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@@ -1077,3 +1077,6 @@ vila/lib/python3.10/site-packages/pandas/tests/io/__pycache__/test_sql.cpython-3
 vila/lib/python3.10/site-packages/pandas/tests/tools/__pycache__/test_to_datetime.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
 vila/lib/python3.10/site-packages/av/bitstream.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
 vila/lib/python3.10/site-packages/av/enum.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
+vila/lib/python3.10/site-packages/scipy/optimize/_pava_pybind.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
+vila/lib/python3.10/site-packages/scipy/optimize/_bglu_dense.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
+vila/lib/python3.10/site-packages/scipy/optimize/_moduleTNC.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text

vila/lib/python3.10/site-packages/scipy/optimize/_basinhopping.py

@@ -0,0 +1,753 @@
+"""
+basinhopping: The basinhopping global optimization algorithm
+"""
+import numpy as np
+import math
+import inspect
+import scipy.optimize
+from scipy._lib._util import check_random_state
+
+__all__ = ['basinhopping']
+
+
+_params = (inspect.Parameter('res_new', kind=inspect.Parameter.KEYWORD_ONLY),
+           inspect.Parameter('res_old', kind=inspect.Parameter.KEYWORD_ONLY))
+_new_accept_test_signature = inspect.Signature(parameters=_params)
+
+
+class Storage:
+    """
+    Class used to store the lowest energy structure
+    """
+    def __init__(self, minres):
+        self._add(minres)
+
+    def _add(self, minres):
+        self.minres = minres
+        self.minres.x = np.copy(minres.x)
+
+    def update(self, minres):
+        if minres.success and (minres.fun < self.minres.fun
+                               or not self.minres.success):
+            self._add(minres)
+            return True
+        else:
+            return False
+
+    def get_lowest(self):
+        return self.minres
+
+
+class BasinHoppingRunner:
+    """This class implements the core of the basinhopping algorithm.
+
+    x0 : ndarray
+        The starting coordinates.
+    minimizer : callable
+        The local minimizer, with signature ``result = minimizer(x)``.
+        The return value is an `optimize.OptimizeResult` object.
+    step_taking : callable
+        This function displaces the coordinates randomly. Signature should
+        be ``x_new = step_taking(x)``. Note that `x` may be modified in-place.
+    accept_tests : list of callables
+        Each test is passed the kwargs `f_new`, `x_new`, `f_old` and
+        `x_old`. These tests will be used to judge whether or not to accept
+        the step. The acceptable return values are True, False, or ``"force
+        accept"``. If any of the tests return False then the step is rejected.
+        If ``"force accept"``, then this will override any other tests in
+        order to accept the step. This can be used, for example, to forcefully
+        escape from a local minimum that ``basinhopping`` is trapped in.
+    disp : bool, optional
+        Display status messages.
+
+    """
+    def __init__(self, x0, minimizer, step_taking, accept_tests, disp=False):
+        self.x = np.copy(x0)
+        self.minimizer = minimizer
+        self.step_taking = step_taking
+        self.accept_tests = accept_tests
+        self.disp = disp
+
+        self.nstep = 0
+
+        # initialize return object
+        self.res = scipy.optimize.OptimizeResult()
+        self.res.minimization_failures = 0
+
+        # do initial minimization
+        minres = minimizer(self.x)
+        if not minres.success:
+            self.res.minimization_failures += 1
+            if self.disp:
+                print("warning: basinhopping: local minimization failure")
+        self.x = np.copy(minres.x)
+        self.energy = minres.fun
+        self.incumbent_minres = minres  # best minimize result found so far
+        if self.disp:
+            print("basinhopping step %d: f %g" % (self.nstep, self.energy))
+
+        # initialize storage class
+        self.storage = Storage(minres)
+
+        if hasattr(minres, "nfev"):
+            self.res.nfev = minres.nfev
+        if hasattr(minres, "njev"):
+            self.res.njev = minres.njev
+        if hasattr(minres, "nhev"):
+            self.res.nhev = minres.nhev
+
+    def _monte_carlo_step(self):
+        """Do one Monte Carlo iteration
+
+        Randomly displace the coordinates, minimize, and decide whether
+        or not to accept the new coordinates.
+        """
+        # Take a random step.  Make a copy of x because the step_taking
+        # algorithm might change x in place
+        x_after_step = np.copy(self.x)
+        x_after_step = self.step_taking(x_after_step)
+
+        # do a local minimization
+        minres = self.minimizer(x_after_step)
+        x_after_quench = minres.x
+        energy_after_quench = minres.fun
+        if not minres.success:
+            self.res.minimization_failures += 1
+            if self.disp:
+                print("warning: basinhopping: local minimization failure")
+        if hasattr(minres, "nfev"):
+            self.res.nfev += minres.nfev
+        if hasattr(minres, "njev"):
+            self.res.njev += minres.njev
+        if hasattr(minres, "nhev"):
+            self.res.nhev += minres.nhev
+
+        # accept the move based on self.accept_tests. If any test is False,
+        # then reject the step.  If any test returns the special string
+        # 'force accept', then accept the step regardless. This can be used
+        # to forcefully escape from a local minimum if normal basin hopping
+        # steps are not sufficient.
+        accept = True
+        for test in self.accept_tests:
+            if inspect.signature(test) == _new_accept_test_signature:
+                testres = test(res_new=minres, res_old=self.incumbent_minres)
+            else:
+                testres = test(f_new=energy_after_quench, x_new=x_after_quench,
+                               f_old=self.energy, x_old=self.x)
+
+            if testres == 'force accept':
+                accept = True
+                break
+            elif testres is None:
+                raise ValueError("accept_tests must return True, False, or "
+                                 "'force accept'")
+            elif not testres:
+                accept = False
+
+        # Report the result of the acceptance test to the take step class.
+        # This is for adaptive step taking
+        if hasattr(self.step_taking, "report"):
+            self.step_taking.report(accept, f_new=energy_after_quench,
+                                    x_new=x_after_quench, f_old=self.energy,
+                                    x_old=self.x)
+
+        return accept, minres
+
+    def one_cycle(self):
+        """Do one cycle of the basinhopping algorithm
+        """
+        self.nstep += 1
+        new_global_min = False
+
+        accept, minres = self._monte_carlo_step()
+
+        if accept:
+            self.energy = minres.fun
+            self.x = np.copy(minres.x)
+            self.incumbent_minres = minres  # best minimize result found so far
+            new_global_min = self.storage.update(minres)
+
+        # print some information
+        if self.disp:
+            self.print_report(minres.fun, accept)
+            if new_global_min:
+                print("found new global minimum on step %d with function"
+                      " value %g" % (self.nstep, self.energy))
+
+        # save some variables as BasinHoppingRunner attributes
+        self.xtrial = minres.x
+        self.energy_trial = minres.fun
+        self.accept = accept
+
+        return new_global_min
+
+    def print_report(self, energy_trial, accept):
+        """print a status update"""
+        minres = self.storage.get_lowest()
+        print("basinhopping step %d: f %g trial_f %g accepted %d "
+              " lowest_f %g" % (self.nstep, self.energy, energy_trial,
+                                accept, minres.fun))
+
+
+class AdaptiveStepsize:
+    """
+    Class to implement adaptive stepsize.
+
+    This class wraps the step taking class and modifies the stepsize to
+    ensure the true acceptance rate is as close as possible to the target.
+
+    Parameters
+    ----------
+    takestep : callable
+        The step taking routine.  Must contain modifiable attribute
+        takestep.stepsize
+    accept_rate : float, optional
+        The target step acceptance rate
+    interval : int, optional
+        Interval for how often to update the stepsize
+    factor : float, optional
+        The step size is multiplied or divided by this factor upon each
+        update.
+    verbose : bool, optional
+        Print information about each update
+
+    """
+    def __init__(self, takestep, accept_rate=0.5, interval=50, factor=0.9,
+                 verbose=True):
+        self.takestep = takestep
+        self.target_accept_rate = accept_rate
+        self.interval = interval
+        self.factor = factor
+        self.verbose = verbose
+
+        self.nstep = 0
+        self.nstep_tot = 0
+        self.naccept = 0
+
+    def __call__(self, x):
+        return self.take_step(x)
+
+    def _adjust_step_size(self):
+        old_stepsize = self.takestep.stepsize
+        accept_rate = float(self.naccept) / self.nstep
+        if accept_rate > self.target_accept_rate:
+            # We're accepting too many steps. This generally means we're
+            # trapped in a basin. Take bigger steps.
+            self.takestep.stepsize /= self.factor
+        else:
+            # We're not accepting enough steps. Take smaller steps.
+            self.takestep.stepsize *= self.factor
+        if self.verbose:
+            print(f"adaptive stepsize: acceptance rate {accept_rate:f} target "
+                  f"{self.target_accept_rate:f} new stepsize "
+                  f"{self.takestep.stepsize:g} old stepsize {old_stepsize:g}")
+
+    def take_step(self, x):
+        self.nstep += 1
+        self.nstep_tot += 1
+        if self.nstep % self.interval == 0:
+            self._adjust_step_size()
+        return self.takestep(x)
+
+    def report(self, accept, **kwargs):
+        "called by basinhopping to report the result of the step"
+        if accept:
+            self.naccept += 1
+
+
+class RandomDisplacement:
+    """Add a random displacement of maximum size `stepsize` to each coordinate.
+
+    Calling this updates `x` in-place.
+
+    Parameters
+    ----------
+    stepsize : float, optional
+        Maximum stepsize in any dimension
+    random_gen : {None, int, `numpy.random.Generator`,
+                  `numpy.random.RandomState`}, optional
+
+        If `seed` is None (or `np.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+
+    """
+
+    def __init__(self, stepsize=0.5, random_gen=None):
+        self.stepsize = stepsize
+        self.random_gen = check_random_state(random_gen)
+
+    def __call__(self, x):
+        x += self.random_gen.uniform(-self.stepsize, self.stepsize,
+                                     np.shape(x))
+        return x
+
+
+class MinimizerWrapper:
+    """
+    wrap a minimizer function as a minimizer class
+    """
+    def __init__(self, minimizer, func=None, **kwargs):
+        self.minimizer = minimizer
+        self.func = func
+        self.kwargs = kwargs
+
+    def __call__(self, x0):
+        if self.func is None:
+            return self.minimizer(x0, **self.kwargs)
+        else:
+            return self.minimizer(self.func, x0, **self.kwargs)
+
+
+class Metropolis:
+    """Metropolis acceptance criterion.
+
+    Parameters
+    ----------
+    T : float
+        The "temperature" parameter for the accept or reject criterion.
+    random_gen : {None, int, `numpy.random.Generator`,
+                  `numpy.random.RandomState`}, optional
+
+        If `seed` is None (or `np.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+        Random number generator used for acceptance test.
+
+    """
+
+    def __init__(self, T, random_gen=None):
+        # Avoid ZeroDivisionError since "MBH can be regarded as a special case
+        # of the BH framework with the Metropolis criterion, where temperature
+        # T = 0." (Reject all steps that increase energy.)
+        self.beta = 1.0 / T if T != 0 else float('inf')
+        self.random_gen = check_random_state(random_gen)
+
+    def accept_reject(self, res_new, res_old):
+        """
+        Assuming the local search underlying res_new was successful:
+        If new energy is lower than old, it will always be accepted.
+        If new is higher than old, there is a chance it will be accepted,
+        less likely for larger differences.
+        """
+        with np.errstate(invalid='ignore'):
+            # The energy values being fed to Metropolis are 1-length arrays, and if
+            # they are equal, their difference is 0, which gets multiplied by beta,
+            # which is inf, and array([0]) * float('inf') causes
+            #
+            # RuntimeWarning: invalid value encountered in multiply
+            #
+            # Ignore this warning so when the algorithm is on a flat plane, it always
+            # accepts the step, to try to move off the plane.
+            prod = -(res_new.fun - res_old.fun) * self.beta
+            w = math.exp(min(0, prod))
+
+        rand = self.random_gen.uniform()
+        return w >= rand and (res_new.success or not res_old.success)
+
+    def __call__(self, *, res_new, res_old):
+        """
+        f_new and f_old are mandatory in kwargs
+        """
+        return bool(self.accept_reject(res_new, res_old))
+
+
+def basinhopping(func, x0, niter=100, T=1.0, stepsize=0.5,
+                 minimizer_kwargs=None, take_step=None, accept_test=None,
+                 callback=None, interval=50, disp=False, niter_success=None,
+                 seed=None, *, target_accept_rate=0.5, stepwise_factor=0.9):
+    """Find the global minimum of a function using the basin-hopping algorithm.
+
+    Basin-hopping is a two-phase method that combines a global stepping
+    algorithm with local minimization at each step. Designed to mimic
+    the natural process of energy minimization of clusters of atoms, it works
+    well for similar problems with "funnel-like, but rugged" energy landscapes
+    [5]_.
+
+    As the step-taking, step acceptance, and minimization methods are all
+    customizable, this function can also be used to implement other two-phase
+    methods.
+
+    Parameters
+    ----------
+    func : callable ``f(x, *args)``
+        Function to be optimized.  ``args`` can be passed as an optional item
+        in the dict `minimizer_kwargs`
+    x0 : array_like
+        Initial guess.
+    niter : integer, optional
+        The number of basin-hopping iterations. There will be a total of
+        ``niter + 1`` runs of the local minimizer.
+    T : float, optional
+        The "temperature" parameter for the acceptance or rejection criterion.
+        Higher "temperatures" mean that larger jumps in function value will be
+        accepted.  For best results `T` should be comparable to the
+        separation (in function value) between local minima.
+    stepsize : float, optional
+        Maximum step size for use in the random displacement.
+    minimizer_kwargs : dict, optional
+        Extra keyword arguments to be passed to the local minimizer
+        `scipy.optimize.minimize` Some important options could be:
+
+            method : str
+                The minimization method (e.g. ``"L-BFGS-B"``)
+            args : tuple
+                Extra arguments passed to the objective function (`func`) and
+                its derivatives (Jacobian, Hessian).
+
+    take_step : callable ``take_step(x)``, optional
+        Replace the default step-taking routine with this routine. The default
+        step-taking routine is a random displacement of the coordinates, but
+        other step-taking algorithms may be better for some systems.
+        `take_step` can optionally have the attribute ``take_step.stepsize``.
+        If this attribute exists, then `basinhopping` will adjust
+        ``take_step.stepsize`` in order to try to optimize the global minimum
+        search.
+    accept_test : callable, ``accept_test(f_new=f_new, x_new=x_new, f_old=fold, x_old=x_old)``, optional
+        Define a test which will be used to judge whether to accept the
+        step. This will be used in addition to the Metropolis test based on
+        "temperature" `T`. The acceptable return values are True,
+        False, or ``"force accept"``. If any of the tests return False
+        then the step is rejected. If the latter, then this will override any
+        other tests in order to accept the step. This can be used, for example,
+        to forcefully escape from a local minimum that `basinhopping` is
+        trapped in.
+    callback : callable, ``callback(x, f, accept)``, optional
+        A callback function which will be called for all minima found. ``x``
+        and ``f`` are the coordinates and function value of the trial minimum,
+        and ``accept`` is whether that minimum was accepted. This can
+        be used, for example, to save the lowest N minima found. Also,
+        `callback` can be used to specify a user defined stop criterion by
+        optionally returning True to stop the `basinhopping` routine.
+    interval : integer, optional
+        interval for how often to update the `stepsize`
+    disp : bool, optional
+        Set to True to print status messages
+    niter_success : integer, optional
+        Stop the run if the global minimum candidate remains the same for this
+        number of iterations.
+    seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional
+
+        If `seed` is None (or `np.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+        Specify `seed` for repeatable minimizations. The random numbers
+        generated with this seed only affect the default Metropolis
+        `accept_test` and the default `take_step`. If you supply your own
+        `take_step` and `accept_test`, and these functions use random
+        number generation, then those functions are responsible for the state
+        of their random number generator.
+    target_accept_rate : float, optional
+        The target acceptance rate that is used to adjust the `stepsize`.
+        If the current acceptance rate is greater than the target,
+        then the `stepsize` is increased. Otherwise, it is decreased.
+        Range is (0, 1). Default is 0.5.
+
+        .. versionadded:: 1.8.0
+
+    stepwise_factor : float, optional
+        The `stepsize` is multiplied or divided by this stepwise factor upon
+        each update. Range is (0, 1). Default is 0.9.
+
+        .. versionadded:: 1.8.0
+
+    Returns
+    -------
+    res : OptimizeResult
+        The optimization result represented as a `OptimizeResult` object.
+        Important attributes are: ``x`` the solution array, ``fun`` the value
+        of the function at the solution, and ``message`` which describes the
+        cause of the termination. The ``OptimizeResult`` object returned by the
+        selected minimizer at the lowest minimum is also contained within this
+        object and can be accessed through the ``lowest_optimization_result``
+        attribute.  See `OptimizeResult` for a description of other attributes.
+
+    See Also
+    --------
+    minimize :
+        The local minimization function called once for each basinhopping step.
+        `minimizer_kwargs` is passed to this routine.
+
+    Notes
+    -----
+    Basin-hopping is a stochastic algorithm which attempts to find the global
+    minimum of a smooth scalar function of one or more variables [1]_ [2]_ [3]_
+    [4]_. The algorithm in its current form was described by David Wales and
+    Jonathan Doye [2]_ http://www-wales.ch.cam.ac.uk/.
+
+    The algorithm is iterative with each cycle composed of the following
+    features
+
+    1) random perturbation of the coordinates
+
+    2) local minimization
+
+    3) accept or reject the new coordinates based on the minimized function
+       value
+
+    The acceptance test used here is the Metropolis criterion of standard Monte
+    Carlo algorithms, although there are many other possibilities [3]_.
+
+    This global minimization method has been shown to be extremely efficient
+    for a wide variety of problems in physics and chemistry. It is
+    particularly useful when the function has many minima separated by large
+    barriers. See the `Cambridge Cluster Database
+    <https://www-wales.ch.cam.ac.uk/CCD.html>`_ for databases of molecular
+    systems that have been optimized primarily using basin-hopping. This
+    database includes minimization problems exceeding 300 degrees of freedom.
+
+    See the free software program `GMIN <https://www-wales.ch.cam.ac.uk/GMIN>`_
+    for a Fortran implementation of basin-hopping. This implementation has many
+    variations of the procedure described above, including more
+    advanced step taking algorithms and alternate acceptance criterion.
+
+    For stochastic global optimization there is no way to determine if the true
+    global minimum has actually been found. Instead, as a consistency check,
+    the algorithm can be run from a number of different random starting points
+    to ensure the lowest minimum found in each example has converged to the
+    global minimum. For this reason, `basinhopping` will by default simply
+    run for the number of iterations `niter` and return the lowest minimum
+    found. It is left to the user to ensure that this is in fact the global
+    minimum.
+
+    Choosing `stepsize`:  This is a crucial parameter in `basinhopping` and
+    depends on the problem being solved. The step is chosen uniformly in the
+    region from x0-stepsize to x0+stepsize, in each dimension. Ideally, it
+    should be comparable to the typical separation (in argument values) between
+    local minima of the function being optimized. `basinhopping` will, by
+    default, adjust `stepsize` to find an optimal value, but this may take
+    many iterations. You will get quicker results if you set a sensible
+    initial value for ``stepsize``.
+
+    Choosing `T`: The parameter `T` is the "temperature" used in the
+    Metropolis criterion. Basinhopping steps are always accepted if
+    ``func(xnew) < func(xold)``. Otherwise, they are accepted with
+    probability::
+
+        exp( -(func(xnew) - func(xold)) / T )
+
+    So, for best results, `T` should to be comparable to the typical
+    difference (in function values) between local minima. (The height of
+    "walls" between local minima is irrelevant.)
+
+    If `T` is 0, the algorithm becomes Monotonic Basin-Hopping, in which all
+    steps that increase energy are rejected.
+
+    .. versionadded:: 0.12.0
+
+    References
+    ----------
+    .. [1] Wales, David J. 2003, Energy Landscapes, Cambridge University Press,
+        Cambridge, UK.
+    .. [2] Wales, D J, and Doye J P K, Global Optimization by Basin-Hopping and
+        the Lowest Energy Structures of Lennard-Jones Clusters Containing up to
+        110 Atoms.  Journal of Physical Chemistry A, 1997, 101, 5111.
+    .. [3] Li, Z. and Scheraga, H. A., Monte Carlo-minimization approach to the
+        multiple-minima problem in protein folding, Proc. Natl. Acad. Sci. USA,
+        1987, 84, 6611.
+    .. [4] Wales, D. J. and Scheraga, H. A., Global optimization of clusters,
+        crystals, and biomolecules, Science, 1999, 285, 1368.
+    .. [5] Olson, B., Hashmi, I., Molloy, K., and Shehu1, A., Basin Hopping as
+        a General and Versatile Optimization Framework for the Characterization
+        of Biological Macromolecules, Advances in Artificial Intelligence,
+        Volume 2012 (2012), Article ID 674832, :doi:`10.1155/2012/674832`
+
+    Examples
+    --------
+    The following example is a 1-D minimization problem, with many
+    local minima superimposed on a parabola.
+
+    >>> import numpy as np
+    >>> from scipy.optimize import basinhopping
+    >>> func = lambda x: np.cos(14.5 * x - 0.3) + (x + 0.2) * x
+    >>> x0 = [1.]
+
+    Basinhopping, internally, uses a local minimization algorithm. We will use
+    the parameter `minimizer_kwargs` to tell basinhopping which algorithm to
+    use and how to set up that minimizer. This parameter will be passed to
+    `scipy.optimize.minimize`.
+
+    >>> minimizer_kwargs = {"method": "BFGS"}
+    >>> ret = basinhopping(func, x0, minimizer_kwargs=minimizer_kwargs,
+    ...                    niter=200)
+    >>> # the global minimum is:
+    >>> ret.x, ret.fun
+    -0.1951, -1.0009
+
+    Next consider a 2-D minimization problem. Also, this time, we
+    will use gradient information to significantly speed up the search.
+
+    >>> def func2d(x):
+    ...     f = np.cos(14.5 * x[0] - 0.3) + (x[1] + 0.2) * x[1] + (x[0] +
+    ...                                                            0.2) * x[0]
+    ...     df = np.zeros(2)
+    ...     df[0] = -14.5 * np.sin(14.5 * x[0] - 0.3) + 2. * x[0] + 0.2
+    ...     df[1] = 2. * x[1] + 0.2
+    ...     return f, df
+
+    We'll also use a different local minimization algorithm. Also, we must tell
+    the minimizer that our function returns both energy and gradient (Jacobian).
+
+    >>> minimizer_kwargs = {"method":"L-BFGS-B", "jac":True}
+    >>> x0 = [1.0, 1.0]
+    >>> ret = basinhopping(func2d, x0, minimizer_kwargs=minimizer_kwargs,
+    ...                    niter=200)
+    >>> print("global minimum: x = [%.4f, %.4f], f(x) = %.4f" % (ret.x[0],
+    ...                                                           ret.x[1],
+    ...                                                           ret.fun))
+    global minimum: x = [-0.1951, -0.1000], f(x) = -1.0109
+
+    Here is an example using a custom step-taking routine. Imagine you want
+    the first coordinate to take larger steps than the rest of the coordinates.
+    This can be implemented like so:
+
+    >>> class MyTakeStep:
+    ...    def __init__(self, stepsize=0.5):
+    ...        self.stepsize = stepsize
+    ...        self.rng = np.random.default_rng()
+    ...    def __call__(self, x):
+    ...        s = self.stepsize
+    ...        x[0] += self.rng.uniform(-2.*s, 2.*s)
+    ...        x[1:] += self.rng.uniform(-s, s, x[1:].shape)
+    ...        return x
+
+    Since ``MyTakeStep.stepsize`` exists basinhopping will adjust the magnitude
+    of `stepsize` to optimize the search. We'll use the same 2-D function as
+    before
+
+    >>> mytakestep = MyTakeStep()
+    >>> ret = basinhopping(func2d, x0, minimizer_kwargs=minimizer_kwargs,
+    ...                    niter=200, take_step=mytakestep)
+    >>> print("global minimum: x = [%.4f, %.4f], f(x) = %.4f" % (ret.x[0],
+    ...                                                           ret.x[1],
+    ...                                                           ret.fun))
+    global minimum: x = [-0.1951, -0.1000], f(x) = -1.0109
+
+    Now, let's do an example using a custom callback function which prints the
+    value of every minimum found
+
+    >>> def print_fun(x, f, accepted):
+    ...         print("at minimum %.4f accepted %d" % (f, int(accepted)))
+
+    We'll run it for only 10 basinhopping steps this time.
+
+    >>> rng = np.random.default_rng()
+    >>> ret = basinhopping(func2d, x0, minimizer_kwargs=minimizer_kwargs,
+    ...                    niter=10, callback=print_fun, seed=rng)
+    at minimum 0.4159 accepted 1
+    at minimum -0.4317 accepted 1
+    at minimum -1.0109 accepted 1
+    at minimum -0.9073 accepted 1
+    at minimum -0.4317 accepted 0
+    at minimum -0.1021 accepted 1
+    at minimum -0.7425 accepted 1
+    at minimum -0.9073 accepted 1
+    at minimum -0.4317 accepted 0
+    at minimum -0.7425 accepted 1
+    at minimum -0.9073 accepted 1
+
+    The minimum at -1.0109 is actually the global minimum, found already on the
+    8th iteration.
+
+    """ # numpy/numpydoc#87  # noqa: E501
+    if target_accept_rate <= 0. or target_accept_rate >= 1.:
+        raise ValueError('target_accept_rate has to be in range (0, 1)')
+    if stepwise_factor <= 0. or stepwise_factor >= 1.:
+        raise ValueError('stepwise_factor has to be in range (0, 1)')
+
+    x0 = np.array(x0)
+
+    # set up the np.random generator
+    rng = check_random_state(seed)
+
+    # set up minimizer
+    if minimizer_kwargs is None:
+        minimizer_kwargs = dict()
+    wrapped_minimizer = MinimizerWrapper(scipy.optimize.minimize, func,
+                                         **minimizer_kwargs)
+
+    # set up step-taking algorithm
+    if take_step is not None:
+        if not callable(take_step):
+            raise TypeError("take_step must be callable")
+        # if take_step.stepsize exists then use AdaptiveStepsize to control
+        # take_step.stepsize
+        if hasattr(take_step, "stepsize"):
+            take_step_wrapped = AdaptiveStepsize(
+                take_step, interval=interval,
+                accept_rate=target_accept_rate,
+                factor=stepwise_factor,
+                verbose=disp)
+        else:
+            take_step_wrapped = take_step
+    else:
+        # use default
+        displace = RandomDisplacement(stepsize=stepsize, random_gen=rng)
+        take_step_wrapped = AdaptiveStepsize(displace, interval=interval,
+                                             accept_rate=target_accept_rate,
+                                             factor=stepwise_factor,
+                                             verbose=disp)
+
+    # set up accept tests
+    accept_tests = []
+    if accept_test is not None:
+        if not callable(accept_test):
+            raise TypeError("accept_test must be callable")
+        accept_tests = [accept_test]
+
+    # use default
+    metropolis = Metropolis(T, random_gen=rng)
+    accept_tests.append(metropolis)
+
+    if niter_success is None:
+        niter_success = niter + 2
+
+    bh = BasinHoppingRunner(x0, wrapped_minimizer, take_step_wrapped,
+                            accept_tests, disp=disp)
+
+    # The wrapped minimizer is called once during construction of
+    # BasinHoppingRunner, so run the callback
+    if callable(callback):
+        callback(bh.storage.minres.x, bh.storage.minres.fun, True)
+
+    # start main iteration loop
+    count, i = 0, 0
+    message = ["requested number of basinhopping iterations completed"
+               " successfully"]
+    for i in range(niter):
+        new_global_min = bh.one_cycle()
+
+        if callable(callback):
+            # should we pass a copy of x?
+            val = callback(bh.xtrial, bh.energy_trial, bh.accept)
+            if val is not None:
+                if val:
+                    message = ["callback function requested stop early by"
+                               "returning True"]
+                    break
+
+        count += 1
+        if new_global_min:
+            count = 0
+        elif count > niter_success:
+            message = ["success condition satisfied"]
+            break
+
+    # prepare return object
+    res = bh.res
+    res.lowest_optimization_result = bh.storage.get_lowest()
+    res.x = np.copy(res.lowest_optimization_result.x)
+    res.fun = res.lowest_optimization_result.fun
+    res.message = message
+    res.nit = i + 1
+    res.success = res.lowest_optimization_result.success
+    return res

vila/lib/python3.10/site-packages/scipy/optimize/_bglu_dense.cpython-310-x86_64-linux-gnu.so

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c45eca1a2737717c4e47975adcd7b7c1c1d02e98dba7d5103eea7e67787a6fea
+size 364392

vila/lib/python3.10/site-packages/scipy/optimize/_cobyqa_py.py

@@ -0,0 +1,62 @@
+import numpy as np
+
+from ._optimize import _check_unknown_options
+
+
+def _minimize_cobyqa(fun, x0, args=(), bounds=None, constraints=(),
+                     callback=None, disp=False, maxfev=None, maxiter=None,
+                     f_target=-np.inf, feasibility_tol=1e-8,
+                     initial_tr_radius=1.0, final_tr_radius=1e-6, scale=False,
+                     **unknown_options):
+    """
+    Minimize a scalar function of one or more variables using the
+    Constrained Optimization BY Quadratic Approximations (COBYQA) algorithm [1]_.
+
+    .. versionadded:: 1.14.0
+
+    Options
+    -------
+    disp : bool
+        Set to True to print information about the optimization procedure.
+    maxfev : int
+        Maximum number of function evaluations.
+    maxiter : int
+        Maximum number of iterations.
+    f_target : float
+        Target value for the objective function. The optimization procedure is
+        terminated when the objective function value of a feasible point (see
+        `feasibility_tol` below) is less than or equal to this target.
+    feasibility_tol : float
+        Absolute tolerance for the constraint violation.
+    initial_tr_radius : float
+        Initial trust-region radius. Typically, this value should be in the
+        order of one tenth of the greatest expected change to the variables.
+    final_tr_radius : float
+        Final trust-region radius. It should indicate the accuracy required in
+        the final values of the variables. If provided, this option overrides
+        the value of `tol` in the `minimize` function.
+    scale : bool
+        Set to True to scale the variables according to the bounds. If True and
+        if all the lower and upper bounds are finite, the variables are scaled
+        to be within the range :math:`[-1, 1]`. If any of the lower or upper
+        bounds is infinite, the variables are not scaled.
+
+    References
+    ----------
+    .. [1] COBYQA
+           https://www.cobyqa.com/stable/
+    """
+    from .._lib.cobyqa import minimize  # import here to avoid circular imports
+
+    _check_unknown_options(unknown_options)
+    options = {
+        'disp': bool(disp),
+        'maxfev': int(maxfev) if maxfev is not None else 500 * len(x0),
+        'maxiter': int(maxiter) if maxiter is not None else 1000 * len(x0),
+        'target': float(f_target),
+        'feasibility_tol': float(feasibility_tol),
+        'radius_init': float(initial_tr_radius),
+        'radius_final': float(final_tr_radius),
+        'scale': bool(scale),
+    }
+    return minimize(fun, x0, args, bounds, constraints, callback, options)

vila/lib/python3.10/site-packages/scipy/optimize/_constraints.py

@@ -0,0 +1,590 @@
+"""Constraints definition for minimize."""
+import numpy as np
+from ._hessian_update_strategy import BFGS
+from ._differentiable_functions import (
+    VectorFunction, LinearVectorFunction, IdentityVectorFunction)
+from ._optimize import OptimizeWarning
+from warnings import warn, catch_warnings, simplefilter, filterwarnings
+from scipy.sparse import issparse
+
+
+def _arr_to_scalar(x):
+    # If x is a numpy array, return x.item().  This will
+    # fail if the array has more than one element.
+    return x.item() if isinstance(x, np.ndarray) else x
+
+
+class NonlinearConstraint:
+    """Nonlinear constraint on the variables.
+
+    The constraint has the general inequality form::
+
+        lb <= fun(x) <= ub
+
+    Here the vector of independent variables x is passed as ndarray of shape
+    (n,) and ``fun`` returns a vector with m components.
+
+    It is possible to use equal bounds to represent an equality constraint or
+    infinite bounds to represent a one-sided constraint.
+
+    Parameters
+    ----------
+    fun : callable
+        The function defining the constraint.
+        The signature is ``fun(x) -> array_like, shape (m,)``.
+    lb, ub : array_like
+        Lower and upper bounds on the constraint. Each array must have the
+        shape (m,) or be a scalar, in the latter case a bound will be the same
+        for all components of the constraint. Use ``np.inf`` with an
+        appropriate sign to specify a one-sided constraint.
+        Set components of `lb` and `ub` equal to represent an equality
+        constraint. Note that you can mix constraints of different types:
+        interval, one-sided or equality, by setting different components of
+        `lb` and `ub` as  necessary.
+    jac : {callable,  '2-point', '3-point', 'cs'}, optional
+        Method of computing the Jacobian matrix (an m-by-n matrix,
+        where element (i, j) is the partial derivative of f[i] with
+        respect to x[j]).  The keywords {'2-point', '3-point',
+        'cs'} select a finite difference scheme for the numerical estimation.
+        A callable must have the following signature:
+        ``jac(x) -> {ndarray, sparse matrix}, shape (m, n)``.
+        Default is '2-point'.
+    hess : {callable, '2-point', '3-point', 'cs', HessianUpdateStrategy, None}, optional
+        Method for computing the Hessian matrix. The keywords
+        {'2-point', '3-point', 'cs'} select a finite difference scheme for
+        numerical  estimation.  Alternatively, objects implementing
+        `HessianUpdateStrategy` interface can be used to approximate the
+        Hessian. Currently available implementations are:
+
+            - `BFGS` (default option)
+            - `SR1`
+
+        A callable must return the Hessian matrix of ``dot(fun, v)`` and
+        must have the following signature:
+        ``hess(x, v) -> {LinearOperator, sparse matrix, array_like}, shape (n, n)``.
+        Here ``v`` is ndarray with shape (m,) containing Lagrange multipliers.
+    keep_feasible : array_like of bool, optional
+        Whether to keep the constraint components feasible throughout
+        iterations. A single value set this property for all components.
+        Default is False. Has no effect for equality constraints.
+    finite_diff_rel_step: None or array_like, optional
+        Relative step size for the finite difference approximation. Default is
+        None, which will select a reasonable value automatically depending
+        on a finite difference scheme.
+    finite_diff_jac_sparsity: {None, array_like, sparse matrix}, optional
+        Defines the sparsity structure of the Jacobian matrix for finite
+        difference estimation, its shape must be (m, n). If the Jacobian has
+        only few non-zero elements in *each* row, providing the sparsity
+        structure will greatly speed up the computations. A zero entry means
+        that a corresponding element in the Jacobian is identically zero.
+        If provided, forces the use of 'lsmr' trust-region solver.
+        If None (default) then dense differencing will be used.
+
+    Notes
+    -----
+    Finite difference schemes {'2-point', '3-point', 'cs'} may be used for
+    approximating either the Jacobian or the Hessian. We, however, do not allow
+    its use for approximating both simultaneously. Hence whenever the Jacobian
+    is estimated via finite-differences, we require the Hessian to be estimated
+    using one of the quasi-Newton strategies.
+
+    The scheme 'cs' is potentially the most accurate, but requires the function
+    to correctly handles complex inputs and be analytically continuable to the
+    complex plane. The scheme '3-point' is more accurate than '2-point' but
+    requires twice as many operations.
+
+    Examples
+    --------
+    Constrain ``x[0] < sin(x[1]) + 1.9``
+
+    >>> from scipy.optimize import NonlinearConstraint
+    >>> import numpy as np
+    >>> con = lambda x: x[0] - np.sin(x[1])
+    >>> nlc = NonlinearConstraint(con, -np.inf, 1.9)
+
+    """
+    def __init__(self, fun, lb, ub, jac='2-point', hess=BFGS(),
+                 keep_feasible=False, finite_diff_rel_step=None,
+                 finite_diff_jac_sparsity=None):
+        self.fun = fun
+        self.lb = lb
+        self.ub = ub
+        self.finite_diff_rel_step = finite_diff_rel_step
+        self.finite_diff_jac_sparsity = finite_diff_jac_sparsity
+        self.jac = jac
+        self.hess = hess
+        self.keep_feasible = keep_feasible
+
+
+class LinearConstraint:
+    """Linear constraint on the variables.
+
+    The constraint has the general inequality form::
+
+        lb <= A.dot(x) <= ub
+
+    Here the vector of independent variables x is passed as ndarray of shape
+    (n,) and the matrix A has shape (m, n).
+
+    It is possible to use equal bounds to represent an equality constraint or
+    infinite bounds to represent a one-sided constraint.
+
+    Parameters
+    ----------
+    A : {array_like, sparse matrix}, shape (m, n)
+        Matrix defining the constraint.
+    lb, ub : dense array_like, optional
+        Lower and upper limits on the constraint. Each array must have the
+        shape (m,) or be a scalar, in the latter case a bound will be the same
+        for all components of the constraint. Use ``np.inf`` with an
+        appropriate sign to specify a one-sided constraint.
+        Set components of `lb` and `ub` equal to represent an equality
+        constraint. Note that you can mix constraints of different types:
+        interval, one-sided or equality, by setting different components of
+        `lb` and `ub` as  necessary. Defaults to ``lb = -np.inf``
+        and ``ub = np.inf`` (no limits).
+    keep_feasible : dense array_like of bool, optional
+        Whether to keep the constraint components feasible throughout
+        iterations. A single value set this property for all components.
+        Default is False. Has no effect for equality constraints.
+    """
+    def _input_validation(self):
+        if self.A.ndim != 2:
+            message = "`A` must have exactly two dimensions."
+            raise ValueError(message)
+
+        try:
+            shape = self.A.shape[0:1]
+            self.lb = np.broadcast_to(self.lb, shape)
+            self.ub = np.broadcast_to(self.ub, shape)
+            self.keep_feasible = np.broadcast_to(self.keep_feasible, shape)
+        except ValueError:
+            message = ("`lb`, `ub`, and `keep_feasible` must be broadcastable "
+                       "to shape `A.shape[0:1]`")
+            raise ValueError(message)
+
+    def __init__(self, A, lb=-np.inf, ub=np.inf, keep_feasible=False):
+        if not issparse(A):
+            # In some cases, if the constraint is not valid, this emits a
+            # VisibleDeprecationWarning about ragged nested sequences
+            # before eventually causing an error. `scipy.optimize.milp` would
+            # prefer that this just error out immediately so it can handle it
+            # rather than concerning the user.
+            with catch_warnings():
+                simplefilter("error")
+                self.A = np.atleast_2d(A).astype(np.float64)
+        else:
+            self.A = A
+        if issparse(lb) or issparse(ub):
+            raise ValueError("Constraint limits must be dense arrays.")
+        self.lb = np.atleast_1d(lb).astype(np.float64)
+        self.ub = np.atleast_1d(ub).astype(np.float64)
+
+        if issparse(keep_feasible):
+            raise ValueError("`keep_feasible` must be a dense array.")
+        self.keep_feasible = np.atleast_1d(keep_feasible).astype(bool)
+        self._input_validation()
+
+    def residual(self, x):
+        """
+        Calculate the residual between the constraint function and the limits
+
+        For a linear constraint of the form::
+
+            lb <= A@x <= ub
+
+        the lower and upper residuals between ``A@x`` and the limits are values
+        ``sl`` and ``sb`` such that::
+
+            lb + sl == A@x == ub - sb
+
+        When all elements of ``sl`` and ``sb`` are positive, all elements of
+        the constraint are satisfied; a negative element in ``sl`` or ``sb``
+        indicates that the corresponding element of the constraint is not
+        satisfied.
+
+        Parameters
+        ----------
+        x: array_like
+            Vector of independent variables
+
+        Returns
+        -------
+        sl, sb : array-like
+            The lower and upper residuals
+        """
+        return self.A@x - self.lb, self.ub - self.A@x
+
+
+class Bounds:
+    """Bounds constraint on the variables.
+
+    The constraint has the general inequality form::
+
+        lb <= x <= ub
+
+    It is possible to use equal bounds to represent an equality constraint or
+    infinite bounds to represent a one-sided constraint.
+
+    Parameters
+    ----------
+    lb, ub : dense array_like, optional
+        Lower and upper bounds on independent variables. `lb`, `ub`, and
+        `keep_feasible` must be the same shape or broadcastable.
+        Set components of `lb` and `ub` equal
+        to fix a variable. Use ``np.inf`` with an appropriate sign to disable
+        bounds on all or some variables. Note that you can mix constraints of
+        different types: interval, one-sided or equality, by setting different
+        components of `lb` and `ub` as necessary. Defaults to ``lb = -np.inf``
+        and ``ub = np.inf`` (no bounds).
+    keep_feasible : dense array_like of bool, optional
+        Whether to keep the constraint components feasible throughout
+        iterations. Must be broadcastable with `lb` and `ub`.
+        Default is False. Has no effect for equality constraints.
+    """
+    def _input_validation(self):
+        try:
+            res = np.broadcast_arrays(self.lb, self.ub, self.keep_feasible)
+            self.lb, self.ub, self.keep_feasible = res
+        except ValueError:
+            message = "`lb`, `ub`, and `keep_feasible` must be broadcastable."
+            raise ValueError(message)
+
+    def __init__(self, lb=-np.inf, ub=np.inf, keep_feasible=False):
+        if issparse(lb) or issparse(ub):
+            raise ValueError("Lower and upper bounds must be dense arrays.")
+        self.lb = np.atleast_1d(lb)
+        self.ub = np.atleast_1d(ub)
+
+        if issparse(keep_feasible):
+            raise ValueError("`keep_feasible` must be a dense array.")
+        self.keep_feasible = np.atleast_1d(keep_feasible).astype(bool)
+        self._input_validation()
+
+    def __repr__(self):
+        start = f"{type(self).__name__}({self.lb!r}, {self.ub!r}"
+        if np.any(self.keep_feasible):
+            end = f", keep_feasible={self.keep_feasible!r})"
+        else:
+            end = ")"
+        return start + end
+
+    def residual(self, x):
+        """Calculate the residual (slack) between the input and the bounds
+
+        For a bound constraint of the form::
+
+            lb <= x <= ub
+
+        the lower and upper residuals between `x` and the bounds are values
+        ``sl`` and ``sb`` such that::
+
+            lb + sl == x == ub - sb
+
+        When all elements of ``sl`` and ``sb`` are positive, all elements of
+        ``x`` lie within the bounds; a negative element in ``sl`` or ``sb``
+        indicates that the corresponding element of ``x`` is out of bounds.
+
+        Parameters
+        ----------
+        x: array_like
+            Vector of independent variables
+
+        Returns
+        -------
+        sl, sb : array-like
+            The lower and upper residuals
+        """
+        return x - self.lb, self.ub - x
+
+
+class PreparedConstraint:
+    """Constraint prepared from a user defined constraint.
+
+    On creation it will check whether a constraint definition is valid and
+    the initial point is feasible. If created successfully, it will contain
+    the attributes listed below.
+
+    Parameters
+    ----------
+    constraint : {NonlinearConstraint, LinearConstraint`, Bounds}
+        Constraint to check and prepare.
+    x0 : array_like
+        Initial vector of independent variables.
+    sparse_jacobian : bool or None, optional
+        If bool, then the Jacobian of the constraint will be converted
+        to the corresponded format if necessary. If None (default), such
+        conversion is not made.
+    finite_diff_bounds : 2-tuple, optional
+        Lower and upper bounds on the independent variables for the finite
+        difference approximation, if applicable. Defaults to no bounds.
+
+    Attributes
+    ----------
+    fun : {VectorFunction, LinearVectorFunction, IdentityVectorFunction}
+        Function defining the constraint wrapped by one of the convenience
+        classes.
+    bounds : 2-tuple
+        Contains lower and upper bounds for the constraints --- lb and ub.
+        These are converted to ndarray and have a size equal to the number of
+        the constraints.
+    keep_feasible : ndarray
+         Array indicating which components must be kept feasible with a size
+         equal to the number of the constraints.
+    """
+    def __init__(self, constraint, x0, sparse_jacobian=None,
+                 finite_diff_bounds=(-np.inf, np.inf)):
+        if isinstance(constraint, NonlinearConstraint):
+            fun = VectorFunction(constraint.fun, x0,
+                                 constraint.jac, constraint.hess,
+                                 constraint.finite_diff_rel_step,
+                                 constraint.finite_diff_jac_sparsity,
+                                 finite_diff_bounds, sparse_jacobian)
+        elif isinstance(constraint, LinearConstraint):
+            fun = LinearVectorFunction(constraint.A, x0, sparse_jacobian)
+        elif isinstance(constraint, Bounds):
+            fun = IdentityVectorFunction(x0, sparse_jacobian)
+        else:
+            raise ValueError("`constraint` of an unknown type is passed.")
+
+        m = fun.m
+
+        lb = np.asarray(constraint.lb, dtype=float)
+        ub = np.asarray(constraint.ub, dtype=float)
+        keep_feasible = np.asarray(constraint.keep_feasible, dtype=bool)
+
+        lb = np.broadcast_to(lb, m)
+        ub = np.broadcast_to(ub, m)
+        keep_feasible = np.broadcast_to(keep_feasible, m)
+
+        if keep_feasible.shape != (m,):
+            raise ValueError("`keep_feasible` has a wrong shape.")
+
+        mask = keep_feasible & (lb != ub)
+        f0 = fun.f
+        if np.any(f0[mask] < lb[mask]) or np.any(f0[mask] > ub[mask]):
+            raise ValueError("`x0` is infeasible with respect to some "
+                             "inequality constraint with `keep_feasible` "
+                             "set to True.")
+
+        self.fun = fun
+        self.bounds = (lb, ub)
+        self.keep_feasible = keep_feasible
+
+    def violation(self, x):
+        """How much the constraint is exceeded by.
+
+        Parameters
+        ----------
+        x : array-like
+            Vector of independent variables
+
+        Returns
+        -------
+        excess : array-like
+            How much the constraint is exceeded by, for each of the
+            constraints specified by `PreparedConstraint.fun`.
+        """
+        with catch_warnings():
+            # Ignore the following warning, it's not important when
+            # figuring out total violation
+            # UserWarning: delta_grad == 0.0. Check if the approximated
+            # function is linear
+            filterwarnings("ignore", "delta_grad", UserWarning)
+            ev = self.fun.fun(np.asarray(x))
+
+        excess_lb = np.maximum(self.bounds[0] - ev, 0)
+        excess_ub = np.maximum(ev - self.bounds[1], 0)
+
+        return excess_lb + excess_ub
+
+
+def new_bounds_to_old(lb, ub, n):
+    """Convert the new bounds representation to the old one.
+
+    The new representation is a tuple (lb, ub) and the old one is a list
+    containing n tuples, ith containing lower and upper bound on a ith
+    variable.
+    If any of the entries in lb/ub are -np.inf/np.inf they are replaced by
+    None.
+    """
+    lb = np.broadcast_to(lb, n)
+    ub = np.broadcast_to(ub, n)
+
+    lb = [float(x) if x > -np.inf else None for x in lb]
+    ub = [float(x) if x < np.inf else None for x in ub]
+
+    return list(zip(lb, ub))
+
+
+def old_bound_to_new(bounds):
+    """Convert the old bounds representation to the new one.
+
+    The new representation is a tuple (lb, ub) and the old one is a list
+    containing n tuples, ith containing lower and upper bound on a ith
+    variable.
+    If any of the entries in lb/ub are None they are replaced by
+    -np.inf/np.inf.
+    """
+    lb, ub = zip(*bounds)
+
+    # Convert occurrences of None to -inf or inf, and replace occurrences of
+    # any numpy array x with x.item(). Then wrap the results in numpy arrays.
+    lb = np.array([float(_arr_to_scalar(x)) if x is not None else -np.inf
+                   for x in lb])
+    ub = np.array([float(_arr_to_scalar(x)) if x is not None else np.inf
+                   for x in ub])
+
+    return lb, ub
+
+
+def strict_bounds(lb, ub, keep_feasible, n_vars):
+    """Remove bounds which are not asked to be kept feasible."""
+    strict_lb = np.resize(lb, n_vars).astype(float)
+    strict_ub = np.resize(ub, n_vars).astype(float)
+    keep_feasible = np.resize(keep_feasible, n_vars)
+    strict_lb[~keep_feasible] = -np.inf
+    strict_ub[~keep_feasible] = np.inf
+    return strict_lb, strict_ub
+
+
+def new_constraint_to_old(con, x0):
+    """
+    Converts new-style constraint objects to old-style constraint dictionaries.
+    """
+    if isinstance(con, NonlinearConstraint):
+        if (con.finite_diff_jac_sparsity is not None or
+                con.finite_diff_rel_step is not None or
+                not isinstance(con.hess, BFGS) or  # misses user specified BFGS
+                con.keep_feasible):
+            warn("Constraint options `finite_diff_jac_sparsity`, "
+                 "`finite_diff_rel_step`, `keep_feasible`, and `hess`"
+                 "are ignored by this method.",
+                 OptimizeWarning, stacklevel=3)
+
+        fun = con.fun
+        if callable(con.jac):
+            jac = con.jac
+        else:
+            jac = None
+
+    else:  # LinearConstraint
+        if np.any(con.keep_feasible):
+            warn("Constraint option `keep_feasible` is ignored by this method.",
+                 OptimizeWarning, stacklevel=3)
+
+        A = con.A
+        if issparse(A):
+            A = A.toarray()
+        def fun(x):
+            return np.dot(A, x)
+        def jac(x):
+            return A
+
+    # FIXME: when bugs in VectorFunction/LinearVectorFunction are worked out,
+    # use pcon.fun.fun and pcon.fun.jac. Until then, get fun/jac above.
+    pcon = PreparedConstraint(con, x0)
+    lb, ub = pcon.bounds
+
+    i_eq = lb == ub
+    i_bound_below = np.logical_xor(lb != -np.inf, i_eq)
+    i_bound_above = np.logical_xor(ub != np.inf, i_eq)
+    i_unbounded = np.logical_and(lb == -np.inf, ub == np.inf)
+
+    if np.any(i_unbounded):
+        warn("At least one constraint is unbounded above and below. Such "
+             "constraints are ignored.",
+             OptimizeWarning, stacklevel=3)
+
+    ceq = []
+    if np.any(i_eq):
+        def f_eq(x):
+            y = np.array(fun(x)).flatten()
+            return y[i_eq] - lb[i_eq]
+        ceq = [{"type": "eq", "fun": f_eq}]
+
+        if jac is not None:
+            def j_eq(x):
+                dy = jac(x)
+                if issparse(dy):
+                    dy = dy.toarray()
+                dy = np.atleast_2d(dy)
+                return dy[i_eq, :]
+            ceq[0]["jac"] = j_eq
+
+    cineq = []
+    n_bound_below = np.sum(i_bound_below)
+    n_bound_above = np.sum(i_bound_above)
+    if n_bound_below + n_bound_above:
+        def f_ineq(x):
+            y = np.zeros(n_bound_below + n_bound_above)
+            y_all = np.array(fun(x)).flatten()
+            y[:n_bound_below] = y_all[i_bound_below] - lb[i_bound_below]
+            y[n_bound_below:] = -(y_all[i_bound_above] - ub[i_bound_above])
+            return y
+        cineq = [{"type": "ineq", "fun": f_ineq}]
+
+        if jac is not None:
+            def j_ineq(x):
+                dy = np.zeros((n_bound_below + n_bound_above, len(x0)))
+                dy_all = jac(x)
+                if issparse(dy_all):
+                    dy_all = dy_all.toarray()
+                dy_all = np.atleast_2d(dy_all)
+                dy[:n_bound_below, :] = dy_all[i_bound_below]
+                dy[n_bound_below:, :] = -dy_all[i_bound_above]
+                return dy
+            cineq[0]["jac"] = j_ineq
+
+    old_constraints = ceq + cineq
+
+    if len(old_constraints) > 1:
+        warn("Equality and inequality constraints are specified in the same "
+             "element of the constraint list. For efficient use with this "
+             "method, equality and inequality constraints should be specified "
+             "in separate elements of the constraint list. ",
+             OptimizeWarning, stacklevel=3)
+    return old_constraints
+
+
+def old_constraint_to_new(ic, con):
+    """
+    Converts old-style constraint dictionaries to new-style constraint objects.
+    """
+    # check type
+    try:
+        ctype = con['type'].lower()
+    except KeyError as e:
+        raise KeyError('Constraint %d has no type defined.' % ic) from e
+    except TypeError as e:
+        raise TypeError(
+            'Constraints must be a sequence of dictionaries.'
+        ) from e
+    except AttributeError as e:
+        raise TypeError("Constraint's type must be a string.") from e
+    else:
+        if ctype not in ['eq', 'ineq']:
+            raise ValueError("Unknown constraint type '%s'." % con['type'])
+    if 'fun' not in con:
+        raise ValueError('Constraint %d has no function defined.' % ic)
+
+    lb = 0
+    if ctype == 'eq':
+        ub = 0
+    else:
+        ub = np.inf
+
+    jac = '2-point'
+    if 'args' in con:
+        args = con['args']
+        def fun(x):
+            return con["fun"](x, *args)
+        if 'jac' in con:
+            def jac(x):
+                return con["jac"](x, *args)
+    else:
+        fun = con['fun']
+        if 'jac' in con:
+            jac = con['jac']
+
+    return NonlinearConstraint(fun, lb, ub, jac)

vila/lib/python3.10/site-packages/scipy/optimize/_dcsrch.py

@@ -0,0 +1,728 @@
+import numpy as np
+
+"""
+# 2023 - ported from minpack2.dcsrch, dcstep (Fortran) to Python
+c     MINPACK-1 Project. June 1983.
+c     Argonne National Laboratory.
+c     Jorge J. More' and David J. Thuente.
+c
+c     MINPACK-2 Project. November 1993.
+c     Argonne National Laboratory and University of Minnesota.
+c     Brett M. Averick, Richard G. Carter, and Jorge J. More'.
+"""
+
+# NOTE this file was linted by black on first commit, and can be kept that way.
+
+
+class DCSRCH:
+    """
+    Parameters
+    ----------
+    phi : callable phi(alpha)
+        Function at point `alpha`
+    derphi : callable phi'(alpha)
+        Objective function derivative. Returns a scalar.
+    ftol : float
+        A nonnegative tolerance for the sufficient decrease condition.
+    gtol : float
+        A nonnegative tolerance for the curvature condition.
+    xtol : float
+        A nonnegative relative tolerance for an acceptable step. The
+        subroutine exits with a warning if the relative difference between
+        sty and stx is less than xtol.
+    stpmin : float
+        A nonnegative lower bound for the step.
+    stpmax :
+        A nonnegative upper bound for the step.
+
+    Notes
+    -----
+
+    This subroutine finds a step that satisfies a sufficient
+    decrease condition and a curvature condition.
+
+    Each call of the subroutine updates an interval with
+    endpoints stx and sty. The interval is initially chosen
+    so that it contains a minimizer of the modified function
+
+           psi(stp) = f(stp) - f(0) - ftol*stp*f'(0).
+
+    If psi(stp) <= 0 and f'(stp) >= 0 for some step, then the
+    interval is chosen so that it contains a minimizer of f.
+
+    The algorithm is designed to find a step that satisfies
+    the sufficient decrease condition
+
+           f(stp) <= f(0) + ftol*stp*f'(0),
+
+    and the curvature condition
+
+           abs(f'(stp)) <= gtol*abs(f'(0)).
+
+    If ftol is less than gtol and if, for example, the function
+    is bounded below, then there is always a step which satisfies
+    both conditions.
+
+    If no step can be found that satisfies both conditions, then
+    the algorithm stops with a warning. In this case stp only
+    satisfies the sufficient decrease condition.
+
+    A typical invocation of dcsrch has the following outline:
+
+    Evaluate the function at stp = 0.0d0; store in f.
+    Evaluate the gradient at stp = 0.0d0; store in g.
+    Choose a starting step stp.
+
+    task = 'START'
+    10 continue
+        call dcsrch(stp,f,g,ftol,gtol,xtol,task,stpmin,stpmax,
+                   isave,dsave)
+        if (task .eq. 'FG') then
+           Evaluate the function and the gradient at stp
+           go to 10
+           end if
+
+    NOTE: The user must not alter work arrays between calls.
+
+    The subroutine statement is
+
+        subroutine dcsrch(f,g,stp,ftol,gtol,xtol,stpmin,stpmax,
+                         task,isave,dsave)
+        where
+
+    stp is a double precision variable.
+        On entry stp is the current estimate of a satisfactory
+            step. On initial entry, a positive initial estimate
+            must be provided.
+        On exit stp is the current estimate of a satisfactory step
+            if task = 'FG'. If task = 'CONV' then stp satisfies
+            the sufficient decrease and curvature condition.
+
+    f is a double precision variable.
+        On initial entry f is the value of the function at 0.
+        On subsequent entries f is the value of the
+            function at stp.
+        On exit f is the value of the function at stp.
+
+    g is a double precision variable.
+        On initial entry g is the derivative of the function at 0.
+        On subsequent entries g is the derivative of the
+           function at stp.
+        On exit g is the derivative of the function at stp.
+
+    ftol is a double precision variable.
+        On entry ftol specifies a nonnegative tolerance for the
+           sufficient decrease condition.
+        On exit ftol is unchanged.
+
+    gtol is a double precision variable.
+        On entry gtol specifies a nonnegative tolerance for the
+           curvature condition.
+        On exit gtol is unchanged.
+
+    xtol is a double precision variable.
+        On entry xtol specifies a nonnegative relative tolerance
+          for an acceptable step. The subroutine exits with a
+          warning if the relative difference between sty and stx
+          is less than xtol.
+
+        On exit xtol is unchanged.
+
+    task is a character variable of length at least 60.
+        On initial entry task must be set to 'START'.
+        On exit task indicates the required action:
+
+           If task(1:2) = 'FG' then evaluate the function and
+           derivative at stp and call dcsrch again.
+
+           If task(1:4) = 'CONV' then the search is successful.
+
+           If task(1:4) = 'WARN' then the subroutine is not able
+           to satisfy the convergence conditions. The exit value of
+           stp contains the best point found during the search.
+
+          If task(1:5) = 'ERROR' then there is an error in the
+          input arguments.
+
+        On exit with convergence, a warning or an error, the
+           variable task contains additional information.
+
+    stpmin is a double precision variable.
+        On entry stpmin is a nonnegative lower bound for the step.
+        On exit stpmin is unchanged.
+
+    stpmax is a double precision variable.
+        On entry stpmax is a nonnegative upper bound for the step.
+        On exit stpmax is unchanged.
+
+    isave is an integer work array of dimension 2.
+
+    dsave is a double precision work array of dimension 13.
+
+    Subprograms called
+
+      MINPACK-2 ... dcstep
+    MINPACK-1 Project. June 1983.
+    Argonne National Laboratory.
+    Jorge J. More' and David J. Thuente.
+
+    MINPACK-2 Project. November 1993.
+    Argonne National Laboratory and University of Minnesota.
+    Brett M. Averick, Richard G. Carter, and Jorge J. More'.
+    """
+
+    def __init__(self, phi, derphi, ftol, gtol, xtol, stpmin, stpmax):
+        self.stage = None
+        self.ginit = None
+        self.gtest = None
+        self.gx = None
+        self.gy = None
+        self.finit = None
+        self.fx = None
+        self.fy = None
+        self.stx = None
+        self.sty = None
+        self.stmin = None
+        self.stmax = None
+        self.width = None
+        self.width1 = None
+
+        # leave all assessment of tolerances/limits to the first call of
+        # this object
+        self.ftol = ftol
+        self.gtol = gtol
+        self.xtol = xtol
+        self.stpmin = stpmin
+        self.stpmax = stpmax
+
+        self.phi = phi
+        self.derphi = derphi
+
+    def __call__(self, alpha1, phi0=None, derphi0=None, maxiter=100):
+        """
+        Parameters
+        ----------
+        alpha1 : float
+            alpha1 is the current estimate of a satisfactory
+            step. A positive initial estimate must be provided.
+        phi0 : float
+            the value of `phi` at 0 (if known).
+        derphi0 : float
+            the derivative of `derphi` at 0 (if known).
+        maxiter : int
+
+        Returns
+        -------
+        alpha : float
+            Step size, or None if no suitable step was found.
+        phi : float
+            Value of `phi` at the new point `alpha`.
+        phi0 : float
+            Value of `phi` at `alpha=0`.
+        task : bytes
+            On exit task indicates status information.
+
+           If task[:4] == b'CONV' then the search is successful.
+
+           If task[:4] == b'WARN' then the subroutine is not able
+           to satisfy the convergence conditions. The exit value of
+           stp contains the best point found during the search.
+
+           If task[:5] == b'ERROR' then there is an error in the
+           input arguments.
+        """
+        if phi0 is None:
+            phi0 = self.phi(0.0)
+        if derphi0 is None:
+            derphi0 = self.derphi(0.0)
+
+        phi1 = phi0
+        derphi1 = derphi0
+
+        task = b"START"
+        for i in range(maxiter):
+            stp, phi1, derphi1, task = self._iterate(
+                alpha1, phi1, derphi1, task
+            )
+
+            if not np.isfinite(stp):
+                task = b"WARN"
+                stp = None
+                break
+
+            if task[:2] == b"FG":
+                alpha1 = stp
+                phi1 = self.phi(stp)
+                derphi1 = self.derphi(stp)
+            else:
+                break
+        else:
+            # maxiter reached, the line search did not converge
+            stp = None
+            task = b"WARNING: dcsrch did not converge within max iterations"
+
+        if task[:5] == b"ERROR" or task[:4] == b"WARN":
+            stp = None  # failed
+
+        return stp, phi1, phi0, task
+
+    def _iterate(self, stp, f, g, task):
+        """
+        Parameters
+        ----------
+        stp : float
+            The current estimate of a satisfactory step. On initial entry, a
+            positive initial estimate must be provided.
+        f : float
+            On first call f is the value of the function at 0. On subsequent
+            entries f should be the value of the function at stp.
+        g : float
+            On initial entry g is the derivative of the function at 0. On
+            subsequent entries g is the derivative of the function at stp.
+        task : bytes
+            On initial entry task must be set to 'START'.
+
+        On exit with convergence, a warning or an error, the
+           variable task contains additional information.
+
+
+        Returns
+        -------
+        stp, f, g, task: tuple
+
+            stp : float
+                the current estimate of a satisfactory step if task = 'FG'. If
+                task = 'CONV' then stp satisfies the sufficient decrease and
+                curvature condition.
+            f : float
+                the value of the function at stp.
+            g : float
+                the derivative of the function at stp.
+            task : bytes
+                On exit task indicates the required action:
+
+               If task(1:2) == b'FG' then evaluate the function and
+               derivative at stp and call dcsrch again.
+
+               If task(1:4) == b'CONV' then the search is successful.
+
+               If task(1:4) == b'WARN' then the subroutine is not able
+               to satisfy the convergence conditions. The exit value of
+               stp contains the best point found during the search.
+
+              If task(1:5) == b'ERROR' then there is an error in the
+              input arguments.
+        """
+        p5 = 0.5
+        p66 = 0.66
+        xtrapl = 1.1
+        xtrapu = 4.0
+
+        if task[:5] == b"START":
+            if stp < self.stpmin:
+                task = b"ERROR: STP .LT. STPMIN"
+            if stp > self.stpmax:
+                task = b"ERROR: STP .GT. STPMAX"
+            if g >= 0:
+                task = b"ERROR: INITIAL G .GE. ZERO"
+            if self.ftol < 0:
+                task = b"ERROR: FTOL .LT. ZERO"
+            if self.gtol < 0:
+                task = b"ERROR: GTOL .LT. ZERO"
+            if self.xtol < 0:
+                task = b"ERROR: XTOL .LT. ZERO"
+            if self.stpmin < 0:
+                task = b"ERROR: STPMIN .LT. ZERO"
+            if self.stpmax < self.stpmin:
+                task = b"ERROR: STPMAX .LT. STPMIN"
+
+            if task[:5] == b"ERROR":
+                return stp, f, g, task
+
+            # Initialize local variables.
+
+            self.brackt = False
+            self.stage = 1
+            self.finit = f
+            self.ginit = g
+            self.gtest = self.ftol * self.ginit
+            self.width = self.stpmax - self.stpmin
+            self.width1 = self.width / p5
+
+            # The variables stx, fx, gx contain the values of the step,
+            # function, and derivative at the best step.
+            # The variables sty, fy, gy contain the value of the step,
+            # function, and derivative at sty.
+            # The variables stp, f, g contain the values of the step,
+            # function, and derivative at stp.
+
+            self.stx = 0.0
+            self.fx = self.finit
+            self.gx = self.ginit
+            self.sty = 0.0
+            self.fy = self.finit
+            self.gy = self.ginit
+            self.stmin = 0
+            self.stmax = stp + xtrapu * stp
+            task = b"FG"
+            return stp, f, g, task
+
+        # in the original Fortran this was a location to restore variables
+        # we don't need to do that because they're attributes.
+
+        # If psi(stp) <= 0 and f'(stp) >= 0 for some step, then the
+        # algorithm enters the second stage.
+        ftest = self.finit + stp * self.gtest
+
+        if self.stage == 1 and f <= ftest and g >= 0:
+            self.stage = 2
+
+        # test for warnings
+        if self.brackt and (stp <= self.stmin or stp >= self.stmax):
+            task = b"WARNING: ROUNDING ERRORS PREVENT PROGRESS"
+        if self.brackt and self.stmax - self.stmin <= self.xtol * self.stmax:
+            task = b"WARNING: XTOL TEST SATISFIED"
+        if stp == self.stpmax and f <= ftest and g <= self.gtest:
+            task = b"WARNING: STP = STPMAX"
+        if stp == self.stpmin and (f > ftest or g >= self.gtest):
+            task = b"WARNING: STP = STPMIN"
+
+        # test for convergence
+        if f <= ftest and abs(g) <= self.gtol * -self.ginit:
+            task = b"CONVERGENCE"
+
+        # test for termination
+        if task[:4] == b"WARN" or task[:4] == b"CONV":
+            return stp, f, g, task
+
+        # A modified function is used to predict the step during the
+        # first stage if a lower function value has been obtained but
+        # the decrease is not sufficient.
+        if self.stage == 1 and f <= self.fx and f > ftest:
+            # Define the modified function and derivative values.
+            fm = f - stp * self.gtest
+            fxm = self.fx - self.stx * self.gtest
+            fym = self.fy - self.sty * self.gtest
+            gm = g - self.gtest
+            gxm = self.gx - self.gtest
+            gym = self.gy - self.gtest
+
+            # Call dcstep to update stx, sty, and to compute the new step.
+            # dcstep can have several operations which can produce NaN
+            # e.g. inf/inf. Filter these out.
+            with np.errstate(invalid="ignore", over="ignore"):
+                tup = dcstep(
+                    self.stx,
+                    fxm,
+                    gxm,
+                    self.sty,
+                    fym,
+                    gym,
+                    stp,
+                    fm,
+                    gm,
+                    self.brackt,
+                    self.stmin,
+                    self.stmax,
+                )
+                self.stx, fxm, gxm, self.sty, fym, gym, stp, self.brackt = tup
+
+            # Reset the function and derivative values for f
+            self.fx = fxm + self.stx * self.gtest
+            self.fy = fym + self.sty * self.gtest
+            self.gx = gxm + self.gtest
+            self.gy = gym + self.gtest
+
+        else:
+            # Call dcstep to update stx, sty, and to compute the new step.
+            # dcstep can have several operations which can produce NaN
+            # e.g. inf/inf. Filter these out.
+
+            with np.errstate(invalid="ignore", over="ignore"):
+                tup = dcstep(
+                    self.stx,
+                    self.fx,
+                    self.gx,
+                    self.sty,
+                    self.fy,
+                    self.gy,
+                    stp,
+                    f,
+                    g,
+                    self.brackt,
+                    self.stmin,
+                    self.stmax,
+                )
+            (
+                self.stx,
+                self.fx,
+                self.gx,
+                self.sty,
+                self.fy,
+                self.gy,
+                stp,
+                self.brackt,
+            ) = tup
+
+        # Decide if a bisection step is needed
+        if self.brackt:
+            if abs(self.sty - self.stx) >= p66 * self.width1:
+                stp = self.stx + p5 * (self.sty - self.stx)
+            self.width1 = self.width
+            self.width = abs(self.sty - self.stx)
+
+        # Set the minimum and maximum steps allowed for stp.
+        if self.brackt:
+            self.stmin = min(self.stx, self.sty)
+            self.stmax = max(self.stx, self.sty)
+        else:
+            self.stmin = stp + xtrapl * (stp - self.stx)
+            self.stmax = stp + xtrapu * (stp - self.stx)
+
+        # Force the step to be within the bounds stpmax and stpmin.
+        stp = np.clip(stp, self.stpmin, self.stpmax)
+
+        # If further progress is not possible, let stp be the best
+        # point obtained during the search.
+        if (
+            self.brackt
+            and (stp <= self.stmin or stp >= self.stmax)
+            or (
+                self.brackt
+                and self.stmax - self.stmin <= self.xtol * self.stmax
+            )
+        ):
+            stp = self.stx
+
+        # Obtain another function and derivative
+        task = b"FG"
+        return stp, f, g, task
+
+
+def dcstep(stx, fx, dx, sty, fy, dy, stp, fp, dp, brackt, stpmin, stpmax):
+    """
+    Subroutine dcstep
+
+    This subroutine computes a safeguarded step for a search
+    procedure and updates an interval that contains a step that
+    satisfies a sufficient decrease and a curvature condition.
+
+    The parameter stx contains the step with the least function
+    value. If brackt is set to .true. then a minimizer has
+    been bracketed in an interval with endpoints stx and sty.
+    The parameter stp contains the current step.
+    The subroutine assumes that if brackt is set to .true. then
+
+        min(stx,sty) < stp < max(stx,sty),
+
+    and that the derivative at stx is negative in the direction
+    of the step.
+
+    The subroutine statement is
+
+      subroutine dcstep(stx,fx,dx,sty,fy,dy,stp,fp,dp,brackt,
+                        stpmin,stpmax)
+
+    where
+
+    stx is a double precision variable.
+        On entry stx is the best step obtained so far and is an
+          endpoint of the interval that contains the minimizer.
+        On exit stx is the updated best step.
+
+    fx is a double precision variable.
+        On entry fx is the function at stx.
+        On exit fx is the function at stx.
+
+    dx is a double precision variable.
+        On entry dx is the derivative of the function at
+          stx. The derivative must be negative in the direction of
+          the step, that is, dx and stp - stx must have opposite
+          signs.
+        On exit dx is the derivative of the function at stx.
+
+    sty is a double precision variable.
+        On entry sty is the second endpoint of the interval that
+          contains the minimizer.
+        On exit sty is the updated endpoint of the interval that
+          contains the minimizer.
+
+    fy is a double precision variable.
+        On entry fy is the function at sty.
+        On exit fy is the function at sty.
+
+    dy is a double precision variable.
+        On entry dy is the derivative of the function at sty.
+        On exit dy is the derivative of the function at the exit sty.
+
+    stp is a double precision variable.
+        On entry stp is the current step. If brackt is set to .true.
+          then on input stp must be between stx and sty.
+        On exit stp is a new trial step.
+
+    fp is a double precision variable.
+        On entry fp is the function at stp
+        On exit fp is unchanged.
+
+    dp is a double precision variable.
+        On entry dp is the derivative of the function at stp.
+        On exit dp is unchanged.
+
+    brackt is an logical variable.
+        On entry brackt specifies if a minimizer has been bracketed.
+            Initially brackt must be set to .false.
+        On exit brackt specifies if a minimizer has been bracketed.
+            When a minimizer is bracketed brackt is set to .true.
+
+    stpmin is a double precision variable.
+        On entry stpmin is a lower bound for the step.
+        On exit stpmin is unchanged.
+
+    stpmax is a double precision variable.
+        On entry stpmax is an upper bound for the step.
+        On exit stpmax is unchanged.
+
+    MINPACK-1 Project. June 1983
+    Argonne National Laboratory.
+    Jorge J. More' and David J. Thuente.
+
+    MINPACK-2 Project. November 1993.
+    Argonne National Laboratory and University of Minnesota.
+    Brett M. Averick and Jorge J. More'.
+
+    """
+    sgn_dp = np.sign(dp)
+    sgn_dx = np.sign(dx)
+
+    # sgnd = dp * (dx / abs(dx))
+    sgnd = sgn_dp * sgn_dx
+
+    # First case: A higher function value. The minimum is bracketed.
+    # If the cubic step is closer to stx than the quadratic step, the
+    # cubic step is taken, otherwise the average of the cubic and
+    # quadratic steps is taken.
+    if fp > fx:
+        theta = 3.0 * (fx - fp) / (stp - stx) + dx + dp
+        s = max(abs(theta), abs(dx), abs(dp))
+        gamma = s * np.sqrt((theta / s) ** 2 - (dx / s) * (dp / s))
+        if stp < stx:
+            gamma *= -1
+        p = (gamma - dx) + theta
+        q = ((gamma - dx) + gamma) + dp
+        r = p / q
+        stpc = stx + r * (stp - stx)
+        stpq = stx + ((dx / ((fx - fp) / (stp - stx) + dx)) / 2.0) * (stp - stx)
+        if abs(stpc - stx) <= abs(stpq - stx):
+            stpf = stpc
+        else:
+            stpf = stpc + (stpq - stpc) / 2.0
+        brackt = True
+    elif sgnd < 0.0:
+        # Second case: A lower function value and derivatives of opposite
+        # sign. The minimum is bracketed. If the cubic step is farther from
+        # stp than the secant step, the cubic step is taken, otherwise the
+        # secant step is taken.
+        theta = 3 * (fx - fp) / (stp - stx) + dx + dp
+        s = max(abs(theta), abs(dx), abs(dp))
+        gamma = s * np.sqrt((theta / s) ** 2 - (dx / s) * (dp / s))
+        if stp > stx:
+            gamma *= -1
+        p = (gamma - dp) + theta
+        q = ((gamma - dp) + gamma) + dx
+        r = p / q
+        stpc = stp + r * (stx - stp)
+        stpq = stp + (dp / (dp - dx)) * (stx - stp)
+        if abs(stpc - stp) > abs(stpq - stp):
+            stpf = stpc
+        else:
+            stpf = stpq
+        brackt = True
+    elif abs(dp) < abs(dx):
+        # Third case: A lower function value, derivatives of the same sign,
+        # and the magnitude of the derivative decreases.
+
+        # The cubic step is computed only if the cubic tends to infinity
+        # in the direction of the step or if the minimum of the cubic
+        # is beyond stp. Otherwise the cubic step is defined to be the
+        # secant step.
+        theta = 3 * (fx - fp) / (stp - stx) + dx + dp
+        s = max(abs(theta), abs(dx), abs(dp))
+
+        # The case gamma = 0 only arises if the cubic does not tend
+        # to infinity in the direction of the step.
+        gamma = s * np.sqrt(max(0, (theta / s) ** 2 - (dx / s) * (dp / s)))
+        if stp > stx:
+            gamma = -gamma
+        p = (gamma - dp) + theta
+        q = (gamma + (dx - dp)) + gamma
+        r = p / q
+        if r < 0 and gamma != 0:
+            stpc = stp + r * (stx - stp)
+        elif stp > stx:
+            stpc = stpmax
+        else:
+            stpc = stpmin
+        stpq = stp + (dp / (dp - dx)) * (stx - stp)
+
+        if brackt:
+            # A minimizer has been bracketed. If the cubic step is
+            # closer to stp than the secant step, the cubic step is
+            # taken, otherwise the secant step is taken.
+            if abs(stpc - stp) < abs(stpq - stp):
+                stpf = stpc
+            else:
+                stpf = stpq
+
+            if stp > stx:
+                stpf = min(stp + 0.66 * (sty - stp), stpf)
+            else:
+                stpf = max(stp + 0.66 * (sty - stp), stpf)
+        else:
+            # A minimizer has not been bracketed. If the cubic step is
+            # farther from stp than the secant step, the cubic step is
+            # taken, otherwise the secant step is taken.
+            if abs(stpc - stp) > abs(stpq - stp):
+                stpf = stpc
+            else:
+                stpf = stpq
+            stpf = np.clip(stpf, stpmin, stpmax)
+
+    else:
+        # Fourth case: A lower function value, derivatives of the same sign,
+        # and the magnitude of the derivative does not decrease. If the
+        # minimum is not bracketed, the step is either stpmin or stpmax,
+        # otherwise the cubic step is taken.
+        if brackt:
+            theta = 3.0 * (fp - fy) / (sty - stp) + dy + dp
+            s = max(abs(theta), abs(dy), abs(dp))
+            gamma = s * np.sqrt((theta / s) ** 2 - (dy / s) * (dp / s))
+            if stp > sty:
+                gamma = -gamma
+            p = (gamma - dp) + theta
+            q = ((gamma - dp) + gamma) + dy
+            r = p / q
+            stpc = stp + r * (sty - stp)
+            stpf = stpc
+        elif stp > stx:
+            stpf = stpmax
+        else:
+            stpf = stpmin
+
+    # Update the interval which contains a minimizer.
+    if fp > fx:
+        sty = stp
+        fy = fp
+        dy = dp
+    else:
+        if sgnd < 0:
+            sty = stx
+            fy = fx
+            dy = dx
+        stx = stp
+        fx = fp
+        dx = dp
+
+    # Compute the new step.
+    stp = stpf
+
+    return stx, fx, dx, sty, fy, dy, stp, brackt

vila/lib/python3.10/site-packages/scipy/optimize/_direct_py.py

@@ -0,0 +1,278 @@
+from __future__ import annotations
+from typing import (  # noqa: UP035
+    Any, Callable, Iterable, TYPE_CHECKING
+)
+
+import numpy as np
+from scipy.optimize import OptimizeResult
+from ._constraints import old_bound_to_new, Bounds
+from ._direct import direct as _direct  # type: ignore
+
+if TYPE_CHECKING:
+    import numpy.typing as npt
+
+__all__ = ['direct']
+
+ERROR_MESSAGES = (
+    "Number of function evaluations done is larger than maxfun={}",
+    "Number of iterations is larger than maxiter={}",
+    "u[i] < l[i] for some i",
+    "maxfun is too large",
+    "Initialization failed",
+    "There was an error in the creation of the sample points",
+    "An error occurred while the function was sampled",
+    "Maximum number of levels has been reached.",
+    "Forced stop",
+    "Invalid arguments",
+    "Out of memory",
+)
+
+SUCCESS_MESSAGES = (
+    ("The best function value found is within a relative error={} "
+     "of the (known) global optimum f_min"),
+    ("The volume of the hyperrectangle containing the lowest function value "
+     "found is below vol_tol={}"),
+    ("The side length measure of the hyperrectangle containing the lowest "
+     "function value found is below len_tol={}"),
+)
+
+
+def direct(
+    func: Callable[[npt.ArrayLike, tuple[Any]], float],
+    bounds: Iterable | Bounds,
+    *,
+    args: tuple = (),
+    eps: float = 1e-4,
+    maxfun: int | None = None,
+    maxiter: int = 1000,
+    locally_biased: bool = True,
+    f_min: float = -np.inf,
+    f_min_rtol: float = 1e-4,
+    vol_tol: float = 1e-16,
+    len_tol: float = 1e-6,
+    callback: Callable[[npt.ArrayLike], None] | None = None
+) -> OptimizeResult:
+    """
+    Finds the global minimum of a function using the
+    DIRECT algorithm.
+
+    Parameters
+    ----------
+    func : callable
+        The objective function to be minimized.
+        ``func(x, *args) -> float``
+        where ``x`` is an 1-D array with shape (n,) and ``args`` is a tuple of
+        the fixed parameters needed to completely specify the function.
+    bounds : sequence or `Bounds`
+        Bounds for variables. There are two ways to specify the bounds:
+
+        1. Instance of `Bounds` class.
+        2. ``(min, max)`` pairs for each element in ``x``.
+
+    args : tuple, optional
+        Any additional fixed parameters needed to
+        completely specify the objective function.
+    eps : float, optional
+        Minimal required difference of the objective function values
+        between the current best hyperrectangle and the next potentially
+        optimal hyperrectangle to be divided. In consequence, `eps` serves as a
+        tradeoff between local and global search: the smaller, the more local
+        the search becomes. Default is 1e-4.
+    maxfun : int or None, optional
+        Approximate upper bound on objective function evaluations.
+        If `None`, will be automatically set to ``1000 * N`` where ``N``
+        represents the number of dimensions. Will be capped if necessary to
+        limit DIRECT's RAM usage to app. 1GiB. This will only occur for very
+        high dimensional problems and excessive `max_fun`. Default is `None`.
+    maxiter : int, optional
+        Maximum number of iterations. Default is 1000.
+    locally_biased : bool, optional
+        If `True` (default), use the locally biased variant of the
+        algorithm known as DIRECT_L. If `False`, use the original unbiased
+        DIRECT algorithm. For hard problems with many local minima,
+        `False` is recommended.
+    f_min : float, optional
+        Function value of the global optimum. Set this value only if the
+        global optimum is known. Default is ``-np.inf``, so that this
+        termination criterion is deactivated.
+    f_min_rtol : float, optional
+        Terminate the optimization once the relative error between the
+        current best minimum `f` and the supplied global minimum `f_min`
+        is smaller than `f_min_rtol`. This parameter is only used if
+        `f_min` is also set. Must lie between 0 and 1. Default is 1e-4.
+    vol_tol : float, optional
+        Terminate the optimization once the volume of the hyperrectangle
+        containing the lowest function value is smaller than `vol_tol`
+        of the complete search space. Must lie between 0 and 1.
+        Default is 1e-16.
+    len_tol : float, optional
+        If `locally_biased=True`, terminate the optimization once half of
+        the normalized maximal side length of the hyperrectangle containing
+        the lowest function value is smaller than `len_tol`.
+        If `locally_biased=False`, terminate the optimization once half of
+        the normalized diagonal of the hyperrectangle containing the lowest
+        function value is smaller than `len_tol`. Must lie between 0 and 1.
+        Default is 1e-6.
+    callback : callable, optional
+        A callback function with signature ``callback(xk)`` where ``xk``
+        represents the best function value found so far.
+
+    Returns
+    -------
+    res : OptimizeResult
+        The optimization result represented as a ``OptimizeResult`` object.
+        Important attributes are: ``x`` the solution array, ``success`` a
+        Boolean flag indicating if the optimizer exited successfully and
+        ``message`` which describes the cause of the termination. See
+        `OptimizeResult` for a description of other attributes.
+
+    Notes
+    -----
+    DIviding RECTangles (DIRECT) is a deterministic global
+    optimization algorithm capable of minimizing a black box function with
+    its variables subject to lower and upper bound constraints by sampling
+    potential solutions in the search space [1]_. The algorithm starts by
+    normalising the search space to an n-dimensional unit hypercube.
+    It samples the function at the center of this hypercube and at 2n
+    (n is the number of variables) more points, 2 in each coordinate
+    direction. Using these function values, DIRECT then divides the
+    domain into hyperrectangles, each having exactly one of the sampling
+    points as its center. In each iteration, DIRECT chooses, using the `eps`
+    parameter which defaults to 1e-4, some of the existing hyperrectangles
+    to be further divided. This division process continues until either the
+    maximum number of iterations or maximum function evaluations allowed
+    are exceeded, or the hyperrectangle containing the minimal value found
+    so far becomes small enough. If `f_min` is specified, the optimization
+    will stop once this function value is reached within a relative tolerance.
+    The locally biased variant of DIRECT (originally called DIRECT_L) [2]_ is
+    used by default. It makes the search more locally biased and more
+    efficient for cases with only a few local minima.
+
+    A note about termination criteria: `vol_tol` refers to the volume of the
+    hyperrectangle containing the lowest function value found so far. This
+    volume decreases exponentially with increasing dimensionality of the
+    problem. Therefore `vol_tol` should be decreased to avoid premature
+    termination of the algorithm for higher dimensions. This does not hold
+    for `len_tol`: it refers either to half of the maximal side length
+    (for ``locally_biased=True``) or half of the diagonal of the
+    hyperrectangle (for ``locally_biased=False``).
+
+    This code is based on the DIRECT 2.0.4 Fortran code by Gablonsky et al. at
+    https://ctk.math.ncsu.edu/SOFTWARE/DIRECTv204.tar.gz .
+    This original version was initially converted via f2c and then cleaned up
+    and reorganized by Steven G. Johnson, August 2007, for the NLopt project.
+    The `direct` function wraps the C implementation.
+
+    .. versionadded:: 1.9.0
+
+    References
+    ----------
+    .. [1] Jones, D.R., Perttunen, C.D. & Stuckman, B.E. Lipschitzian
+        optimization without the Lipschitz constant. J Optim Theory Appl
+        79, 157-181 (1993).
+    .. [2] Gablonsky, J., Kelley, C. A Locally-Biased form of the DIRECT
+        Algorithm. Journal of Global Optimization 21, 27-37 (2001).
+
+    Examples
+    --------
+    The following example is a 2-D problem with four local minima: minimizing
+    the Styblinski-Tang function
+    (https://en.wikipedia.org/wiki/Test_functions_for_optimization).
+
+    >>> from scipy.optimize import direct, Bounds
+    >>> def styblinski_tang(pos):
+    ...     x, y = pos
+    ...     return 0.5 * (x**4 - 16*x**2 + 5*x + y**4 - 16*y**2 + 5*y)
+    >>> bounds = Bounds([-4., -4.], [4., 4.])
+    >>> result = direct(styblinski_tang, bounds)
+    >>> result.x, result.fun, result.nfev
+    array([-2.90321597, -2.90321597]), -78.3323279095383, 2011
+
+    The correct global minimum was found but with a huge number of function
+    evaluations (2011). Loosening the termination tolerances `vol_tol` and
+    `len_tol` can be used to stop DIRECT earlier.
+
+    >>> result = direct(styblinski_tang, bounds, len_tol=1e-3)
+    >>> result.x, result.fun, result.nfev
+    array([-2.9044353, -2.9044353]), -78.33230330754142, 207
+
+    """
+    # convert bounds to new Bounds class if necessary
+    if not isinstance(bounds, Bounds):
+        if isinstance(bounds, list) or isinstance(bounds, tuple):
+            lb, ub = old_bound_to_new(bounds)
+            bounds = Bounds(lb, ub)
+        else:
+            message = ("bounds must be a sequence or "
+                       "instance of Bounds class")
+            raise ValueError(message)
+
+    lb = np.ascontiguousarray(bounds.lb, dtype=np.float64)
+    ub = np.ascontiguousarray(bounds.ub, dtype=np.float64)
+
+    # validate bounds
+    # check that lower bounds are smaller than upper bounds
+    if not np.all(lb < ub):
+        raise ValueError('Bounds are not consistent min < max')
+    # check for infs
+    if (np.any(np.isinf(lb)) or np.any(np.isinf(ub))):
+        raise ValueError("Bounds must not be inf.")
+
+    # validate tolerances
+    if (vol_tol < 0 or vol_tol > 1):
+        raise ValueError("vol_tol must be between 0 and 1.")
+    if (len_tol < 0 or len_tol > 1):
+        raise ValueError("len_tol must be between 0 and 1.")
+    if (f_min_rtol < 0 or f_min_rtol > 1):
+        raise ValueError("f_min_rtol must be between 0 and 1.")
+
+    # validate maxfun and maxiter
+    if maxfun is None:
+        maxfun = 1000 * lb.shape[0]
+    if not isinstance(maxfun, int):
+        raise ValueError("maxfun must be of type int.")
+    if maxfun < 0:
+        raise ValueError("maxfun must be > 0.")
+    if not isinstance(maxiter, int):
+        raise ValueError("maxiter must be of type int.")
+    if maxiter < 0:
+        raise ValueError("maxiter must be > 0.")
+
+    # validate boolean parameters
+    if not isinstance(locally_biased, bool):
+        raise ValueError("locally_biased must be True or False.")
+
+    def _func_wrap(x, args=None):
+        x = np.asarray(x)
+        if args is None:
+            f = func(x)
+        else:
+            f = func(x, *args)
+        # always return a float
+        return np.asarray(f).item()
+
+    # TODO: fix disp argument
+    x, fun, ret_code, nfev, nit = _direct(
+        _func_wrap,
+        np.asarray(lb), np.asarray(ub),
+        args,
+        False, eps, maxfun, maxiter,
+        locally_biased,
+        f_min, f_min_rtol,
+        vol_tol, len_tol, callback
+    )
+
+    format_val = (maxfun, maxiter, f_min_rtol, vol_tol, len_tol)
+    if ret_code > 2:
+        message = SUCCESS_MESSAGES[ret_code - 3].format(
+                    format_val[ret_code - 1])
+    elif 0 < ret_code <= 2:
+        message = ERROR_MESSAGES[ret_code - 1].format(format_val[ret_code - 1])
+    elif 0 > ret_code > -100:
+        message = ERROR_MESSAGES[abs(ret_code) + 1]
+    else:
+        message = ERROR_MESSAGES[ret_code + 99]
+
+    return OptimizeResult(x=np.asarray(x), fun=fun, status=ret_code,
+                          success=ret_code > 2, message=message,
+                          nfev=nfev, nit=nit)

vila/lib/python3.10/site-packages/scipy/optimize/_hessian_update_strategy.py

@@ -0,0 +1,475 @@
+"""Hessian update strategies for quasi-Newton optimization methods."""
+import numpy as np
+from numpy.linalg import norm
+from scipy.linalg import get_blas_funcs, issymmetric
+from warnings import warn
+
+
+__all__ = ['HessianUpdateStrategy', 'BFGS', 'SR1']
+
+
+class HessianUpdateStrategy:
+    """Interface for implementing Hessian update strategies.
+
+    Many optimization methods make use of Hessian (or inverse Hessian)
+    approximations, such as the quasi-Newton methods BFGS, SR1, L-BFGS.
+    Some of these  approximations, however, do not actually need to store
+    the entire matrix or can compute the internal matrix product with a
+    given vector in a very efficiently manner. This class serves as an
+    abstract interface between the optimization algorithm and the
+    quasi-Newton update strategies, giving freedom of implementation
+    to store and update the internal matrix as efficiently as possible.
+    Different choices of initialization and update procedure will result
+    in different quasi-Newton strategies.
+
+    Four methods should be implemented in derived classes: ``initialize``,
+    ``update``, ``dot`` and ``get_matrix``.
+
+    Notes
+    -----
+    Any instance of a class that implements this interface,
+    can be accepted by the method ``minimize`` and used by
+    the compatible solvers to approximate the Hessian (or
+    inverse Hessian) used by the optimization algorithms.
+    """
+
+    def initialize(self, n, approx_type):
+        """Initialize internal matrix.
+
+        Allocate internal memory for storing and updating
+        the Hessian or its inverse.
+
+        Parameters
+        ----------
+        n : int
+            Problem dimension.
+        approx_type : {'hess', 'inv_hess'}
+            Selects either the Hessian or the inverse Hessian.
+            When set to 'hess' the Hessian will be stored and updated.
+            When set to 'inv_hess' its inverse will be used instead.
+        """
+        raise NotImplementedError("The method ``initialize(n, approx_type)``"
+                                  " is not implemented.")
+
+    def update(self, delta_x, delta_grad):
+        """Update internal matrix.
+
+        Update Hessian matrix or its inverse (depending on how 'approx_type'
+        is defined) using information about the last evaluated points.
+
+        Parameters
+        ----------
+        delta_x : ndarray
+            The difference between two points the gradient
+            function have been evaluated at: ``delta_x = x2 - x1``.
+        delta_grad : ndarray
+            The difference between the gradients:
+            ``delta_grad = grad(x2) - grad(x1)``.
+        """
+        raise NotImplementedError("The method ``update(delta_x, delta_grad)``"
+                                  " is not implemented.")
+
+    def dot(self, p):
+        """Compute the product of the internal matrix with the given vector.
+
+        Parameters
+        ----------
+        p : array_like
+            1-D array representing a vector.
+
+        Returns
+        -------
+        Hp : array
+            1-D represents the result of multiplying the approximation matrix
+            by vector p.
+        """
+        raise NotImplementedError("The method ``dot(p)``"
+                                  " is not implemented.")
+
+    def get_matrix(self):
+        """Return current internal matrix.
+
+        Returns
+        -------
+        H : ndarray, shape (n, n)
+            Dense matrix containing either the Hessian
+            or its inverse (depending on how 'approx_type'
+            is defined).
+        """
+        raise NotImplementedError("The method ``get_matrix(p)``"
+                                  " is not implemented.")
+
+
+class FullHessianUpdateStrategy(HessianUpdateStrategy):
+    """Hessian update strategy with full dimensional internal representation.
+    """
+    _syr = get_blas_funcs('syr', dtype='d')  # Symmetric rank 1 update
+    _syr2 = get_blas_funcs('syr2', dtype='d')  # Symmetric rank 2 update
+    # Symmetric matrix-vector product
+    _symv = get_blas_funcs('symv', dtype='d')
+
+    def __init__(self, init_scale='auto'):
+        self.init_scale = init_scale
+        # Until initialize is called we can't really use the class,
+        # so it makes sense to set everything to None.
+        self.first_iteration = None
+        self.approx_type = None
+        self.B = None
+        self.H = None
+
+    def initialize(self, n, approx_type):
+        """Initialize internal matrix.
+
+        Allocate internal memory for storing and updating
+        the Hessian or its inverse.
+
+        Parameters
+        ----------
+        n : int
+            Problem dimension.
+        approx_type : {'hess', 'inv_hess'}
+            Selects either the Hessian or the inverse Hessian.
+            When set to 'hess' the Hessian will be stored and updated.
+            When set to 'inv_hess' its inverse will be used instead.
+        """
+        self.first_iteration = True
+        self.n = n
+        self.approx_type = approx_type
+        if approx_type not in ('hess', 'inv_hess'):
+            raise ValueError("`approx_type` must be 'hess' or 'inv_hess'.")
+        # Create matrix
+        if self.approx_type == 'hess':
+            self.B = np.eye(n, dtype=float)
+        else:
+            self.H = np.eye(n, dtype=float)
+
+    def _auto_scale(self, delta_x, delta_grad):
+        # Heuristic to scale matrix at first iteration.
+        # Described in Nocedal and Wright "Numerical Optimization"
+        # p.143 formula (6.20).
+        s_norm2 = np.dot(delta_x, delta_x)
+        y_norm2 = np.dot(delta_grad, delta_grad)
+        ys = np.abs(np.dot(delta_grad, delta_x))
+        if ys == 0.0 or y_norm2 == 0 or s_norm2 == 0:
+            return 1
+        if self.approx_type == 'hess':
+            return y_norm2 / ys
+        else:
+            return ys / y_norm2
+
+    def _update_implementation(self, delta_x, delta_grad):
+        raise NotImplementedError("The method ``_update_implementation``"
+                                  " is not implemented.")
+
+    def update(self, delta_x, delta_grad):
+        """Update internal matrix.
+
+        Update Hessian matrix or its inverse (depending on how 'approx_type'
+        is defined) using information about the last evaluated points.
+
+        Parameters
+        ----------
+        delta_x : ndarray
+            The difference between two points the gradient
+            function have been evaluated at: ``delta_x = x2 - x1``.
+        delta_grad : ndarray
+            The difference between the gradients:
+            ``delta_grad = grad(x2) - grad(x1)``.
+        """
+        if np.all(delta_x == 0.0):
+            return
+        if np.all(delta_grad == 0.0):
+            warn('delta_grad == 0.0. Check if the approximated '
+                 'function is linear. If the function is linear '
+                 'better results can be obtained by defining the '
+                 'Hessian as zero instead of using quasi-Newton '
+                 'approximations.',
+                 UserWarning, stacklevel=2)
+            return
+        if self.first_iteration:
+            # Get user specific scale
+            if isinstance(self.init_scale, str) and self.init_scale == "auto":
+                scale = self._auto_scale(delta_x, delta_grad)
+            else:
+                scale = self.init_scale
+
+            # Check for complex: numpy will silently cast a complex array to
+            # a real one but not so for scalar as it raises a TypeError.
+            # Checking here brings a consistent behavior.
+            replace = False
+            if np.size(scale) == 1:
+                # to account for the legacy behavior having the exact same cast
+                scale = float(scale)
+            elif np.iscomplexobj(scale):
+                raise TypeError("init_scale contains complex elements, "
+                                "must be real.")
+            else:  # test explicitly for allowed shapes and values
+                replace = True
+                if self.approx_type == 'hess':
+                    shape = np.shape(self.B)
+                    dtype = self.B.dtype
+                else:
+                    shape = np.shape(self.H)
+                    dtype = self.H.dtype
+                # copy, will replace the original
+                scale = np.array(scale, dtype=dtype, copy=True)
+
+                # it has to match the shape of the matrix for the multiplication,
+                # no implicit broadcasting is allowed
+                if shape != (init_shape := np.shape(scale)):
+                    raise ValueError("If init_scale is an array, it must have the "
+                                     f"dimensions of the hess/inv_hess: {shape}."
+                                     f" Got {init_shape}.")
+                if not issymmetric(scale):
+                    raise ValueError("If init_scale is an array, it must be"
+                                     " symmetric (passing scipy.linalg.issymmetric)"
+                                     " to be an approximation of a hess/inv_hess.")
+
+            # Scale initial matrix with ``scale * np.eye(n)`` or replace
+            # This is not ideal, we could assign the scale directly in
+            # initialize, but we would need to
+            if self.approx_type == 'hess':
+                if replace:
+                    self.B = scale
+                else:
+                    self.B *= scale
+            else:
+                if replace:
+                    self.H = scale
+                else:
+                    self.H *= scale
+            self.first_iteration = False
+        self._update_implementation(delta_x, delta_grad)
+
+    def dot(self, p):
+        """Compute the product of the internal matrix with the given vector.
+
+        Parameters
+        ----------
+        p : array_like
+            1-D array representing a vector.
+
+        Returns
+        -------
+        Hp : array
+            1-D represents the result of multiplying the approximation matrix
+            by vector p.
+        """
+        if self.approx_type == 'hess':
+            return self._symv(1, self.B, p)
+        else:
+            return self._symv(1, self.H, p)
+
+    def get_matrix(self):
+        """Return the current internal matrix.
+
+        Returns
+        -------
+        M : ndarray, shape (n, n)
+            Dense matrix containing either the Hessian or its inverse
+            (depending on how `approx_type` was defined).
+        """
+        if self.approx_type == 'hess':
+            M = np.copy(self.B)
+        else:
+            M = np.copy(self.H)
+        li = np.tril_indices_from(M, k=-1)
+        M[li] = M.T[li]
+        return M
+
+
+class BFGS(FullHessianUpdateStrategy):
+    """Broyden-Fletcher-Goldfarb-Shanno (BFGS) Hessian update strategy.
+
+    Parameters
+    ----------
+    exception_strategy : {'skip_update', 'damp_update'}, optional
+        Define how to proceed when the curvature condition is violated.
+        Set it to 'skip_update' to just skip the update. Or, alternatively,
+        set it to 'damp_update' to interpolate between the actual BFGS
+        result and the unmodified matrix. Both exceptions strategies
+        are explained  in [1]_, p.536-537.
+    min_curvature : float
+        This number, scaled by a normalization factor, defines the
+        minimum curvature ``dot(delta_grad, delta_x)`` allowed to go
+        unaffected by the exception strategy. By default is equal to
+        1e-8 when ``exception_strategy = 'skip_update'`` and equal
+        to 0.2 when ``exception_strategy = 'damp_update'``.
+    init_scale : {float, np.array, 'auto'}
+        This parameter can be used to initialize the Hessian or its
+        inverse. When a float is given, the relevant array is initialized
+        to ``np.eye(n) * init_scale``, where ``n`` is the problem dimension.
+        Alternatively, if a precisely ``(n, n)`` shaped, symmetric array is given,
+        this array will be used. Otherwise an error is generated.
+        Set it to 'auto' in order to use an automatic heuristic for choosing
+        the initial scale. The heuristic is described in [1]_, p.143.
+        The default is 'auto'.
+
+    Notes
+    -----
+    The update is based on the description in [1]_, p.140.
+
+    References
+    ----------
+    .. [1] Nocedal, Jorge, and Stephen J. Wright. "Numerical optimization"
+           Second Edition (2006).
+    """
+
+    def __init__(self, exception_strategy='skip_update', min_curvature=None,
+                 init_scale='auto'):
+        if exception_strategy == 'skip_update':
+            if min_curvature is not None:
+                self.min_curvature = min_curvature
+            else:
+                self.min_curvature = 1e-8
+        elif exception_strategy == 'damp_update':
+            if min_curvature is not None:
+                self.min_curvature = min_curvature
+            else:
+                self.min_curvature = 0.2
+        else:
+            raise ValueError("`exception_strategy` must be 'skip_update' "
+                             "or 'damp_update'.")
+
+        super().__init__(init_scale)
+        self.exception_strategy = exception_strategy
+
+    def _update_inverse_hessian(self, ys, Hy, yHy, s):
+        """Update the inverse Hessian matrix.
+
+        BFGS update using the formula:
+
+            ``H <- H + ((H*y).T*y + s.T*y)/(s.T*y)^2 * (s*s.T)
+                     - 1/(s.T*y) * ((H*y)*s.T + s*(H*y).T)``
+
+        where ``s = delta_x`` and ``y = delta_grad``. This formula is
+        equivalent to (6.17) in [1]_ written in a more efficient way
+        for implementation.
+
+        References
+        ----------
+        .. [1] Nocedal, Jorge, and Stephen J. Wright. "Numerical optimization"
+               Second Edition (2006).
+        """
+        self.H = self._syr2(-1.0 / ys, s, Hy, a=self.H)
+        self.H = self._syr((ys + yHy) / ys ** 2, s, a=self.H)
+
+    def _update_hessian(self, ys, Bs, sBs, y):
+        """Update the Hessian matrix.
+
+        BFGS update using the formula:
+
+            ``B <- B - (B*s)*(B*s).T/s.T*(B*s) + y*y^T/s.T*y``
+
+        where ``s`` is short for ``delta_x`` and ``y`` is short
+        for ``delta_grad``. Formula (6.19) in [1]_.
+
+        References
+        ----------
+        .. [1] Nocedal, Jorge, and Stephen J. Wright. "Numerical optimization"
+               Second Edition (2006).
+        """
+        self.B = self._syr(1.0 / ys, y, a=self.B)
+        self.B = self._syr(-1.0 / sBs, Bs, a=self.B)
+
+    def _update_implementation(self, delta_x, delta_grad):
+        # Auxiliary variables w and z
+        if self.approx_type == 'hess':
+            w = delta_x
+            z = delta_grad
+        else:
+            w = delta_grad
+            z = delta_x
+        # Do some common operations
+        wz = np.dot(w, z)
+        Mw = self.dot(w)
+        wMw = Mw.dot(w)
+        # Guarantee that wMw > 0 by reinitializing matrix.
+        # While this is always true in exact arithmetic,
+        # indefinite matrix may appear due to roundoff errors.
+        if wMw <= 0.0:
+            scale = self._auto_scale(delta_x, delta_grad)
+            # Reinitialize matrix
+            if self.approx_type == 'hess':
+                self.B = scale * np.eye(self.n, dtype=float)
+            else:
+                self.H = scale * np.eye(self.n, dtype=float)
+            # Do common operations for new matrix
+            Mw = self.dot(w)
+            wMw = Mw.dot(w)
+        # Check if curvature condition is violated
+        if wz <= self.min_curvature * wMw:
+            # If the option 'skip_update' is set
+            # we just skip the update when the condition
+            # is violated.
+            if self.exception_strategy == 'skip_update':
+                return
+            # If the option 'damp_update' is set we
+            # interpolate between the actual BFGS
+            # result and the unmodified matrix.
+            elif self.exception_strategy == 'damp_update':
+                update_factor = (1-self.min_curvature) / (1 - wz/wMw)
+                z = update_factor*z + (1-update_factor)*Mw
+                wz = np.dot(w, z)
+        # Update matrix
+        if self.approx_type == 'hess':
+            self._update_hessian(wz, Mw, wMw, z)
+        else:
+            self._update_inverse_hessian(wz, Mw, wMw, z)
+
+
+class SR1(FullHessianUpdateStrategy):
+    """Symmetric-rank-1 Hessian update strategy.
+
+    Parameters
+    ----------
+    min_denominator : float
+        This number, scaled by a normalization factor,
+        defines the minimum denominator magnitude allowed
+        in the update. When the condition is violated we skip
+        the update. By default uses ``1e-8``.
+    init_scale : {float, np.array, 'auto'}, optional
+        This parameter can be used to initialize the Hessian or its
+        inverse. When a float is given, the relevant array is initialized
+        to ``np.eye(n) * init_scale``, where ``n`` is the problem dimension.
+        Alternatively, if a precisely ``(n, n)`` shaped, symmetric array is given,
+        this array will be used. Otherwise an error is generated.
+        Set it to 'auto' in order to use an automatic heuristic for choosing
+        the initial scale. The heuristic is described in [1]_, p.143.
+        The default is 'auto'.
+
+    Notes
+    -----
+    The update is based on the description in [1]_, p.144-146.
+
+    References
+    ----------
+    .. [1] Nocedal, Jorge, and Stephen J. Wright. "Numerical optimization"
+           Second Edition (2006).
+    """
+
+    def __init__(self, min_denominator=1e-8, init_scale='auto'):
+        self.min_denominator = min_denominator
+        super().__init__(init_scale)
+
+    def _update_implementation(self, delta_x, delta_grad):
+        # Auxiliary variables w and z
+        if self.approx_type == 'hess':
+            w = delta_x
+            z = delta_grad
+        else:
+            w = delta_grad
+            z = delta_x
+        # Do some common operations
+        Mw = self.dot(w)
+        z_minus_Mw = z - Mw
+        denominator = np.dot(w, z_minus_Mw)
+        # If the denominator is too small
+        # we just skip the update.
+        if np.abs(denominator) <= self.min_denominator*norm(w)*norm(z_minus_Mw):
+            return
+        # Update matrix
+        if self.approx_type == 'hess':
+            self.B = self._syr(1/denominator, z_minus_Mw, a=self.B)
+        else:
+            self.H = self._syr(1/denominator, z_minus_Mw, a=self.H)

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HConst.pxd

@@ -0,0 +1,106 @@
+# cython: language_level=3
+
+from libcpp cimport bool
+from libcpp.string cimport string
+
+cdef extern from "HConst.h" nogil:
+
+    const int HIGHS_CONST_I_INF "kHighsIInf"
+    const double HIGHS_CONST_INF "kHighsInf"
+    const double kHighsTiny
+    const double kHighsZero
+    const int kHighsThreadLimit
+
+    cdef enum HighsDebugLevel:
+      HighsDebugLevel_kHighsDebugLevelNone "kHighsDebugLevelNone" = 0
+      HighsDebugLevel_kHighsDebugLevelCheap "kHighsDebugLevelCheap"
+      HighsDebugLevel_kHighsDebugLevelCostly "kHighsDebugLevelCostly"
+      HighsDebugLevel_kHighsDebugLevelExpensive "kHighsDebugLevelExpensive"
+      HighsDebugLevel_kHighsDebugLevelMin "kHighsDebugLevelMin" = HighsDebugLevel_kHighsDebugLevelNone
+      HighsDebugLevel_kHighsDebugLevelMax "kHighsDebugLevelMax" = HighsDebugLevel_kHighsDebugLevelExpensive
+
+    ctypedef enum HighsModelStatus:
+        HighsModelStatusNOTSET "HighsModelStatus::kNotset" = 0
+        HighsModelStatusLOAD_ERROR "HighsModelStatus::kLoadError"
+        HighsModelStatusMODEL_ERROR "HighsModelStatus::kModelError"
+        HighsModelStatusPRESOLVE_ERROR "HighsModelStatus::kPresolveError"
+        HighsModelStatusSOLVE_ERROR "HighsModelStatus::kSolveError"
+        HighsModelStatusPOSTSOLVE_ERROR "HighsModelStatus::kPostsolveError"
+        HighsModelStatusMODEL_EMPTY "HighsModelStatus::kModelEmpty"
+        HighsModelStatusOPTIMAL "HighsModelStatus::kOptimal"
+        HighsModelStatusINFEASIBLE "HighsModelStatus::kInfeasible"
+        HighsModelStatus_UNBOUNDED_OR_INFEASIBLE "HighsModelStatus::kUnboundedOrInfeasible"
+        HighsModelStatusUNBOUNDED "HighsModelStatus::kUnbounded"
+        HighsModelStatusREACHED_DUAL_OBJECTIVE_VALUE_UPPER_BOUND "HighsModelStatus::kObjectiveBound"
+        HighsModelStatusREACHED_OBJECTIVE_TARGET "HighsModelStatus::kObjectiveTarget"
+        HighsModelStatusREACHED_TIME_LIMIT "HighsModelStatus::kTimeLimit"
+        HighsModelStatusREACHED_ITERATION_LIMIT "HighsModelStatus::kIterationLimit"
+        HighsModelStatusUNKNOWN "HighsModelStatus::kUnknown"
+        HighsModelStatusHIGHS_MODEL_STATUS_MIN "HighsModelStatus::kMin" = HighsModelStatusNOTSET
+        HighsModelStatusHIGHS_MODEL_STATUS_MAX "HighsModelStatus::kMax" = HighsModelStatusUNKNOWN
+
+    cdef enum HighsBasisStatus:
+        HighsBasisStatusLOWER "HighsBasisStatus::kLower" = 0, # (slack) variable is at its lower bound [including fixed variables]
+        HighsBasisStatusBASIC "HighsBasisStatus::kBasic" # (slack) variable is basic
+        HighsBasisStatusUPPER "HighsBasisStatus::kUpper" # (slack) variable is at its upper bound
+        HighsBasisStatusZERO "HighsBasisStatus::kZero" # free variable is non-basic and set to zero
+        HighsBasisStatusNONBASIC "HighsBasisStatus::kNonbasic" # nonbasic with no specific bound information - useful for users and postsolve
+
+    cdef enum SolverOption:
+        SOLVER_OPTION_SIMPLEX "SolverOption::SOLVER_OPTION_SIMPLEX" = -1
+        SOLVER_OPTION_CHOOSE "SolverOption::SOLVER_OPTION_CHOOSE"
+        SOLVER_OPTION_IPM "SolverOption::SOLVER_OPTION_IPM"
+
+    cdef enum PrimalDualStatus:
+        PrimalDualStatusSTATUS_NOT_SET "PrimalDualStatus::STATUS_NOT_SET" = -1
+        PrimalDualStatusSTATUS_MIN "PrimalDualStatus::STATUS_MIN" = PrimalDualStatusSTATUS_NOT_SET
+        PrimalDualStatusSTATUS_NO_SOLUTION "PrimalDualStatus::STATUS_NO_SOLUTION"
+        PrimalDualStatusSTATUS_UNKNOWN "PrimalDualStatus::STATUS_UNKNOWN"
+        PrimalDualStatusSTATUS_INFEASIBLE_POINT "PrimalDualStatus::STATUS_INFEASIBLE_POINT"
+        PrimalDualStatusSTATUS_FEASIBLE_POINT "PrimalDualStatus::STATUS_FEASIBLE_POINT"
+        PrimalDualStatusSTATUS_MAX "PrimalDualStatus::STATUS_MAX" = PrimalDualStatusSTATUS_FEASIBLE_POINT
+
+    cdef enum HighsOptionType:
+        HighsOptionTypeBOOL "HighsOptionType::kBool" = 0
+        HighsOptionTypeINT "HighsOptionType::kInt"
+        HighsOptionTypeDOUBLE "HighsOptionType::kDouble"
+        HighsOptionTypeSTRING "HighsOptionType::kString"
+
+    # workaround for lack of enum class support in Cython < 3.x
+    # cdef enum class ObjSense(int):
+    #     ObjSenseMINIMIZE "ObjSense::kMinimize" = 1
+    #     ObjSenseMAXIMIZE "ObjSense::kMaximize" = -1
+
+    cdef cppclass ObjSense:
+        pass
+
+    cdef ObjSense ObjSenseMINIMIZE "ObjSense::kMinimize"
+    cdef ObjSense ObjSenseMAXIMIZE "ObjSense::kMaximize"
+
+    # cdef enum class MatrixFormat(int):
+    #     MatrixFormatkColwise "MatrixFormat::kColwise" = 1
+    #     MatrixFormatkRowwise "MatrixFormat::kRowwise"
+    #     MatrixFormatkRowwisePartitioned "MatrixFormat::kRowwisePartitioned"
+
+    cdef cppclass MatrixFormat:
+        pass
+
+    cdef MatrixFormat MatrixFormatkColwise "MatrixFormat::kColwise"
+    cdef MatrixFormat MatrixFormatkRowwise "MatrixFormat::kRowwise"
+    cdef MatrixFormat MatrixFormatkRowwisePartitioned "MatrixFormat::kRowwisePartitioned"
+
+    # cdef enum class HighsVarType(int):
+    #     kContinuous "HighsVarType::kContinuous"
+    #     kInteger "HighsVarType::kInteger"
+    #     kSemiContinuous "HighsVarType::kSemiContinuous"
+    #     kSemiInteger "HighsVarType::kSemiInteger"
+    #     kImplicitInteger "HighsVarType::kImplicitInteger"
+
+    cdef cppclass HighsVarType:
+        pass
+
+    cdef HighsVarType kContinuous "HighsVarType::kContinuous"
+    cdef HighsVarType kInteger "HighsVarType::kInteger"
+    cdef HighsVarType kSemiContinuous "HighsVarType::kSemiContinuous"
+    cdef HighsVarType kSemiInteger "HighsVarType::kSemiInteger"
+    cdef HighsVarType kImplicitInteger "HighsVarType::kImplicitInteger"

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/Highs.pxd

@@ -0,0 +1,56 @@
+# cython: language_level=3
+
+from libc.stdio cimport FILE
+
+from libcpp cimport bool
+from libcpp.string cimport string
+
+from .HighsStatus cimport HighsStatus
+from .HighsOptions cimport HighsOptions
+from .HighsInfo cimport HighsInfo
+from .HighsLp cimport (
+    HighsLp,
+    HighsSolution,
+    HighsBasis,
+    ObjSense,
+)
+from .HConst cimport HighsModelStatus
+
+cdef extern from "Highs.h":
+    # From HiGHS/src/Highs.h
+    cdef cppclass Highs:
+        HighsStatus passHighsOptions(const HighsOptions& options)
+        HighsStatus passModel(const HighsLp& lp)
+        HighsStatus run()
+        HighsStatus setHighsLogfile(FILE* logfile)
+        HighsStatus setHighsOutput(FILE* output)
+        HighsStatus writeHighsOptions(const string filename, const bool report_only_non_default_values = true)
+
+        # split up for cython below
+        #const HighsModelStatus& getModelStatus(const bool scaled_model = False) const
+        const HighsModelStatus & getModelStatus() const
+
+        const HighsInfo& getHighsInfo "getInfo" () const
+        string modelStatusToString(const HighsModelStatus model_status) const
+        #HighsStatus getHighsInfoValue(const string& info, int& value)
+        HighsStatus getHighsInfoValue(const string& info, double& value) const
+        const HighsOptions& getHighsOptions() const
+
+        const HighsLp& getLp() const
+
+        HighsStatus writeSolution(const string filename, const bool pretty) const
+
+        HighsStatus setBasis()
+        const HighsSolution& getSolution() const
+        const HighsBasis& getBasis() const
+
+        bool changeObjectiveSense(const ObjSense sense)
+
+        HighsStatus setHighsOptionValueBool "setOptionValue" (const string & option, const bool value)
+        HighsStatus setHighsOptionValueInt "setOptionValue" (const string & option, const int value)
+        HighsStatus setHighsOptionValueStr "setOptionValue" (const string & option, const string & value)
+        HighsStatus setHighsOptionValueDbl "setOptionValue" (const string & option, const double value)
+
+        string primalDualStatusToString(const int primal_dual_status)
+
+        void resetGlobalScheduler(bool blocking)

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsInfo.pxd

@@ -0,0 +1,22 @@
+# cython: language_level=3
+
+cdef extern from "HighsInfo.h" nogil:
+    # From HiGHS/src/lp_data/HighsInfo.h
+    cdef cppclass HighsInfo:
+        # Inherited from HighsInfoStruct:
+        int mip_node_count
+        int simplex_iteration_count
+        int ipm_iteration_count
+        int crossover_iteration_count
+        int primal_solution_status
+        int dual_solution_status
+        int basis_validity
+        double objective_function_value
+        double mip_dual_bound
+        double mip_gap
+        int num_primal_infeasibilities
+        double max_primal_infeasibility
+        double sum_primal_infeasibilities
+        int num_dual_infeasibilities
+        double max_dual_infeasibility
+        double sum_dual_infeasibilities

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsLp.pxd

@@ -0,0 +1,46 @@
+# cython: language_level=3
+
+from libcpp cimport bool
+from libcpp.string cimport string
+from libcpp.vector cimport vector
+
+from .HConst cimport HighsBasisStatus, ObjSense, HighsVarType
+from .HighsSparseMatrix cimport HighsSparseMatrix
+
+
+cdef extern from "HighsLp.h" nogil:
+    # From HiGHS/src/lp_data/HighsLp.h
+    cdef cppclass HighsLp:
+        int num_col_
+        int num_row_
+
+        vector[double] col_cost_
+        vector[double] col_lower_
+        vector[double] col_upper_
+        vector[double] row_lower_
+        vector[double] row_upper_
+
+        HighsSparseMatrix a_matrix_
+
+        ObjSense sense_
+        double offset_
+
+        string model_name_
+
+        vector[string] row_names_
+        vector[string] col_names_
+
+        vector[HighsVarType] integrality_
+
+        bool isMip() const
+
+    cdef cppclass HighsSolution:
+        vector[double] col_value
+        vector[double] col_dual
+        vector[double] row_value
+        vector[double] row_dual
+
+    cdef cppclass HighsBasis:
+        bool valid_
+        vector[HighsBasisStatus] col_status
+        vector[HighsBasisStatus] row_status

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsLpUtils.pxd

@@ -0,0 +1,9 @@
+# cython: language_level=3
+
+from .HighsStatus cimport HighsStatus
+from .HighsLp cimport HighsLp
+from .HighsOptions cimport HighsOptions
+
+cdef extern from "HighsLpUtils.h" nogil:
+    # From HiGHS/src/lp_data/HighsLpUtils.h
+    HighsStatus assessLp(HighsLp& lp, const HighsOptions& options)

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsModelUtils.pxd

@@ -0,0 +1,10 @@
+# cython: language_level=3
+
+from libcpp.string cimport string
+
+from .HConst cimport HighsModelStatus
+
+cdef extern from "HighsModelUtils.h" nogil:
+    # From HiGHS/src/lp_data/HighsModelUtils.h
+    string utilHighsModelStatusToString(const HighsModelStatus model_status)
+    string utilBasisStatusToString(const int primal_dual_status)

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsOptions.pxd

@@ -0,0 +1,110 @@
+# cython: language_level=3
+
+from libc.stdio cimport FILE
+
+from libcpp cimport bool
+from libcpp.string cimport string
+from libcpp.vector cimport vector
+
+from .HConst cimport HighsOptionType
+
+cdef extern from "HighsOptions.h" nogil:
+
+    cdef cppclass OptionRecord:
+        HighsOptionType type
+        string name
+        string description
+        bool advanced
+
+    cdef cppclass OptionRecordBool(OptionRecord):
+        bool* value
+        bool default_value
+
+    cdef cppclass OptionRecordInt(OptionRecord):
+        int* value
+        int lower_bound
+        int default_value
+        int upper_bound
+
+    cdef cppclass OptionRecordDouble(OptionRecord):
+        double* value
+        double lower_bound
+        double default_value
+        double upper_bound
+
+    cdef cppclass OptionRecordString(OptionRecord):
+        string* value
+        string default_value
+
+    cdef cppclass HighsOptions:
+        # From HighsOptionsStruct:
+
+        # Options read from the command line
+        string model_file
+        string presolve
+        string solver
+        string parallel
+        double time_limit
+        string options_file
+
+        # Options read from the file
+        double infinite_cost
+        double infinite_bound
+        double small_matrix_value
+        double large_matrix_value
+        double primal_feasibility_tolerance
+        double dual_feasibility_tolerance
+        double ipm_optimality_tolerance
+        double dual_objective_value_upper_bound
+        int highs_debug_level
+        int simplex_strategy
+        int simplex_scale_strategy
+        int simplex_crash_strategy
+        int simplex_dual_edge_weight_strategy
+        int simplex_primal_edge_weight_strategy
+        int simplex_iteration_limit
+        int simplex_update_limit
+        int ipm_iteration_limit
+        int highs_min_threads
+        int highs_max_threads
+        int message_level
+        string solution_file
+        bool write_solution_to_file
+        bool write_solution_pretty
+
+        # Advanced options
+        bool run_crossover
+        bool mps_parser_type_free
+        int keep_n_rows
+        int allowed_simplex_matrix_scale_factor
+        int allowed_simplex_cost_scale_factor
+        int simplex_dualise_strategy
+        int simplex_permute_strategy
+        int dual_simplex_cleanup_strategy
+        int simplex_price_strategy
+        int dual_chuzc_sort_strategy
+        bool simplex_initial_condition_check
+        double simplex_initial_condition_tolerance
+        double dual_steepest_edge_weight_log_error_threshhold
+        double dual_simplex_cost_perturbation_multiplier
+        double start_crossover_tolerance
+        bool less_infeasible_DSE_check
+        bool less_infeasible_DSE_choose_row
+        bool use_original_HFactor_logic
+
+        # Options for MIP solver
+        int mip_max_nodes
+        int mip_report_level
+
+        # Switch for MIP solver
+        bool mip
+
+        # Options for HighsPrintMessage and HighsLogMessage
+        FILE* logfile
+        FILE* output
+        int message_level
+        string solution_file
+        bool write_solution_to_file
+        bool write_solution_pretty
+
+        vector[OptionRecord*] records

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsRuntimeOptions.pxd

@@ -0,0 +1,9 @@
+# cython: language_level=3
+
+from libcpp cimport bool
+
+from .HighsOptions cimport HighsOptions
+
+cdef extern from "HighsRuntimeOptions.h" nogil:
+    # From HiGHS/src/lp_data/HighsRuntimeOptions.h
+    bool loadOptions(int argc, char** argv, HighsOptions& options)

vila/lib/python3.10/site-packages/scipy/optimize/_highs/src/cython/HighsStatus.pxd

@@ -0,0 +1,12 @@
+# cython: language_level=3
+
+from libcpp.string cimport string
+
+cdef extern from "HighsStatus.h" nogil:
+    ctypedef enum HighsStatus:
+        HighsStatusError "HighsStatus::kError" = -1
+        HighsStatusOK "HighsStatus::kOk" = 0
+        HighsStatusWarning "HighsStatus::kWarning" = 1
+
+
+    string highsStatusToString(HighsStatus status)

vila/lib/python3.10/site-packages/scipy/optimize/_lbfgsb_py.py

@@ -0,0 +1,543 @@
+"""
+Functions
+---------
+.. autosummary::
+   :toctree: generated/
+
+    fmin_l_bfgs_b
+
+"""
+
+## License for the Python wrapper
+## ==============================
+
+## Copyright (c) 2004 David M. Cooke <cookedm@physics.mcmaster.ca>
+
+## Permission is hereby granted, free of charge, to any person obtaining a
+## copy of this software and associated documentation files (the "Software"),
+## to deal in the Software without restriction, including without limitation
+## the rights to use, copy, modify, merge, publish, distribute, sublicense,
+## and/or sell copies of the Software, and to permit persons to whom the
+## Software is furnished to do so, subject to the following conditions:
+
+## The above copyright notice and this permission notice shall be included in
+## all copies or substantial portions of the Software.
+
+## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+## AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+## DEALINGS IN THE SOFTWARE.
+
+## Modifications by Travis Oliphant and Enthought, Inc. for inclusion in SciPy
+
+import numpy as np
+from numpy import array, asarray, float64, zeros
+from . import _lbfgsb
+from ._optimize import (MemoizeJac, OptimizeResult, _call_callback_maybe_halt,
+                        _wrap_callback, _check_unknown_options,
+                        _prepare_scalar_function)
+from ._constraints import old_bound_to_new
+
+from scipy.sparse.linalg import LinearOperator
+
+__all__ = ['fmin_l_bfgs_b', 'LbfgsInvHessProduct']
+
+
+def fmin_l_bfgs_b(func, x0, fprime=None, args=(),
+                  approx_grad=0,
+                  bounds=None, m=10, factr=1e7, pgtol=1e-5,
+                  epsilon=1e-8,
+                  iprint=-1, maxfun=15000, maxiter=15000, disp=None,
+                  callback=None, maxls=20):
+    """
+    Minimize a function func using the L-BFGS-B algorithm.
+
+    Parameters
+    ----------
+    func : callable f(x,*args)
+        Function to minimize.
+    x0 : ndarray
+        Initial guess.
+    fprime : callable fprime(x,*args), optional
+        The gradient of `func`. If None, then `func` returns the function
+        value and the gradient (``f, g = func(x, *args)``), unless
+        `approx_grad` is True in which case `func` returns only ``f``.
+    args : sequence, optional
+        Arguments to pass to `func` and `fprime`.
+    approx_grad : bool, optional
+        Whether to approximate the gradient numerically (in which case
+        `func` returns only the function value).
+    bounds : list, optional
+        ``(min, max)`` pairs for each element in ``x``, defining
+        the bounds on that parameter. Use None or +-inf for one of ``min`` or
+        ``max`` when there is no bound in that direction.
+    m : int, optional
+        The maximum number of variable metric corrections
+        used to define the limited memory matrix. (The limited memory BFGS
+        method does not store the full hessian but uses this many terms in an
+        approximation to it.)
+    factr : float, optional
+        The iteration stops when
+        ``(f^k - f^{k+1})/max{|f^k|,|f^{k+1}|,1} <= factr * eps``,
+        where ``eps`` is the machine precision, which is automatically
+        generated by the code. Typical values for `factr` are: 1e12 for
+        low accuracy; 1e7 for moderate accuracy; 10.0 for extremely
+        high accuracy. See Notes for relationship to `ftol`, which is exposed
+        (instead of `factr`) by the `scipy.optimize.minimize` interface to
+        L-BFGS-B.
+    pgtol : float, optional
+        The iteration will stop when
+        ``max{|proj g_i | i = 1, ..., n} <= pgtol``
+        where ``proj g_i`` is the i-th component of the projected gradient.
+    epsilon : float, optional
+        Step size used when `approx_grad` is True, for numerically
+        calculating the gradient
+    iprint : int, optional
+        Controls the frequency of output. ``iprint < 0`` means no output;
+        ``iprint = 0``    print only one line at the last iteration;
+        ``0 < iprint < 99`` print also f and ``|proj g|`` every iprint iterations;
+        ``iprint = 99``   print details of every iteration except n-vectors;
+        ``iprint = 100``  print also the changes of active set and final x;
+        ``iprint > 100``  print details of every iteration including x and g.
+    disp : int, optional
+        If zero, then no output. If a positive number, then this over-rides
+        `iprint` (i.e., `iprint` gets the value of `disp`).
+    maxfun : int, optional
+        Maximum number of function evaluations. Note that this function
+        may violate the limit because of evaluating gradients by numerical
+        differentiation.
+    maxiter : int, optional
+        Maximum number of iterations.
+    callback : callable, optional
+        Called after each iteration, as ``callback(xk)``, where ``xk`` is the
+        current parameter vector.
+    maxls : int, optional
+        Maximum number of line search steps (per iteration). Default is 20.
+
+    Returns
+    -------
+    x : array_like
+        Estimated position of the minimum.
+    f : float
+        Value of `func` at the minimum.
+    d : dict
+        Information dictionary.
+
+        * d['warnflag'] is
+
+          - 0 if converged,
+          - 1 if too many function evaluations or too many iterations,
+          - 2 if stopped for another reason, given in d['task']
+
+        * d['grad'] is the gradient at the minimum (should be 0 ish)
+        * d['funcalls'] is the number of function calls made.
+        * d['nit'] is the number of iterations.
+
+    See also
+    --------
+    minimize: Interface to minimization algorithms for multivariate
+        functions. See the 'L-BFGS-B' `method` in particular. Note that the
+        `ftol` option is made available via that interface, while `factr` is
+        provided via this interface, where `factr` is the factor multiplying
+        the default machine floating-point precision to arrive at `ftol`:
+        ``ftol = factr * numpy.finfo(float).eps``.
+
+    Notes
+    -----
+    License of L-BFGS-B (FORTRAN code):
+
+    The version included here (in fortran code) is 3.0
+    (released April 25, 2011). It was written by Ciyou Zhu, Richard Byrd,
+    and Jorge Nocedal <nocedal@ece.nwu.edu>. It carries the following
+    condition for use:
+
+    This software is freely available, but we expect that all publications
+    describing work using this software, or all commercial products using it,
+    quote at least one of the references given below. This software is released
+    under the BSD License.
+
+    References
+    ----------
+    * R. H. Byrd, P. Lu and J. Nocedal. A Limited Memory Algorithm for Bound
+      Constrained Optimization, (1995), SIAM Journal on Scientific and
+      Statistical Computing, 16, 5, pp. 1190-1208.
+    * C. Zhu, R. H. Byrd and J. Nocedal. L-BFGS-B: Algorithm 778: L-BFGS-B,
+      FORTRAN routines for large scale bound constrained optimization (1997),
+      ACM Transactions on Mathematical Software, 23, 4, pp. 550 - 560.
+    * J.L. Morales and J. Nocedal. L-BFGS-B: Remark on Algorithm 778: L-BFGS-B,
+      FORTRAN routines for large scale bound constrained optimization (2011),
+      ACM Transactions on Mathematical Software, 38, 1.
+
+    Examples
+    --------
+    Solve a linear regression problem via `fmin_l_bfgs_b`. To do this, first we define
+    an objective function ``f(m, b) = (y - y_model)**2``, where `y` describes the
+    observations and `y_model` the prediction of the linear model as
+    ``y_model = m*x + b``. The bounds for the parameters, ``m`` and ``b``, are arbitrarily
+    chosen as ``(0,5)`` and ``(5,10)`` for this example.
+
+    >>> import numpy as np
+    >>> from scipy.optimize import fmin_l_bfgs_b
+    >>> X = np.arange(0, 10, 1)
+    >>> M = 2
+    >>> B = 3
+    >>> Y = M * X + B
+    >>> def func(parameters, *args):
+    ...     x = args[0]
+    ...     y = args[1]
+    ...     m, b = parameters
+    ...     y_model = m*x + b
+    ...     error = sum(np.power((y - y_model), 2))
+    ...     return error
+
+    >>> initial_values = np.array([0.0, 1.0])
+
+    >>> x_opt, f_opt, info = fmin_l_bfgs_b(func, x0=initial_values, args=(X, Y),
+    ...                                    approx_grad=True)
+    >>> x_opt, f_opt
+    array([1.99999999, 3.00000006]), 1.7746231151323805e-14  # may vary
+
+    The optimized parameters in ``x_opt`` agree with the ground truth parameters
+    ``m`` and ``b``. Next, let us perform a bound contrained optimization using the `bounds`
+    parameter. 
+
+    >>> bounds = [(0, 5), (5, 10)]
+    >>> x_opt, f_op, info = fmin_l_bfgs_b(func, x0=initial_values, args=(X, Y),
+    ...                                   approx_grad=True, bounds=bounds)
+    >>> x_opt, f_opt
+    array([1.65990508, 5.31649385]), 15.721334516453945  # may vary    
+    """
+    # handle fprime/approx_grad
+    if approx_grad:
+        fun = func
+        jac = None
+    elif fprime is None:
+        fun = MemoizeJac(func)
+        jac = fun.derivative
+    else:
+        fun = func
+        jac = fprime
+
+    # build options
+    callback = _wrap_callback(callback)
+    opts = {'disp': disp,
+            'iprint': iprint,
+            'maxcor': m,
+            'ftol': factr * np.finfo(float).eps,
+            'gtol': pgtol,
+            'eps': epsilon,
+            'maxfun': maxfun,
+            'maxiter': maxiter,
+            'callback': callback,
+            'maxls': maxls}
+
+    res = _minimize_lbfgsb(fun, x0, args=args, jac=jac, bounds=bounds,
+                           **opts)
+    d = {'grad': res['jac'],
+         'task': res['message'],
+         'funcalls': res['nfev'],
+         'nit': res['nit'],
+         'warnflag': res['status']}
+    f = res['fun']
+    x = res['x']
+
+    return x, f, d
+
+
+def _minimize_lbfgsb(fun, x0, args=(), jac=None, bounds=None,
+                     disp=None, maxcor=10, ftol=2.2204460492503131e-09,
+                     gtol=1e-5, eps=1e-8, maxfun=15000, maxiter=15000,
+                     iprint=-1, callback=None, maxls=20,
+                     finite_diff_rel_step=None, **unknown_options):
+    """
+    Minimize a scalar function of one or more variables using the L-BFGS-B
+    algorithm.
+
+    Options
+    -------
+    disp : None or int
+        If `disp is None` (the default), then the supplied version of `iprint`
+        is used. If `disp is not None`, then it overrides the supplied version
+        of `iprint` with the behaviour you outlined.
+    maxcor : int
+        The maximum number of variable metric corrections used to
+        define the limited memory matrix. (The limited memory BFGS
+        method does not store the full hessian but uses this many terms
+        in an approximation to it.)
+    ftol : float
+        The iteration stops when ``(f^k -
+        f^{k+1})/max{|f^k|,|f^{k+1}|,1} <= ftol``.
+    gtol : float
+        The iteration will stop when ``max{|proj g_i | i = 1, ..., n}
+        <= gtol`` where ``proj g_i`` is the i-th component of the
+        projected gradient.
+    eps : float or ndarray
+        If `jac is None` the absolute step size used for numerical
+        approximation of the jacobian via forward differences.
+    maxfun : int
+        Maximum number of function evaluations. Note that this function
+        may violate the limit because of evaluating gradients by numerical
+        differentiation.
+    maxiter : int
+        Maximum number of iterations.
+    iprint : int, optional
+        Controls the frequency of output. ``iprint < 0`` means no output;
+        ``iprint = 0``    print only one line at the last iteration;
+        ``0 < iprint < 99`` print also f and ``|proj g|`` every iprint iterations;
+        ``iprint = 99``   print details of every iteration except n-vectors;
+        ``iprint = 100``  print also the changes of active set and final x;
+        ``iprint > 100``  print details of every iteration including x and g.
+    maxls : int, optional
+        Maximum number of line search steps (per iteration). Default is 20.
+    finite_diff_rel_step : None or array_like, optional
+        If `jac in ['2-point', '3-point', 'cs']` the relative step size to
+        use for numerical approximation of the jacobian. The absolute step
+        size is computed as ``h = rel_step * sign(x) * max(1, abs(x))``,
+        possibly adjusted to fit into the bounds. For ``method='3-point'``
+        the sign of `h` is ignored. If None (default) then step is selected
+        automatically.
+
+    Notes
+    -----
+    The option `ftol` is exposed via the `scipy.optimize.minimize` interface,
+    but calling `scipy.optimize.fmin_l_bfgs_b` directly exposes `factr`. The
+    relationship between the two is ``ftol = factr * numpy.finfo(float).eps``.
+    I.e., `factr` multiplies the default machine floating-point precision to
+    arrive at `ftol`.
+
+    """
+    _check_unknown_options(unknown_options)
+    m = maxcor
+    pgtol = gtol
+    factr = ftol / np.finfo(float).eps
+
+    x0 = asarray(x0).ravel()
+    n, = x0.shape
+
+    # historically old-style bounds were/are expected by lbfgsb.
+    # That's still the case but we'll deal with new-style from here on,
+    # it's easier
+    if bounds is None:
+        pass
+    elif len(bounds) != n:
+        raise ValueError('length of x0 != length of bounds')
+    else:
+        bounds = np.array(old_bound_to_new(bounds))
+
+        # check bounds
+        if (bounds[0] > bounds[1]).any():
+            raise ValueError(
+                "LBFGSB - one of the lower bounds is greater than an upper bound."
+            )
+
+        # initial vector must lie within the bounds. Otherwise ScalarFunction and
+        # approx_derivative will cause problems
+        x0 = np.clip(x0, bounds[0], bounds[1])
+
+    if disp is not None:
+        if disp == 0:
+            iprint = -1
+        else:
+            iprint = disp
+
+    # _prepare_scalar_function can use bounds=None to represent no bounds
+    sf = _prepare_scalar_function(fun, x0, jac=jac, args=args, epsilon=eps,
+                                  bounds=bounds,
+                                  finite_diff_rel_step=finite_diff_rel_step)
+
+    func_and_grad = sf.fun_and_grad
+
+    fortran_int = _lbfgsb.types.intvar.dtype
+
+    nbd = zeros(n, fortran_int)
+    low_bnd = zeros(n, float64)
+    upper_bnd = zeros(n, float64)
+    bounds_map = {(-np.inf, np.inf): 0,
+                  (1, np.inf): 1,
+                  (1, 1): 2,
+                  (-np.inf, 1): 3}
+
+    if bounds is not None:
+        for i in range(0, n):
+            l, u = bounds[0, i], bounds[1, i]
+            if not np.isinf(l):
+                low_bnd[i] = l
+                l = 1
+            if not np.isinf(u):
+                upper_bnd[i] = u
+                u = 1
+            nbd[i] = bounds_map[l, u]
+
+    if not maxls > 0:
+        raise ValueError('maxls must be positive.')
+
+    x = array(x0, float64)
+    f = array(0.0, float64)
+    g = zeros((n,), float64)
+    wa = zeros(2*m*n + 5*n + 11*m*m + 8*m, float64)
+    iwa = zeros(3*n, fortran_int)
+    task = zeros(1, 'S60')
+    csave = zeros(1, 'S60')
+    lsave = zeros(4, fortran_int)
+    isave = zeros(44, fortran_int)
+    dsave = zeros(29, float64)
+
+    task[:] = 'START'
+
+    n_iterations = 0
+
+    while 1:
+        # g may become float32 if a user provides a function that calculates
+        # the Jacobian in float32 (see gh-18730). The underlying Fortran code
+        # expects float64, so upcast it
+        g = g.astype(np.float64)
+        # x, f, g, wa, iwa, task, csave, lsave, isave, dsave = \
+        _lbfgsb.setulb(m, x, low_bnd, upper_bnd, nbd, f, g, factr,
+                       pgtol, wa, iwa, task, iprint, csave, lsave,
+                       isave, dsave, maxls)
+        task_str = task.tobytes()
+        if task_str.startswith(b'FG'):
+            # The minimization routine wants f and g at the current x.
+            # Note that interruptions due to maxfun are postponed
+            # until the completion of the current minimization iteration.
+            # Overwrite f and g:
+            f, g = func_and_grad(x)
+        elif task_str.startswith(b'NEW_X'):
+            # new iteration
+            n_iterations += 1
+
+            intermediate_result = OptimizeResult(x=x, fun=f)
+            if _call_callback_maybe_halt(callback, intermediate_result):
+                task[:] = 'STOP: CALLBACK REQUESTED HALT'
+            if n_iterations >= maxiter:
+                task[:] = 'STOP: TOTAL NO. of ITERATIONS REACHED LIMIT'
+            elif sf.nfev > maxfun:
+                task[:] = ('STOP: TOTAL NO. of f AND g EVALUATIONS '
+                           'EXCEEDS LIMIT')
+        else:
+            break
+
+    task_str = task.tobytes().strip(b'\x00').strip()
+    if task_str.startswith(b'CONV'):
+        warnflag = 0
+    elif sf.nfev > maxfun or n_iterations >= maxiter:
+        warnflag = 1
+    else:
+        warnflag = 2
+
+    # These two portions of the workspace are described in the mainlb
+    # subroutine in lbfgsb.f. See line 363.
+    s = wa[0: m*n].reshape(m, n)
+    y = wa[m*n: 2*m*n].reshape(m, n)
+
+    # See lbfgsb.f line 160 for this portion of the workspace.
+    # isave(31) = the total number of BFGS updates prior the current iteration;
+    n_bfgs_updates = isave[30]
+
+    n_corrs = min(n_bfgs_updates, maxcor)
+    hess_inv = LbfgsInvHessProduct(s[:n_corrs], y[:n_corrs])
+
+    task_str = task_str.decode()
+    return OptimizeResult(fun=f, jac=g, nfev=sf.nfev,
+                          njev=sf.ngev,
+                          nit=n_iterations, status=warnflag, message=task_str,
+                          x=x, success=(warnflag == 0), hess_inv=hess_inv)
+
+
+class LbfgsInvHessProduct(LinearOperator):
+    """Linear operator for the L-BFGS approximate inverse Hessian.
+
+    This operator computes the product of a vector with the approximate inverse
+    of the Hessian of the objective function, using the L-BFGS limited
+    memory approximation to the inverse Hessian, accumulated during the
+    optimization.
+
+    Objects of this class implement the ``scipy.sparse.linalg.LinearOperator``
+    interface.
+
+    Parameters
+    ----------
+    sk : array_like, shape=(n_corr, n)
+        Array of `n_corr` most recent updates to the solution vector.
+        (See [1]).
+    yk : array_like, shape=(n_corr, n)
+        Array of `n_corr` most recent updates to the gradient. (See [1]).
+
+    References
+    ----------
+    .. [1] Nocedal, Jorge. "Updating quasi-Newton matrices with limited
+       storage." Mathematics of computation 35.151 (1980): 773-782.
+
+    """
+
+    def __init__(self, sk, yk):
+        """Construct the operator."""
+        if sk.shape != yk.shape or sk.ndim != 2:
+            raise ValueError('sk and yk must have matching shape, (n_corrs, n)')
+        n_corrs, n = sk.shape
+
+        super().__init__(dtype=np.float64, shape=(n, n))
+
+        self.sk = sk
+        self.yk = yk
+        self.n_corrs = n_corrs
+        self.rho = 1 / np.einsum('ij,ij->i', sk, yk)
+
+    def _matvec(self, x):
+        """Efficient matrix-vector multiply with the BFGS matrices.
+
+        This calculation is described in Section (4) of [1].
+
+        Parameters
+        ----------
+        x : ndarray
+            An array with shape (n,) or (n,1).
+
+        Returns
+        -------
+        y : ndarray
+            The matrix-vector product
+
+        """
+        s, y, n_corrs, rho = self.sk, self.yk, self.n_corrs, self.rho
+        q = np.array(x, dtype=self.dtype, copy=True)
+        if q.ndim == 2 and q.shape[1] == 1:
+            q = q.reshape(-1)
+
+        alpha = np.empty(n_corrs)
+
+        for i in range(n_corrs-1, -1, -1):
+            alpha[i] = rho[i] * np.dot(s[i], q)
+            q = q - alpha[i]*y[i]
+
+        r = q
+        for i in range(n_corrs):
+            beta = rho[i] * np.dot(y[i], r)
+            r = r + s[i] * (alpha[i] - beta)
+
+        return r
+
+    def todense(self):
+        """Return a dense array representation of this operator.
+
+        Returns
+        -------
+        arr : ndarray, shape=(n, n)
+            An array with the same shape and containing
+            the same data represented by this `LinearOperator`.
+
+        """
+        s, y, n_corrs, rho = self.sk, self.yk, self.n_corrs, self.rho
+        I = np.eye(*self.shape, dtype=self.dtype)
+        Hk = I
+
+        for i in range(n_corrs):
+            A1 = I - s[i][:, np.newaxis] * y[i][np.newaxis, :] * rho[i]
+            A2 = I - y[i][:, np.newaxis] * s[i][np.newaxis, :] * rho[i]
+
+            Hk = np.dot(A1, np.dot(Hk, A2)) + (rho[i] * s[i][:, np.newaxis] *
+                                                        s[i][np.newaxis, :])
+        return Hk

vila/lib/python3.10/site-packages/scipy/optimize/_linprog.py

@@ -0,0 +1,716 @@
+"""
+A top-level linear programming interface.
+
+.. versionadded:: 0.15.0
+
+Functions
+---------
+.. autosummary::
+   :toctree: generated/
+
+    linprog
+    linprog_verbose_callback
+    linprog_terse_callback
+
+"""
+
+import numpy as np
+
+from ._optimize import OptimizeResult, OptimizeWarning
+from warnings import warn
+from ._linprog_highs import _linprog_highs
+from ._linprog_ip import _linprog_ip
+from ._linprog_simplex import _linprog_simplex
+from ._linprog_rs import _linprog_rs
+from ._linprog_doc import (_linprog_highs_doc, _linprog_ip_doc,  # noqa: F401
+                           _linprog_rs_doc, _linprog_simplex_doc,
+                           _linprog_highs_ipm_doc, _linprog_highs_ds_doc)
+from ._linprog_util import (
+    _parse_linprog, _presolve, _get_Abc, _LPProblem, _autoscale,
+    _postsolve, _check_result, _display_summary)
+from copy import deepcopy
+
+__all__ = ['linprog', 'linprog_verbose_callback', 'linprog_terse_callback']
+
+__docformat__ = "restructuredtext en"
+
+LINPROG_METHODS = [
+    'simplex', 'revised simplex', 'interior-point', 'highs', 'highs-ds', 'highs-ipm'
+]
+
+
+def linprog_verbose_callback(res):
+    """
+    A sample callback function demonstrating the linprog callback interface.
+    This callback produces detailed output to sys.stdout before each iteration
+    and after the final iteration of the simplex algorithm.
+
+    Parameters
+    ----------
+    res : A `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+        x : 1-D array
+            The independent variable vector which optimizes the linear
+            programming problem.
+        fun : float
+            Value of the objective function.
+        success : bool
+            True if the algorithm succeeded in finding an optimal solution.
+        slack : 1-D array
+            The values of the slack variables. Each slack variable corresponds
+            to an inequality constraint. If the slack is zero, then the
+            corresponding constraint is active.
+        con : 1-D array
+            The (nominally zero) residuals of the equality constraints, that is,
+            ``b - A_eq @ x``
+        phase : int
+            The phase of the optimization being executed. In phase 1 a basic
+            feasible solution is sought and the T has an additional row
+            representing an alternate objective function.
+        status : int
+            An integer representing the exit status of the optimization::
+
+                 0 : Optimization terminated successfully
+                 1 : Iteration limit reached
+                 2 : Problem appears to be infeasible
+                 3 : Problem appears to be unbounded
+                 4 : Serious numerical difficulties encountered
+
+        nit : int
+            The number of iterations performed.
+        message : str
+            A string descriptor of the exit status of the optimization.
+    """
+    x = res['x']
+    fun = res['fun']
+    phase = res['phase']
+    status = res['status']
+    nit = res['nit']
+    message = res['message']
+    complete = res['complete']
+
+    saved_printoptions = np.get_printoptions()
+    np.set_printoptions(linewidth=500,
+                        formatter={'float': lambda x: f"{x: 12.4f}"})
+    if status:
+        print('--------- Simplex Early Exit -------\n')
+        print(f'The simplex method exited early with status {status:d}')
+        print(message)
+    elif complete:
+        print('--------- Simplex Complete --------\n')
+        print(f'Iterations required: {nit}')
+    else:
+        print(f'--------- Iteration {nit:d}  ---------\n')
+
+    if nit > 0:
+        if phase == 1:
+            print('Current Pseudo-Objective Value:')
+        else:
+            print('Current Objective Value:')
+        print('f = ', fun)
+        print()
+        print('Current Solution Vector:')
+        print('x = ', x)
+        print()
+
+    np.set_printoptions(**saved_printoptions)
+
+
+def linprog_terse_callback(res):
+    """
+    A sample callback function demonstrating the linprog callback interface.
+    This callback produces brief output to sys.stdout before each iteration
+    and after the final iteration of the simplex algorithm.
+
+    Parameters
+    ----------
+    res : A `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+        x : 1-D array
+            The independent variable vector which optimizes the linear
+            programming problem.
+        fun : float
+            Value of the objective function.
+        success : bool
+            True if the algorithm succeeded in finding an optimal solution.
+        slack : 1-D array
+            The values of the slack variables. Each slack variable corresponds
+            to an inequality constraint. If the slack is zero, then the
+            corresponding constraint is active.
+        con : 1-D array
+            The (nominally zero) residuals of the equality constraints, that is,
+            ``b - A_eq @ x``.
+        phase : int
+            The phase of the optimization being executed. In phase 1 a basic
+            feasible solution is sought and the T has an additional row
+            representing an alternate objective function.
+        status : int
+            An integer representing the exit status of the optimization::
+
+                 0 : Optimization terminated successfully
+                 1 : Iteration limit reached
+                 2 : Problem appears to be infeasible
+                 3 : Problem appears to be unbounded
+                 4 : Serious numerical difficulties encountered
+
+        nit : int
+            The number of iterations performed.
+        message : str
+            A string descriptor of the exit status of the optimization.
+    """
+    nit = res['nit']
+    x = res['x']
+
+    if nit == 0:
+        print("Iter:   X:")
+    print(f"{nit: <5d}   ", end="")
+    print(x)
+
+
+def linprog(c, A_ub=None, b_ub=None, A_eq=None, b_eq=None,
+            bounds=(0, None), method='highs', callback=None,
+            options=None, x0=None, integrality=None):
+    r"""
+    Linear programming: minimize a linear objective function subject to linear
+    equality and inequality constraints.
+
+    Linear programming solves problems of the following form:
+
+    .. math::
+
+        \min_x \ & c^T x \\
+        \mbox{such that} \ & A_{ub} x \leq b_{ub},\\
+        & A_{eq} x = b_{eq},\\
+        & l \leq x \leq u ,
+
+    where :math:`x` is a vector of decision variables; :math:`c`,
+    :math:`b_{ub}`, :math:`b_{eq}`, :math:`l`, and :math:`u` are vectors; and
+    :math:`A_{ub}` and :math:`A_{eq}` are matrices.
+
+    Alternatively, that's:
+
+        - minimize ::
+
+            c @ x
+
+        - such that ::
+
+            A_ub @ x <= b_ub
+            A_eq @ x == b_eq
+            lb <= x <= ub
+
+    Note that by default ``lb = 0`` and ``ub = None``. Other bounds can be
+    specified with ``bounds``.
+
+    Parameters
+    ----------
+    c : 1-D array
+        The coefficients of the linear objective function to be minimized.
+    A_ub : 2-D array, optional
+        The inequality constraint matrix. Each row of ``A_ub`` specifies the
+        coefficients of a linear inequality constraint on ``x``.
+    b_ub : 1-D array, optional
+        The inequality constraint vector. Each element represents an
+        upper bound on the corresponding value of ``A_ub @ x``.
+    A_eq : 2-D array, optional
+        The equality constraint matrix. Each row of ``A_eq`` specifies the
+        coefficients of a linear equality constraint on ``x``.
+    b_eq : 1-D array, optional
+        The equality constraint vector. Each element of ``A_eq @ x`` must equal
+        the corresponding element of ``b_eq``.
+    bounds : sequence, optional
+        A sequence of ``(min, max)`` pairs for each element in ``x``, defining
+        the minimum and maximum values of that decision variable.
+        If a single tuple ``(min, max)`` is provided, then ``min`` and ``max``
+        will serve as bounds for all decision variables.
+        Use ``None`` to indicate that there is no bound. For instance, the
+        default bound ``(0, None)`` means that all decision variables are
+        non-negative, and the pair ``(None, None)`` means no bounds at all,
+        i.e. all variables are allowed to be any real.
+    method : str, optional
+        The algorithm used to solve the standard form problem.
+        :ref:`'highs' <optimize.linprog-highs>` (default),
+        :ref:`'highs-ds' <optimize.linprog-highs-ds>`,
+        :ref:`'highs-ipm' <optimize.linprog-highs-ipm>`,
+        :ref:`'interior-point' <optimize.linprog-interior-point>` (legacy),
+        :ref:`'revised simplex' <optimize.linprog-revised_simplex>` (legacy),
+        and
+        :ref:`'simplex' <optimize.linprog-simplex>` (legacy) are supported.
+        The legacy methods are deprecated and will be removed in SciPy 1.11.0.
+    callback : callable, optional
+        If a callback function is provided, it will be called at least once per
+        iteration of the algorithm. The callback function must accept a single
+        `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+        x : 1-D array
+            The current solution vector.
+        fun : float
+            The current value of the objective function ``c @ x``.
+        success : bool
+            ``True`` when the algorithm has completed successfully.
+        slack : 1-D array
+            The (nominally positive) values of the slack,
+            ``b_ub - A_ub @ x``.
+        con : 1-D array
+            The (nominally zero) residuals of the equality constraints,
+            ``b_eq - A_eq @ x``.
+        phase : int
+            The phase of the algorithm being executed.
+        status : int
+            An integer representing the status of the algorithm.
+
+            ``0`` : Optimization proceeding nominally.
+
+            ``1`` : Iteration limit reached.
+
+            ``2`` : Problem appears to be infeasible.
+
+            ``3`` : Problem appears to be unbounded.
+
+            ``4`` : Numerical difficulties encountered.
+
+            nit : int
+                The current iteration number.
+            message : str
+                A string descriptor of the algorithm status.
+
+        Callback functions are not currently supported by the HiGHS methods.
+
+    options : dict, optional
+        A dictionary of solver options. All methods accept the following
+        options:
+
+        maxiter : int
+            Maximum number of iterations to perform.
+            Default: see method-specific documentation.
+        disp : bool
+            Set to ``True`` to print convergence messages.
+            Default: ``False``.
+        presolve : bool
+            Set to ``False`` to disable automatic presolve.
+            Default: ``True``.
+
+        All methods except the HiGHS solvers also accept:
+
+        tol : float
+            A tolerance which determines when a residual is "close enough" to
+            zero to be considered exactly zero.
+        autoscale : bool
+            Set to ``True`` to automatically perform equilibration.
+            Consider using this option if the numerical values in the
+            constraints are separated by several orders of magnitude.
+            Default: ``False``.
+        rr : bool
+            Set to ``False`` to disable automatic redundancy removal.
+            Default: ``True``.
+        rr_method : string
+            Method used to identify and remove redundant rows from the
+            equality constraint matrix after presolve. For problems with
+            dense input, the available methods for redundancy removal are:
+
+            "SVD":
+                Repeatedly performs singular value decomposition on
+                the matrix, detecting redundant rows based on nonzeros
+                in the left singular vectors that correspond with
+                zero singular values. May be fast when the matrix is
+                nearly full rank.
+            "pivot":
+                Uses the algorithm presented in [5]_ to identify
+                redundant rows.
+            "ID":
+                Uses a randomized interpolative decomposition.
+                Identifies columns of the matrix transpose not used in
+                a full-rank interpolative decomposition of the matrix.
+            None:
+                Uses "svd" if the matrix is nearly full rank, that is,
+                the difference between the matrix rank and the number
+                of rows is less than five. If not, uses "pivot". The
+                behavior of this default is subject to change without
+                prior notice.
+
+            Default: None.
+            For problems with sparse input, this option is ignored, and the
+            pivot-based algorithm presented in [5]_ is used.
+
+        For method-specific options, see
+        :func:`show_options('linprog') <show_options>`.
+
+    x0 : 1-D array, optional
+        Guess values of the decision variables, which will be refined by
+        the optimization algorithm. This argument is currently used only by the
+        'revised simplex' method, and can only be used if `x0` represents a
+        basic feasible solution.
+
+    integrality : 1-D array or int, optional
+        Indicates the type of integrality constraint on each decision variable.
+
+        ``0`` : Continuous variable; no integrality constraint.
+
+        ``1`` : Integer variable; decision variable must be an integer
+        within `bounds`.
+
+        ``2`` : Semi-continuous variable; decision variable must be within
+        `bounds` or take value ``0``.
+
+        ``3`` : Semi-integer variable; decision variable must be an integer
+        within `bounds` or take value ``0``.
+
+        By default, all variables are continuous.
+
+        For mixed integrality constraints, supply an array of shape `c.shape`.
+        To infer a constraint on each decision variable from shorter inputs,
+        the argument will be broadcasted to `c.shape` using `np.broadcast_to`.
+
+        This argument is currently used only by the ``'highs'`` method and
+        ignored otherwise.
+
+    Returns
+    -------
+    res : OptimizeResult
+        A :class:`scipy.optimize.OptimizeResult` consisting of the fields
+        below. Note that the return types of the fields may depend on whether
+        the optimization was successful, therefore it is recommended to check
+        `OptimizeResult.status` before relying on the other fields:
+
+        x : 1-D array
+            The values of the decision variables that minimizes the
+            objective function while satisfying the constraints.
+        fun : float
+            The optimal value of the objective function ``c @ x``.
+        slack : 1-D array
+            The (nominally positive) values of the slack variables,
+            ``b_ub - A_ub @ x``.
+        con : 1-D array
+            The (nominally zero) residuals of the equality constraints,
+            ``b_eq - A_eq @ x``.
+        success : bool
+            ``True`` when the algorithm succeeds in finding an optimal
+            solution.
+        status : int
+            An integer representing the exit status of the algorithm.
+
+            ``0`` : Optimization terminated successfully.
+
+            ``1`` : Iteration limit reached.
+
+            ``2`` : Problem appears to be infeasible.
+
+            ``3`` : Problem appears to be unbounded.
+
+            ``4`` : Numerical difficulties encountered.
+
+        nit : int
+            The total number of iterations performed in all phases.
+        message : str
+            A string descriptor of the exit status of the algorithm.
+
+    See Also
+    --------
+    show_options : Additional options accepted by the solvers.
+
+    Notes
+    -----
+    This section describes the available solvers that can be selected by the
+    'method' parameter.
+
+    `'highs-ds'` and
+    `'highs-ipm'` are interfaces to the
+    HiGHS simplex and interior-point method solvers [13]_, respectively.
+    `'highs'` (default) chooses between
+    the two automatically. These are the fastest linear
+    programming solvers in SciPy, especially for large, sparse problems;
+    which of these two is faster is problem-dependent.
+    The other solvers (`'interior-point'`, `'revised simplex'`, and
+    `'simplex'`) are legacy methods and will be removed in SciPy 1.11.0.
+
+    Method *highs-ds* is a wrapper of the C++ high performance dual
+    revised simplex implementation (HSOL) [13]_, [14]_. Method *highs-ipm*
+    is a wrapper of a C++ implementation of an **i**\ nterior-\ **p**\ oint
+    **m**\ ethod [13]_; it features a crossover routine, so it is as accurate
+    as a simplex solver. Method *highs* chooses between the two automatically.
+    For new code involving `linprog`, we recommend explicitly choosing one of
+    these three method values.
+
+    .. versionadded:: 1.6.0
+
+    Method *interior-point* uses the primal-dual path following algorithm
+    as outlined in [4]_. This algorithm supports sparse constraint matrices and
+    is typically faster than the simplex methods, especially for large, sparse
+    problems. Note, however, that the solution returned may be slightly less
+    accurate than those of the simplex methods and will not, in general,
+    correspond with a vertex of the polytope defined by the constraints.
+
+    .. versionadded:: 1.0.0
+
+    Method *revised simplex* uses the revised simplex method as described in
+    [9]_, except that a factorization [11]_ of the basis matrix, rather than
+    its inverse, is efficiently maintained and used to solve the linear systems
+    at each iteration of the algorithm.
+
+    .. versionadded:: 1.3.0
+
+    Method *simplex* uses a traditional, full-tableau implementation of
+    Dantzig's simplex algorithm [1]_, [2]_ (*not* the
+    Nelder-Mead simplex). This algorithm is included for backwards
+    compatibility and educational purposes.
+
+    .. versionadded:: 0.15.0
+
+    Before applying *interior-point*, *revised simplex*, or *simplex*,
+    a presolve procedure based on [8]_ attempts
+    to identify trivial infeasibilities, trivial unboundedness, and potential
+    problem simplifications. Specifically, it checks for:
+
+    - rows of zeros in ``A_eq`` or ``A_ub``, representing trivial constraints;
+    - columns of zeros in ``A_eq`` `and` ``A_ub``, representing unconstrained
+      variables;
+    - column singletons in ``A_eq``, representing fixed variables; and
+    - column singletons in ``A_ub``, representing simple bounds.
+
+    If presolve reveals that the problem is unbounded (e.g. an unconstrained
+    and unbounded variable has negative cost) or infeasible (e.g., a row of
+    zeros in ``A_eq`` corresponds with a nonzero in ``b_eq``), the solver
+    terminates with the appropriate status code. Note that presolve terminates
+    as soon as any sign of unboundedness is detected; consequently, a problem
+    may be reported as unbounded when in reality the problem is infeasible
+    (but infeasibility has not been detected yet). Therefore, if it is
+    important to know whether the problem is actually infeasible, solve the
+    problem again with option ``presolve=False``.
+
+    If neither infeasibility nor unboundedness are detected in a single pass
+    of the presolve, bounds are tightened where possible and fixed
+    variables are removed from the problem. Then, linearly dependent rows
+    of the ``A_eq`` matrix are removed, (unless they represent an
+    infeasibility) to avoid numerical difficulties in the primary solve
+    routine. Note that rows that are nearly linearly dependent (within a
+    prescribed tolerance) may also be removed, which can change the optimal
+    solution in rare cases. If this is a concern, eliminate redundancy from
+    your problem formulation and run with option ``rr=False`` or
+    ``presolve=False``.
+
+    Several potential improvements can be made here: additional presolve
+    checks outlined in [8]_ should be implemented, the presolve routine should
+    be run multiple times (until no further simplifications can be made), and
+    more of the efficiency improvements from [5]_ should be implemented in the
+    redundancy removal routines.
+
+    After presolve, the problem is transformed to standard form by converting
+    the (tightened) simple bounds to upper bound constraints, introducing
+    non-negative slack variables for inequality constraints, and expressing
+    unbounded variables as the difference between two non-negative variables.
+    Optionally, the problem is automatically scaled via equilibration [12]_.
+    The selected algorithm solves the standard form problem, and a
+    postprocessing routine converts the result to a solution to the original
+    problem.
+
+    References
+    ----------
+    .. [1] Dantzig, George B., Linear programming and extensions. Rand
+           Corporation Research Study Princeton Univ. Press, Princeton, NJ,
+           1963
+    .. [2] Hillier, S.H. and Lieberman, G.J. (1995), "Introduction to
+           Mathematical Programming", McGraw-Hill, Chapter 4.
+    .. [3] Bland, Robert G. New finite pivoting rules for the simplex method.
+           Mathematics of Operations Research (2), 1977: pp. 103-107.
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+    .. [5] Andersen, Erling D. "Finding all linearly dependent rows in
+           large-scale linear programming." Optimization Methods and Software
+           6.3 (1995): 219-227.
+    .. [6] Freund, Robert M. "Primal-Dual Interior-Point Methods for Linear
+           Programming based on Newton's Method." Unpublished Course Notes,
+           March 2004. Available 2/25/2017 at
+           https://ocw.mit.edu/courses/sloan-school-of-management/15-084j-nonlinear-programming-spring-2004/lecture-notes/lec14_int_pt_mthd.pdf
+    .. [7] Fourer, Robert. "Solving Linear Programs by Interior-Point Methods."
+           Unpublished Course Notes, August 26, 2005. Available 2/25/2017 at
+           http://www.4er.org/CourseNotes/Book%20B/B-III.pdf
+    .. [8] Andersen, Erling D., and Knud D. Andersen. "Presolving in linear
+           programming." Mathematical Programming 71.2 (1995): 221-245.
+    .. [9] Bertsimas, Dimitris, and J. Tsitsiklis. "Introduction to linear
+           programming." Athena Scientific 1 (1997): 997.
+    .. [10] Andersen, Erling D., et al. Implementation of interior point
+            methods for large scale linear programming. HEC/Universite de
+            Geneve, 1996.
+    .. [11] Bartels, Richard H. "A stabilization of the simplex method."
+            Journal in  Numerische Mathematik 16.5 (1971): 414-434.
+    .. [12] Tomlin, J. A. "On scaling linear programming problems."
+            Mathematical Programming Study 4 (1975): 146-166.
+    .. [13] Huangfu, Q., Galabova, I., Feldmeier, M., and Hall, J. A. J.
+            "HiGHS - high performance software for linear optimization."
+            https://highs.dev/
+    .. [14] Huangfu, Q. and Hall, J. A. J. "Parallelizing the dual revised
+            simplex method." Mathematical Programming Computation, 10 (1),
+            119-142, 2018. DOI: 10.1007/s12532-017-0130-5
+
+    Examples
+    --------
+    Consider the following problem:
+
+    .. math::
+
+        \min_{x_0, x_1} \ -x_0 + 4x_1 & \\
+        \mbox{such that} \ -3x_0 + x_1 & \leq 6,\\
+        -x_0 - 2x_1 & \geq -4,\\
+        x_1 & \geq -3.
+
+    The problem is not presented in the form accepted by `linprog`. This is
+    easily remedied by converting the "greater than" inequality
+    constraint to a "less than" inequality constraint by
+    multiplying both sides by a factor of :math:`-1`. Note also that the last
+    constraint is really the simple bound :math:`-3 \leq x_1 \leq \infty`.
+    Finally, since there are no bounds on :math:`x_0`, we must explicitly
+    specify the bounds :math:`-\infty \leq x_0 \leq \infty`, as the
+    default is for variables to be non-negative. After collecting coeffecients
+    into arrays and tuples, the input for this problem is:
+
+    >>> from scipy.optimize import linprog
+    >>> c = [-1, 4]
+    >>> A = [[-3, 1], [1, 2]]
+    >>> b = [6, 4]
+    >>> x0_bounds = (None, None)
+    >>> x1_bounds = (-3, None)
+    >>> res = linprog(c, A_ub=A, b_ub=b, bounds=[x0_bounds, x1_bounds])
+    >>> res.fun
+    -22.0
+    >>> res.x
+    array([10., -3.])
+    >>> res.message
+    'Optimization terminated successfully. (HiGHS Status 7: Optimal)'
+
+    The marginals (AKA dual values / shadow prices / Lagrange multipliers)
+    and residuals (slacks) are also available.
+
+    >>> res.ineqlin
+      residual: [ 3.900e+01  0.000e+00]
+     marginals: [-0.000e+00 -1.000e+00]
+
+    For example, because the marginal associated with the second inequality
+    constraint is -1, we expect the optimal value of the objective function
+    to decrease by ``eps`` if we add a small amount ``eps`` to the right hand
+    side of the second inequality constraint:
+
+    >>> eps = 0.05
+    >>> b[1] += eps
+    >>> linprog(c, A_ub=A, b_ub=b, bounds=[x0_bounds, x1_bounds]).fun
+    -22.05
+
+    Also, because the residual on the first inequality constraint is 39, we
+    can decrease the right hand side of the first constraint by 39 without
+    affecting the optimal solution.
+
+    >>> b = [6, 4]  # reset to original values
+    >>> b[0] -= 39
+    >>> linprog(c, A_ub=A, b_ub=b, bounds=[x0_bounds, x1_bounds]).fun
+    -22.0
+
+    """
+
+    meth = method.lower()
+    methods = {"highs", "highs-ds", "highs-ipm",
+               "simplex", "revised simplex", "interior-point"}
+
+    if meth not in methods:
+        raise ValueError(f"Unknown solver '{method}'")
+
+    if x0 is not None and meth != "revised simplex":
+        warning_message = "x0 is used only when method is 'revised simplex'. "
+        warn(warning_message, OptimizeWarning, stacklevel=2)
+
+    if np.any(integrality) and not meth == "highs":
+        integrality = None
+        warning_message = ("Only `method='highs'` supports integer "
+                           "constraints. Ignoring `integrality`.")
+        warn(warning_message, OptimizeWarning, stacklevel=2)
+    elif np.any(integrality):
+        integrality = np.broadcast_to(integrality, np.shape(c))
+    else:
+        integrality = None
+
+    lp = _LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0, integrality)
+    lp, solver_options = _parse_linprog(lp, options, meth)
+    tol = solver_options.get('tol', 1e-9)
+
+    # Give unmodified problem to HiGHS
+    if meth.startswith('highs'):
+        if callback is not None:
+            raise NotImplementedError("HiGHS solvers do not support the "
+                                      "callback interface.")
+        highs_solvers = {'highs-ipm': 'ipm', 'highs-ds': 'simplex',
+                         'highs': None}
+
+        sol = _linprog_highs(lp, solver=highs_solvers[meth],
+                             **solver_options)
+        sol['status'], sol['message'] = (
+            _check_result(sol['x'], sol['fun'], sol['status'], sol['slack'],
+                          sol['con'], lp.bounds, tol, sol['message'],
+                          integrality))
+        sol['success'] = sol['status'] == 0
+        return OptimizeResult(sol)
+
+    warn(f"`method='{meth}'` is deprecated and will be removed in SciPy "
+         "1.11.0. Please use one of the HiGHS solvers (e.g. "
+         "`method='highs'`) in new code.", DeprecationWarning, stacklevel=2)
+
+    iteration = 0
+    complete = False  # will become True if solved in presolve
+    undo = []
+
+    # Keep the original arrays to calculate slack/residuals for original
+    # problem.
+    lp_o = deepcopy(lp)
+
+    # Solve trivial problem, eliminate variables, tighten bounds, etc.
+    rr_method = solver_options.pop('rr_method', None)  # need to pop these;
+    rr = solver_options.pop('rr', True)  # they're not passed to methods
+    c0 = 0  # we might get a constant term in the objective
+    if solver_options.pop('presolve', True):
+        (lp, c0, x, undo, complete, status, message) = _presolve(lp, rr,
+                                                                 rr_method,
+                                                                 tol)
+
+    C, b_scale = 1, 1  # for trivial unscaling if autoscale is not used
+    postsolve_args = (lp_o._replace(bounds=lp.bounds), undo, C, b_scale)
+
+    if not complete:
+        A, b, c, c0, x0 = _get_Abc(lp, c0)
+        if solver_options.pop('autoscale', False):
+            A, b, c, x0, C, b_scale = _autoscale(A, b, c, x0)
+            postsolve_args = postsolve_args[:-2] + (C, b_scale)
+
+        if meth == 'simplex':
+            x, status, message, iteration = _linprog_simplex(
+                c, c0=c0, A=A, b=b, callback=callback,
+                postsolve_args=postsolve_args, **solver_options)
+        elif meth == 'interior-point':
+            x, status, message, iteration = _linprog_ip(
+                c, c0=c0, A=A, b=b, callback=callback,
+                postsolve_args=postsolve_args, **solver_options)
+        elif meth == 'revised simplex':
+            x, status, message, iteration = _linprog_rs(
+                c, c0=c0, A=A, b=b, x0=x0, callback=callback,
+                postsolve_args=postsolve_args, **solver_options)
+
+    # Eliminate artificial variables, re-introduce presolved variables, etc.
+    disp = solver_options.get('disp', False)
+
+    x, fun, slack, con = _postsolve(x, postsolve_args, complete)
+
+    status, message = _check_result(x, fun, status, slack, con, lp_o.bounds,
+                                    tol, message, integrality)
+
+    if disp:
+        _display_summary(message, status, fun, iteration)
+
+    sol = {
+        'x': x,
+        'fun': fun,
+        'slack': slack,
+        'con': con,
+        'status': status,
+        'message': message,
+        'nit': iteration,
+        'success': status == 0}
+
+    return OptimizeResult(sol)

vila/lib/python3.10/site-packages/scipy/optimize/_linprog_highs.py

@@ -0,0 +1,440 @@
+"""HiGHS Linear Optimization Methods
+
+Interface to HiGHS linear optimization software.
+https://highs.dev/
+
+.. versionadded:: 1.5.0
+
+References
+----------
+.. [1] Q. Huangfu and J.A.J. Hall. "Parallelizing the dual revised simplex
+           method." Mathematical Programming Computation, 10 (1), 119-142,
+           2018. DOI: 10.1007/s12532-017-0130-5
+
+"""
+
+import inspect
+import numpy as np
+from ._optimize import OptimizeWarning, OptimizeResult
+from warnings import warn
+from ._highs._highs_wrapper import _highs_wrapper
+from ._highs._highs_constants import (
+    CONST_INF,
+    MESSAGE_LEVEL_NONE,
+    HIGHS_OBJECTIVE_SENSE_MINIMIZE,
+
+    MODEL_STATUS_NOTSET,
+    MODEL_STATUS_LOAD_ERROR,
+    MODEL_STATUS_MODEL_ERROR,
+    MODEL_STATUS_PRESOLVE_ERROR,
+    MODEL_STATUS_SOLVE_ERROR,
+    MODEL_STATUS_POSTSOLVE_ERROR,
+    MODEL_STATUS_MODEL_EMPTY,
+    MODEL_STATUS_OPTIMAL,
+    MODEL_STATUS_INFEASIBLE,
+    MODEL_STATUS_UNBOUNDED_OR_INFEASIBLE,
+    MODEL_STATUS_UNBOUNDED,
+    MODEL_STATUS_REACHED_DUAL_OBJECTIVE_VALUE_UPPER_BOUND
+    as MODEL_STATUS_RDOVUB,
+    MODEL_STATUS_REACHED_OBJECTIVE_TARGET,
+    MODEL_STATUS_REACHED_TIME_LIMIT,
+    MODEL_STATUS_REACHED_ITERATION_LIMIT,
+
+    HIGHS_SIMPLEX_STRATEGY_DUAL,
+
+    HIGHS_SIMPLEX_CRASH_STRATEGY_OFF,
+
+    HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_CHOOSE,
+    HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_DANTZIG,
+    HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_DEVEX,
+    HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_STEEPEST_EDGE,
+)
+from scipy.sparse import csc_matrix, vstack, issparse
+
+
+def _highs_to_scipy_status_message(highs_status, highs_message):
+    """Converts HiGHS status number/message to SciPy status number/message"""
+
+    scipy_statuses_messages = {
+        None: (4, "HiGHS did not provide a status code. "),
+        MODEL_STATUS_NOTSET: (4, ""),
+        MODEL_STATUS_LOAD_ERROR: (4, ""),
+        MODEL_STATUS_MODEL_ERROR: (2, ""),
+        MODEL_STATUS_PRESOLVE_ERROR: (4, ""),
+        MODEL_STATUS_SOLVE_ERROR: (4, ""),
+        MODEL_STATUS_POSTSOLVE_ERROR: (4, ""),
+        MODEL_STATUS_MODEL_EMPTY: (4, ""),
+        MODEL_STATUS_RDOVUB: (4, ""),
+        MODEL_STATUS_REACHED_OBJECTIVE_TARGET: (4, ""),
+        MODEL_STATUS_OPTIMAL: (0, "Optimization terminated successfully. "),
+        MODEL_STATUS_REACHED_TIME_LIMIT: (1, "Time limit reached. "),
+        MODEL_STATUS_REACHED_ITERATION_LIMIT: (1, "Iteration limit reached. "),
+        MODEL_STATUS_INFEASIBLE: (2, "The problem is infeasible. "),
+        MODEL_STATUS_UNBOUNDED: (3, "The problem is unbounded. "),
+        MODEL_STATUS_UNBOUNDED_OR_INFEASIBLE: (4, "The problem is unbounded "
+                                               "or infeasible. ")}
+    unrecognized = (4, "The HiGHS status code was not recognized. ")
+    scipy_status, scipy_message = (
+        scipy_statuses_messages.get(highs_status, unrecognized))
+    scipy_message = (f"{scipy_message}"
+                     f"(HiGHS Status {highs_status}: {highs_message})")
+    return scipy_status, scipy_message
+
+
+def _replace_inf(x):
+    # Replace `np.inf` with CONST_INF
+    infs = np.isinf(x)
+    with np.errstate(invalid="ignore"):
+        x[infs] = np.sign(x[infs])*CONST_INF
+    return x
+
+
+def _convert_to_highs_enum(option, option_str, choices):
+    # If option is in the choices we can look it up, if not use
+    # the default value taken from function signature and warn:
+    try:
+        return choices[option.lower()]
+    except AttributeError:
+        return choices[option]
+    except KeyError:
+        sig = inspect.signature(_linprog_highs)
+        default_str = sig.parameters[option_str].default
+        warn(f"Option {option_str} is {option}, but only values in "
+             f"{set(choices.keys())} are allowed. Using default: "
+             f"{default_str}.",
+             OptimizeWarning, stacklevel=3)
+        return choices[default_str]
+
+
+def _linprog_highs(lp, solver, time_limit=None, presolve=True,
+                   disp=False, maxiter=None,
+                   dual_feasibility_tolerance=None,
+                   primal_feasibility_tolerance=None,
+                   ipm_optimality_tolerance=None,
+                   simplex_dual_edge_weight_strategy=None,
+                   mip_rel_gap=None,
+                   mip_max_nodes=None,
+                   **unknown_options):
+    r"""
+    Solve the following linear programming problem using one of the HiGHS
+    solvers:
+
+    User-facing documentation is in _linprog_doc.py.
+
+    Parameters
+    ----------
+    lp :  _LPProblem
+        A ``scipy.optimize._linprog_util._LPProblem`` ``namedtuple``.
+    solver : "ipm" or "simplex" or None
+        Which HiGHS solver to use.  If ``None``, "simplex" will be used.
+
+    Options
+    -------
+    maxiter : int
+        The maximum number of iterations to perform in either phase. For
+        ``solver='ipm'``, this does not include the number of crossover
+        iterations.  Default is the largest possible value for an ``int``
+        on the platform.
+    disp : bool
+        Set to ``True`` if indicators of optimization status are to be printed
+        to the console each iteration; default ``False``.
+    time_limit : float
+        The maximum time in seconds allotted to solve the problem; default is
+        the largest possible value for a ``double`` on the platform.
+    presolve : bool
+        Presolve attempts to identify trivial infeasibilities,
+        identify trivial unboundedness, and simplify the problem before
+        sending it to the main solver. It is generally recommended
+        to keep the default setting ``True``; set to ``False`` if presolve is
+        to be disabled.
+    dual_feasibility_tolerance : double
+        Dual feasibility tolerance.  Default is 1e-07.
+        The minimum of this and ``primal_feasibility_tolerance``
+        is used for the feasibility tolerance when ``solver='ipm'``.
+    primal_feasibility_tolerance : double
+        Primal feasibility tolerance.  Default is 1e-07.
+        The minimum of this and ``dual_feasibility_tolerance``
+        is used for the feasibility tolerance when ``solver='ipm'``.
+    ipm_optimality_tolerance : double
+        Optimality tolerance for ``solver='ipm'``.  Default is 1e-08.
+        Minimum possible value is 1e-12 and must be smaller than the largest
+        possible value for a ``double`` on the platform.
+    simplex_dual_edge_weight_strategy : str (default: None)
+        Strategy for simplex dual edge weights. The default, ``None``,
+        automatically selects one of the following.
+
+        ``'dantzig'`` uses Dantzig's original strategy of choosing the most
+        negative reduced cost.
+
+        ``'devex'`` uses the strategy described in [15]_.
+
+        ``steepest`` uses the exact steepest edge strategy as described in
+        [16]_.
+
+        ``'steepest-devex'`` begins with the exact steepest edge strategy
+        until the computation is too costly or inexact and then switches to
+        the devex method.
+
+        Currently, using ``None`` always selects ``'steepest-devex'``, but this
+        may change as new options become available.
+
+    mip_max_nodes : int
+        The maximum number of nodes allotted to solve the problem; default is
+        the largest possible value for a ``HighsInt`` on the platform.
+        Ignored if not using the MIP solver.
+    unknown_options : dict
+        Optional arguments not used by this particular solver. If
+        ``unknown_options`` is non-empty, a warning is issued listing all
+        unused options.
+
+    Returns
+    -------
+    sol : dict
+        A dictionary consisting of the fields:
+
+            x : 1D array
+                The values of the decision variables that minimizes the
+                objective function while satisfying the constraints.
+            fun : float
+                The optimal value of the objective function ``c @ x``.
+            slack : 1D array
+                The (nominally positive) values of the slack,
+                ``b_ub - A_ub @ x``.
+            con : 1D array
+                The (nominally zero) residuals of the equality constraints,
+                ``b_eq - A_eq @ x``.
+            success : bool
+                ``True`` when the algorithm succeeds in finding an optimal
+                solution.
+            status : int
+                An integer representing the exit status of the algorithm.
+
+                ``0`` : Optimization terminated successfully.
+
+                ``1`` : Iteration or time limit reached.
+
+                ``2`` : Problem appears to be infeasible.
+
+                ``3`` : Problem appears to be unbounded.
+
+                ``4`` : The HiGHS solver ran into a problem.
+
+            message : str
+                A string descriptor of the exit status of the algorithm.
+            nit : int
+                The total number of iterations performed.
+                For ``solver='simplex'``, this includes iterations in all
+                phases. For ``solver='ipm'``, this does not include
+                crossover iterations.
+            crossover_nit : int
+                The number of primal/dual pushes performed during the
+                crossover routine for ``solver='ipm'``.  This is ``0``
+                for ``solver='simplex'``.
+            ineqlin : OptimizeResult
+                Solution and sensitivity information corresponding to the
+                inequality constraints, `b_ub`. A dictionary consisting of the
+                fields:
+
+                residual : np.ndnarray
+                    The (nominally positive) values of the slack variables,
+                    ``b_ub - A_ub @ x``.  This quantity is also commonly
+                    referred to as "slack".
+
+                marginals : np.ndarray
+                    The sensitivity (partial derivative) of the objective
+                    function with respect to the right-hand side of the
+                    inequality constraints, `b_ub`.
+
+            eqlin : OptimizeResult
+                Solution and sensitivity information corresponding to the
+                equality constraints, `b_eq`.  A dictionary consisting of the
+                fields:
+
+                residual : np.ndarray
+                    The (nominally zero) residuals of the equality constraints,
+                    ``b_eq - A_eq @ x``.
+
+                marginals : np.ndarray
+                    The sensitivity (partial derivative) of the objective
+                    function with respect to the right-hand side of the
+                    equality constraints, `b_eq`.
+
+            lower, upper : OptimizeResult
+                Solution and sensitivity information corresponding to the
+                lower and upper bounds on decision variables, `bounds`.
+
+                residual : np.ndarray
+                    The (nominally positive) values of the quantity
+                    ``x - lb`` (lower) or ``ub - x`` (upper).
+
+                marginals : np.ndarray
+                    The sensitivity (partial derivative) of the objective
+                    function with respect to the lower and upper
+                    `bounds`.
+
+            mip_node_count : int
+                The number of subproblems or "nodes" solved by the MILP
+                solver. Only present when `integrality` is not `None`.
+
+            mip_dual_bound : float
+                The MILP solver's final estimate of the lower bound on the
+                optimal solution. Only present when `integrality` is not
+                `None`.
+
+            mip_gap : float
+                The difference between the final objective function value
+                and the final dual bound, scaled by the final objective
+                function value. Only present when `integrality` is not
+                `None`.
+
+    Notes
+    -----
+    The result fields `ineqlin`, `eqlin`, `lower`, and `upper` all contain
+    `marginals`, or partial derivatives of the objective function with respect
+    to the right-hand side of each constraint. These partial derivatives are
+    also referred to as "Lagrange multipliers", "dual values", and
+    "shadow prices". The sign convention of `marginals` is opposite that
+    of Lagrange multipliers produced by many nonlinear solvers.
+
+    References
+    ----------
+    .. [15] Harris, Paula MJ. "Pivot selection methods of the Devex LP code."
+            Mathematical programming 5.1 (1973): 1-28.
+    .. [16] Goldfarb, Donald, and John Ker Reid. "A practicable steepest-edge
+            simplex algorithm." Mathematical Programming 12.1 (1977): 361-371.
+    """
+    if unknown_options:
+        message = (f"Unrecognized options detected: {unknown_options}. "
+                   "These will be passed to HiGHS verbatim.")
+        warn(message, OptimizeWarning, stacklevel=3)
+
+    # Map options to HiGHS enum values
+    simplex_dual_edge_weight_strategy_enum = _convert_to_highs_enum(
+        simplex_dual_edge_weight_strategy,
+        'simplex_dual_edge_weight_strategy',
+        choices={'dantzig': HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_DANTZIG,
+                 'devex': HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_DEVEX,
+                 'steepest-devex': HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_CHOOSE,
+                 'steepest':
+                 HIGHS_SIMPLEX_EDGE_WEIGHT_STRATEGY_STEEPEST_EDGE,
+                 None: None})
+
+    c, A_ub, b_ub, A_eq, b_eq, bounds, x0, integrality = lp
+
+    lb, ub = bounds.T.copy()  # separate bounds, copy->C-cntgs
+    # highs_wrapper solves LHS <= A*x <= RHS, not equality constraints
+    with np.errstate(invalid="ignore"):
+        lhs_ub = -np.ones_like(b_ub)*np.inf  # LHS of UB constraints is -inf
+    rhs_ub = b_ub  # RHS of UB constraints is b_ub
+    lhs_eq = b_eq  # Equality constraint is inequality
+    rhs_eq = b_eq  # constraint with LHS=RHS
+    lhs = np.concatenate((lhs_ub, lhs_eq))
+    rhs = np.concatenate((rhs_ub, rhs_eq))
+
+    if issparse(A_ub) or issparse(A_eq):
+        A = vstack((A_ub, A_eq))
+    else:
+        A = np.vstack((A_ub, A_eq))
+    A = csc_matrix(A)
+
+    options = {
+        'presolve': presolve,
+        'sense': HIGHS_OBJECTIVE_SENSE_MINIMIZE,
+        'solver': solver,
+        'time_limit': time_limit,
+        'highs_debug_level': MESSAGE_LEVEL_NONE,
+        'dual_feasibility_tolerance': dual_feasibility_tolerance,
+        'ipm_optimality_tolerance': ipm_optimality_tolerance,
+        'log_to_console': disp,
+        'mip_max_nodes': mip_max_nodes,
+        'output_flag': disp,
+        'primal_feasibility_tolerance': primal_feasibility_tolerance,
+        'simplex_dual_edge_weight_strategy':
+            simplex_dual_edge_weight_strategy_enum,
+        'simplex_strategy': HIGHS_SIMPLEX_STRATEGY_DUAL,
+        'simplex_crash_strategy': HIGHS_SIMPLEX_CRASH_STRATEGY_OFF,
+        'ipm_iteration_limit': maxiter,
+        'simplex_iteration_limit': maxiter,
+        'mip_rel_gap': mip_rel_gap,
+    }
+    options.update(unknown_options)
+
+    # np.inf doesn't work; use very large constant
+    rhs = _replace_inf(rhs)
+    lhs = _replace_inf(lhs)
+    lb = _replace_inf(lb)
+    ub = _replace_inf(ub)
+
+    if integrality is None or np.sum(integrality) == 0:
+        integrality = np.empty(0)
+    else:
+        integrality = np.array(integrality)
+
+    res = _highs_wrapper(c, A.indptr, A.indices, A.data, lhs, rhs,
+                         lb, ub, integrality.astype(np.uint8), options)
+
+    # HiGHS represents constraints as lhs/rhs, so
+    # Ax + s = b => Ax = b - s
+    # and we need to split up s by A_ub and A_eq
+    if 'slack' in res:
+        slack = res['slack']
+        con = np.array(slack[len(b_ub):])
+        slack = np.array(slack[:len(b_ub)])
+    else:
+        slack, con = None, None
+
+    # lagrange multipliers for equalities/inequalities and upper/lower bounds
+    if 'lambda' in res:
+        lamda = res['lambda']
+        marg_ineqlin = np.array(lamda[:len(b_ub)])
+        marg_eqlin = np.array(lamda[len(b_ub):])
+        marg_upper = np.array(res['marg_bnds'][1, :])
+        marg_lower = np.array(res['marg_bnds'][0, :])
+    else:
+        marg_ineqlin, marg_eqlin = None, None
+        marg_upper, marg_lower = None, None
+
+    # this needs to be updated if we start choosing the solver intelligently
+
+    # Convert to scipy-style status and message
+    highs_status = res.get('status', None)
+    highs_message = res.get('message', None)
+    status, message = _highs_to_scipy_status_message(highs_status,
+                                                     highs_message)
+
+    x = np.array(res['x']) if 'x' in res else None
+    sol = {'x': x,
+           'slack': slack,
+           'con': con,
+           'ineqlin': OptimizeResult({
+               'residual': slack,
+               'marginals': marg_ineqlin,
+           }),
+           'eqlin': OptimizeResult({
+               'residual': con,
+               'marginals': marg_eqlin,
+           }),
+           'lower': OptimizeResult({
+               'residual': None if x is None else x - lb,
+               'marginals': marg_lower,
+           }),
+           'upper': OptimizeResult({
+               'residual': None if x is None else ub - x,
+               'marginals': marg_upper
+            }),
+           'fun': res.get('fun'),
+           'status': status,
+           'success': res['status'] == MODEL_STATUS_OPTIMAL,
+           'message': message,
+           'nit': res.get('simplex_nit', 0) or res.get('ipm_nit', 0),
+           'crossover_nit': res.get('crossover_nit'),
+           }
+
+    if np.any(x) and integrality is not None:
+        sol.update({
+            'mip_node_count': res.get('mip_node_count', 0),
+            'mip_dual_bound': res.get('mip_dual_bound', 0.0),
+            'mip_gap': res.get('mip_gap', 0.0),
+        })
+
+    return sol

vila/lib/python3.10/site-packages/scipy/optimize/_linprog_ip.py

@@ -0,0 +1,1126 @@
+"""Interior-point method for linear programming
+
+The *interior-point* method uses the primal-dual path following algorithm
+outlined in [1]_. This algorithm supports sparse constraint matrices and
+is typically faster than the simplex methods, especially for large, sparse
+problems. Note, however, that the solution returned may be slightly less
+accurate than those of the simplex methods and will not, in general,
+correspond with a vertex of the polytope defined by the constraints.
+
+    .. versionadded:: 1.0.0
+
+References
+----------
+.. [1] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+       optimizer for linear programming: an implementation of the
+       homogeneous algorithm." High performance optimization. Springer US,
+       2000. 197-232.
+"""
+# Author: Matt Haberland
+
+import numpy as np
+import scipy as sp
+import scipy.sparse as sps
+from warnings import warn
+from scipy.linalg import LinAlgError
+from ._optimize import OptimizeWarning, OptimizeResult, _check_unknown_options
+from ._linprog_util import _postsolve
+has_umfpack = True
+has_cholmod = True
+try:
+    import sksparse  # noqa: F401
+    from sksparse.cholmod import cholesky as cholmod  # noqa: F401
+    from sksparse.cholmod import analyze as cholmod_analyze
+except ImportError:
+    has_cholmod = False
+try:
+    import scikits.umfpack  # test whether to use factorized  # noqa: F401
+except ImportError:
+    has_umfpack = False
+
+
+def _get_solver(M, sparse=False, lstsq=False, sym_pos=True,
+                cholesky=True, permc_spec='MMD_AT_PLUS_A'):
+    """
+    Given solver options, return a handle to the appropriate linear system
+    solver.
+
+    Parameters
+    ----------
+    M : 2-D array
+        As defined in [4] Equation 8.31
+    sparse : bool (default = False)
+        True if the system to be solved is sparse. This is typically set
+        True when the original ``A_ub`` and ``A_eq`` arrays are sparse.
+    lstsq : bool (default = False)
+        True if the system is ill-conditioned and/or (nearly) singular and
+        thus a more robust least-squares solver is desired. This is sometimes
+        needed as the solution is approached.
+    sym_pos : bool (default = True)
+        True if the system matrix is symmetric positive definite
+        Sometimes this needs to be set false as the solution is approached,
+        even when the system should be symmetric positive definite, due to
+        numerical difficulties.
+    cholesky : bool (default = True)
+        True if the system is to be solved by Cholesky, rather than LU,
+        decomposition. This is typically faster unless the problem is very
+        small or prone to numerical difficulties.
+    permc_spec : str (default = 'MMD_AT_PLUS_A')
+        Sparsity preservation strategy used by SuperLU. Acceptable values are:
+
+        - ``NATURAL``: natural ordering.
+        - ``MMD_ATA``: minimum degree ordering on the structure of A^T A.
+        - ``MMD_AT_PLUS_A``: minimum degree ordering on the structure of A^T+A.
+        - ``COLAMD``: approximate minimum degree column ordering.
+
+        See SuperLU documentation.
+
+    Returns
+    -------
+    solve : function
+        Handle to the appropriate solver function
+
+    """
+    try:
+        if sparse:
+            if lstsq:
+                def solve(r, sym_pos=False):
+                    return sps.linalg.lsqr(M, r)[0]
+            elif cholesky:
+                try:
+                    # Will raise an exception in the first call,
+                    # or when the matrix changes due to a new problem
+                    _get_solver.cholmod_factor.cholesky_inplace(M)
+                except Exception:
+                    _get_solver.cholmod_factor = cholmod_analyze(M)
+                    _get_solver.cholmod_factor.cholesky_inplace(M)
+                solve = _get_solver.cholmod_factor
+            else:
+                if has_umfpack and sym_pos:
+                    solve = sps.linalg.factorized(M)
+                else:  # factorized doesn't pass permc_spec
+                    solve = sps.linalg.splu(M, permc_spec=permc_spec).solve
+
+        else:
+            if lstsq:  # sometimes necessary as solution is approached
+                def solve(r):
+                    return sp.linalg.lstsq(M, r)[0]
+            elif cholesky:
+                L = sp.linalg.cho_factor(M)
+
+                def solve(r):
+                    return sp.linalg.cho_solve(L, r)
+            else:
+                # this seems to cache the matrix factorization, so solving
+                # with multiple right hand sides is much faster
+                def solve(r, sym_pos=sym_pos):
+                    if sym_pos:
+                        return sp.linalg.solve(M, r, assume_a="pos")
+                    else:
+                        return sp.linalg.solve(M, r)
+    # There are many things that can go wrong here, and it's hard to say
+    # what all of them are. It doesn't really matter: if the matrix can't be
+    # factorized, return None. get_solver will be called again with different
+    # inputs, and a new routine will try to factorize the matrix.
+    except KeyboardInterrupt:
+        raise
+    except Exception:
+        return None
+    return solve
+
+
+def _get_delta(A, b, c, x, y, z, tau, kappa, gamma, eta, sparse=False,
+               lstsq=False, sym_pos=True, cholesky=True, pc=True, ip=False,
+               permc_spec='MMD_AT_PLUS_A'):
+    """
+    Given standard form problem defined by ``A``, ``b``, and ``c``;
+    current variable estimates ``x``, ``y``, ``z``, ``tau``, and ``kappa``;
+    algorithmic parameters ``gamma and ``eta;
+    and options ``sparse``, ``lstsq``, ``sym_pos``, ``cholesky``, ``pc``
+    (predictor-corrector), and ``ip`` (initial point improvement),
+    get the search direction for increments to the variable estimates.
+
+    Parameters
+    ----------
+    As defined in [4], except:
+    sparse : bool
+        True if the system to be solved is sparse. This is typically set
+        True when the original ``A_ub`` and ``A_eq`` arrays are sparse.
+    lstsq : bool
+        True if the system is ill-conditioned and/or (nearly) singular and
+        thus a more robust least-squares solver is desired. This is sometimes
+        needed as the solution is approached.
+    sym_pos : bool
+        True if the system matrix is symmetric positive definite
+        Sometimes this needs to be set false as the solution is approached,
+        even when the system should be symmetric positive definite, due to
+        numerical difficulties.
+    cholesky : bool
+        True if the system is to be solved by Cholesky, rather than LU,
+        decomposition. This is typically faster unless the problem is very
+        small or prone to numerical difficulties.
+    pc : bool
+        True if the predictor-corrector method of Mehrota is to be used. This
+        is almost always (if not always) beneficial. Even though it requires
+        the solution of an additional linear system, the factorization
+        is typically (implicitly) reused so solution is efficient, and the
+        number of algorithm iterations is typically reduced.
+    ip : bool
+        True if the improved initial point suggestion due to [4] section 4.3
+        is desired. It's unclear whether this is beneficial.
+    permc_spec : str (default = 'MMD_AT_PLUS_A')
+        (Has effect only with ``sparse = True``, ``lstsq = False``, ``sym_pos =
+        True``.) A matrix is factorized in each iteration of the algorithm.
+        This option specifies how to permute the columns of the matrix for
+        sparsity preservation. Acceptable values are:
+
+        - ``NATURAL``: natural ordering.
+        - ``MMD_ATA``: minimum degree ordering on the structure of A^T A.
+        - ``MMD_AT_PLUS_A``: minimum degree ordering on the structure of A^T+A.
+        - ``COLAMD``: approximate minimum degree column ordering.
+
+        This option can impact the convergence of the
+        interior point algorithm; test different values to determine which
+        performs best for your problem. For more information, refer to
+        ``scipy.sparse.linalg.splu``.
+
+    Returns
+    -------
+    Search directions as defined in [4]
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+    if A.shape[0] == 0:
+        # If there are no constraints, some solvers fail (understandably)
+        # rather than returning empty solution. This gets the job done.
+        sparse, lstsq, sym_pos, cholesky = False, False, True, False
+    n_x = len(x)
+
+    # [4] Equation 8.8
+    r_P = b * tau - A.dot(x)
+    r_D = c * tau - A.T.dot(y) - z
+    r_G = c.dot(x) - b.transpose().dot(y) + kappa
+    mu = (x.dot(z) + tau * kappa) / (n_x + 1)
+
+    #  Assemble M from [4] Equation 8.31
+    Dinv = x / z
+
+    if sparse:
+        M = A.dot(sps.diags(Dinv, 0, format="csc").dot(A.T))
+    else:
+        M = A.dot(Dinv.reshape(-1, 1) * A.T)
+    solve = _get_solver(M, sparse, lstsq, sym_pos, cholesky, permc_spec)
+
+    # pc: "predictor-corrector" [4] Section 4.1
+    # In development this option could be turned off
+    # but it always seems to improve performance substantially
+    n_corrections = 1 if pc else 0
+
+    i = 0
+    alpha, d_x, d_z, d_tau, d_kappa = 0, 0, 0, 0, 0
+    while i <= n_corrections:
+        # Reference [4] Eq. 8.6
+        rhatp = eta(gamma) * r_P
+        rhatd = eta(gamma) * r_D
+        rhatg = eta(gamma) * r_G
+
+        # Reference [4] Eq. 8.7
+        rhatxs = gamma * mu - x * z
+        rhattk = gamma * mu - tau * kappa
+
+        if i == 1:
+            if ip:  # if the correction is to get "initial point"
+                # Reference [4] Eq. 8.23
+                rhatxs = ((1 - alpha) * gamma * mu -
+                          x * z - alpha**2 * d_x * d_z)
+                rhattk = ((1 - alpha) * gamma * mu -
+                    tau * kappa -
+                    alpha**2 * d_tau * d_kappa)
+            else:  # if the correction is for "predictor-corrector"
+                # Reference [4] Eq. 8.13
+                rhatxs -= d_x * d_z
+                rhattk -= d_tau * d_kappa
+
+        # sometimes numerical difficulties arise as the solution is approached
+        # this loop tries to solve the equations using a sequence of functions
+        # for solve. For dense systems, the order is:
+        # 1. scipy.linalg.cho_factor/scipy.linalg.cho_solve,
+        # 2. scipy.linalg.solve w/ sym_pos = True,
+        # 3. scipy.linalg.solve w/ sym_pos = False, and if all else fails
+        # 4. scipy.linalg.lstsq
+        # For sparse systems, the order is:
+        # 1. sksparse.cholmod.cholesky (if available)
+        # 2. scipy.sparse.linalg.factorized (if umfpack available)
+        # 3. scipy.sparse.linalg.splu
+        # 4. scipy.sparse.linalg.lsqr
+        solved = False
+        while not solved:
+            try:
+                # [4] Equation 8.28
+                p, q = _sym_solve(Dinv, A, c, b, solve)
+                # [4] Equation 8.29
+                u, v = _sym_solve(Dinv, A, rhatd -
+                                  (1 / x) * rhatxs, rhatp, solve)
+                if np.any(np.isnan(p)) or np.any(np.isnan(q)):
+                    raise LinAlgError
+                solved = True
+            except (LinAlgError, ValueError, TypeError) as e:
+                # Usually this doesn't happen. If it does, it happens when
+                # there are redundant constraints or when approaching the
+                # solution. If so, change solver.
+                if cholesky:
+                    cholesky = False
+                    warn(
+                        "Solving system with option 'cholesky':True "
+                        "failed. It is normal for this to happen "
+                        "occasionally, especially as the solution is "
+                        "approached. However, if you see this frequently, "
+                        "consider setting option 'cholesky' to False.",
+                        OptimizeWarning, stacklevel=5)
+                elif sym_pos:
+                    sym_pos = False
+                    warn(
+                        "Solving system with option 'sym_pos':True "
+                        "failed. It is normal for this to happen "
+                        "occasionally, especially as the solution is "
+                        "approached. However, if you see this frequently, "
+                        "consider setting option 'sym_pos' to False.",
+                        OptimizeWarning, stacklevel=5)
+                elif not lstsq:
+                    lstsq = True
+                    warn(
+                        "Solving system with option 'sym_pos':False "
+                        "failed. This may happen occasionally, "
+                        "especially as the solution is "
+                        "approached. However, if you see this frequently, "
+                        "your problem may be numerically challenging. "
+                        "If you cannot improve the formulation, consider "
+                        "setting 'lstsq' to True. Consider also setting "
+                        "`presolve` to True, if it is not already.",
+                        OptimizeWarning, stacklevel=5)
+                else:
+                    raise e
+                solve = _get_solver(M, sparse, lstsq, sym_pos,
+                                    cholesky, permc_spec)
+        # [4] Results after 8.29
+        d_tau = ((rhatg + 1 / tau * rhattk - (-c.dot(u) + b.dot(v))) /
+                 (1 / tau * kappa + (-c.dot(p) + b.dot(q))))
+        d_x = u + p * d_tau
+        d_y = v + q * d_tau
+
+        # [4] Relations between  after 8.25 and 8.26
+        d_z = (1 / x) * (rhatxs - z * d_x)
+        d_kappa = 1 / tau * (rhattk - kappa * d_tau)
+
+        # [4] 8.12 and "Let alpha be the maximal possible step..." before 8.23
+        alpha = _get_step(x, d_x, z, d_z, tau, d_tau, kappa, d_kappa, 1)
+        if ip:  # initial point - see [4] 4.4
+            gamma = 10
+        else:  # predictor-corrector, [4] definition after 8.12
+            beta1 = 0.1  # [4] pg. 220 (Table 8.1)
+            gamma = (1 - alpha)**2 * min(beta1, (1 - alpha))
+        i += 1
+
+    return d_x, d_y, d_z, d_tau, d_kappa
+
+
+def _sym_solve(Dinv, A, r1, r2, solve):
+    """
+    An implementation of [4] equation 8.31 and 8.32
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+    # [4] 8.31
+    r = r2 + A.dot(Dinv * r1)
+    v = solve(r)
+    # [4] 8.32
+    u = Dinv * (A.T.dot(v) - r1)
+    return u, v
+
+
+def _get_step(x, d_x, z, d_z, tau, d_tau, kappa, d_kappa, alpha0):
+    """
+    An implementation of [4] equation 8.21
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+    # [4] 4.3 Equation 8.21, ignoring 8.20 requirement
+    # same step is taken in primal and dual spaces
+    # alpha0 is basically beta3 from [4] Table 8.1, but instead of beta3
+    # the value 1 is used in Mehrota corrector and initial point correction
+    i_x = d_x < 0
+    i_z = d_z < 0
+    alpha_x = alpha0 * np.min(x[i_x] / -d_x[i_x]) if np.any(i_x) else 1
+    alpha_tau = alpha0 * tau / -d_tau if d_tau < 0 else 1
+    alpha_z = alpha0 * np.min(z[i_z] / -d_z[i_z]) if np.any(i_z) else 1
+    alpha_kappa = alpha0 * kappa / -d_kappa if d_kappa < 0 else 1
+    alpha = np.min([1, alpha_x, alpha_tau, alpha_z, alpha_kappa])
+    return alpha
+
+
+def _get_message(status):
+    """
+    Given problem status code, return a more detailed message.
+
+    Parameters
+    ----------
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Serious numerical difficulties encountered
+
+    Returns
+    -------
+    message : str
+        A string descriptor of the exit status of the optimization.
+
+    """
+    messages = (
+        ["Optimization terminated successfully.",
+         "The iteration limit was reached before the algorithm converged.",
+         "The algorithm terminated successfully and determined that the "
+         "problem is infeasible.",
+         "The algorithm terminated successfully and determined that the "
+         "problem is unbounded.",
+         "Numerical difficulties were encountered before the problem "
+         "converged. Please check your problem formulation for errors, "
+         "independence of linear equality constraints, and reasonable "
+         "scaling and matrix condition numbers. If you continue to "
+         "encounter this error, please submit a bug report."
+         ])
+    return messages[status]
+
+
+def _do_step(x, y, z, tau, kappa, d_x, d_y, d_z, d_tau, d_kappa, alpha):
+    """
+    An implementation of [4] Equation 8.9
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+    x = x + alpha * d_x
+    tau = tau + alpha * d_tau
+    z = z + alpha * d_z
+    kappa = kappa + alpha * d_kappa
+    y = y + alpha * d_y
+    return x, y, z, tau, kappa
+
+
+def _get_blind_start(shape):
+    """
+    Return the starting point from [4] 4.4
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+    m, n = shape
+    x0 = np.ones(n)
+    y0 = np.zeros(m)
+    z0 = np.ones(n)
+    tau0 = 1
+    kappa0 = 1
+    return x0, y0, z0, tau0, kappa0
+
+
+def _indicators(A, b, c, c0, x, y, z, tau, kappa):
+    """
+    Implementation of several equations from [4] used as indicators of
+    the status of optimization.
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+
+    # residuals for termination are relative to initial values
+    x0, y0, z0, tau0, kappa0 = _get_blind_start(A.shape)
+
+    # See [4], Section 4 - The Homogeneous Algorithm, Equation 8.8
+    def r_p(x, tau):
+        return b * tau - A.dot(x)
+
+    def r_d(y, z, tau):
+        return c * tau - A.T.dot(y) - z
+
+    def r_g(x, y, kappa):
+        return kappa + c.dot(x) - b.dot(y)
+
+    # np.dot unpacks if they are arrays of size one
+    def mu(x, tau, z, kappa):
+        return (x.dot(z) + np.dot(tau, kappa)) / (len(x) + 1)
+
+    obj = c.dot(x / tau) + c0
+
+    def norm(a):
+        return np.linalg.norm(a)
+
+    # See [4], Section 4.5 - The Stopping Criteria
+    r_p0 = r_p(x0, tau0)
+    r_d0 = r_d(y0, z0, tau0)
+    r_g0 = r_g(x0, y0, kappa0)
+    mu_0 = mu(x0, tau0, z0, kappa0)
+    rho_A = norm(c.T.dot(x) - b.T.dot(y)) / (tau + norm(b.T.dot(y)))
+    rho_p = norm(r_p(x, tau)) / max(1, norm(r_p0))
+    rho_d = norm(r_d(y, z, tau)) / max(1, norm(r_d0))
+    rho_g = norm(r_g(x, y, kappa)) / max(1, norm(r_g0))
+    rho_mu = mu(x, tau, z, kappa) / mu_0
+    return rho_p, rho_d, rho_A, rho_g, rho_mu, obj
+
+
+def _display_iter(rho_p, rho_d, rho_g, alpha, rho_mu, obj, header=False):
+    """
+    Print indicators of optimization status to the console.
+
+    Parameters
+    ----------
+    rho_p : float
+        The (normalized) primal feasibility, see [4] 4.5
+    rho_d : float
+        The (normalized) dual feasibility, see [4] 4.5
+    rho_g : float
+        The (normalized) duality gap, see [4] 4.5
+    alpha : float
+        The step size, see [4] 4.3
+    rho_mu : float
+        The (normalized) path parameter, see [4] 4.5
+    obj : float
+        The objective function value of the current iterate
+    header : bool
+        True if a header is to be printed
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+
+    """
+    if header:
+        print("Primal Feasibility ",
+              "Dual Feasibility   ",
+              "Duality Gap        ",
+              "Step            ",
+              "Path Parameter     ",
+              "Objective          ")
+
+    # no clue why this works
+    fmt = '{0:<20.13}{1:<20.13}{2:<20.13}{3:<17.13}{4:<20.13}{5:<20.13}'
+    print(fmt.format(
+        float(rho_p),
+        float(rho_d),
+        float(rho_g),
+        alpha if isinstance(alpha, str) else float(alpha),
+        float(rho_mu),
+        float(obj)))
+
+
+def _ip_hsd(A, b, c, c0, alpha0, beta, maxiter, disp, tol, sparse, lstsq,
+            sym_pos, cholesky, pc, ip, permc_spec, callback, postsolve_args):
+    r"""
+    Solve a linear programming problem in standard form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    using the interior point method of [4].
+
+    Parameters
+    ----------
+    A : 2-D array
+        2-D array such that ``A @ x``, gives the values of the equality
+        constraints at ``x``.
+    b : 1-D array
+        1-D array of values representing the RHS of each equality constraint
+        (row) in ``A`` (for standard form problem).
+    c : 1-D array
+        Coefficients of the linear objective function to be minimized (for
+        standard form problem).
+    c0 : float
+        Constant term in objective function due to fixed (and eliminated)
+        variables. (Purely for display.)
+    alpha0 : float
+        The maximal step size for Mehrota's predictor-corrector search
+        direction; see :math:`\beta_3`of [4] Table 8.1
+    beta : float
+        The desired reduction of the path parameter :math:`\mu` (see  [6]_)
+    maxiter : int
+        The maximum number of iterations of the algorithm.
+    disp : bool
+        Set to ``True`` if indicators of optimization status are to be printed
+        to the console each iteration.
+    tol : float
+        Termination tolerance; see [4]_ Section 4.5.
+    sparse : bool
+        Set to ``True`` if the problem is to be treated as sparse. However,
+        the inputs ``A_eq`` and ``A_ub`` should nonetheless be provided as
+        (dense) arrays rather than sparse matrices.
+    lstsq : bool
+        Set to ``True`` if the problem is expected to be very poorly
+        conditioned. This should always be left as ``False`` unless severe
+        numerical difficulties are frequently encountered, and a better option
+        would be to improve the formulation of the problem.
+    sym_pos : bool
+        Leave ``True`` if the problem is expected to yield a well conditioned
+        symmetric positive definite normal equation matrix (almost always).
+    cholesky : bool
+        Set to ``True`` if the normal equations are to be solved by explicit
+        Cholesky decomposition followed by explicit forward/backward
+        substitution. This is typically faster for moderate, dense problems
+        that are numerically well-behaved.
+    pc : bool
+        Leave ``True`` if the predictor-corrector method of Mehrota is to be
+        used. This is almost always (if not always) beneficial.
+    ip : bool
+        Set to ``True`` if the improved initial point suggestion due to [4]_
+        Section 4.3 is desired. It's unclear whether this is beneficial.
+    permc_spec : str (default = 'MMD_AT_PLUS_A')
+        (Has effect only with ``sparse = True``, ``lstsq = False``, ``sym_pos =
+        True``.) A matrix is factorized in each iteration of the algorithm.
+        This option specifies how to permute the columns of the matrix for
+        sparsity preservation. Acceptable values are:
+
+        - ``NATURAL``: natural ordering.
+        - ``MMD_ATA``: minimum degree ordering on the structure of A^T A.
+        - ``MMD_AT_PLUS_A``: minimum degree ordering on the structure of A^T+A.
+        - ``COLAMD``: approximate minimum degree column ordering.
+
+        This option can impact the convergence of the
+        interior point algorithm; test different values to determine which
+        performs best for your problem. For more information, refer to
+        ``scipy.sparse.linalg.splu``.
+    callback : callable, optional
+        If a callback function is provided, it will be called within each
+        iteration of the algorithm. The callback function must accept a single
+        `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+            x : 1-D array
+                Current solution vector
+            fun : float
+                Current value of the objective function
+            success : bool
+                True only when an algorithm has completed successfully,
+                so this is always False as the callback function is called
+                only while the algorithm is still iterating.
+            slack : 1-D array
+                The values of the slack variables. Each slack variable
+                corresponds to an inequality constraint. If the slack is zero,
+                the corresponding constraint is active.
+            con : 1-D array
+                The (nominally zero) residuals of the equality constraints,
+                that is, ``b - A_eq @ x``
+            phase : int
+                The phase of the algorithm being executed. This is always
+                1 for the interior-point method because it has only one phase.
+            status : int
+                For revised simplex, this is always 0 because if a different
+                status is detected, the algorithm terminates.
+            nit : int
+                The number of iterations performed.
+            message : str
+                A string descriptor of the exit status of the optimization.
+    postsolve_args : tuple
+        Data needed by _postsolve to convert the solution to the standard-form
+        problem into the solution to the original problem.
+
+    Returns
+    -------
+    x_hat : float
+        Solution vector (for standard form problem).
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Serious numerical difficulties encountered
+
+    message : str
+        A string descriptor of the exit status of the optimization.
+    iteration : int
+        The number of iterations taken to solve the problem
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+    .. [6] Freund, Robert M. "Primal-Dual Interior-Point Methods for Linear
+           Programming based on Newton's Method." Unpublished Course Notes,
+           March 2004. Available 2/25/2017 at:
+           https://ocw.mit.edu/courses/sloan-school-of-management/15-084j-nonlinear-programming-spring-2004/lecture-notes/lec14_int_pt_mthd.pdf
+
+    """
+
+    iteration = 0
+
+    # default initial point
+    x, y, z, tau, kappa = _get_blind_start(A.shape)
+
+    # first iteration is special improvement of initial point
+    ip = ip if pc else False
+
+    # [4] 4.5
+    rho_p, rho_d, rho_A, rho_g, rho_mu, obj = _indicators(
+        A, b, c, c0, x, y, z, tau, kappa)
+    go = rho_p > tol or rho_d > tol or rho_A > tol  # we might get lucky : )
+
+    if disp:
+        _display_iter(rho_p, rho_d, rho_g, "-", rho_mu, obj, header=True)
+    if callback is not None:
+        x_o, fun, slack, con = _postsolve(x/tau, postsolve_args)
+        res = OptimizeResult({'x': x_o, 'fun': fun, 'slack': slack,
+                              'con': con, 'nit': iteration, 'phase': 1,
+                              'complete': False, 'status': 0,
+                              'message': "", 'success': False})
+        callback(res)
+
+    status = 0
+    message = "Optimization terminated successfully."
+
+    if sparse:
+        A = sps.csc_matrix(A)
+
+    while go:
+
+        iteration += 1
+
+        if ip:  # initial point
+            # [4] Section 4.4
+            gamma = 1
+
+            def eta(g):
+                return 1
+        else:
+            # gamma = 0 in predictor step according to [4] 4.1
+            # if predictor/corrector is off, use mean of complementarity [6]
+            # 5.1 / [4] Below Figure 10-4
+            gamma = 0 if pc else beta * np.mean(z * x)
+            # [4] Section 4.1
+
+            def eta(g=gamma):
+                return 1 - g
+
+        try:
+            # Solve [4] 8.6 and 8.7/8.13/8.23
+            d_x, d_y, d_z, d_tau, d_kappa = _get_delta(
+                A, b, c, x, y, z, tau, kappa, gamma, eta,
+                sparse, lstsq, sym_pos, cholesky, pc, ip, permc_spec)
+
+            if ip:  # initial point
+                # [4] 4.4
+                # Formula after 8.23 takes a full step regardless if this will
+                # take it negative
+                alpha = 1.0
+                x, y, z, tau, kappa = _do_step(
+                    x, y, z, tau, kappa, d_x, d_y,
+                    d_z, d_tau, d_kappa, alpha)
+                x[x < 1] = 1
+                z[z < 1] = 1
+                tau = max(1, tau)
+                kappa = max(1, kappa)
+                ip = False  # done with initial point
+            else:
+                # [4] Section 4.3
+                alpha = _get_step(x, d_x, z, d_z, tau,
+                                  d_tau, kappa, d_kappa, alpha0)
+                # [4] Equation 8.9
+                x, y, z, tau, kappa = _do_step(
+                    x, y, z, tau, kappa, d_x, d_y, d_z, d_tau, d_kappa, alpha)
+
+        except (LinAlgError, FloatingPointError,
+                ValueError, ZeroDivisionError):
+            # this can happen when sparse solver is used and presolve
+            # is turned off. Also observed ValueError in AppVeyor Python 3.6
+            # Win32 build (PR #8676). I've never seen it otherwise.
+            status = 4
+            message = _get_message(status)
+            break
+
+        # [4] 4.5
+        rho_p, rho_d, rho_A, rho_g, rho_mu, obj = _indicators(
+            A, b, c, c0, x, y, z, tau, kappa)
+        go = rho_p > tol or rho_d > tol or rho_A > tol
+
+        if disp:
+            _display_iter(rho_p, rho_d, rho_g, alpha, rho_mu, obj)
+        if callback is not None:
+            x_o, fun, slack, con = _postsolve(x/tau, postsolve_args)
+            res = OptimizeResult({'x': x_o, 'fun': fun, 'slack': slack,
+                                  'con': con, 'nit': iteration, 'phase': 1,
+                                  'complete': False, 'status': 0,
+                                  'message': "", 'success': False})
+            callback(res)
+
+        # [4] 4.5
+        inf1 = (rho_p < tol and rho_d < tol and rho_g < tol and tau < tol *
+                max(1, kappa))
+        inf2 = rho_mu < tol and tau < tol * min(1, kappa)
+        if inf1 or inf2:
+            # [4] Lemma 8.4 / Theorem 8.3
+            if b.transpose().dot(y) > tol:
+                status = 2
+            else:  # elif c.T.dot(x) < tol: ? Probably not necessary.
+                status = 3
+            message = _get_message(status)
+            break
+        elif iteration >= maxiter:
+            status = 1
+            message = _get_message(status)
+            break
+
+    x_hat = x / tau
+    # [4] Statement after Theorem 8.2
+    return x_hat, status, message, iteration
+
+
+def _linprog_ip(c, c0, A, b, callback, postsolve_args, maxiter=1000, tol=1e-8,
+                disp=False, alpha0=.99995, beta=0.1, sparse=False, lstsq=False,
+                sym_pos=True, cholesky=None, pc=True, ip=False,
+                permc_spec='MMD_AT_PLUS_A', **unknown_options):
+    r"""
+    Minimize a linear objective function subject to linear
+    equality and non-negativity constraints using the interior point method
+    of [4]_. Linear programming is intended to solve problems
+    of the following form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    User-facing documentation is in _linprog_doc.py.
+
+    Parameters
+    ----------
+    c : 1-D array
+        Coefficients of the linear objective function to be minimized.
+    c0 : float
+        Constant term in objective function due to fixed (and eliminated)
+        variables. (Purely for display.)
+    A : 2-D array
+        2-D array such that ``A @ x``, gives the values of the equality
+        constraints at ``x``.
+    b : 1-D array
+        1-D array of values representing the right hand side of each equality
+        constraint (row) in ``A``.
+    callback : callable, optional
+        Callback function to be executed once per iteration.
+    postsolve_args : tuple
+        Data needed by _postsolve to convert the solution to the standard-form
+        problem into the solution to the original problem.
+
+    Options
+    -------
+    maxiter : int (default = 1000)
+        The maximum number of iterations of the algorithm.
+    tol : float (default = 1e-8)
+        Termination tolerance to be used for all termination criteria;
+        see [4]_ Section 4.5.
+    disp : bool (default = False)
+        Set to ``True`` if indicators of optimization status are to be printed
+        to the console each iteration.
+    alpha0 : float (default = 0.99995)
+        The maximal step size for Mehrota's predictor-corrector search
+        direction; see :math:`\beta_{3}` of [4]_ Table 8.1.
+    beta : float (default = 0.1)
+        The desired reduction of the path parameter :math:`\mu` (see [6]_)
+        when Mehrota's predictor-corrector is not in use (uncommon).
+    sparse : bool (default = False)
+        Set to ``True`` if the problem is to be treated as sparse after
+        presolve. If either ``A_eq`` or ``A_ub`` is a sparse matrix,
+        this option will automatically be set ``True``, and the problem
+        will be treated as sparse even during presolve. If your constraint
+        matrices contain mostly zeros and the problem is not very small (less
+        than about 100 constraints or variables), consider setting ``True``
+        or providing ``A_eq`` and ``A_ub`` as sparse matrices.
+    lstsq : bool (default = False)
+        Set to ``True`` if the problem is expected to be very poorly
+        conditioned. This should always be left ``False`` unless severe
+        numerical difficulties are encountered. Leave this at the default
+        unless you receive a warning message suggesting otherwise.
+    sym_pos : bool (default = True)
+        Leave ``True`` if the problem is expected to yield a well conditioned
+        symmetric positive definite normal equation matrix
+        (almost always). Leave this at the default unless you receive
+        a warning message suggesting otherwise.
+    cholesky : bool (default = True)
+        Set to ``True`` if the normal equations are to be solved by explicit
+        Cholesky decomposition followed by explicit forward/backward
+        substitution. This is typically faster for problems
+        that are numerically well-behaved.
+    pc : bool (default = True)
+        Leave ``True`` if the predictor-corrector method of Mehrota is to be
+        used. This is almost always (if not always) beneficial.
+    ip : bool (default = False)
+        Set to ``True`` if the improved initial point suggestion due to [4]_
+        Section 4.3 is desired. Whether this is beneficial or not
+        depends on the problem.
+    permc_spec : str (default = 'MMD_AT_PLUS_A')
+        (Has effect only with ``sparse = True``, ``lstsq = False``, ``sym_pos =
+        True``, and no SuiteSparse.)
+        A matrix is factorized in each iteration of the algorithm.
+        This option specifies how to permute the columns of the matrix for
+        sparsity preservation. Acceptable values are:
+
+        - ``NATURAL``: natural ordering.
+        - ``MMD_ATA``: minimum degree ordering on the structure of A^T A.
+        - ``MMD_AT_PLUS_A``: minimum degree ordering on the structure of A^T+A.
+        - ``COLAMD``: approximate minimum degree column ordering.
+
+        This option can impact the convergence of the
+        interior point algorithm; test different values to determine which
+        performs best for your problem. For more information, refer to
+        ``scipy.sparse.linalg.splu``.
+    unknown_options : dict
+        Optional arguments not used by this particular solver. If
+        `unknown_options` is non-empty a warning is issued listing all
+        unused options.
+
+    Returns
+    -------
+    x : 1-D array
+        Solution vector.
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Serious numerical difficulties encountered
+
+    message : str
+        A string descriptor of the exit status of the optimization.
+    iteration : int
+        The number of iterations taken to solve the problem.
+
+    Notes
+    -----
+    This method implements the algorithm outlined in [4]_ with ideas from [8]_
+    and a structure inspired by the simpler methods of [6]_.
+
+    The primal-dual path following method begins with initial 'guesses' of
+    the primal and dual variables of the standard form problem and iteratively
+    attempts to solve the (nonlinear) Karush-Kuhn-Tucker conditions for the
+    problem with a gradually reduced logarithmic barrier term added to the
+    objective. This particular implementation uses a homogeneous self-dual
+    formulation, which provides certificates of infeasibility or unboundedness
+    where applicable.
+
+    The default initial point for the primal and dual variables is that
+    defined in [4]_ Section 4.4 Equation 8.22. Optionally (by setting initial
+    point option ``ip=True``), an alternate (potentially improved) starting
+    point can be calculated according to the additional recommendations of
+    [4]_ Section 4.4.
+
+    A search direction is calculated using the predictor-corrector method
+    (single correction) proposed by Mehrota and detailed in [4]_ Section 4.1.
+    (A potential improvement would be to implement the method of multiple
+    corrections described in [4]_ Section 4.2.) In practice, this is
+    accomplished by solving the normal equations, [4]_ Section 5.1 Equations
+    8.31 and 8.32, derived from the Newton equations [4]_ Section 5 Equations
+    8.25 (compare to [4]_ Section 4 Equations 8.6-8.8). The advantage of
+    solving the normal equations rather than 8.25 directly is that the
+    matrices involved are symmetric positive definite, so Cholesky
+    decomposition can be used rather than the more expensive LU factorization.
+
+    With default options, the solver used to perform the factorization depends
+    on third-party software availability and the conditioning of the problem.
+
+    For dense problems, solvers are tried in the following order:
+
+    1. ``scipy.linalg.cho_factor``
+
+    2. ``scipy.linalg.solve`` with option ``sym_pos=True``
+
+    3. ``scipy.linalg.solve`` with option ``sym_pos=False``
+
+    4. ``scipy.linalg.lstsq``
+
+    For sparse problems:
+
+    1. ``sksparse.cholmod.cholesky`` (if scikit-sparse and SuiteSparse are installed)
+
+    2. ``scipy.sparse.linalg.factorized``
+        (if scikit-umfpack and SuiteSparse are installed)
+
+    3. ``scipy.sparse.linalg.splu`` (which uses SuperLU distributed with SciPy)
+
+    4. ``scipy.sparse.linalg.lsqr``
+
+    If the solver fails for any reason, successively more robust (but slower)
+    solvers are attempted in the order indicated. Attempting, failing, and
+    re-starting factorization can be time consuming, so if the problem is
+    numerically challenging, options can be set to  bypass solvers that are
+    failing. Setting ``cholesky=False`` skips to solver 2,
+    ``sym_pos=False`` skips to solver 3, and ``lstsq=True`` skips
+    to solver 4 for both sparse and dense problems.
+
+    Potential improvements for combatting issues associated with dense
+    columns in otherwise sparse problems are outlined in [4]_ Section 5.3 and
+    [10]_ Section 4.1-4.2; the latter also discusses the alleviation of
+    accuracy issues associated with the substitution approach to free
+    variables.
+
+    After calculating the search direction, the maximum possible step size
+    that does not activate the non-negativity constraints is calculated, and
+    the smaller of this step size and unity is applied (as in [4]_ Section
+    4.1.) [4]_ Section 4.3 suggests improvements for choosing the step size.
+
+    The new point is tested according to the termination conditions of [4]_
+    Section 4.5. The same tolerance, which can be set using the ``tol`` option,
+    is used for all checks. (A potential improvement would be to expose
+    the different tolerances to be set independently.) If optimality,
+    unboundedness, or infeasibility is detected, the solve procedure
+    terminates; otherwise it repeats.
+
+    The expected problem formulation differs between the top level ``linprog``
+    module and the method specific solvers. The method specific solvers expect a
+    problem in standard form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    Whereas the top level ``linprog`` module expects a problem of form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A_ub @ x <= b_ub
+        A_eq @ x == b_eq
+         lb <= x <= ub
+
+    where ``lb = 0`` and ``ub = None`` unless set in ``bounds``.
+
+    The original problem contains equality, upper-bound and variable constraints
+    whereas the method specific solver requires equality constraints and
+    variable non-negativity.
+
+    ``linprog`` module converts the original problem to standard form by
+    converting the simple bounds to upper bound constraints, introducing
+    non-negative slack variables for inequality constraints, and expressing
+    unbounded variables as the difference between two non-negative variables.
+
+
+    References
+    ----------
+    .. [4] Andersen, Erling D., and Knud D. Andersen. "The MOSEK interior point
+           optimizer for linear programming: an implementation of the
+           homogeneous algorithm." High performance optimization. Springer US,
+           2000. 197-232.
+    .. [6] Freund, Robert M. "Primal-Dual Interior-Point Methods for Linear
+           Programming based on Newton's Method." Unpublished Course Notes,
+           March 2004. Available 2/25/2017 at
+           https://ocw.mit.edu/courses/sloan-school-of-management/15-084j-nonlinear-programming-spring-2004/lecture-notes/lec14_int_pt_mthd.pdf
+    .. [8] Andersen, Erling D., and Knud D. Andersen. "Presolving in linear
+           programming." Mathematical Programming 71.2 (1995): 221-245.
+    .. [9] Bertsimas, Dimitris, and J. Tsitsiklis. "Introduction to linear
+           programming." Athena Scientific 1 (1997): 997.
+    .. [10] Andersen, Erling D., et al. Implementation of interior point methods
+            for large scale linear programming. HEC/Universite de Geneve, 1996.
+
+    """
+
+    _check_unknown_options(unknown_options)
+
+    # These should be warnings, not errors
+    if (cholesky or cholesky is None) and sparse and not has_cholmod:
+        if cholesky:
+            warn("Sparse cholesky is only available with scikit-sparse. "
+                 "Setting `cholesky = False`",
+                 OptimizeWarning, stacklevel=3)
+        cholesky = False
+
+    if sparse and lstsq:
+        warn("Option combination 'sparse':True and 'lstsq':True "
+             "is not recommended.",
+             OptimizeWarning, stacklevel=3)
+
+    if lstsq and cholesky:
+        warn("Invalid option combination 'lstsq':True "
+             "and 'cholesky':True; option 'cholesky' has no effect when "
+             "'lstsq' is set True.",
+             OptimizeWarning, stacklevel=3)
+
+    valid_permc_spec = ('NATURAL', 'MMD_ATA', 'MMD_AT_PLUS_A', 'COLAMD')
+    if permc_spec.upper() not in valid_permc_spec:
+        warn("Invalid permc_spec option: '" + str(permc_spec) + "'. "
+             "Acceptable values are 'NATURAL', 'MMD_ATA', 'MMD_AT_PLUS_A', "
+             "and 'COLAMD'. Reverting to default.",
+             OptimizeWarning, stacklevel=3)
+        permc_spec = 'MMD_AT_PLUS_A'
+
+    # This can be an error
+    if not sym_pos and cholesky:
+        raise ValueError(
+            "Invalid option combination 'sym_pos':False "
+            "and 'cholesky':True: Cholesky decomposition is only possible "
+            "for symmetric positive definite matrices.")
+
+    cholesky = cholesky or (cholesky is None and sym_pos and not lstsq)
+
+    x, status, message, iteration = _ip_hsd(A, b, c, c0, alpha0, beta,
+                                            maxiter, disp, tol, sparse,
+                                            lstsq, sym_pos, cholesky,
+                                            pc, ip, permc_spec, callback,
+                                            postsolve_args)
+
+    return x, status, message, iteration

vila/lib/python3.10/site-packages/scipy/optimize/_linprog_rs.py

@@ -0,0 +1,572 @@
+"""Revised simplex method for linear programming
+
+The *revised simplex* method uses the method described in [1]_, except
+that a factorization [2]_ of the basis matrix, rather than its inverse,
+is efficiently maintained and used to solve the linear systems at each
+iteration of the algorithm.
+
+.. versionadded:: 1.3.0
+
+References
+----------
+.. [1] Bertsimas, Dimitris, and J. Tsitsiklis. "Introduction to linear
+           programming." Athena Scientific 1 (1997): 997.
+.. [2] Bartels, Richard H. "A stabilization of the simplex method."
+            Journal in  Numerische Mathematik 16.5 (1971): 414-434.
+
+"""
+# Author: Matt Haberland
+
+import numpy as np
+from numpy.linalg import LinAlgError
+
+from scipy.linalg import solve
+from ._optimize import _check_unknown_options
+from ._bglu_dense import LU
+from ._bglu_dense import BGLU as BGLU
+from ._linprog_util import _postsolve
+from ._optimize import OptimizeResult
+
+
+def _phase_one(A, b, x0, callback, postsolve_args, maxiter, tol, disp,
+               maxupdate, mast, pivot):
+    """
+    The purpose of phase one is to find an initial basic feasible solution
+    (BFS) to the original problem.
+
+    Generates an auxiliary problem with a trivial BFS and an objective that
+    minimizes infeasibility of the original problem. Solves the auxiliary
+    problem using the main simplex routine (phase two). This either yields
+    a BFS to the original problem or determines that the original problem is
+    infeasible. If feasible, phase one detects redundant rows in the original
+    constraint matrix and removes them, then chooses additional indices as
+    necessary to complete a basis/BFS for the original problem.
+    """
+
+    m, n = A.shape
+    status = 0
+
+    # generate auxiliary problem to get initial BFS
+    A, b, c, basis, x, status = _generate_auxiliary_problem(A, b, x0, tol)
+
+    if status == 6:
+        residual = c.dot(x)
+        iter_k = 0
+        return x, basis, A, b, residual, status, iter_k
+
+    # solve auxiliary problem
+    phase_one_n = n
+    iter_k = 0
+    x, basis, status, iter_k = _phase_two(c, A, x, basis, callback,
+                                          postsolve_args,
+                                          maxiter, tol, disp,
+                                          maxupdate, mast, pivot,
+                                          iter_k, phase_one_n)
+
+    # check for infeasibility
+    residual = c.dot(x)
+    if status == 0 and residual > tol:
+        status = 2
+
+    # drive artificial variables out of basis
+    # TODO: test redundant row removal better
+    # TODO: make solve more efficient with BGLU? This could take a while.
+    keep_rows = np.ones(m, dtype=bool)
+    for basis_column in basis[basis >= n]:
+        B = A[:, basis]
+        try:
+            basis_finder = np.abs(solve(B, A))  # inefficient
+            pertinent_row = np.argmax(basis_finder[:, basis_column])
+            eligible_columns = np.ones(n, dtype=bool)
+            eligible_columns[basis[basis < n]] = 0
+            eligible_column_indices = np.where(eligible_columns)[0]
+            index = np.argmax(basis_finder[:, :n]
+                              [pertinent_row, eligible_columns])
+            new_basis_column = eligible_column_indices[index]
+            if basis_finder[pertinent_row, new_basis_column] < tol:
+                keep_rows[pertinent_row] = False
+            else:
+                basis[basis == basis_column] = new_basis_column
+        except LinAlgError:
+            status = 4
+
+    # form solution to original problem
+    A = A[keep_rows, :n]
+    basis = basis[keep_rows]
+    x = x[:n]
+    m = A.shape[0]
+    return x, basis, A, b, residual, status, iter_k
+
+
+def _get_more_basis_columns(A, basis):
+    """
+    Called when the auxiliary problem terminates with artificial columns in
+    the basis, which must be removed and replaced with non-artificial
+    columns. Finds additional columns that do not make the matrix singular.
+    """
+    m, n = A.shape
+
+    # options for inclusion are those that aren't already in the basis
+    a = np.arange(m+n)
+    bl = np.zeros(len(a), dtype=bool)
+    bl[basis] = 1
+    options = a[~bl]
+    options = options[options < n]  # and they have to be non-artificial
+
+    # form basis matrix
+    B = np.zeros((m, m))
+    B[:, 0:len(basis)] = A[:, basis]
+
+    if (basis.size > 0 and
+            np.linalg.matrix_rank(B[:, :len(basis)]) < len(basis)):
+        raise Exception("Basis has dependent columns")
+
+    rank = 0  # just enter the loop
+    for i in range(n):  # somewhat arbitrary, but we need another way out
+        # permute the options, and take as many as needed
+        new_basis = np.random.permutation(options)[:m-len(basis)]
+        B[:, len(basis):] = A[:, new_basis]  # update the basis matrix
+        rank = np.linalg.matrix_rank(B)      # check the rank
+        if rank == m:
+            break
+
+    return np.concatenate((basis, new_basis))
+
+
+def _generate_auxiliary_problem(A, b, x0, tol):
+    """
+    Modifies original problem to create an auxiliary problem with a trivial
+    initial basic feasible solution and an objective that minimizes
+    infeasibility in the original problem.
+
+    Conceptually, this is done by stacking an identity matrix on the right of
+    the original constraint matrix, adding artificial variables to correspond
+    with each of these new columns, and generating a cost vector that is all
+    zeros except for ones corresponding with each of the new variables.
+
+    A initial basic feasible solution is trivial: all variables are zero
+    except for the artificial variables, which are set equal to the
+    corresponding element of the right hand side `b`.
+
+    Running the simplex method on this auxiliary problem drives all of the
+    artificial variables - and thus the cost - to zero if the original problem
+    is feasible. The original problem is declared infeasible otherwise.
+
+    Much of the complexity below is to improve efficiency by using singleton
+    columns in the original problem where possible, thus generating artificial
+    variables only as necessary, and using an initial 'guess' basic feasible
+    solution.
+    """
+    status = 0
+    m, n = A.shape
+
+    if x0 is not None:
+        x = x0
+    else:
+        x = np.zeros(n)
+
+    r = b - A@x  # residual; this must be all zeros for feasibility
+
+    A[r < 0] = -A[r < 0]  # express problem with RHS positive for trivial BFS
+    b[r < 0] = -b[r < 0]  # to the auxiliary problem
+    r[r < 0] *= -1
+
+    # Rows which we will need to find a trivial way to zero.
+    # This should just be the rows where there is a nonzero residual.
+    # But then we would not necessarily have a column singleton in every row.
+    # This makes it difficult to find an initial basis.
+    if x0 is None:
+        nonzero_constraints = np.arange(m)
+    else:
+        nonzero_constraints = np.where(r > tol)[0]
+
+    # these are (at least some of) the initial basis columns
+    basis = np.where(np.abs(x) > tol)[0]
+
+    if len(nonzero_constraints) == 0 and len(basis) <= m:  # already a BFS
+        c = np.zeros(n)
+        basis = _get_more_basis_columns(A, basis)
+        return A, b, c, basis, x, status
+    elif (len(nonzero_constraints) > m - len(basis) or
+          np.any(x < 0)):  # can't get trivial BFS
+        c = np.zeros(n)
+        status = 6
+        return A, b, c, basis, x, status
+
+    # chooses existing columns appropriate for inclusion in initial basis
+    cols, rows = _select_singleton_columns(A, r)
+
+    # find the rows we need to zero that we _can_ zero with column singletons
+    i_tofix = np.isin(rows, nonzero_constraints)
+    # these columns can't already be in the basis, though
+    # we are going to add them to the basis and change the corresponding x val
+    i_notinbasis = np.logical_not(np.isin(cols, basis))
+    i_fix_without_aux = np.logical_and(i_tofix, i_notinbasis)
+    rows = rows[i_fix_without_aux]
+    cols = cols[i_fix_without_aux]
+
+    # indices of the rows we can only zero with auxiliary variable
+    # these rows will get a one in each auxiliary column
+    arows = nonzero_constraints[np.logical_not(
+                                np.isin(nonzero_constraints, rows))]
+    n_aux = len(arows)
+    acols = n + np.arange(n_aux)          # indices of auxiliary columns
+
+    basis_ng = np.concatenate((cols, acols))   # basis columns not from guess
+    basis_ng_rows = np.concatenate((rows, arows))  # rows we need to zero
+
+    # add auxiliary singleton columns
+    A = np.hstack((A, np.zeros((m, n_aux))))
+    A[arows, acols] = 1
+
+    # generate initial BFS
+    x = np.concatenate((x, np.zeros(n_aux)))
+    x[basis_ng] = r[basis_ng_rows]/A[basis_ng_rows, basis_ng]
+
+    # generate costs to minimize infeasibility
+    c = np.zeros(n_aux + n)
+    c[acols] = 1
+
+    # basis columns correspond with nonzeros in guess, those with column
+    # singletons we used to zero remaining constraints, and any additional
+    # columns to get a full set (m columns)
+    basis = np.concatenate((basis, basis_ng))
+    basis = _get_more_basis_columns(A, basis)  # add columns as needed
+
+    return A, b, c, basis, x, status
+
+
+def _select_singleton_columns(A, b):
+    """
+    Finds singleton columns for which the singleton entry is of the same sign
+    as the right-hand side; these columns are eligible for inclusion in an
+    initial basis. Determines the rows in which the singleton entries are
+    located. For each of these rows, returns the indices of the one singleton
+    column and its corresponding row.
+    """
+    # find indices of all singleton columns and corresponding row indices
+    column_indices = np.nonzero(np.sum(np.abs(A) != 0, axis=0) == 1)[0]
+    columns = A[:, column_indices]          # array of singleton columns
+    row_indices = np.zeros(len(column_indices), dtype=int)
+    nonzero_rows, nonzero_columns = np.nonzero(columns)
+    row_indices[nonzero_columns] = nonzero_rows   # corresponding row indices
+
+    # keep only singletons with entries that have same sign as RHS
+    # this is necessary because all elements of BFS must be non-negative
+    same_sign = A[row_indices, column_indices]*b[row_indices] >= 0
+    column_indices = column_indices[same_sign][::-1]
+    row_indices = row_indices[same_sign][::-1]
+    # Reversing the order so that steps below select rightmost columns
+    # for initial basis, which will tend to be slack variables. (If the
+    # guess corresponds with a basic feasible solution but a constraint
+    # is not satisfied with the corresponding slack variable zero, the slack
+    # variable must be basic.)
+
+    # for each row, keep rightmost singleton column with an entry in that row
+    unique_row_indices, first_columns = np.unique(row_indices,
+                                                  return_index=True)
+    return column_indices[first_columns], unique_row_indices
+
+
+def _find_nonzero_rows(A, tol):
+    """
+    Returns logical array indicating the locations of rows with at least
+    one nonzero element.
+    """
+    return np.any(np.abs(A) > tol, axis=1)
+
+
+def _select_enter_pivot(c_hat, bl, a, rule="bland", tol=1e-12):
+    """
+    Selects a pivot to enter the basis. Currently Bland's rule - the smallest
+    index that has a negative reduced cost - is the default.
+    """
+    if rule.lower() == "mrc":  # index with minimum reduced cost
+        return a[~bl][np.argmin(c_hat)]
+    else:  # smallest index w/ negative reduced cost
+        return a[~bl][c_hat < -tol][0]
+
+
+def _display_iter(phase, iteration, slack, con, fun):
+    """
+    Print indicators of optimization status to the console.
+    """
+    header = True if not iteration % 20 else False
+
+    if header:
+        print("Phase",
+              "Iteration",
+              "Minimum Slack      ",
+              "Constraint Residual",
+              "Objective          ")
+
+    # :<X.Y left aligns Y digits in X digit spaces
+    fmt = '{0:<6}{1:<10}{2:<20.13}{3:<20.13}{4:<20.13}'
+    try:
+        slack = np.min(slack)
+    except ValueError:
+        slack = "NA"
+    print(fmt.format(phase, iteration, slack, np.linalg.norm(con), fun))
+
+
+def _display_and_callback(phase_one_n, x, postsolve_args, status,
+                          iteration, disp, callback):
+    if phase_one_n is not None:
+        phase = 1
+        x_postsolve = x[:phase_one_n]
+    else:
+        phase = 2
+        x_postsolve = x
+    x_o, fun, slack, con = _postsolve(x_postsolve,
+                                      postsolve_args)
+
+    if callback is not None:
+        res = OptimizeResult({'x': x_o, 'fun': fun, 'slack': slack,
+                              'con': con, 'nit': iteration,
+                              'phase': phase, 'complete': False,
+                              'status': status, 'message': "",
+                              'success': False})
+        callback(res)
+    if disp:
+        _display_iter(phase, iteration, slack, con, fun)
+
+
+def _phase_two(c, A, x, b, callback, postsolve_args, maxiter, tol, disp,
+               maxupdate, mast, pivot, iteration=0, phase_one_n=None):
+    """
+    The heart of the simplex method. Beginning with a basic feasible solution,
+    moves to adjacent basic feasible solutions successively lower reduced cost.
+    Terminates when there are no basic feasible solutions with lower reduced
+    cost or if the problem is determined to be unbounded.
+
+    This implementation follows the revised simplex method based on LU
+    decomposition. Rather than maintaining a tableau or an inverse of the
+    basis matrix, we keep a factorization of the basis matrix that allows
+    efficient solution of linear systems while avoiding stability issues
+    associated with inverted matrices.
+    """
+    m, n = A.shape
+    status = 0
+    a = np.arange(n)                    # indices of columns of A
+    ab = np.arange(m)                   # indices of columns of B
+    if maxupdate:
+        # basis matrix factorization object; similar to B = A[:, b]
+        B = BGLU(A, b, maxupdate, mast)
+    else:
+        B = LU(A, b)
+
+    for iteration in range(iteration, maxiter):
+
+        if disp or callback is not None:
+            _display_and_callback(phase_one_n, x, postsolve_args, status,
+                                  iteration, disp, callback)
+
+        bl = np.zeros(len(a), dtype=bool)
+        bl[b] = 1
+
+        xb = x[b]       # basic variables
+        cb = c[b]       # basic costs
+
+        try:
+            v = B.solve(cb, transposed=True)    # similar to v = solve(B.T, cb)
+        except LinAlgError:
+            status = 4
+            break
+
+        # TODO: cythonize?
+        c_hat = c - v.dot(A)    # reduced cost
+        c_hat = c_hat[~bl]
+        # Above is much faster than:
+        # N = A[:, ~bl]                 # slow!
+        # c_hat = c[~bl] - v.T.dot(N)
+        # Can we perform the multiplication only on the nonbasic columns?
+
+        if np.all(c_hat >= -tol):  # all reduced costs positive -> terminate
+            break
+
+        j = _select_enter_pivot(c_hat, bl, a, rule=pivot, tol=tol)
+        u = B.solve(A[:, j])        # similar to u = solve(B, A[:, j])
+
+        i = u > tol                 # if none of the u are positive, unbounded
+        if not np.any(i):
+            status = 3
+            break
+
+        th = xb[i]/u[i]
+        l = np.argmin(th)           # implicitly selects smallest subscript
+        th_star = th[l]             # step size
+
+        x[b] = x[b] - th_star*u     # take step
+        x[j] = th_star
+        B.update(ab[i][l], j)       # modify basis
+        b = B.b                     # similar to b[ab[i][l]] =
+
+    else:
+        # If the end of the for loop is reached (without a break statement),
+        # then another step has been taken, so the iteration counter should
+        # increment, info should be displayed, and callback should be called.
+        iteration += 1
+        status = 1
+        if disp or callback is not None:
+            _display_and_callback(phase_one_n, x, postsolve_args, status,
+                                  iteration, disp, callback)
+
+    return x, b, status, iteration
+
+
+def _linprog_rs(c, c0, A, b, x0, callback, postsolve_args,
+                maxiter=5000, tol=1e-12, disp=False,
+                maxupdate=10, mast=False, pivot="mrc",
+                **unknown_options):
+    """
+    Solve the following linear programming problem via a two-phase
+    revised simplex algorithm.::
+
+        minimize:     c @ x
+
+        subject to:  A @ x == b
+                     0 <= x < oo
+
+    User-facing documentation is in _linprog_doc.py.
+
+    Parameters
+    ----------
+    c : 1-D array
+        Coefficients of the linear objective function to be minimized.
+    c0 : float
+        Constant term in objective function due to fixed (and eliminated)
+        variables. (Currently unused.)
+    A : 2-D array
+        2-D array which, when matrix-multiplied by ``x``, gives the values of
+        the equality constraints at ``x``.
+    b : 1-D array
+        1-D array of values representing the RHS of each equality constraint
+        (row) in ``A_eq``.
+    x0 : 1-D array, optional
+        Starting values of the independent variables, which will be refined by
+        the optimization algorithm. For the revised simplex method, these must
+        correspond with a basic feasible solution.
+    callback : callable, optional
+        If a callback function is provided, it will be called within each
+        iteration of the algorithm. The callback function must accept a single
+        `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+            x : 1-D array
+                Current solution vector.
+            fun : float
+                Current value of the objective function ``c @ x``.
+            success : bool
+                True only when an algorithm has completed successfully,
+                so this is always False as the callback function is called
+                only while the algorithm is still iterating.
+            slack : 1-D array
+                The values of the slack variables. Each slack variable
+                corresponds to an inequality constraint. If the slack is zero,
+                the corresponding constraint is active.
+            con : 1-D array
+                The (nominally zero) residuals of the equality constraints,
+                that is, ``b - A_eq @ x``.
+            phase : int
+                The phase of the algorithm being executed.
+            status : int
+                For revised simplex, this is always 0 because if a different
+                status is detected, the algorithm terminates.
+            nit : int
+                The number of iterations performed.
+            message : str
+                A string descriptor of the exit status of the optimization.
+    postsolve_args : tuple
+        Data needed by _postsolve to convert the solution to the standard-form
+        problem into the solution to the original problem.
+
+    Options
+    -------
+    maxiter : int
+       The maximum number of iterations to perform in either phase.
+    tol : float
+        The tolerance which determines when a solution is "close enough" to
+        zero in Phase 1 to be considered a basic feasible solution or close
+        enough to positive to serve as an optimal solution.
+    disp : bool
+        Set to ``True`` if indicators of optimization status are to be printed
+        to the console each iteration.
+    maxupdate : int
+        The maximum number of updates performed on the LU factorization.
+        After this many updates is reached, the basis matrix is factorized
+        from scratch.
+    mast : bool
+        Minimize Amortized Solve Time. If enabled, the average time to solve
+        a linear system using the basis factorization is measured. Typically,
+        the average solve time will decrease with each successive solve after
+        initial factorization, as factorization takes much more time than the
+        solve operation (and updates). Eventually, however, the updated
+        factorization becomes sufficiently complex that the average solve time
+        begins to increase. When this is detected, the basis is refactorized
+        from scratch. Enable this option to maximize speed at the risk of
+        nondeterministic behavior. Ignored if ``maxupdate`` is 0.
+    pivot : "mrc" or "bland"
+        Pivot rule: Minimum Reduced Cost (default) or Bland's rule. Choose
+        Bland's rule if iteration limit is reached and cycling is suspected.
+    unknown_options : dict
+        Optional arguments not used by this particular solver. If
+        `unknown_options` is non-empty a warning is issued listing all
+        unused options.
+
+    Returns
+    -------
+    x : 1-D array
+        Solution vector.
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Numerical difficulties encountered
+         5 : No constraints; turn presolve on
+         6 : Guess x0 cannot be converted to a basic feasible solution
+
+    message : str
+        A string descriptor of the exit status of the optimization.
+    iteration : int
+        The number of iterations taken to solve the problem.
+    """
+
+    _check_unknown_options(unknown_options)
+
+    messages = ["Optimization terminated successfully.",
+                "Iteration limit reached.",
+                "The problem appears infeasible, as the phase one auxiliary "
+                "problem terminated successfully with a residual of {0:.1e}, "
+                "greater than the tolerance {1} required for the solution to "
+                "be considered feasible. Consider increasing the tolerance to "
+                "be greater than {0:.1e}. If this tolerance is unnaceptably "
+                "large, the problem is likely infeasible.",
+                "The problem is unbounded, as the simplex algorithm found "
+                "a basic feasible solution from which there is a direction "
+                "with negative reduced cost in which all decision variables "
+                "increase.",
+                "Numerical difficulties encountered; consider trying "
+                "method='interior-point'.",
+                "Problems with no constraints are trivially solved; please "
+                "turn presolve on.",
+                "The guess x0 cannot be converted to a basic feasible "
+                "solution. "
+                ]
+
+    if A.size == 0:  # address test_unbounded_below_no_presolve_corrected
+        return np.zeros(c.shape), 5, messages[5], 0
+
+    x, basis, A, b, residual, status, iteration = (
+        _phase_one(A, b, x0, callback, postsolve_args,
+                   maxiter, tol, disp, maxupdate, mast, pivot))
+
+    if status == 0:
+        x, basis, status, iteration = _phase_two(c, A, x, basis, callback,
+                                                 postsolve_args,
+                                                 maxiter, tol, disp,
+                                                 maxupdate, mast, pivot,
+                                                 iteration)
+
+    return x, status, messages[status].format(residual, tol), iteration

vila/lib/python3.10/site-packages/scipy/optimize/_linprog_simplex.py

@@ -0,0 +1,661 @@
+"""Simplex method for  linear programming
+
+The *simplex* method uses a traditional, full-tableau implementation of
+Dantzig's simplex algorithm [1]_, [2]_ (*not* the Nelder-Mead simplex).
+This algorithm is included for backwards compatibility and educational
+purposes.
+
+    .. versionadded:: 0.15.0
+
+Warnings
+--------
+
+The simplex method may encounter numerical difficulties when pivot
+values are close to the specified tolerance. If encountered try
+remove any redundant constraints, change the pivot strategy to Bland's
+rule or increase the tolerance value.
+
+Alternatively, more robust methods maybe be used. See
+:ref:`'interior-point' <optimize.linprog-interior-point>` and
+:ref:`'revised simplex' <optimize.linprog-revised_simplex>`.
+
+References
+----------
+.. [1] Dantzig, George B., Linear programming and extensions. Rand
+       Corporation Research Study Princeton Univ. Press, Princeton, NJ,
+       1963
+.. [2] Hillier, S.H. and Lieberman, G.J. (1995), "Introduction to
+       Mathematical Programming", McGraw-Hill, Chapter 4.
+"""
+
+import numpy as np
+from warnings import warn
+from ._optimize import OptimizeResult, OptimizeWarning, _check_unknown_options
+from ._linprog_util import _postsolve
+
+
+def _pivot_col(T, tol=1e-9, bland=False):
+    """
+    Given a linear programming simplex tableau, determine the column
+    of the variable to enter the basis.
+
+    Parameters
+    ----------
+    T : 2-D array
+        A 2-D array representing the simplex tableau, T, corresponding to the
+        linear programming problem. It should have the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],    0]]
+
+        for a Phase 2 problem, or the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],   0],
+         [c'[0],  c'[1], ...,  c'[n_total],  0]]
+
+         for a Phase 1 problem (a problem in which a basic feasible solution is
+         sought prior to maximizing the actual objective. ``T`` is modified in
+         place by ``_solve_simplex``.
+    tol : float
+        Elements in the objective row larger than -tol will not be considered
+        for pivoting. Nominally this value is zero, but numerical issues
+        cause a tolerance about zero to be necessary.
+    bland : bool
+        If True, use Bland's rule for selection of the column (select the
+        first column with a negative coefficient in the objective row,
+        regardless of magnitude).
+
+    Returns
+    -------
+    status: bool
+        True if a suitable pivot column was found, otherwise False.
+        A return of False indicates that the linear programming simplex
+        algorithm is complete.
+    col: int
+        The index of the column of the pivot element.
+        If status is False, col will be returned as nan.
+    """
+    ma = np.ma.masked_where(T[-1, :-1] >= -tol, T[-1, :-1], copy=False)
+    if ma.count() == 0:
+        return False, np.nan
+    if bland:
+        # ma.mask is sometimes 0d
+        return True, np.nonzero(np.logical_not(np.atleast_1d(ma.mask)))[0][0]
+    return True, np.ma.nonzero(ma == ma.min())[0][0]
+
+
+def _pivot_row(T, basis, pivcol, phase, tol=1e-9, bland=False):
+    """
+    Given a linear programming simplex tableau, determine the row for the
+    pivot operation.
+
+    Parameters
+    ----------
+    T : 2-D array
+        A 2-D array representing the simplex tableau, T, corresponding to the
+        linear programming problem. It should have the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],    0]]
+
+        for a Phase 2 problem, or the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],   0],
+         [c'[0],  c'[1], ...,  c'[n_total],  0]]
+
+         for a Phase 1 problem (a Problem in which a basic feasible solution is
+         sought prior to maximizing the actual objective. ``T`` is modified in
+         place by ``_solve_simplex``.
+    basis : array
+        A list of the current basic variables.
+    pivcol : int
+        The index of the pivot column.
+    phase : int
+        The phase of the simplex algorithm (1 or 2).
+    tol : float
+        Elements in the pivot column smaller than tol will not be considered
+        for pivoting. Nominally this value is zero, but numerical issues
+        cause a tolerance about zero to be necessary.
+    bland : bool
+        If True, use Bland's rule for selection of the row (if more than one
+        row can be used, choose the one with the lowest variable index).
+
+    Returns
+    -------
+    status: bool
+        True if a suitable pivot row was found, otherwise False. A return
+        of False indicates that the linear programming problem is unbounded.
+    row: int
+        The index of the row of the pivot element. If status is False, row
+        will be returned as nan.
+    """
+    if phase == 1:
+        k = 2
+    else:
+        k = 1
+    ma = np.ma.masked_where(T[:-k, pivcol] <= tol, T[:-k, pivcol], copy=False)
+    if ma.count() == 0:
+        return False, np.nan
+    mb = np.ma.masked_where(T[:-k, pivcol] <= tol, T[:-k, -1], copy=False)
+    q = mb / ma
+    min_rows = np.ma.nonzero(q == q.min())[0]
+    if bland:
+        return True, min_rows[np.argmin(np.take(basis, min_rows))]
+    return True, min_rows[0]
+
+
+def _apply_pivot(T, basis, pivrow, pivcol, tol=1e-9):
+    """
+    Pivot the simplex tableau inplace on the element given by (pivrow, pivol).
+    The entering variable corresponds to the column given by pivcol forcing
+    the variable basis[pivrow] to leave the basis.
+
+    Parameters
+    ----------
+    T : 2-D array
+        A 2-D array representing the simplex tableau, T, corresponding to the
+        linear programming problem. It should have the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],    0]]
+
+        for a Phase 2 problem, or the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],   0],
+         [c'[0],  c'[1], ...,  c'[n_total],  0]]
+
+         for a Phase 1 problem (a problem in which a basic feasible solution is
+         sought prior to maximizing the actual objective. ``T`` is modified in
+         place by ``_solve_simplex``.
+    basis : 1-D array
+        An array of the indices of the basic variables, such that basis[i]
+        contains the column corresponding to the basic variable for row i.
+        Basis is modified in place by _apply_pivot.
+    pivrow : int
+        Row index of the pivot.
+    pivcol : int
+        Column index of the pivot.
+    """
+    basis[pivrow] = pivcol
+    pivval = T[pivrow, pivcol]
+    T[pivrow] = T[pivrow] / pivval
+    for irow in range(T.shape[0]):
+        if irow != pivrow:
+            T[irow] = T[irow] - T[pivrow] * T[irow, pivcol]
+
+    # The selected pivot should never lead to a pivot value less than the tol.
+    if np.isclose(pivval, tol, atol=0, rtol=1e4):
+        message = (
+            f"The pivot operation produces a pivot value of:{pivval: .1e}, "
+            "which is only slightly greater than the specified "
+            f"tolerance{tol: .1e}. This may lead to issues regarding the "
+            "numerical stability of the simplex method. "
+            "Removing redundant constraints, changing the pivot strategy "
+            "via Bland's rule or increasing the tolerance may "
+            "help reduce the issue.")
+        warn(message, OptimizeWarning, stacklevel=5)
+
+
+def _solve_simplex(T, n, basis, callback, postsolve_args,
+                   maxiter=1000, tol=1e-9, phase=2, bland=False, nit0=0,
+                   ):
+    """
+    Solve a linear programming problem in "standard form" using the Simplex
+    Method. Linear Programming is intended to solve the following problem form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    Parameters
+    ----------
+    T : 2-D array
+        A 2-D array representing the simplex tableau, T, corresponding to the
+        linear programming problem. It should have the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],    0]]
+
+        for a Phase 2 problem, or the form:
+
+        [[A[0, 0], A[0, 1], ..., A[0, n_total], b[0]],
+         [A[1, 0], A[1, 1], ..., A[1, n_total], b[1]],
+         .
+         .
+         .
+         [A[m, 0], A[m, 1], ..., A[m, n_total], b[m]],
+         [c[0],   c[1], ...,   c[n_total],   0],
+         [c'[0],  c'[1], ...,  c'[n_total],  0]]
+
+         for a Phase 1 problem (a problem in which a basic feasible solution is
+         sought prior to maximizing the actual objective. ``T`` is modified in
+         place by ``_solve_simplex``.
+    n : int
+        The number of true variables in the problem.
+    basis : 1-D array
+        An array of the indices of the basic variables, such that basis[i]
+        contains the column corresponding to the basic variable for row i.
+        Basis is modified in place by _solve_simplex
+    callback : callable, optional
+        If a callback function is provided, it will be called within each
+        iteration of the algorithm. The callback must accept a
+        `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+            x : 1-D array
+                Current solution vector
+            fun : float
+                Current value of the objective function
+            success : bool
+                True only when a phase has completed successfully. This
+                will be False for most iterations.
+            slack : 1-D array
+                The values of the slack variables. Each slack variable
+                corresponds to an inequality constraint. If the slack is zero,
+                the corresponding constraint is active.
+            con : 1-D array
+                The (nominally zero) residuals of the equality constraints,
+                that is, ``b - A_eq @ x``
+            phase : int
+                The phase of the optimization being executed. In phase 1 a basic
+                feasible solution is sought and the T has an additional row
+                representing an alternate objective function.
+            status : int
+                An integer representing the exit status of the optimization::
+
+                     0 : Optimization terminated successfully
+                     1 : Iteration limit reached
+                     2 : Problem appears to be infeasible
+                     3 : Problem appears to be unbounded
+                     4 : Serious numerical difficulties encountered
+
+            nit : int
+                The number of iterations performed.
+            message : str
+                A string descriptor of the exit status of the optimization.
+    postsolve_args : tuple
+        Data needed by _postsolve to convert the solution to the standard-form
+        problem into the solution to the original problem.
+    maxiter : int
+        The maximum number of iterations to perform before aborting the
+        optimization.
+    tol : float
+        The tolerance which determines when a solution is "close enough" to
+        zero in Phase 1 to be considered a basic feasible solution or close
+        enough to positive to serve as an optimal solution.
+    phase : int
+        The phase of the optimization being executed. In phase 1 a basic
+        feasible solution is sought and the T has an additional row
+        representing an alternate objective function.
+    bland : bool
+        If True, choose pivots using Bland's rule [3]_. In problems which
+        fail to converge due to cycling, using Bland's rule can provide
+        convergence at the expense of a less optimal path about the simplex.
+    nit0 : int
+        The initial iteration number used to keep an accurate iteration total
+        in a two-phase problem.
+
+    Returns
+    -------
+    nit : int
+        The number of iterations. Used to keep an accurate iteration total
+        in the two-phase problem.
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Serious numerical difficulties encountered
+
+    """
+    nit = nit0
+    status = 0
+    message = ''
+    complete = False
+
+    if phase == 1:
+        m = T.shape[1]-2
+    elif phase == 2:
+        m = T.shape[1]-1
+    else:
+        raise ValueError("Argument 'phase' to _solve_simplex must be 1 or 2")
+
+    if phase == 2:
+        # Check if any artificial variables are still in the basis.
+        # If yes, check if any coefficients from this row and a column
+        # corresponding to one of the non-artificial variable is non-zero.
+        # If found, pivot at this term. If not, start phase 2.
+        # Do this for all artificial variables in the basis.
+        # Ref: "An Introduction to Linear Programming and Game Theory"
+        # by Paul R. Thie, Gerard E. Keough, 3rd Ed,
+        # Chapter 3.7 Redundant Systems (pag 102)
+        for pivrow in [row for row in range(basis.size)
+                       if basis[row] > T.shape[1] - 2]:
+            non_zero_row = [col for col in range(T.shape[1] - 1)
+                            if abs(T[pivrow, col]) > tol]
+            if len(non_zero_row) > 0:
+                pivcol = non_zero_row[0]
+                _apply_pivot(T, basis, pivrow, pivcol, tol)
+                nit += 1
+
+    if len(basis[:m]) == 0:
+        solution = np.empty(T.shape[1] - 1, dtype=np.float64)
+    else:
+        solution = np.empty(max(T.shape[1] - 1, max(basis[:m]) + 1),
+                            dtype=np.float64)
+
+    while not complete:
+        # Find the pivot column
+        pivcol_found, pivcol = _pivot_col(T, tol, bland)
+        if not pivcol_found:
+            pivcol = np.nan
+            pivrow = np.nan
+            status = 0
+            complete = True
+        else:
+            # Find the pivot row
+            pivrow_found, pivrow = _pivot_row(T, basis, pivcol, phase, tol, bland)
+            if not pivrow_found:
+                status = 3
+                complete = True
+
+        if callback is not None:
+            solution[:] = 0
+            solution[basis[:n]] = T[:n, -1]
+            x = solution[:m]
+            x, fun, slack, con = _postsolve(
+                x, postsolve_args
+            )
+            res = OptimizeResult({
+                'x': x,
+                'fun': fun,
+                'slack': slack,
+                'con': con,
+                'status': status,
+                'message': message,
+                'nit': nit,
+                'success': status == 0 and complete,
+                'phase': phase,
+                'complete': complete,
+                })
+            callback(res)
+
+        if not complete:
+            if nit >= maxiter:
+                # Iteration limit exceeded
+                status = 1
+                complete = True
+            else:
+                _apply_pivot(T, basis, pivrow, pivcol, tol)
+                nit += 1
+    return nit, status
+
+
+def _linprog_simplex(c, c0, A, b, callback, postsolve_args,
+                     maxiter=1000, tol=1e-9, disp=False, bland=False,
+                     **unknown_options):
+    """
+    Minimize a linear objective function subject to linear equality and
+    non-negativity constraints using the two phase simplex method.
+    Linear programming is intended to solve problems of the following form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    User-facing documentation is in _linprog_doc.py.
+
+    Parameters
+    ----------
+    c : 1-D array
+        Coefficients of the linear objective function to be minimized.
+    c0 : float
+        Constant term in objective function due to fixed (and eliminated)
+        variables. (Purely for display.)
+    A : 2-D array
+        2-D array such that ``A @ x``, gives the values of the equality
+        constraints at ``x``.
+    b : 1-D array
+        1-D array of values representing the right hand side of each equality
+        constraint (row) in ``A``.
+    callback : callable, optional
+        If a callback function is provided, it will be called within each
+        iteration of the algorithm. The callback function must accept a single
+        `scipy.optimize.OptimizeResult` consisting of the following fields:
+
+            x : 1-D array
+                Current solution vector
+            fun : float
+                Current value of the objective function
+            success : bool
+                True when an algorithm has completed successfully.
+            slack : 1-D array
+                The values of the slack variables. Each slack variable
+                corresponds to an inequality constraint. If the slack is zero,
+                the corresponding constraint is active.
+            con : 1-D array
+                The (nominally zero) residuals of the equality constraints,
+                that is, ``b - A_eq @ x``
+            phase : int
+                The phase of the algorithm being executed.
+            status : int
+                An integer representing the status of the optimization::
+
+                     0 : Algorithm proceeding nominally
+                     1 : Iteration limit reached
+                     2 : Problem appears to be infeasible
+                     3 : Problem appears to be unbounded
+                     4 : Serious numerical difficulties encountered
+            nit : int
+                The number of iterations performed.
+            message : str
+                A string descriptor of the exit status of the optimization.
+    postsolve_args : tuple
+        Data needed by _postsolve to convert the solution to the standard-form
+        problem into the solution to the original problem.
+
+    Options
+    -------
+    maxiter : int
+       The maximum number of iterations to perform.
+    disp : bool
+        If True, print exit status message to sys.stdout
+    tol : float
+        The tolerance which determines when a solution is "close enough" to
+        zero in Phase 1 to be considered a basic feasible solution or close
+        enough to positive to serve as an optimal solution.
+    bland : bool
+        If True, use Bland's anti-cycling rule [3]_ to choose pivots to
+        prevent cycling. If False, choose pivots which should lead to a
+        converged solution more quickly. The latter method is subject to
+        cycling (non-convergence) in rare instances.
+    unknown_options : dict
+        Optional arguments not used by this particular solver. If
+        `unknown_options` is non-empty a warning is issued listing all
+        unused options.
+
+    Returns
+    -------
+    x : 1-D array
+        Solution vector.
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Serious numerical difficulties encountered
+
+    message : str
+        A string descriptor of the exit status of the optimization.
+    iteration : int
+        The number of iterations taken to solve the problem.
+
+    References
+    ----------
+    .. [1] Dantzig, George B., Linear programming and extensions. Rand
+           Corporation Research Study Princeton Univ. Press, Princeton, NJ,
+           1963
+    .. [2] Hillier, S.H. and Lieberman, G.J. (1995), "Introduction to
+           Mathematical Programming", McGraw-Hill, Chapter 4.
+    .. [3] Bland, Robert G. New finite pivoting rules for the simplex method.
+           Mathematics of Operations Research (2), 1977: pp. 103-107.
+
+
+    Notes
+    -----
+    The expected problem formulation differs between the top level ``linprog``
+    module and the method specific solvers. The method specific solvers expect a
+    problem in standard form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    Whereas the top level ``linprog`` module expects a problem of form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A_ub @ x <= b_ub
+        A_eq @ x == b_eq
+         lb <= x <= ub
+
+    where ``lb = 0`` and ``ub = None`` unless set in ``bounds``.
+
+    The original problem contains equality, upper-bound and variable constraints
+    whereas the method specific solver requires equality constraints and
+    variable non-negativity.
+
+    ``linprog`` module converts the original problem to standard form by
+    converting the simple bounds to upper bound constraints, introducing
+    non-negative slack variables for inequality constraints, and expressing
+    unbounded variables as the difference between two non-negative variables.
+    """
+    _check_unknown_options(unknown_options)
+
+    status = 0
+    messages = {0: "Optimization terminated successfully.",
+                1: "Iteration limit reached.",
+                2: "Optimization failed. Unable to find a feasible"
+                   " starting point.",
+                3: "Optimization failed. The problem appears to be unbounded.",
+                4: "Optimization failed. Singular matrix encountered."}
+
+    n, m = A.shape
+
+    # All constraints must have b >= 0.
+    is_negative_constraint = np.less(b, 0)
+    A[is_negative_constraint] *= -1
+    b[is_negative_constraint] *= -1
+
+    # As all constraints are equality constraints the artificial variables
+    # will also be basic variables.
+    av = np.arange(n) + m
+    basis = av.copy()
+
+    # Format the phase one tableau by adding artificial variables and stacking
+    # the constraints, the objective row and pseudo-objective row.
+    row_constraints = np.hstack((A, np.eye(n), b[:, np.newaxis]))
+    row_objective = np.hstack((c, np.zeros(n), c0))
+    row_pseudo_objective = -row_constraints.sum(axis=0)
+    row_pseudo_objective[av] = 0
+    T = np.vstack((row_constraints, row_objective, row_pseudo_objective))
+
+    nit1, status = _solve_simplex(T, n, basis, callback=callback,
+                                  postsolve_args=postsolve_args,
+                                  maxiter=maxiter, tol=tol, phase=1,
+                                  bland=bland
+                                  )
+    # if pseudo objective is zero, remove the last row from the tableau and
+    # proceed to phase 2
+    nit2 = nit1
+    if abs(T[-1, -1]) < tol:
+        # Remove the pseudo-objective row from the tableau
+        T = T[:-1, :]
+        # Remove the artificial variable columns from the tableau
+        T = np.delete(T, av, 1)
+    else:
+        # Failure to find a feasible starting point
+        status = 2
+        messages[status] = (
+            "Phase 1 of the simplex method failed to find a feasible "
+            "solution. The pseudo-objective function evaluates to {0:.1e} "
+            "which exceeds the required tolerance of {1} for a solution to be "
+            "considered 'close enough' to zero to be a basic solution. "
+            "Consider increasing the tolerance to be greater than {0:.1e}. "
+            "If this tolerance is unacceptably  large the problem may be "
+            "infeasible.".format(abs(T[-1, -1]), tol)
+        )
+
+    if status == 0:
+        # Phase 2
+        nit2, status = _solve_simplex(T, n, basis, callback=callback,
+                                      postsolve_args=postsolve_args,
+                                      maxiter=maxiter, tol=tol, phase=2,
+                                      bland=bland, nit0=nit1
+                                      )
+
+    solution = np.zeros(n + m)
+    solution[basis[:n]] = T[:n, -1]
+    x = solution[:m]
+
+    return x, status, messages[status], int(nit2)

vila/lib/python3.10/site-packages/scipy/optimize/_linprog_util.py

@@ -0,0 +1,1522 @@
+"""
+Method agnostic utility functions for linear programming
+"""
+
+import numpy as np
+import scipy.sparse as sps
+from warnings import warn
+from ._optimize import OptimizeWarning
+from scipy.optimize._remove_redundancy import (
+    _remove_redundancy_svd, _remove_redundancy_pivot_sparse,
+    _remove_redundancy_pivot_dense, _remove_redundancy_id
+    )
+from collections import namedtuple
+
+_LPProblem = namedtuple('_LPProblem',
+                        'c A_ub b_ub A_eq b_eq bounds x0 integrality')
+_LPProblem.__new__.__defaults__ = (None,) * 7  # make c the only required arg
+_LPProblem.__doc__ = \
+    """ Represents a linear-programming problem.
+
+    Attributes
+    ----------
+    c : 1D array
+        The coefficients of the linear objective function to be minimized.
+    A_ub : 2D array, optional
+        The inequality constraint matrix. Each row of ``A_ub`` specifies the
+        coefficients of a linear inequality constraint on ``x``.
+    b_ub : 1D array, optional
+        The inequality constraint vector. Each element represents an
+        upper bound on the corresponding value of ``A_ub @ x``.
+    A_eq : 2D array, optional
+        The equality constraint matrix. Each row of ``A_eq`` specifies the
+        coefficients of a linear equality constraint on ``x``.
+    b_eq : 1D array, optional
+        The equality constraint vector. Each element of ``A_eq @ x`` must equal
+        the corresponding element of ``b_eq``.
+    bounds : various valid formats, optional
+        The bounds of ``x``, as ``min`` and ``max`` pairs.
+        If bounds are specified for all N variables separately, valid formats
+        are:
+        * a 2D array (N x 2);
+        * a sequence of N sequences, each with 2 values.
+        If all variables have the same bounds, the bounds can be specified as
+        a 1-D or 2-D array or sequence with 2 scalar values.
+        If all variables have a lower bound of 0 and no upper bound, the bounds
+        parameter can be omitted (or given as None).
+        Absent lower and/or upper bounds can be specified as -numpy.inf (no
+        lower bound), numpy.inf (no upper bound) or None (both).
+    x0 : 1D array, optional
+        Guess values of the decision variables, which will be refined by
+        the optimization algorithm. This argument is currently used only by the
+        'revised simplex' method, and can only be used if `x0` represents a
+        basic feasible solution.
+    integrality : 1-D array or int, optional
+        Indicates the type of integrality constraint on each decision variable.
+
+        ``0`` : Continuous variable; no integrality constraint.
+
+        ``1`` : Integer variable; decision variable must be an integer
+        within `bounds`.
+
+        ``2`` : Semi-continuous variable; decision variable must be within
+        `bounds` or take value ``0``.
+
+        ``3`` : Semi-integer variable; decision variable must be an integer
+        within `bounds` or take value ``0``.
+
+        By default, all variables are continuous.
+
+        For mixed integrality constraints, supply an array of shape `c.shape`.
+        To infer a constraint on each decision variable from shorter inputs,
+        the argument will be broadcasted to `c.shape` using `np.broadcast_to`.
+
+        This argument is currently used only by the ``'highs'`` method and
+        ignored otherwise.
+
+    Notes
+    -----
+    This namedtuple supports 2 ways of initialization:
+    >>> lp1 = _LPProblem(c=[-1, 4], A_ub=[[-3, 1], [1, 2]], b_ub=[6, 4])
+    >>> lp2 = _LPProblem([-1, 4], [[-3, 1], [1, 2]], [6, 4])
+
+    Note that only ``c`` is a required argument here, whereas all other arguments
+    ``A_ub``, ``b_ub``, ``A_eq``, ``b_eq``, ``bounds``, ``x0`` are optional with
+    default values of None.
+    For example, ``A_eq`` and ``b_eq`` can be set without ``A_ub`` or ``b_ub``:
+    >>> lp3 = _LPProblem(c=[-1, 4], A_eq=[[2, 1]], b_eq=[10])
+    """
+
+
+def _check_sparse_inputs(options, meth, A_ub, A_eq):
+    """
+    Check the provided ``A_ub`` and ``A_eq`` matrices conform to the specified
+    optional sparsity variables.
+
+    Parameters
+    ----------
+    A_ub : 2-D array, optional
+        2-D array such that ``A_ub @ x`` gives the values of the upper-bound
+        inequality constraints at ``x``.
+    A_eq : 2-D array, optional
+        2-D array such that ``A_eq @ x`` gives the values of the equality
+        constraints at ``x``.
+    options : dict
+        A dictionary of solver options. All methods accept the following
+        generic options:
+
+            maxiter : int
+                Maximum number of iterations to perform.
+            disp : bool
+                Set to True to print convergence messages.
+
+        For method-specific options, see :func:`show_options('linprog')`.
+    method : str, optional
+        The algorithm used to solve the standard form problem.
+
+    Returns
+    -------
+    A_ub : 2-D array, optional
+        2-D array such that ``A_ub @ x`` gives the values of the upper-bound
+        inequality constraints at ``x``.
+    A_eq : 2-D array, optional
+        2-D array such that ``A_eq @ x`` gives the values of the equality
+        constraints at ``x``.
+    options : dict
+        A dictionary of solver options. All methods accept the following
+        generic options:
+
+            maxiter : int
+                Maximum number of iterations to perform.
+            disp : bool
+                Set to True to print convergence messages.
+
+        For method-specific options, see :func:`show_options('linprog')`.
+    """
+    # This is an undocumented option for unit testing sparse presolve
+    _sparse_presolve = options.pop('_sparse_presolve', False)
+    if _sparse_presolve and A_eq is not None:
+        A_eq = sps.coo_matrix(A_eq)
+    if _sparse_presolve and A_ub is not None:
+        A_ub = sps.coo_matrix(A_ub)
+
+    sparse_constraint = sps.issparse(A_eq) or sps.issparse(A_ub)
+
+    preferred_methods = {"highs", "highs-ds", "highs-ipm"}
+    dense_methods = {"simplex", "revised simplex"}
+    if meth in dense_methods and sparse_constraint:
+        raise ValueError(f"Method '{meth}' does not support sparse "
+                         "constraint matrices. Please consider using one of "
+                         f"{preferred_methods}.")
+
+    sparse = options.get('sparse', False)
+    if not sparse and sparse_constraint and meth == 'interior-point':
+        options['sparse'] = True
+        warn("Sparse constraint matrix detected; setting 'sparse':True.",
+             OptimizeWarning, stacklevel=4)
+    return options, A_ub, A_eq
+
+
+def _format_A_constraints(A, n_x, sparse_lhs=False):
+    """Format the left hand side of the constraints to a 2-D array
+
+    Parameters
+    ----------
+    A : 2-D array
+        2-D array such that ``A @ x`` gives the values of the upper-bound
+        (in)equality constraints at ``x``.
+    n_x : int
+        The number of variables in the linear programming problem.
+    sparse_lhs : bool
+        Whether either of `A_ub` or `A_eq` are sparse. If true return a
+        coo_matrix instead of a numpy array.
+
+    Returns
+    -------
+    np.ndarray or sparse.coo_matrix
+        2-D array such that ``A @ x`` gives the values of the upper-bound
+        (in)equality constraints at ``x``.
+
+    """
+    if sparse_lhs:
+        return sps.coo_matrix(
+            (0, n_x) if A is None else A, dtype=float, copy=True
+        )
+    elif A is None:
+        return np.zeros((0, n_x), dtype=float)
+    else:
+        return np.array(A, dtype=float, copy=True)
+
+
+def _format_b_constraints(b):
+    """Format the upper bounds of the constraints to a 1-D array
+
+    Parameters
+    ----------
+    b : 1-D array
+        1-D array of values representing the upper-bound of each (in)equality
+        constraint (row) in ``A``.
+
+    Returns
+    -------
+    1-D np.array
+        1-D array of values representing the upper-bound of each (in)equality
+        constraint (row) in ``A``.
+
+    """
+    if b is None:
+        return np.array([], dtype=float)
+    b = np.array(b, dtype=float, copy=True).squeeze()
+    return b if b.size != 1 else b.reshape(-1)
+
+
+def _clean_inputs(lp):
+    """
+    Given user inputs for a linear programming problem, return the
+    objective vector, upper bound constraints, equality constraints,
+    and simple bounds in a preferred format.
+
+    Parameters
+    ----------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : various valid formats, optional
+            The bounds of ``x``, as ``min`` and ``max`` pairs.
+            If bounds are specified for all N variables separately, valid formats are:
+            * a 2D array (2 x N or N x 2);
+            * a sequence of N sequences, each with 2 values.
+            If all variables have the same bounds, a single pair of values can
+            be specified. Valid formats are:
+            * a sequence with 2 scalar values;
+            * a sequence with a single element containing 2 scalar values.
+            If all variables have a lower bound of 0 and no upper bound, the bounds
+            parameter can be omitted (or given as None).
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    Returns
+    -------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : 2D array
+            The bounds of ``x``, as ``min`` and ``max`` pairs, one for each of the N
+            elements of ``x``. The N x 2 array contains lower bounds in the first
+            column and upper bounds in the 2nd. Unbounded variables have lower
+            bound -np.inf and/or upper bound np.inf.
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    """
+    c, A_ub, b_ub, A_eq, b_eq, bounds, x0, integrality = lp
+
+    if c is None:
+        raise TypeError
+
+    try:
+        c = np.array(c, dtype=np.float64, copy=True).squeeze()
+    except ValueError as e:
+        raise TypeError(
+            "Invalid input for linprog: c must be a 1-D array of numerical "
+            "coefficients") from e
+    else:
+        # If c is a single value, convert it to a 1-D array.
+        if c.size == 1:
+            c = c.reshape(-1)
+
+        n_x = len(c)
+        if n_x == 0 or len(c.shape) != 1:
+            raise ValueError(
+                "Invalid input for linprog: c must be a 1-D array and must "
+                "not have more than one non-singleton dimension")
+        if not np.isfinite(c).all():
+            raise ValueError(
+                "Invalid input for linprog: c must not contain values "
+                "inf, nan, or None")
+
+    sparse_lhs = sps.issparse(A_eq) or sps.issparse(A_ub)
+    try:
+        A_ub = _format_A_constraints(A_ub, n_x, sparse_lhs=sparse_lhs)
+    except ValueError as e:
+        raise TypeError(
+            "Invalid input for linprog: A_ub must be a 2-D array "
+            "of numerical values") from e
+    else:
+        n_ub = A_ub.shape[0]
+        if len(A_ub.shape) != 2 or A_ub.shape[1] != n_x:
+            raise ValueError(
+                "Invalid input for linprog: A_ub must have exactly two "
+                "dimensions, and the number of columns in A_ub must be "
+                "equal to the size of c")
+        if (sps.issparse(A_ub) and not np.isfinite(A_ub.data).all()
+                or not sps.issparse(A_ub) and not np.isfinite(A_ub).all()):
+            raise ValueError(
+                "Invalid input for linprog: A_ub must not contain values "
+                "inf, nan, or None")
+
+    try:
+        b_ub = _format_b_constraints(b_ub)
+    except ValueError as e:
+        raise TypeError(
+            "Invalid input for linprog: b_ub must be a 1-D array of "
+            "numerical values, each representing the upper bound of an "
+            "inequality constraint (row) in A_ub") from e
+    else:
+        if b_ub.shape != (n_ub,):
+            raise ValueError(
+                "Invalid input for linprog: b_ub must be a 1-D array; b_ub "
+                "must not have more than one non-singleton dimension and "
+                "the number of rows in A_ub must equal the number of values "
+                "in b_ub")
+        if not np.isfinite(b_ub).all():
+            raise ValueError(
+                "Invalid input for linprog: b_ub must not contain values "
+                "inf, nan, or None")
+
+    try:
+        A_eq = _format_A_constraints(A_eq, n_x, sparse_lhs=sparse_lhs)
+    except ValueError as e:
+        raise TypeError(
+            "Invalid input for linprog: A_eq must be a 2-D array "
+            "of numerical values") from e
+    else:
+        n_eq = A_eq.shape[0]
+        if len(A_eq.shape) != 2 or A_eq.shape[1] != n_x:
+            raise ValueError(
+                "Invalid input for linprog: A_eq must have exactly two "
+                "dimensions, and the number of columns in A_eq must be "
+                "equal to the size of c")
+
+        if (sps.issparse(A_eq) and not np.isfinite(A_eq.data).all()
+                or not sps.issparse(A_eq) and not np.isfinite(A_eq).all()):
+            raise ValueError(
+                "Invalid input for linprog: A_eq must not contain values "
+                "inf, nan, or None")
+
+    try:
+        b_eq = _format_b_constraints(b_eq)
+    except ValueError as e:
+        raise TypeError(
+            "Invalid input for linprog: b_eq must be a dense, 1-D array of "
+            "numerical values, each representing the right hand side of an "
+            "equality constraint (row) in A_eq") from e
+    else:
+        if b_eq.shape != (n_eq,):
+            raise ValueError(
+                "Invalid input for linprog: b_eq must be a 1-D array; b_eq "
+                "must not have more than one non-singleton dimension and "
+                "the number of rows in A_eq must equal the number of values "
+                "in b_eq")
+        if not np.isfinite(b_eq).all():
+            raise ValueError(
+                "Invalid input for linprog: b_eq must not contain values "
+                "inf, nan, or None")
+
+    # x0 gives a (optional) starting solution to the solver. If x0 is None,
+    # skip the checks. Initial solution will be generated automatically.
+    if x0 is not None:
+        try:
+            x0 = np.array(x0, dtype=float, copy=True).squeeze()
+        except ValueError as e:
+            raise TypeError(
+                "Invalid input for linprog: x0 must be a 1-D array of "
+                "numerical coefficients") from e
+        if x0.ndim == 0:
+            x0 = x0.reshape(-1)
+        if len(x0) == 0 or x0.ndim != 1:
+            raise ValueError(
+                "Invalid input for linprog: x0 should be a 1-D array; it "
+                "must not have more than one non-singleton dimension")
+        if not x0.size == c.size:
+            raise ValueError(
+                "Invalid input for linprog: x0 and c should contain the "
+                "same number of elements")
+        if not np.isfinite(x0).all():
+            raise ValueError(
+                "Invalid input for linprog: x0 must not contain values "
+                "inf, nan, or None")
+
+    # Bounds can be one of these formats:
+    # (1) a 2-D array or sequence, with shape N x 2
+    # (2) a 1-D or 2-D sequence or array with 2 scalars
+    # (3) None (or an empty sequence or array)
+    # Unspecified bounds can be represented by None or (-)np.inf.
+    # All formats are converted into a N x 2 np.array with (-)np.inf where
+    # bounds are unspecified.
+
+    # Prepare clean bounds array
+    bounds_clean = np.zeros((n_x, 2), dtype=float)
+
+    # Convert to a numpy array.
+    # np.array(..,dtype=float) raises an error if dimensions are inconsistent
+    # or if there are invalid data types in bounds. Just add a linprog prefix
+    # to the error and re-raise.
+    # Creating at least a 2-D array simplifies the cases to distinguish below.
+    if bounds is None or np.array_equal(bounds, []) or np.array_equal(bounds, [[]]):
+        bounds = (0, np.inf)
+    try:
+        bounds_conv = np.atleast_2d(np.array(bounds, dtype=float))
+    except ValueError as e:
+        raise ValueError(
+            "Invalid input for linprog: unable to interpret bounds, "
+            "check values and dimensions: " + e.args[0]) from e
+    except TypeError as e:
+        raise TypeError(
+            "Invalid input for linprog: unable to interpret bounds, "
+            "check values and dimensions: " + e.args[0]) from e
+
+    # Check bounds options
+    bsh = bounds_conv.shape
+    if len(bsh) > 2:
+        # Do not try to handle multidimensional bounds input
+        raise ValueError(
+            "Invalid input for linprog: provide a 2-D array for bounds, "
+            f"not a {len(bsh):d}-D array.")
+    elif np.all(bsh == (n_x, 2)):
+        # Regular N x 2 array
+        bounds_clean = bounds_conv
+    elif (np.all(bsh == (2, 1)) or np.all(bsh == (1, 2))):
+        # 2 values: interpret as overall lower and upper bound
+        bounds_flat = bounds_conv.flatten()
+        bounds_clean[:, 0] = bounds_flat[0]
+        bounds_clean[:, 1] = bounds_flat[1]
+    elif np.all(bsh == (2, n_x)):
+        # Reject a 2 x N array
+        raise ValueError(
+            f"Invalid input for linprog: provide a {n_x:d} x 2 array for bounds, "
+            f"not a 2 x {n_x:d} array.")
+    else:
+        raise ValueError(
+            "Invalid input for linprog: unable to interpret bounds with this "
+            f"dimension tuple: {bsh}.")
+
+    # The process above creates nan-s where the input specified None
+    # Convert the nan-s in the 1st column to -np.inf and in the 2nd column
+    # to np.inf
+    i_none = np.isnan(bounds_clean[:, 0])
+    bounds_clean[i_none, 0] = -np.inf
+    i_none = np.isnan(bounds_clean[:, 1])
+    bounds_clean[i_none, 1] = np.inf
+
+    return _LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds_clean, x0, integrality)
+
+
+def _presolve(lp, rr, rr_method, tol=1e-9):
+    """
+    Given inputs for a linear programming problem in preferred format,
+    presolve the problem: identify trivial infeasibilities, redundancies,
+    and unboundedness, tighten bounds where possible, and eliminate fixed
+    variables.
+
+    Parameters
+    ----------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : 2D array
+            The bounds of ``x``, as ``min`` and ``max`` pairs, one for each of the N
+            elements of ``x``. The N x 2 array contains lower bounds in the first
+            column and upper bounds in the 2nd. Unbounded variables have lower
+            bound -np.inf and/or upper bound np.inf.
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    rr : bool
+        If ``True`` attempts to eliminate any redundant rows in ``A_eq``.
+        Set False if ``A_eq`` is known to be of full row rank, or if you are
+        looking for a potential speedup (at the expense of reliability).
+    rr_method : string
+        Method used to identify and remove redundant rows from the
+        equality constraint matrix after presolve.
+    tol : float
+        The tolerance which determines when a solution is "close enough" to
+        zero in Phase 1 to be considered a basic feasible solution or close
+        enough to positive to serve as an optimal solution.
+
+    Returns
+    -------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : 2D array
+            The bounds of ``x``, as ``min`` and ``max`` pairs, possibly tightened.
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    c0 : 1D array
+        Constant term in objective function due to fixed (and eliminated)
+        variables.
+    x : 1D array
+        Solution vector (when the solution is trivial and can be determined
+        in presolve)
+    revstack: list of functions
+        the functions in the list reverse the operations of _presolve()
+        the function signature is x_org = f(x_mod), where x_mod is the result
+        of a presolve step and x_org the value at the start of the step
+        (currently, the revstack contains only one function)
+    complete: bool
+        Whether the solution is complete (solved or determined to be infeasible
+        or unbounded in presolve)
+    status : int
+        An integer representing the exit status of the optimization::
+
+         0 : Optimization terminated successfully
+         1 : Iteration limit reached
+         2 : Problem appears to be infeasible
+         3 : Problem appears to be unbounded
+         4 : Serious numerical difficulties encountered
+
+    message : str
+        A string descriptor of the exit status of the optimization.
+
+    References
+    ----------
+    .. [5] Andersen, Erling D. "Finding all linearly dependent rows in
+           large-scale linear programming." Optimization Methods and Software
+           6.3 (1995): 219-227.
+    .. [8] Andersen, Erling D., and Knud D. Andersen. "Presolving in linear
+           programming." Mathematical Programming 71.2 (1995): 221-245.
+
+    """
+    # ideas from Reference [5] by Andersen and Andersen
+    # however, unlike the reference, this is performed before converting
+    # problem to standard form
+    # There are a few advantages:
+    #  * artificial variables have not been added, so matrices are smaller
+    #  * bounds have not been converted to constraints yet. (It is better to
+    #    do that after presolve because presolve may adjust the simple bounds.)
+    # There are many improvements that can be made, namely:
+    #  * implement remaining checks from [5]
+    #  * loop presolve until no additional changes are made
+    #  * implement additional efficiency improvements in redundancy removal [2]
+
+    c, A_ub, b_ub, A_eq, b_eq, bounds, x0, _ = lp
+
+    revstack = []               # record of variables eliminated from problem
+    # constant term in cost function may be added if variables are eliminated
+    c0 = 0
+    complete = False        # complete is True if detected infeasible/unbounded
+    x = np.zeros(c.shape)   # this is solution vector if completed in presolve
+
+    status = 0              # all OK unless determined otherwise
+    message = ""
+
+    # Lower and upper bounds. Copy to prevent feedback.
+    lb = bounds[:, 0].copy()
+    ub = bounds[:, 1].copy()
+
+    m_eq, n = A_eq.shape
+    m_ub, n = A_ub.shape
+
+    if (rr_method is not None
+            and rr_method.lower() not in {"svd", "pivot", "id"}):
+        message = ("'" + str(rr_method) + "' is not a valid option "
+                   "for redundancy removal. Valid options are 'SVD', "
+                   "'pivot', and 'ID'.")
+        raise ValueError(message)
+
+    if sps.issparse(A_eq):
+        A_eq = A_eq.tocsr()
+        A_ub = A_ub.tocsr()
+
+        def where(A):
+            return A.nonzero()
+
+        vstack = sps.vstack
+    else:
+        where = np.where
+        vstack = np.vstack
+
+    # upper bounds > lower bounds
+    if np.any(ub < lb) or np.any(lb == np.inf) or np.any(ub == -np.inf):
+        status = 2
+        message = ("The problem is (trivially) infeasible since one "
+                   "or more upper bounds are smaller than the corresponding "
+                   "lower bounds, a lower bound is np.inf or an upper bound "
+                   "is -np.inf.")
+        complete = True
+        return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                c0, x, revstack, complete, status, message)
+
+    # zero row in equality constraints
+    zero_row = np.array(np.sum(A_eq != 0, axis=1) == 0).flatten()
+    if np.any(zero_row):
+        if np.any(
+            np.logical_and(
+                zero_row,
+                np.abs(b_eq) > tol)):  # test_zero_row_1
+            # infeasible if RHS is not zero
+            status = 2
+            message = ("The problem is (trivially) infeasible due to a row "
+                       "of zeros in the equality constraint matrix with a "
+                       "nonzero corresponding constraint value.")
+            complete = True
+            return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                    c0, x, revstack, complete, status, message)
+        else:  # test_zero_row_2
+            # if RHS is zero, we can eliminate this equation entirely
+            A_eq = A_eq[np.logical_not(zero_row), :]
+            b_eq = b_eq[np.logical_not(zero_row)]
+
+    # zero row in inequality constraints
+    zero_row = np.array(np.sum(A_ub != 0, axis=1) == 0).flatten()
+    if np.any(zero_row):
+        if np.any(np.logical_and(zero_row, b_ub < -tol)):  # test_zero_row_1
+            # infeasible if RHS is less than zero (because LHS is zero)
+            status = 2
+            message = ("The problem is (trivially) infeasible due to a row "
+                       "of zeros in the equality constraint matrix with a "
+                       "nonzero corresponding  constraint value.")
+            complete = True
+            return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                    c0, x, revstack, complete, status, message)
+        else:  # test_zero_row_2
+            # if LHS is >= 0, we can eliminate this constraint entirely
+            A_ub = A_ub[np.logical_not(zero_row), :]
+            b_ub = b_ub[np.logical_not(zero_row)]
+
+    # zero column in (both) constraints
+    # this indicates that a variable isn't constrained and can be removed
+    A = vstack((A_eq, A_ub))
+    if A.shape[0] > 0:
+        zero_col = np.array(np.sum(A != 0, axis=0) == 0).flatten()
+        # variable will be at upper or lower bound, depending on objective
+        x[np.logical_and(zero_col, c < 0)] = ub[
+            np.logical_and(zero_col, c < 0)]
+        x[np.logical_and(zero_col, c > 0)] = lb[
+            np.logical_and(zero_col, c > 0)]
+        if np.any(np.isinf(x)):  # if an unconstrained variable has no bound
+            status = 3
+            message = ("If feasible, the problem is (trivially) unbounded "
+                       "due  to a zero column in the constraint matrices. If "
+                       "you wish to check whether the problem is infeasible, "
+                       "turn presolve off.")
+            complete = True
+            return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                    c0, x, revstack, complete, status, message)
+        # variables will equal upper/lower bounds will be removed later
+        lb[np.logical_and(zero_col, c < 0)] = ub[
+            np.logical_and(zero_col, c < 0)]
+        ub[np.logical_and(zero_col, c > 0)] = lb[
+            np.logical_and(zero_col, c > 0)]
+
+    # row singleton in equality constraints
+    # this fixes a variable and removes the constraint
+    singleton_row = np.array(np.sum(A_eq != 0, axis=1) == 1).flatten()
+    rows = where(singleton_row)[0]
+    cols = where(A_eq[rows, :])[1]
+    if len(rows) > 0:
+        for row, col in zip(rows, cols):
+            val = b_eq[row] / A_eq[row, col]
+            if not lb[col] - tol <= val <= ub[col] + tol:
+                # infeasible if fixed value is not within bounds
+                status = 2
+                message = ("The problem is (trivially) infeasible because a "
+                           "singleton row in the equality constraints is "
+                           "inconsistent with the bounds.")
+                complete = True
+                return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                        c0, x, revstack, complete, status, message)
+            else:
+                # sets upper and lower bounds at that fixed value - variable
+                # will be removed later
+                lb[col] = val
+                ub[col] = val
+        A_eq = A_eq[np.logical_not(singleton_row), :]
+        b_eq = b_eq[np.logical_not(singleton_row)]
+
+    # row singleton in inequality constraints
+    # this indicates a simple bound and the constraint can be removed
+    # simple bounds may be adjusted here
+    # After all of the simple bound information is combined here, get_Abc will
+    # turn the simple bounds into constraints
+    singleton_row = np.array(np.sum(A_ub != 0, axis=1) == 1).flatten()
+    cols = where(A_ub[singleton_row, :])[1]
+    rows = where(singleton_row)[0]
+    if len(rows) > 0:
+        for row, col in zip(rows, cols):
+            val = b_ub[row] / A_ub[row, col]
+            if A_ub[row, col] > 0:  # upper bound
+                if val < lb[col] - tol:  # infeasible
+                    complete = True
+                elif val < ub[col]:  # new upper bound
+                    ub[col] = val
+            else:  # lower bound
+                if val > ub[col] + tol:  # infeasible
+                    complete = True
+                elif val > lb[col]:  # new lower bound
+                    lb[col] = val
+            if complete:
+                status = 2
+                message = ("The problem is (trivially) infeasible because a "
+                           "singleton row in the upper bound constraints is "
+                           "inconsistent with the bounds.")
+                return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                        c0, x, revstack, complete, status, message)
+        A_ub = A_ub[np.logical_not(singleton_row), :]
+        b_ub = b_ub[np.logical_not(singleton_row)]
+
+    # identical bounds indicate that variable can be removed
+    i_f = np.abs(lb - ub) < tol   # indices of "fixed" variables
+    i_nf = np.logical_not(i_f)  # indices of "not fixed" variables
+
+    # test_bounds_equal_but_infeasible
+    if np.all(i_f):  # if bounds define solution, check for consistency
+        residual = b_eq - A_eq.dot(lb)
+        slack = b_ub - A_ub.dot(lb)
+        if ((A_ub.size > 0 and np.any(slack < 0)) or
+                (A_eq.size > 0 and not np.allclose(residual, 0))):
+            status = 2
+            message = ("The problem is (trivially) infeasible because the "
+                       "bounds fix all variables to values inconsistent with "
+                       "the constraints")
+            complete = True
+            return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                    c0, x, revstack, complete, status, message)
+
+    ub_mod = ub
+    lb_mod = lb
+    if np.any(i_f):
+        c0 += c[i_f].dot(lb[i_f])
+        b_eq = b_eq - A_eq[:, i_f].dot(lb[i_f])
+        b_ub = b_ub - A_ub[:, i_f].dot(lb[i_f])
+        c = c[i_nf]
+        x_undo = lb[i_f]  # not x[i_f], x is just zeroes
+        x = x[i_nf]
+        # user guess x0 stays separate from presolve solution x
+        if x0 is not None:
+            x0 = x0[i_nf]
+        A_eq = A_eq[:, i_nf]
+        A_ub = A_ub[:, i_nf]
+        # modify bounds
+        lb_mod = lb[i_nf]
+        ub_mod = ub[i_nf]
+
+        def rev(x_mod):
+            # Function to restore x: insert x_undo into x_mod.
+            # When elements have been removed at positions k1, k2, k3, ...
+            # then these must be replaced at (after) positions k1-1, k2-2,
+            # k3-3, ... in the modified array to recreate the original
+            i = np.flatnonzero(i_f)
+            # Number of variables to restore
+            N = len(i)
+            index_offset = np.arange(N)
+            # Create insert indices
+            insert_indices = i - index_offset
+            x_rev = np.insert(x_mod.astype(float), insert_indices, x_undo)
+            return x_rev
+
+        # Use revstack as a list of functions, currently just this one.
+        revstack.append(rev)
+
+    # no constraints indicates that problem is trivial
+    if A_eq.size == 0 and A_ub.size == 0:
+        b_eq = np.array([])
+        b_ub = np.array([])
+        # test_empty_constraint_1
+        if c.size == 0:
+            status = 0
+            message = ("The solution was determined in presolve as there are "
+                       "no non-trivial constraints.")
+        elif (np.any(np.logical_and(c < 0, ub_mod == np.inf)) or
+              np.any(np.logical_and(c > 0, lb_mod == -np.inf))):
+            # test_no_constraints()
+            # test_unbounded_no_nontrivial_constraints_1
+            # test_unbounded_no_nontrivial_constraints_2
+            status = 3
+            message = ("The problem is (trivially) unbounded "
+                       "because there are no non-trivial constraints and "
+                       "a) at least one decision variable is unbounded "
+                       "above and its corresponding cost is negative, or "
+                       "b) at least one decision variable is unbounded below "
+                       "and its corresponding cost is positive. ")
+        else:  # test_empty_constraint_2
+            status = 0
+            message = ("The solution was determined in presolve as there are "
+                       "no non-trivial constraints.")
+        complete = True
+        x[c < 0] = ub_mod[c < 0]
+        x[c > 0] = lb_mod[c > 0]
+        # where c is zero, set x to a finite bound or zero
+        x_zero_c = ub_mod[c == 0]
+        x_zero_c[np.isinf(x_zero_c)] = ub_mod[c == 0][np.isinf(x_zero_c)]
+        x_zero_c[np.isinf(x_zero_c)] = 0
+        x[c == 0] = x_zero_c
+        # if this is not the last step of presolve, should convert bounds back
+        # to array and return here
+
+    # Convert modified lb and ub back into N x 2 bounds
+    bounds = np.hstack((lb_mod[:, np.newaxis], ub_mod[:, np.newaxis]))
+
+    # remove redundant (linearly dependent) rows from equality constraints
+    n_rows_A = A_eq.shape[0]
+    redundancy_warning = ("A_eq does not appear to be of full row rank. To "
+                          "improve performance, check the problem formulation "
+                          "for redundant equality constraints.")
+    if (sps.issparse(A_eq)):
+        if rr and A_eq.size > 0:  # TODO: Fast sparse rank check?
+            rr_res = _remove_redundancy_pivot_sparse(A_eq, b_eq)
+            A_eq, b_eq, status, message = rr_res
+            if A_eq.shape[0] < n_rows_A:
+                warn(redundancy_warning, OptimizeWarning, stacklevel=1)
+            if status != 0:
+                complete = True
+        return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+                c0, x, revstack, complete, status, message)
+
+    # This is a wild guess for which redundancy removal algorithm will be
+    # faster. More testing would be good.
+    small_nullspace = 5
+    if rr and A_eq.size > 0:
+        try:  # TODO: use results of first SVD in _remove_redundancy_svd
+            rank = np.linalg.matrix_rank(A_eq)
+        # oh well, we'll have to go with _remove_redundancy_pivot_dense
+        except Exception:
+            rank = 0
+    if rr and A_eq.size > 0 and rank < A_eq.shape[0]:
+        warn(redundancy_warning, OptimizeWarning, stacklevel=3)
+        dim_row_nullspace = A_eq.shape[0]-rank
+        if rr_method is None:
+            if dim_row_nullspace <= small_nullspace:
+                rr_res = _remove_redundancy_svd(A_eq, b_eq)
+                A_eq, b_eq, status, message = rr_res
+            if dim_row_nullspace > small_nullspace or status == 4:
+                rr_res = _remove_redundancy_pivot_dense(A_eq, b_eq)
+                A_eq, b_eq, status, message = rr_res
+
+        else:
+            rr_method = rr_method.lower()
+            if rr_method == "svd":
+                rr_res = _remove_redundancy_svd(A_eq, b_eq)
+                A_eq, b_eq, status, message = rr_res
+            elif rr_method == "pivot":
+                rr_res = _remove_redundancy_pivot_dense(A_eq, b_eq)
+                A_eq, b_eq, status, message = rr_res
+            elif rr_method == "id":
+                rr_res = _remove_redundancy_id(A_eq, b_eq, rank)
+                A_eq, b_eq, status, message = rr_res
+            else:  # shouldn't get here; option validity checked above
+                pass
+        if A_eq.shape[0] < rank:
+            message = ("Due to numerical issues, redundant equality "
+                       "constraints could not be removed automatically. "
+                       "Try providing your constraint matrices as sparse "
+                       "matrices to activate sparse presolve, try turning "
+                       "off redundancy removal, or try turning off presolve "
+                       "altogether.")
+            status = 4
+        if status != 0:
+            complete = True
+    return (_LPProblem(c, A_ub, b_ub, A_eq, b_eq, bounds, x0),
+            c0, x, revstack, complete, status, message)
+
+
+def _parse_linprog(lp, options, meth):
+    """
+    Parse the provided linear programming problem
+
+    ``_parse_linprog`` employs two main steps ``_check_sparse_inputs`` and
+    ``_clean_inputs``. ``_check_sparse_inputs`` checks for sparsity in the
+    provided constraints (``A_ub`` and ``A_eq) and if these match the provided
+    sparsity optional values.
+
+    ``_clean inputs`` checks of the provided inputs. If no violations are
+    identified the objective vector, upper bound constraints, equality
+    constraints, and simple bounds are returned in the expected format.
+
+    Parameters
+    ----------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : various valid formats, optional
+            The bounds of ``x``, as ``min`` and ``max`` pairs.
+            If bounds are specified for all N variables separately, valid formats are:
+            * a 2D array (2 x N or N x 2);
+            * a sequence of N sequences, each with 2 values.
+            If all variables have the same bounds, a single pair of values can
+            be specified. Valid formats are:
+            * a sequence with 2 scalar values;
+            * a sequence with a single element containing 2 scalar values.
+            If all variables have a lower bound of 0 and no upper bound, the bounds
+            parameter can be omitted (or given as None).
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    options : dict
+        A dictionary of solver options. All methods accept the following
+        generic options:
+
+            maxiter : int
+                Maximum number of iterations to perform.
+            disp : bool
+                Set to True to print convergence messages.
+
+        For method-specific options, see :func:`show_options('linprog')`.
+
+    Returns
+    -------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : 2D array
+            The bounds of ``x``, as ``min`` and ``max`` pairs, one for each of the N
+            elements of ``x``. The N x 2 array contains lower bounds in the first
+            column and upper bounds in the 2nd. Unbounded variables have lower
+            bound -np.inf and/or upper bound np.inf.
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    options : dict, optional
+        A dictionary of solver options. All methods accept the following
+        generic options:
+
+            maxiter : int
+                Maximum number of iterations to perform.
+            disp : bool
+                Set to True to print convergence messages.
+
+        For method-specific options, see :func:`show_options('linprog')`.
+
+    """
+    if options is None:
+        options = {}
+
+    solver_options = {k: v for k, v in options.items()}
+    solver_options, A_ub, A_eq = _check_sparse_inputs(solver_options, meth,
+                                                      lp.A_ub, lp.A_eq)
+    # Convert lists to numpy arrays, etc...
+    lp = _clean_inputs(lp._replace(A_ub=A_ub, A_eq=A_eq))
+    return lp, solver_options
+
+
+def _get_Abc(lp, c0):
+    """
+    Given a linear programming problem of the form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A_ub @ x <= b_ub
+        A_eq @ x == b_eq
+         lb <= x <= ub
+
+    where ``lb = 0`` and ``ub = None`` unless set in ``bounds``.
+
+    Return the problem in standard form:
+
+    Minimize::
+
+        c @ x
+
+    Subject to::
+
+        A @ x == b
+            x >= 0
+
+    by adding slack variables and making variable substitutions as necessary.
+
+    Parameters
+    ----------
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : 2D array
+            The bounds of ``x``, lower bounds in the 1st column, upper
+            bounds in the 2nd column. The bounds are possibly tightened
+            by the presolve procedure.
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    c0 : float
+        Constant term in objective function due to fixed (and eliminated)
+        variables.
+
+    Returns
+    -------
+    A : 2-D array
+        2-D array such that ``A`` @ ``x``, gives the values of the equality
+        constraints at ``x``.
+    b : 1-D array
+        1-D array of values representing the RHS of each equality constraint
+        (row) in A (for standard form problem).
+    c : 1-D array
+        Coefficients of the linear objective function to be minimized (for
+        standard form problem).
+    c0 : float
+        Constant term in objective function due to fixed (and eliminated)
+        variables.
+    x0 : 1-D array
+        Starting values of the independent variables, which will be refined by
+        the optimization algorithm
+
+    References
+    ----------
+    .. [9] Bertsimas, Dimitris, and J. Tsitsiklis. "Introduction to linear
+           programming." Athena Scientific 1 (1997): 997.
+
+    """
+    c, A_ub, b_ub, A_eq, b_eq, bounds, x0, integrality = lp
+
+    if sps.issparse(A_eq):
+        sparse = True
+        A_eq = sps.csr_matrix(A_eq)
+        A_ub = sps.csr_matrix(A_ub)
+
+        def hstack(blocks):
+            return sps.hstack(blocks, format="csr")
+
+        def vstack(blocks):
+            return sps.vstack(blocks, format="csr")
+
+        zeros = sps.csr_matrix
+        eye = sps.eye
+    else:
+        sparse = False
+        hstack = np.hstack
+        vstack = np.vstack
+        zeros = np.zeros
+        eye = np.eye
+
+    # Variables lbs and ubs (see below) may be changed, which feeds back into
+    # bounds, so copy.
+    bounds = np.array(bounds, copy=True)
+
+    # modify problem such that all variables have only non-negativity bounds
+    lbs = bounds[:, 0]
+    ubs = bounds[:, 1]
+    m_ub, n_ub = A_ub.shape
+
+    lb_none = np.equal(lbs, -np.inf)
+    ub_none = np.equal(ubs, np.inf)
+    lb_some = np.logical_not(lb_none)
+    ub_some = np.logical_not(ub_none)
+
+    # unbounded below: substitute xi = -xi' (unbounded above)
+    # if -inf <= xi <= ub, then -ub <= -xi <= inf, so swap and invert bounds
+    l_nolb_someub = np.logical_and(lb_none, ub_some)
+    i_nolb = np.nonzero(l_nolb_someub)[0]
+    lbs[l_nolb_someub], ubs[l_nolb_someub] = (
+        -ubs[l_nolb_someub], -lbs[l_nolb_someub])
+    lb_none = np.equal(lbs, -np.inf)
+    ub_none = np.equal(ubs, np.inf)
+    lb_some = np.logical_not(lb_none)
+    ub_some = np.logical_not(ub_none)
+    c[i_nolb] *= -1
+    if x0 is not None:
+        x0[i_nolb] *= -1
+    if len(i_nolb) > 0:
+        if A_ub.shape[0] > 0:  # sometimes needed for sparse arrays... weird
+            A_ub[:, i_nolb] *= -1
+        if A_eq.shape[0] > 0:
+            A_eq[:, i_nolb] *= -1
+
+    # upper bound: add inequality constraint
+    i_newub, = ub_some.nonzero()
+    ub_newub = ubs[ub_some]
+    n_bounds = len(i_newub)
+    if n_bounds > 0:
+        shape = (n_bounds, A_ub.shape[1])
+        if sparse:
+            idxs = (np.arange(n_bounds), i_newub)
+            A_ub = vstack((A_ub, sps.csr_matrix((np.ones(n_bounds), idxs),
+                                                shape=shape)))
+        else:
+            A_ub = vstack((A_ub, np.zeros(shape)))
+            A_ub[np.arange(m_ub, A_ub.shape[0]), i_newub] = 1
+        b_ub = np.concatenate((b_ub, np.zeros(n_bounds)))
+        b_ub[m_ub:] = ub_newub
+
+    A1 = vstack((A_ub, A_eq))
+    b = np.concatenate((b_ub, b_eq))
+    c = np.concatenate((c, np.zeros((A_ub.shape[0],))))
+    if x0 is not None:
+        x0 = np.concatenate((x0, np.zeros((A_ub.shape[0],))))
+    # unbounded: substitute xi = xi+ + xi-
+    l_free = np.logical_and(lb_none, ub_none)
+    i_free = np.nonzero(l_free)[0]
+    n_free = len(i_free)
+    c = np.concatenate((c, np.zeros(n_free)))
+    if x0 is not None:
+        x0 = np.concatenate((x0, np.zeros(n_free)))
+    A1 = hstack((A1[:, :n_ub], -A1[:, i_free]))
+    c[n_ub:n_ub+n_free] = -c[i_free]
+    if x0 is not None:
+        i_free_neg = x0[i_free] < 0
+        x0[np.arange(n_ub, A1.shape[1])[i_free_neg]] = -x0[i_free[i_free_neg]]
+        x0[i_free[i_free_neg]] = 0
+
+    # add slack variables
+    A2 = vstack([eye(A_ub.shape[0]), zeros((A_eq.shape[0], A_ub.shape[0]))])
+
+    A = hstack([A1, A2])
+
+    # lower bound: substitute xi = xi' + lb
+    # now there is a constant term in objective
+    i_shift = np.nonzero(lb_some)[0]
+    lb_shift = lbs[lb_some].astype(float)
+    c0 += np.sum(lb_shift * c[i_shift])
+    if sparse:
+        b = b.reshape(-1, 1)
+        A = A.tocsc()
+        b -= (A[:, i_shift] * sps.diags(lb_shift)).sum(axis=1)
+        b = b.ravel()
+    else:
+        b -= (A[:, i_shift] * lb_shift).sum(axis=1)
+    if x0 is not None:
+        x0[i_shift] -= lb_shift
+
+    return A, b, c, c0, x0
+
+
+def _round_to_power_of_two(x):
+    """
+    Round elements of the array to the nearest power of two.
+    """
+    return 2**np.around(np.log2(x))
+
+
+def _autoscale(A, b, c, x0):
+    """
+    Scales the problem according to equilibration from [12].
+    Also normalizes the right hand side vector by its maximum element.
+    """
+    m, n = A.shape
+
+    C = 1
+    R = 1
+
+    if A.size > 0:
+
+        R = np.max(np.abs(A), axis=1)
+        if sps.issparse(A):
+            R = R.toarray().flatten()
+        R[R == 0] = 1
+        R = 1/_round_to_power_of_two(R)
+        A = sps.diags(R)*A if sps.issparse(A) else A*R.reshape(m, 1)
+        b = b*R
+
+        C = np.max(np.abs(A), axis=0)
+        if sps.issparse(A):
+            C = C.toarray().flatten()
+        C[C == 0] = 1
+        C = 1/_round_to_power_of_two(C)
+        A = A*sps.diags(C) if sps.issparse(A) else A*C
+        c = c*C
+
+    b_scale = np.max(np.abs(b)) if b.size > 0 else 1
+    if b_scale == 0:
+        b_scale = 1.
+    b = b/b_scale
+
+    if x0 is not None:
+        x0 = x0/b_scale*(1/C)
+    return A, b, c, x0, C, b_scale
+
+
+def _unscale(x, C, b_scale):
+    """
+    Converts solution to _autoscale problem -> solution to original problem.
+    """
+
+    try:
+        n = len(C)
+        # fails if sparse or scalar; that's OK.
+        # this is only needed for original simplex (never sparse)
+    except TypeError:
+        n = len(x)
+
+    return x[:n]*b_scale*C
+
+
+def _display_summary(message, status, fun, iteration):
+    """
+    Print the termination summary of the linear program
+
+    Parameters
+    ----------
+    message : str
+            A string descriptor of the exit status of the optimization.
+    status : int
+        An integer representing the exit status of the optimization::
+
+                0 : Optimization terminated successfully
+                1 : Iteration limit reached
+                2 : Problem appears to be infeasible
+                3 : Problem appears to be unbounded
+                4 : Serious numerical difficulties encountered
+
+    fun : float
+        Value of the objective function.
+    iteration : iteration
+        The number of iterations performed.
+    """
+    print(message)
+    if status in (0, 1):
+        print(f"         Current function value: {fun: <12.6f}")
+    print(f"         Iterations: {iteration:d}")
+
+
+def _postsolve(x, postsolve_args, complete=False):
+    """
+    Given solution x to presolved, standard form linear program x, add
+    fixed variables back into the problem and undo the variable substitutions
+    to get solution to original linear program. Also, calculate the objective
+    function value, slack in original upper bound constraints, and residuals
+    in original equality constraints.
+
+    Parameters
+    ----------
+    x : 1-D array
+        Solution vector to the standard-form problem.
+    postsolve_args : tuple
+        Data needed by _postsolve to convert the solution to the standard-form
+        problem into the solution to the original problem, including:
+
+    lp : A `scipy.optimize._linprog_util._LPProblem` consisting of the following fields:
+
+        c : 1D array
+            The coefficients of the linear objective function to be minimized.
+        A_ub : 2D array, optional
+            The inequality constraint matrix. Each row of ``A_ub`` specifies the
+            coefficients of a linear inequality constraint on ``x``.
+        b_ub : 1D array, optional
+            The inequality constraint vector. Each element represents an
+            upper bound on the corresponding value of ``A_ub @ x``.
+        A_eq : 2D array, optional
+            The equality constraint matrix. Each row of ``A_eq`` specifies the
+            coefficients of a linear equality constraint on ``x``.
+        b_eq : 1D array, optional
+            The equality constraint vector. Each element of ``A_eq @ x`` must equal
+            the corresponding element of ``b_eq``.
+        bounds : 2D array
+            The bounds of ``x``, lower bounds in the 1st column, upper
+            bounds in the 2nd column. The bounds are possibly tightened
+            by the presolve procedure.
+        x0 : 1D array, optional
+            Guess values of the decision variables, which will be refined by
+            the optimization algorithm. This argument is currently used only by the
+            'revised simplex' method, and can only be used if `x0` represents a
+            basic feasible solution.
+
+    revstack: list of functions
+        the functions in the list reverse the operations of _presolve()
+        the function signature is x_org = f(x_mod), where x_mod is the result
+        of a presolve step and x_org the value at the start of the step
+    complete : bool
+        Whether the solution is was determined in presolve (``True`` if so)
+
+    Returns
+    -------
+    x : 1-D array
+        Solution vector to original linear programming problem
+    fun: float
+        optimal objective value for original problem
+    slack : 1-D array
+        The (non-negative) slack in the upper bound constraints, that is,
+        ``b_ub - A_ub @ x``
+    con : 1-D array
+        The (nominally zero) residuals of the equality constraints, that is,
+        ``b - A_eq @ x``
+    """
+    # note that all the inputs are the ORIGINAL, unmodified versions
+    # no rows, columns have been removed
+
+    c, A_ub, b_ub, A_eq, b_eq, bounds, x0, integrality = postsolve_args[0]
+    revstack, C, b_scale = postsolve_args[1:]
+
+    x = _unscale(x, C, b_scale)
+
+    # Undo variable substitutions of _get_Abc()
+    # if "complete", problem was solved in presolve; don't do anything here
+    n_x = bounds.shape[0]
+    if not complete and bounds is not None:  # bounds are never none, probably
+        n_unbounded = 0
+        for i, bi in enumerate(bounds):
+            lbi = bi[0]
+            ubi = bi[1]
+            if lbi == -np.inf and ubi == np.inf:
+                n_unbounded += 1
+                x[i] = x[i] - x[n_x + n_unbounded - 1]
+            else:
+                if lbi == -np.inf:
+                    x[i] = ubi - x[i]
+                else:
+                    x[i] += lbi
+    # all the rest of the variables were artificial
+    x = x[:n_x]
+
+    # If there were variables removed from the problem, add them back into the
+    # solution vector
+    # Apply the functions in revstack (reverse direction)
+    for rev in reversed(revstack):
+        x = rev(x)
+
+    fun = x.dot(c)
+    slack = b_ub - A_ub.dot(x)  # report slack for ORIGINAL UB constraints
+    # report residuals of ORIGINAL EQ constraints
+    con = b_eq - A_eq.dot(x)
+
+    return x, fun, slack, con
+
+
+def _check_result(x, fun, status, slack, con, bounds, tol, message,
+                  integrality):
+    """
+    Check the validity of the provided solution.
+
+    A valid (optimal) solution satisfies all bounds, all slack variables are
+    negative and all equality constraint residuals are strictly non-zero.
+    Further, the lower-bounds, upper-bounds, slack and residuals contain
+    no nan values.
+
+    Parameters
+    ----------
+    x : 1-D array
+        Solution vector to original linear programming problem
+    fun: float
+        optimal objective value for original problem
+    status : int
+        An integer representing the exit status of the optimization::
+
+             0 : Optimization terminated successfully
+             1 : Iteration limit reached
+             2 : Problem appears to be infeasible
+             3 : Problem appears to be unbounded
+             4 : Serious numerical difficulties encountered
+
+    slack : 1-D array
+        The (non-negative) slack in the upper bound constraints, that is,
+        ``b_ub - A_ub @ x``
+    con : 1-D array
+        The (nominally zero) residuals of the equality constraints, that is,
+        ``b - A_eq @ x``
+    bounds : 2D array
+        The bounds on the original variables ``x``
+    message : str
+        A string descriptor of the exit status of the optimization.
+    tol : float
+        Termination tolerance; see [1]_ Section 4.5.
+
+    Returns
+    -------
+    status : int
+        An integer representing the exit status of the optimization::
+
+             0 : Optimization terminated successfully
+             1 : Iteration limit reached
+             2 : Problem appears to be infeasible
+             3 : Problem appears to be unbounded
+             4 : Serious numerical difficulties encountered
+
+    message : str
+        A string descriptor of the exit status of the optimization.
+    """
+    # Somewhat arbitrary
+    tol = np.sqrt(tol) * 10
+
+    if x is None:
+        # HiGHS does not provide x if infeasible/unbounded
+        if status == 0:  # Observed with HiGHS Simplex Primal
+            status = 4
+            message = ("The solver did not provide a solution nor did it "
+                       "report a failure. Please submit a bug report.")
+        return status, message
+
+    contains_nans = (
+        np.isnan(x).any()
+        or np.isnan(fun)
+        or np.isnan(slack).any()
+        or np.isnan(con).any()
+    )
+
+    if contains_nans:
+        is_feasible = False
+    else:
+        if integrality is None:
+            integrality = 0
+        valid_bounds = (x >= bounds[:, 0] - tol) & (x <= bounds[:, 1] + tol)
+        # When integrality is 2 or 3, x must be within bounds OR take value 0
+        valid_bounds |= (integrality > 1) & np.isclose(x, 0, atol=tol)
+        invalid_bounds = not np.all(valid_bounds)
+
+        invalid_slack = status != 3 and (slack < -tol).any()
+        invalid_con = status != 3 and (np.abs(con) > tol).any()
+        is_feasible = not (invalid_bounds or invalid_slack or invalid_con)
+
+    if status == 0 and not is_feasible:
+        status = 4
+        message = ("The solution does not satisfy the constraints within the "
+                   "required tolerance of " + f"{tol:.2E}" + ", yet "
+                   "no errors were raised and there is no certificate of "
+                   "infeasibility or unboundedness. Check whether "
+                   "the slack and constraint residuals are acceptable; "
+                   "if not, consider enabling presolve, adjusting the "
+                   "tolerance option(s), and/or using a different method. "
+                   "Please consider submitting a bug report.")
+    elif status == 2 and is_feasible:
+        # Occurs if the simplex method exits after phase one with a very
+        # nearly basic feasible solution. Postsolving can make the solution
+        # basic, however, this solution is NOT optimal
+        status = 4
+        message = ("The solution is feasible, but the solver did not report "
+                   "that the solution was optimal. Please try a different "
+                   "method.")
+
+    return status, message

vila/lib/python3.10/site-packages/scipy/optimize/_milp.py

@@ -0,0 +1,392 @@
+import warnings
+import numpy as np
+from scipy.sparse import csc_array, vstack, issparse
+from scipy._lib._util import VisibleDeprecationWarning
+from ._highs._highs_wrapper import _highs_wrapper  # type: ignore[import-not-found,import-untyped]
+from ._constraints import LinearConstraint, Bounds
+from ._optimize import OptimizeResult
+from ._linprog_highs import _highs_to_scipy_status_message
+
+
+def _constraints_to_components(constraints):
+    """
+    Convert sequence of constraints to a single set of components A, b_l, b_u.
+
+    `constraints` could be
+
+    1. A LinearConstraint
+    2. A tuple representing a LinearConstraint
+    3. An invalid object
+    4. A sequence of composed entirely of objects of type 1/2
+    5. A sequence containing at least one object of type 3
+
+    We want to accept 1, 2, and 4 and reject 3 and 5.
+    """
+    message = ("`constraints` (or each element within `constraints`) must be "
+               "convertible into an instance of "
+               "`scipy.optimize.LinearConstraint`.")
+    As = []
+    b_ls = []
+    b_us = []
+
+    # Accept case 1 by standardizing as case 4
+    if isinstance(constraints, LinearConstraint):
+        constraints = [constraints]
+    else:
+        # Reject case 3
+        try:
+            iter(constraints)
+        except TypeError as exc:
+            raise ValueError(message) from exc
+
+        # Accept case 2 by standardizing as case 4
+        if len(constraints) == 3:
+            # argument could be a single tuple representing a LinearConstraint
+            try:
+                constraints = [LinearConstraint(*constraints)]
+            except (TypeError, ValueError, VisibleDeprecationWarning):
+                # argument was not a tuple representing a LinearConstraint
+                pass
+
+    # Address cases 4/5
+    for constraint in constraints:
+        # if it's not a LinearConstraint or something that represents a
+        # LinearConstraint at this point, it's invalid
+        if not isinstance(constraint, LinearConstraint):
+            try:
+                constraint = LinearConstraint(*constraint)
+            except TypeError as exc:
+                raise ValueError(message) from exc
+        As.append(csc_array(constraint.A))
+        b_ls.append(np.atleast_1d(constraint.lb).astype(np.float64))
+        b_us.append(np.atleast_1d(constraint.ub).astype(np.float64))
+
+    if len(As) > 1:
+        A = vstack(As, format="csc")
+        b_l = np.concatenate(b_ls)
+        b_u = np.concatenate(b_us)
+    else:  # avoid unnecessary copying
+        A = As[0]
+        b_l = b_ls[0]
+        b_u = b_us[0]
+
+    return A, b_l, b_u
+
+
+def _milp_iv(c, integrality, bounds, constraints, options):
+    # objective IV
+    if issparse(c):
+        raise ValueError("`c` must be a dense array.")
+    c = np.atleast_1d(c).astype(np.float64)
+    if c.ndim != 1 or c.size == 0 or not np.all(np.isfinite(c)):
+        message = ("`c` must be a one-dimensional array of finite numbers "
+                   "with at least one element.")
+        raise ValueError(message)
+
+    # integrality IV
+    if issparse(integrality):
+        raise ValueError("`integrality` must be a dense array.")
+    message = ("`integrality` must contain integers 0-3 and be broadcastable "
+               "to `c.shape`.")
+    if integrality is None:
+        integrality = 0
+    try:
+        integrality = np.broadcast_to(integrality, c.shape).astype(np.uint8)
+    except ValueError:
+        raise ValueError(message)
+    if integrality.min() < 0 or integrality.max() > 3:
+        raise ValueError(message)
+
+    # bounds IV
+    if bounds is None:
+        bounds = Bounds(0, np.inf)
+    elif not isinstance(bounds, Bounds):
+        message = ("`bounds` must be convertible into an instance of "
+                   "`scipy.optimize.Bounds`.")
+        try:
+            bounds = Bounds(*bounds)
+        except TypeError as exc:
+            raise ValueError(message) from exc
+
+    try:
+        lb = np.broadcast_to(bounds.lb, c.shape).astype(np.float64)
+        ub = np.broadcast_to(bounds.ub, c.shape).astype(np.float64)
+    except (ValueError, TypeError) as exc:
+        message = ("`bounds.lb` and `bounds.ub` must contain reals and "
+                   "be broadcastable to `c.shape`.")
+        raise ValueError(message) from exc
+
+    # constraints IV
+    if not constraints:
+        constraints = [LinearConstraint(np.empty((0, c.size)),
+                                        np.empty((0,)), np.empty((0,)))]
+    try:
+        A, b_l, b_u = _constraints_to_components(constraints)
+    except ValueError as exc:
+        message = ("`constraints` (or each element within `constraints`) must "
+                   "be convertible into an instance of "
+                   "`scipy.optimize.LinearConstraint`.")
+        raise ValueError(message) from exc
+
+    if A.shape != (b_l.size, c.size):
+        message = "The shape of `A` must be (len(b_l), len(c))."
+        raise ValueError(message)
+    indptr, indices, data = A.indptr, A.indices, A.data.astype(np.float64)
+
+    # options IV
+    options = options or {}
+    supported_options = {'disp', 'presolve', 'time_limit', 'node_limit',
+                         'mip_rel_gap'}
+    unsupported_options = set(options).difference(supported_options)
+    if unsupported_options:
+        message = (f"Unrecognized options detected: {unsupported_options}. "
+                   "These will be passed to HiGHS verbatim.")
+        warnings.warn(message, RuntimeWarning, stacklevel=3)
+    options_iv = {'log_to_console': options.pop("disp", False),
+                  'mip_max_nodes': options.pop("node_limit", None)}
+    options_iv.update(options)
+
+    return c, integrality, lb, ub, indptr, indices, data, b_l, b_u, options_iv
+
+
+def milp(c, *, integrality=None, bounds=None, constraints=None, options=None):
+    r"""
+    Mixed-integer linear programming
+
+    Solves problems of the following form:
+
+    .. math::
+
+        \min_x \ & c^T x \\
+        \mbox{such that} \ & b_l \leq A x \leq b_u,\\
+        & l \leq x \leq u, \\
+        & x_i \in \mathbb{Z}, i \in X_i
+
+    where :math:`x` is a vector of decision variables;
+    :math:`c`, :math:`b_l`, :math:`b_u`, :math:`l`, and :math:`u` are vectors;
+    :math:`A` is a matrix, and :math:`X_i` is the set of indices of
+    decision variables that must be integral. (In this context, a
+    variable that can assume only integer values is said to be "integral";
+    it has an "integrality" constraint.)
+
+    Alternatively, that's:
+
+    minimize::
+
+        c @ x
+
+    such that::
+
+        b_l <= A @ x <= b_u
+        l <= x <= u
+        Specified elements of x must be integers
+
+    By default, ``l = 0`` and ``u = np.inf`` unless specified with
+    ``bounds``.
+
+    Parameters
+    ----------
+    c : 1D dense array_like
+        The coefficients of the linear objective function to be minimized.
+        `c` is converted to a double precision array before the problem is
+        solved.
+    integrality : 1D dense array_like, optional
+        Indicates the type of integrality constraint on each decision variable.
+
+        ``0`` : Continuous variable; no integrality constraint.
+
+        ``1`` : Integer variable; decision variable must be an integer
+        within `bounds`.
+
+        ``2`` : Semi-continuous variable; decision variable must be within
+        `bounds` or take value ``0``.
+
+        ``3`` : Semi-integer variable; decision variable must be an integer
+        within `bounds` or take value ``0``.
+
+        By default, all variables are continuous. `integrality` is converted
+        to an array of integers before the problem is solved.
+
+    bounds : scipy.optimize.Bounds, optional
+        Bounds on the decision variables. Lower and upper bounds are converted
+        to double precision arrays before the problem is solved. The
+        ``keep_feasible`` parameter of the `Bounds` object is ignored. If
+        not specified, all decision variables are constrained to be
+        non-negative.
+    constraints : sequence of scipy.optimize.LinearConstraint, optional
+        Linear constraints of the optimization problem. Arguments may be
+        one of the following:
+
+        1. A single `LinearConstraint` object
+        2. A single tuple that can be converted to a `LinearConstraint` object
+           as ``LinearConstraint(*constraints)``
+        3. A sequence composed entirely of objects of type 1. and 2.
+
+        Before the problem is solved, all values are converted to double
+        precision, and the matrices of constraint coefficients are converted to
+        instances of `scipy.sparse.csc_array`. The ``keep_feasible`` parameter
+        of `LinearConstraint` objects is ignored.
+    options : dict, optional
+        A dictionary of solver options. The following keys are recognized.
+
+        disp : bool (default: ``False``)
+            Set to ``True`` if indicators of optimization status are to be
+            printed to the console during optimization.
+        node_limit : int, optional
+            The maximum number of nodes (linear program relaxations) to solve
+            before stopping. Default is no maximum number of nodes.
+        presolve : bool (default: ``True``)
+            Presolve attempts to identify trivial infeasibilities,
+            identify trivial unboundedness, and simplify the problem before
+            sending it to the main solver.
+        time_limit : float, optional
+            The maximum number of seconds allotted to solve the problem.
+            Default is no time limit.
+        mip_rel_gap : float, optional
+            Termination criterion for MIP solver: solver will terminate when
+            the gap between the primal objective value and the dual objective
+            bound, scaled by the primal objective value, is <= mip_rel_gap.
+
+    Returns
+    -------
+    res : OptimizeResult
+        An instance of :class:`scipy.optimize.OptimizeResult`. The object
+        is guaranteed to have the following attributes.
+
+        status : int
+            An integer representing the exit status of the algorithm.
+
+            ``0`` : Optimal solution found.
+
+            ``1`` : Iteration or time limit reached.
+
+            ``2`` : Problem is infeasible.
+
+            ``3`` : Problem is unbounded.
+
+            ``4`` : Other; see message for details.
+
+        success : bool
+            ``True`` when an optimal solution is found and ``False`` otherwise.
+
+        message : str
+            A string descriptor of the exit status of the algorithm.
+
+        The following attributes will also be present, but the values may be
+        ``None``, depending on the solution status.
+
+        x : ndarray
+            The values of the decision variables that minimize the
+            objective function while satisfying the constraints.
+        fun : float
+            The optimal value of the objective function ``c @ x``.
+        mip_node_count : int
+            The number of subproblems or "nodes" solved by the MILP solver.
+        mip_dual_bound : float
+            The MILP solver's final estimate of the lower bound on the optimal
+            solution.
+        mip_gap : float
+            The difference between the primal objective value and the dual
+            objective bound, scaled by the primal objective value.
+
+    Notes
+    -----
+    `milp` is a wrapper of the HiGHS linear optimization software [1]_. The
+    algorithm is deterministic, and it typically finds the global optimum of
+    moderately challenging mixed-integer linear programs (when it exists).
+
+    References
+    ----------
+    .. [1] Huangfu, Q., Galabova, I., Feldmeier, M., and Hall, J. A. J.
+           "HiGHS - high performance software for linear optimization."
+           https://highs.dev/
+    .. [2] Huangfu, Q. and Hall, J. A. J. "Parallelizing the dual revised
+           simplex method." Mathematical Programming Computation, 10 (1),
+           119-142, 2018. DOI: 10.1007/s12532-017-0130-5
+
+    Examples
+    --------
+    Consider the problem at
+    https://en.wikipedia.org/wiki/Integer_programming#Example, which is
+    expressed as a maximization problem of two variables. Since `milp` requires
+    that the problem be expressed as a minimization problem, the objective
+    function coefficients on the decision variables are:
+
+    >>> import numpy as np
+    >>> c = -np.array([0, 1])
+
+    Note the negative sign: we maximize the original objective function
+    by minimizing the negative of the objective function.
+
+    We collect the coefficients of the constraints into arrays like:
+
+    >>> A = np.array([[-1, 1], [3, 2], [2, 3]])
+    >>> b_u = np.array([1, 12, 12])
+    >>> b_l = np.full_like(b_u, -np.inf, dtype=float)
+
+    Because there is no lower limit on these constraints, we have defined a
+    variable ``b_l`` full of values representing negative infinity. This may
+    be unfamiliar to users of `scipy.optimize.linprog`, which only accepts
+    "less than" (or "upper bound") inequality constraints of the form
+    ``A_ub @ x <= b_u``. By accepting both ``b_l`` and ``b_u`` of constraints
+    ``b_l <= A_ub @ x <= b_u``, `milp` makes it easy to specify "greater than"
+    inequality constraints, "less than" inequality constraints, and equality
+    constraints concisely.
+
+    These arrays are collected into a single `LinearConstraint` object like:
+
+    >>> from scipy.optimize import LinearConstraint
+    >>> constraints = LinearConstraint(A, b_l, b_u)
+
+    The non-negativity bounds on the decision variables are enforced by
+    default, so we do not need to provide an argument for `bounds`.
+
+    Finally, the problem states that both decision variables must be integers:
+
+    >>> integrality = np.ones_like(c)
+
+    We solve the problem like:
+
+    >>> from scipy.optimize import milp
+    >>> res = milp(c=c, constraints=constraints, integrality=integrality)
+    >>> res.x
+    [2.0, 2.0]
+
+    Note that had we solved the relaxed problem (without integrality
+    constraints):
+
+    >>> res = milp(c=c, constraints=constraints)  # OR:
+    >>> # from scipy.optimize import linprog; res = linprog(c, A, b_u)
+    >>> res.x
+    [1.8, 2.8]
+
+    we would not have obtained the correct solution by rounding to the nearest
+    integers.
+
+    Other examples are given :ref:`in the tutorial <tutorial-optimize_milp>`.
+
+    """
+    args_iv = _milp_iv(c, integrality, bounds, constraints, options)
+    c, integrality, lb, ub, indptr, indices, data, b_l, b_u, options = args_iv
+
+    highs_res = _highs_wrapper(c, indptr, indices, data, b_l, b_u,
+                               lb, ub, integrality, options)
+
+    res = {}
+
+    # Convert to scipy-style status and message
+    highs_status = highs_res.get('status', None)
+    highs_message = highs_res.get('message', None)
+    status, message = _highs_to_scipy_status_message(highs_status,
+                                                     highs_message)
+    res['status'] = status
+    res['message'] = message
+    res['success'] = (status == 0)
+    x = highs_res.get('x', None)
+    res['x'] = np.array(x) if x is not None else None
+    res['fun'] = highs_res.get('fun', None)
+    res['mip_node_count'] = highs_res.get('mip_node_count', None)
+    res['mip_dual_bound'] = highs_res.get('mip_dual_bound', None)
+    res['mip_gap'] = highs_res.get('mip_gap', None)
+
+    return OptimizeResult(res)

vila/lib/python3.10/site-packages/scipy/optimize/_minpack_py.py

@@ -0,0 +1,1164 @@
+import warnings
+from . import _minpack
+
+import numpy as np
+from numpy import (atleast_1d, triu, shape, transpose, zeros, prod, greater,
+                   asarray, inf,
+                   finfo, inexact, issubdtype, dtype)
+from scipy import linalg
+from scipy.linalg import svd, cholesky, solve_triangular, LinAlgError
+from scipy._lib._util import _asarray_validated, _lazywhere, _contains_nan
+from scipy._lib._util import getfullargspec_no_self as _getfullargspec
+from ._optimize import OptimizeResult, _check_unknown_options, OptimizeWarning
+from ._lsq import least_squares
+# from ._lsq.common import make_strictly_feasible
+from ._lsq.least_squares import prepare_bounds
+from scipy.optimize._minimize import Bounds
+
+__all__ = ['fsolve', 'leastsq', 'fixed_point', 'curve_fit']
+
+
+def _check_func(checker, argname, thefunc, x0, args, numinputs,
+                output_shape=None):
+    res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
+    if (output_shape is not None) and (shape(res) != output_shape):
+        if (output_shape[0] != 1):
+            if len(output_shape) > 1:
+                if output_shape[1] == 1:
+                    return shape(res)
+            msg = f"{checker}: there is a mismatch between the input and output " \
+                  f"shape of the '{argname}' argument"
+            func_name = getattr(thefunc, '__name__', None)
+            if func_name:
+                msg += " '%s'." % func_name
+            else:
+                msg += "."
+            msg += f'Shape should be {output_shape} but it is {shape(res)}.'
+            raise TypeError(msg)
+    if issubdtype(res.dtype, inexact):
+        dt = res.dtype
+    else:
+        dt = dtype(float)
+    return shape(res), dt
+
+
+def fsolve(func, x0, args=(), fprime=None, full_output=0,
+           col_deriv=0, xtol=1.49012e-8, maxfev=0, band=None,
+           epsfcn=None, factor=100, diag=None):
+    """
+    Find the roots of a function.
+
+    Return the roots of the (non-linear) equations defined by
+    ``func(x) = 0`` given a starting estimate.
+
+    Parameters
+    ----------
+    func : callable ``f(x, *args)``
+        A function that takes at least one (possibly vector) argument,
+        and returns a value of the same length.
+    x0 : ndarray
+        The starting estimate for the roots of ``func(x) = 0``.
+    args : tuple, optional
+        Any extra arguments to `func`.
+    fprime : callable ``f(x, *args)``, optional
+        A function to compute the Jacobian of `func` with derivatives
+        across the rows. By default, the Jacobian will be estimated.
+    full_output : bool, optional
+        If True, return optional outputs.
+    col_deriv : bool, optional
+        Specify whether the Jacobian function computes derivatives down
+        the columns (faster, because there is no transpose operation).
+    xtol : float, optional
+        The calculation will terminate if the relative error between two
+        consecutive iterates is at most `xtol`.
+    maxfev : int, optional
+        The maximum number of calls to the function. If zero, then
+        ``100*(N+1)`` is the maximum where N is the number of elements
+        in `x0`.
+    band : tuple, optional
+        If set to a two-sequence containing the number of sub- and
+        super-diagonals within the band of the Jacobi matrix, the
+        Jacobi matrix is considered banded (only for ``fprime=None``).
+    epsfcn : float, optional
+        A suitable step length for the forward-difference
+        approximation of the Jacobian (for ``fprime=None``). If
+        `epsfcn` is less than the machine precision, it is assumed
+        that the relative errors in the functions are of the order of
+        the machine precision.
+    factor : float, optional
+        A parameter determining the initial step bound
+        (``factor * || diag * x||``). Should be in the interval
+        ``(0.1, 100)``.
+    diag : sequence, optional
+        N positive entries that serve as a scale factors for the
+        variables.
+
+    Returns
+    -------
+    x : ndarray
+        The solution (or the result of the last iteration for
+        an unsuccessful call).
+    infodict : dict
+        A dictionary of optional outputs with the keys:
+
+        ``nfev``
+            number of function calls
+        ``njev``
+            number of Jacobian calls
+        ``fvec``
+            function evaluated at the output
+        ``fjac``
+            the orthogonal matrix, q, produced by the QR
+            factorization of the final approximate Jacobian
+            matrix, stored column wise
+        ``r``
+            upper triangular matrix produced by QR factorization
+            of the same matrix
+        ``qtf``
+            the vector ``(transpose(q) * fvec)``
+
+    ier : int
+        An integer flag.  Set to 1 if a solution was found, otherwise refer
+        to `mesg` for more information.
+    mesg : str
+        If no solution is found, `mesg` details the cause of failure.
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See the ``method='hybr'`` in particular.
+
+    Notes
+    -----
+    ``fsolve`` is a wrapper around MINPACK's hybrd and hybrj algorithms.
+
+    Examples
+    --------
+    Find a solution to the system of equations:
+    ``x0*cos(x1) = 4,  x1*x0 - x1 = 5``.
+
+    >>> import numpy as np
+    >>> from scipy.optimize import fsolve
+    >>> def func(x):
+    ...     return [x[0] * np.cos(x[1]) - 4,
+    ...             x[1] * x[0] - x[1] - 5]
+    >>> root = fsolve(func, [1, 1])
+    >>> root
+    array([6.50409711, 0.90841421])
+    >>> np.isclose(func(root), [0.0, 0.0])  # func(root) should be almost 0.0.
+    array([ True,  True])
+
+    """
+    def _wrapped_func(*fargs):
+        """
+        Wrapped `func` to track the number of times
+        the function has been called.
+        """
+        _wrapped_func.nfev += 1
+        return func(*fargs)
+
+    _wrapped_func.nfev = 0
+
+    options = {'col_deriv': col_deriv,
+               'xtol': xtol,
+               'maxfev': maxfev,
+               'band': band,
+               'eps': epsfcn,
+               'factor': factor,
+               'diag': diag}
+
+    res = _root_hybr(_wrapped_func, x0, args, jac=fprime, **options)
+    res.nfev = _wrapped_func.nfev
+
+    if full_output:
+        x = res['x']
+        info = {k: res.get(k)
+                    for k in ('nfev', 'njev', 'fjac', 'r', 'qtf') if k in res}
+        info['fvec'] = res['fun']
+        return x, info, res['status'], res['message']
+    else:
+        status = res['status']
+        msg = res['message']
+        if status == 0:
+            raise TypeError(msg)
+        elif status == 1:
+            pass
+        elif status in [2, 3, 4, 5]:
+            warnings.warn(msg, RuntimeWarning, stacklevel=2)
+        else:
+            raise TypeError(msg)
+        return res['x']
+
+
+def _root_hybr(func, x0, args=(), jac=None,
+               col_deriv=0, xtol=1.49012e-08, maxfev=0, band=None, eps=None,
+               factor=100, diag=None, **unknown_options):
+    """
+    Find the roots of a multivariate function using MINPACK's hybrd and
+    hybrj routines (modified Powell method).
+
+    Options
+    -------
+    col_deriv : bool
+        Specify whether the Jacobian function computes derivatives down
+        the columns (faster, because there is no transpose operation).
+    xtol : float
+        The calculation will terminate if the relative error between two
+        consecutive iterates is at most `xtol`.
+    maxfev : int
+        The maximum number of calls to the function. If zero, then
+        ``100*(N+1)`` is the maximum where N is the number of elements
+        in `x0`.
+    band : tuple
+        If set to a two-sequence containing the number of sub- and
+        super-diagonals within the band of the Jacobi matrix, the
+        Jacobi matrix is considered banded (only for ``fprime=None``).
+    eps : float
+        A suitable step length for the forward-difference
+        approximation of the Jacobian (for ``fprime=None``). If
+        `eps` is less than the machine precision, it is assumed
+        that the relative errors in the functions are of the order of
+        the machine precision.
+    factor : float
+        A parameter determining the initial step bound
+        (``factor * || diag * x||``). Should be in the interval
+        ``(0.1, 100)``.
+    diag : sequence
+        N positive entries that serve as a scale factors for the
+        variables.
+
+    """
+    _check_unknown_options(unknown_options)
+    epsfcn = eps
+
+    x0 = asarray(x0).flatten()
+    n = len(x0)
+    if not isinstance(args, tuple):
+        args = (args,)
+    shape, dtype = _check_func('fsolve', 'func', func, x0, args, n, (n,))
+    if epsfcn is None:
+        epsfcn = finfo(dtype).eps
+    Dfun = jac
+    if Dfun is None:
+        if band is None:
+            ml, mu = -10, -10
+        else:
+            ml, mu = band[:2]
+        if maxfev == 0:
+            maxfev = 200 * (n + 1)
+        retval = _minpack._hybrd(func, x0, args, 1, xtol, maxfev,
+                                 ml, mu, epsfcn, factor, diag)
+    else:
+        _check_func('fsolve', 'fprime', Dfun, x0, args, n, (n, n))
+        if (maxfev == 0):
+            maxfev = 100 * (n + 1)
+        retval = _minpack._hybrj(func, Dfun, x0, args, 1,
+                                 col_deriv, xtol, maxfev, factor, diag)
+
+    x, status = retval[0], retval[-1]
+
+    errors = {0: "Improper input parameters were entered.",
+              1: "The solution converged.",
+              2: "The number of calls to function has "
+                  "reached maxfev = %d." % maxfev,
+              3: "xtol=%f is too small, no further improvement "
+                  "in the approximate\n  solution "
+                  "is possible." % xtol,
+              4: "The iteration is not making good progress, as measured "
+                  "by the \n  improvement from the last five "
+                  "Jacobian evaluations.",
+              5: "The iteration is not making good progress, "
+                  "as measured by the \n  improvement from the last "
+                  "ten iterations.",
+              'unknown': "An error occurred."}
+
+    info = retval[1]
+    info['fun'] = info.pop('fvec')
+    sol = OptimizeResult(x=x, success=(status == 1), status=status,
+                         method="hybr")
+    sol.update(info)
+    try:
+        sol['message'] = errors[status]
+    except KeyError:
+        sol['message'] = errors['unknown']
+
+    return sol
+
+
+LEASTSQ_SUCCESS = [1, 2, 3, 4]
+LEASTSQ_FAILURE = [5, 6, 7, 8]
+
+
+def leastsq(func, x0, args=(), Dfun=None, full_output=False,
+            col_deriv=False, ftol=1.49012e-8, xtol=1.49012e-8,
+            gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None):
+    """
+    Minimize the sum of squares of a set of equations.
+
+    ::
+
+        x = arg min(sum(func(y)**2,axis=0))
+                 y
+
+    Parameters
+    ----------
+    func : callable
+        Should take at least one (possibly length ``N`` vector) argument and
+        returns ``M`` floating point numbers. It must not return NaNs or
+        fitting might fail. ``M`` must be greater than or equal to ``N``.
+    x0 : ndarray
+        The starting estimate for the minimization.
+    args : tuple, optional
+        Any extra arguments to func are placed in this tuple.
+    Dfun : callable, optional
+        A function or method to compute the Jacobian of func with derivatives
+        across the rows. If this is None, the Jacobian will be estimated.
+    full_output : bool, optional
+        If ``True``, return all optional outputs (not just `x` and `ier`).
+    col_deriv : bool, optional
+        If ``True``, specify that the Jacobian function computes derivatives
+        down the columns (faster, because there is no transpose operation).
+    ftol : float, optional
+        Relative error desired in the sum of squares.
+    xtol : float, optional
+        Relative error desired in the approximate solution.
+    gtol : float, optional
+        Orthogonality desired between the function vector and the columns of
+        the Jacobian.
+    maxfev : int, optional
+        The maximum number of calls to the function. If `Dfun` is provided,
+        then the default `maxfev` is 100*(N+1) where N is the number of elements
+        in x0, otherwise the default `maxfev` is 200*(N+1).
+    epsfcn : float, optional
+        A variable used in determining a suitable step length for the forward-
+        difference approximation of the Jacobian (for Dfun=None).
+        Normally the actual step length will be sqrt(epsfcn)*x
+        If epsfcn is less than the machine precision, it is assumed that the
+        relative errors are of the order of the machine precision.
+    factor : float, optional
+        A parameter determining the initial step bound
+        (``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
+    diag : sequence, optional
+        N positive entries that serve as a scale factors for the variables.
+
+    Returns
+    -------
+    x : ndarray
+        The solution (or the result of the last iteration for an unsuccessful
+        call).
+    cov_x : ndarray
+        The inverse of the Hessian. `fjac` and `ipvt` are used to construct an
+        estimate of the Hessian. A value of None indicates a singular matrix,
+        which means the curvature in parameters `x` is numerically flat. To
+        obtain the covariance matrix of the parameters `x`, `cov_x` must be
+        multiplied by the variance of the residuals -- see curve_fit. Only
+        returned if `full_output` is ``True``.
+    infodict : dict
+        a dictionary of optional outputs with the keys:
+
+        ``nfev``
+            The number of function calls
+        ``fvec``
+            The function evaluated at the output
+        ``fjac``
+            A permutation of the R matrix of a QR
+            factorization of the final approximate
+            Jacobian matrix, stored column wise.
+            Together with ipvt, the covariance of the
+            estimate can be approximated.
+        ``ipvt``
+            An integer array of length N which defines
+            a permutation matrix, p, such that
+            fjac*p = q*r, where r is upper triangular
+            with diagonal elements of nonincreasing
+            magnitude. Column j of p is column ipvt(j)
+            of the identity matrix.
+        ``qtf``
+            The vector (transpose(q) * fvec).
+
+        Only returned if `full_output` is ``True``.
+    mesg : str
+        A string message giving information about the cause of failure.
+        Only returned if `full_output` is ``True``.
+    ier : int
+        An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
+        found. Otherwise, the solution was not found. In either case, the
+        optional output variable 'mesg' gives more information.
+
+    See Also
+    --------
+    least_squares : Newer interface to solve nonlinear least-squares problems
+        with bounds on the variables. See ``method='lm'`` in particular.
+
+    Notes
+    -----
+    "leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
+
+    cov_x is a Jacobian approximation to the Hessian of the least squares
+    objective function.
+    This approximation assumes that the objective function is based on the
+    difference between some observed target data (ydata) and a (non-linear)
+    function of the parameters `f(xdata, params)` ::
+
+           func(params) = ydata - f(xdata, params)
+
+    so that the objective function is ::
+
+           min   sum((ydata - f(xdata, params))**2, axis=0)
+         params
+
+    The solution, `x`, is always a 1-D array, regardless of the shape of `x0`,
+    or whether `x0` is a scalar.
+
+    Examples
+    --------
+    >>> from scipy.optimize import leastsq
+    >>> def func(x):
+    ...     return 2*(x-3)**2+1
+    >>> leastsq(func, 0)
+    (array([2.99999999]), 1)
+
+    """
+    x0 = asarray(x0).flatten()
+    n = len(x0)
+    if not isinstance(args, tuple):
+        args = (args,)
+    shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
+    m = shape[0]
+
+    if n > m:
+        raise TypeError(f"Improper input: func input vector length N={n} must"
+                        f" not exceed func output vector length M={m}")
+
+    if epsfcn is None:
+        epsfcn = finfo(dtype).eps
+
+    if Dfun is None:
+        if maxfev == 0:
+            maxfev = 200*(n + 1)
+        retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol,
+                                 gtol, maxfev, epsfcn, factor, diag)
+    else:
+        if col_deriv:
+            _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m))
+        else:
+            _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m, n))
+        if maxfev == 0:
+            maxfev = 100 * (n + 1)
+        retval = _minpack._lmder(func, Dfun, x0, args, full_output,
+                                 col_deriv, ftol, xtol, gtol, maxfev,
+                                 factor, diag)
+
+    errors = {0: ["Improper input parameters.", TypeError],
+              1: ["Both actual and predicted relative reductions "
+                  "in the sum of squares\n  are at most %f" % ftol, None],
+              2: ["The relative error between two consecutive "
+                  "iterates is at most %f" % xtol, None],
+              3: ["Both actual and predicted relative reductions in "
+                  f"the sum of squares\n  are at most {ftol:f} and the "
+                  "relative error between two consecutive "
+                  f"iterates is at \n  most {xtol:f}", None],
+              4: ["The cosine of the angle between func(x) and any "
+                  "column of the\n  Jacobian is at most %f in "
+                  "absolute value" % gtol, None],
+              5: ["Number of calls to function has reached "
+                  "maxfev = %d." % maxfev, ValueError],
+              6: ["ftol=%f is too small, no further reduction "
+                  "in the sum of squares\n  is possible." % ftol,
+                  ValueError],
+              7: ["xtol=%f is too small, no further improvement in "
+                  "the approximate\n  solution is possible." % xtol,
+                  ValueError],
+              8: ["gtol=%f is too small, func(x) is orthogonal to the "
+                  "columns of\n  the Jacobian to machine "
+                  "precision." % gtol, ValueError]}
+
+    # The FORTRAN return value (possible return values are >= 0 and <= 8)
+    info = retval[-1]
+
+    if full_output:
+        cov_x = None
+        if info in LEASTSQ_SUCCESS:
+            # This was
+            # perm = take(eye(n), retval[1]['ipvt'] - 1, 0)
+            # r = triu(transpose(retval[1]['fjac'])[:n, :])
+            # R = dot(r, perm)
+            # cov_x = inv(dot(transpose(R), R))
+            # but the explicit dot product was not necessary and sometimes
+            # the result was not symmetric positive definite. See gh-4555.
+            perm = retval[1]['ipvt'] - 1
+            n = len(perm)
+            r = triu(transpose(retval[1]['fjac'])[:n, :])
+            inv_triu = linalg.get_lapack_funcs('trtri', (r,))
+            try:
+                # inverse of permuted matrix is a permutation of matrix inverse
+                invR, trtri_info = inv_triu(r)  # default: upper, non-unit diag
+                if trtri_info != 0:  # explicit comparison for readability
+                    raise LinAlgError(f'trtri returned info {trtri_info}')
+                invR[perm] = invR.copy()
+                cov_x = invR @ invR.T
+            except (LinAlgError, ValueError):
+                pass
+        return (retval[0], cov_x) + retval[1:-1] + (errors[info][0], info)
+    else:
+        if info in LEASTSQ_FAILURE:
+            warnings.warn(errors[info][0], RuntimeWarning, stacklevel=2)
+        elif info == 0:
+            raise errors[info][1](errors[info][0])
+        return retval[0], info
+
+
+def _lightweight_memoizer(f):
+    # very shallow memoization to address gh-13670: only remember the first set
+    # of parameters and corresponding function value, and only attempt to use
+    # them twice (the number of times the function is evaluated at x0).
+    def _memoized_func(params):
+        if _memoized_func.skip_lookup:
+            return f(params)
+
+        if np.all(_memoized_func.last_params == params):
+            return _memoized_func.last_val
+        elif _memoized_func.last_params is not None:
+            _memoized_func.skip_lookup = True
+
+        val = f(params)
+
+        if _memoized_func.last_params is None:
+            _memoized_func.last_params = np.copy(params)
+            _memoized_func.last_val = val
+
+        return val
+
+    _memoized_func.last_params = None
+    _memoized_func.last_val = None
+    _memoized_func.skip_lookup = False
+    return _memoized_func
+
+
+def _wrap_func(func, xdata, ydata, transform):
+    if transform is None:
+        def func_wrapped(params):
+            return func(xdata, *params) - ydata
+    elif transform.size == 1 or transform.ndim == 1:
+        def func_wrapped(params):
+            return transform * (func(xdata, *params) - ydata)
+    else:
+        # Chisq = (y - yd)^T C^{-1} (y-yd)
+        # transform = L such that C = L L^T
+        # C^{-1} = L^{-T} L^{-1}
+        # Chisq = (y - yd)^T L^{-T} L^{-1} (y-yd)
+        # Define (y-yd)' = L^{-1} (y-yd)
+        # by solving
+        # L (y-yd)' = (y-yd)
+        # and minimize (y-yd)'^T (y-yd)'
+        def func_wrapped(params):
+            return solve_triangular(transform, func(xdata, *params) - ydata, lower=True)
+    return func_wrapped
+
+
+def _wrap_jac(jac, xdata, transform):
+    if transform is None:
+        def jac_wrapped(params):
+            return jac(xdata, *params)
+    elif transform.ndim == 1:
+        def jac_wrapped(params):
+            return transform[:, np.newaxis] * np.asarray(jac(xdata, *params))
+    else:
+        def jac_wrapped(params):
+            return solve_triangular(transform,
+                                    np.asarray(jac(xdata, *params)),
+                                    lower=True)
+    return jac_wrapped
+
+
+def _initialize_feasible(lb, ub):
+    p0 = np.ones_like(lb)
+    lb_finite = np.isfinite(lb)
+    ub_finite = np.isfinite(ub)
+
+    mask = lb_finite & ub_finite
+    p0[mask] = 0.5 * (lb[mask] + ub[mask])
+
+    mask = lb_finite & ~ub_finite
+    p0[mask] = lb[mask] + 1
+
+    mask = ~lb_finite & ub_finite
+    p0[mask] = ub[mask] - 1
+
+    return p0
+
+
+def curve_fit(f, xdata, ydata, p0=None, sigma=None, absolute_sigma=False,
+              check_finite=None, bounds=(-np.inf, np.inf), method=None,
+              jac=None, *, full_output=False, nan_policy=None,
+              **kwargs):
+    """
+    Use non-linear least squares to fit a function, f, to data.
+
+    Assumes ``ydata = f(xdata, *params) + eps``.
+
+    Parameters
+    ----------
+    f : callable
+        The model function, f(x, ...). It must take the independent
+        variable as the first argument and the parameters to fit as
+        separate remaining arguments.
+    xdata : array_like
+        The independent variable where the data is measured.
+        Should usually be an M-length sequence or an (k,M)-shaped array for
+        functions with k predictors, and each element should be float
+        convertible if it is an array like object.
+    ydata : array_like
+        The dependent data, a length M array - nominally ``f(xdata, ...)``.
+    p0 : array_like, optional
+        Initial guess for the parameters (length N). If None, then the
+        initial values will all be 1 (if the number of parameters for the
+        function can be determined using introspection, otherwise a
+        ValueError is raised).
+    sigma : None or scalar or M-length sequence or MxM array, optional
+        Determines the uncertainty in `ydata`. If we define residuals as
+        ``r = ydata - f(xdata, *popt)``, then the interpretation of `sigma`
+        depends on its number of dimensions:
+
+            - A scalar or 1-D `sigma` should contain values of standard deviations of
+              errors in `ydata`. In this case, the optimized function is
+              ``chisq = sum((r / sigma) ** 2)``.
+
+            - A 2-D `sigma` should contain the covariance matrix of
+              errors in `ydata`. In this case, the optimized function is
+              ``chisq = r.T @ inv(sigma) @ r``.
+
+              .. versionadded:: 0.19
+
+        None (default) is equivalent of 1-D `sigma` filled with ones.
+    absolute_sigma : bool, optional
+        If True, `sigma` is used in an absolute sense and the estimated parameter
+        covariance `pcov` reflects these absolute values.
+
+        If False (default), only the relative magnitudes of the `sigma` values matter.
+        The returned parameter covariance matrix `pcov` is based on scaling
+        `sigma` by a constant factor. This constant is set by demanding that the
+        reduced `chisq` for the optimal parameters `popt` when using the
+        *scaled* `sigma` equals unity. In other words, `sigma` is scaled to
+        match the sample variance of the residuals after the fit. Default is False.
+        Mathematically,
+        ``pcov(absolute_sigma=False) = pcov(absolute_sigma=True) * chisq(popt)/(M-N)``
+    check_finite : bool, optional
+        If True, check that the input arrays do not contain nans of infs,
+        and raise a ValueError if they do. Setting this parameter to
+        False may silently produce nonsensical results if the input arrays
+        do contain nans. Default is True if `nan_policy` is not specified
+        explicitly and False otherwise.
+    bounds : 2-tuple of array_like or `Bounds`, optional
+        Lower and upper bounds on parameters. Defaults to no bounds.
+        There are two ways to specify the bounds:
+
+            - Instance of `Bounds` class.
+
+            - 2-tuple of array_like: Each element of the tuple must be either
+              an array with the length equal to the number of parameters, or a
+              scalar (in which case the bound is taken to be the same for all
+              parameters). Use ``np.inf`` with an appropriate sign to disable
+              bounds on all or some parameters.
+
+    method : {'lm', 'trf', 'dogbox'}, optional
+        Method to use for optimization. See `least_squares` for more details.
+        Default is 'lm' for unconstrained problems and 'trf' if `bounds` are
+        provided. The method 'lm' won't work when the number of observations
+        is less than the number of variables, use 'trf' or 'dogbox' in this
+        case.
+
+        .. versionadded:: 0.17
+    jac : callable, string or None, optional
+        Function with signature ``jac(x, ...)`` which computes the Jacobian
+        matrix of the model function with respect to parameters as a dense
+        array_like structure. It will be scaled according to provided `sigma`.
+        If None (default), the Jacobian will be estimated numerically.
+        String keywords for 'trf' and 'dogbox' methods can be used to select
+        a finite difference scheme, see `least_squares`.
+
+        .. versionadded:: 0.18
+    full_output : boolean, optional
+        If True, this function returns additioal information: `infodict`,
+        `mesg`, and `ier`.
+
+        .. versionadded:: 1.9
+    nan_policy : {'raise', 'omit', None}, optional
+        Defines how to handle when input contains nan.
+        The following options are available (default is None):
+
+          * 'raise': throws an error
+          * 'omit': performs the calculations ignoring nan values
+          * None: no special handling of NaNs is performed
+            (except what is done by check_finite); the behavior when NaNs
+            are present is implementation-dependent and may change.
+
+        Note that if this value is specified explicitly (not None),
+        `check_finite` will be set as False.
+
+        .. versionadded:: 1.11
+    **kwargs
+        Keyword arguments passed to `leastsq` for ``method='lm'`` or
+        `least_squares` otherwise.
+
+    Returns
+    -------
+    popt : array
+        Optimal values for the parameters so that the sum of the squared
+        residuals of ``f(xdata, *popt) - ydata`` is minimized.
+    pcov : 2-D array
+        The estimated approximate covariance of popt. The diagonals provide
+        the variance of the parameter estimate. To compute one standard
+        deviation errors on the parameters, use
+        ``perr = np.sqrt(np.diag(pcov))``. Note that the relationship between
+        `cov` and parameter error estimates is derived based on a linear
+        approximation to the model function around the optimum [1].
+        When this approximation becomes inaccurate, `cov` may not provide an
+        accurate measure of uncertainty.
+
+        How the `sigma` parameter affects the estimated covariance
+        depends on `absolute_sigma` argument, as described above.
+
+        If the Jacobian matrix at the solution doesn't have a full rank, then
+        'lm' method returns a matrix filled with ``np.inf``, on the other hand
+        'trf'  and 'dogbox' methods use Moore-Penrose pseudoinverse to compute
+        the covariance matrix. Covariance matrices with large condition numbers
+        (e.g. computed with `numpy.linalg.cond`) may indicate that results are
+        unreliable.
+    infodict : dict (returned only if `full_output` is True)
+        a dictionary of optional outputs with the keys:
+
+        ``nfev``
+            The number of function calls. Methods 'trf' and 'dogbox' do not
+            count function calls for numerical Jacobian approximation,
+            as opposed to 'lm' method.
+        ``fvec``
+            The residual values evaluated at the solution, for a 1-D `sigma`
+            this is ``(f(x, *popt) - ydata)/sigma``.
+        ``fjac``
+            A permutation of the R matrix of a QR
+            factorization of the final approximate
+            Jacobian matrix, stored column wise.
+            Together with ipvt, the covariance of the
+            estimate can be approximated.
+            Method 'lm' only provides this information.
+        ``ipvt``
+            An integer array of length N which defines
+            a permutation matrix, p, such that
+            fjac*p = q*r, where r is upper triangular
+            with diagonal elements of nonincreasing
+            magnitude. Column j of p is column ipvt(j)
+            of the identity matrix.
+            Method 'lm' only provides this information.
+        ``qtf``
+            The vector (transpose(q) * fvec).
+            Method 'lm' only provides this information.
+
+        .. versionadded:: 1.9
+    mesg : str (returned only if `full_output` is True)
+        A string message giving information about the solution.
+
+        .. versionadded:: 1.9
+    ier : int (returned only if `full_output` is True)
+        An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
+        found. Otherwise, the solution was not found. In either case, the
+        optional output variable `mesg` gives more information.
+
+        .. versionadded:: 1.9
+
+    Raises
+    ------
+    ValueError
+        if either `ydata` or `xdata` contain NaNs, or if incompatible options
+        are used.
+
+    RuntimeError
+        if the least-squares minimization fails.
+
+    OptimizeWarning
+        if covariance of the parameters can not be estimated.
+
+    See Also
+    --------
+    least_squares : Minimize the sum of squares of nonlinear functions.
+    scipy.stats.linregress : Calculate a linear least squares regression for
+                             two sets of measurements.
+
+    Notes
+    -----
+    Users should ensure that inputs `xdata`, `ydata`, and the output of `f`
+    are ``float64``, or else the optimization may return incorrect results.
+
+    With ``method='lm'``, the algorithm uses the Levenberg-Marquardt algorithm
+    through `leastsq`. Note that this algorithm can only deal with
+    unconstrained problems.
+
+    Box constraints can be handled by methods 'trf' and 'dogbox'. Refer to
+    the docstring of `least_squares` for more information.
+
+    Parameters to be fitted must have similar scale. Differences of multiple
+    orders of magnitude can lead to incorrect results. For the 'trf' and
+    'dogbox' methods, the `x_scale` keyword argument can be used to scale
+    the parameters.
+
+    References
+    ----------
+    [1] K. Vugrin et al. Confidence region estimation techniques for nonlinear
+        regression in groundwater flow: Three case studies. Water Resources
+        Research, Vol. 43, W03423, :doi:`10.1029/2005WR004804`
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> import matplotlib.pyplot as plt
+    >>> from scipy.optimize import curve_fit
+
+    >>> def func(x, a, b, c):
+    ...     return a * np.exp(-b * x) + c
+
+    Define the data to be fit with some noise:
+
+    >>> xdata = np.linspace(0, 4, 50)
+    >>> y = func(xdata, 2.5, 1.3, 0.5)
+    >>> rng = np.random.default_rng()
+    >>> y_noise = 0.2 * rng.normal(size=xdata.size)
+    >>> ydata = y + y_noise
+    >>> plt.plot(xdata, ydata, 'b-', label='data')
+
+    Fit for the parameters a, b, c of the function `func`:
+
+    >>> popt, pcov = curve_fit(func, xdata, ydata)
+    >>> popt
+    array([2.56274217, 1.37268521, 0.47427475])
+    >>> plt.plot(xdata, func(xdata, *popt), 'r-',
+    ...          label='fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt))
+
+    Constrain the optimization to the region of ``0 <= a <= 3``,
+    ``0 <= b <= 1`` and ``0 <= c <= 0.5``:
+
+    >>> popt, pcov = curve_fit(func, xdata, ydata, bounds=(0, [3., 1., 0.5]))
+    >>> popt
+    array([2.43736712, 1.        , 0.34463856])
+    >>> plt.plot(xdata, func(xdata, *popt), 'g--',
+    ...          label='fit: a=%5.3f, b=%5.3f, c=%5.3f' % tuple(popt))
+
+    >>> plt.xlabel('x')
+    >>> plt.ylabel('y')
+    >>> plt.legend()
+    >>> plt.show()
+
+    For reliable results, the model `func` should not be overparametrized;
+    redundant parameters can cause unreliable covariance matrices and, in some
+    cases, poorer quality fits. As a quick check of whether the model may be
+    overparameterized, calculate the condition number of the covariance matrix:
+
+    >>> np.linalg.cond(pcov)
+    34.571092161547405  # may vary
+
+    The value is small, so it does not raise much concern. If, however, we were
+    to add a fourth parameter ``d`` to `func` with the same effect as ``a``:
+
+    >>> def func2(x, a, b, c, d):
+    ...     return a * d * np.exp(-b * x) + c  # a and d are redundant
+    >>> popt, pcov = curve_fit(func2, xdata, ydata)
+    >>> np.linalg.cond(pcov)
+    1.13250718925596e+32  # may vary
+
+    Such a large value is cause for concern. The diagonal elements of the
+    covariance matrix, which is related to uncertainty of the fit, gives more
+    information:
+
+    >>> np.diag(pcov)
+    array([1.48814742e+29, 3.78596560e-02, 5.39253738e-03, 2.76417220e+28])  # may vary
+
+    Note that the first and last terms are much larger than the other elements,
+    suggesting that the optimal values of these parameters are ambiguous and
+    that only one of these parameters is needed in the model.
+
+    If the optimal parameters of `f` differ by multiple orders of magnitude, the
+    resulting fit can be inaccurate. Sometimes, `curve_fit` can fail to find any
+    results:
+
+    >>> ydata = func(xdata, 500000, 0.01, 15)
+    >>> try:
+    ...     popt, pcov = curve_fit(func, xdata, ydata, method = 'trf')
+    ... except RuntimeError as e:
+    ...     print(e)
+    Optimal parameters not found: The maximum number of function evaluations is
+    exceeded.
+
+    If parameter scale is roughly known beforehand, it can be defined in
+    `x_scale` argument:
+
+    >>> popt, pcov = curve_fit(func, xdata, ydata, method = 'trf',
+    ...                        x_scale = [1000, 1, 1])
+    >>> popt
+    array([5.00000000e+05, 1.00000000e-02, 1.49999999e+01])
+    """
+    if p0 is None:
+        # determine number of parameters by inspecting the function
+        sig = _getfullargspec(f)
+        args = sig.args
+        if len(args) < 2:
+            raise ValueError("Unable to determine number of fit parameters.")
+        n = len(args) - 1
+    else:
+        p0 = np.atleast_1d(p0)
+        n = p0.size
+
+    if isinstance(bounds, Bounds):
+        lb, ub = bounds.lb, bounds.ub
+    else:
+        lb, ub = prepare_bounds(bounds, n)
+    if p0 is None:
+        p0 = _initialize_feasible(lb, ub)
+
+    bounded_problem = np.any((lb > -np.inf) | (ub < np.inf))
+    if method is None:
+        if bounded_problem:
+            method = 'trf'
+        else:
+            method = 'lm'
+
+    if method == 'lm' and bounded_problem:
+        raise ValueError("Method 'lm' only works for unconstrained problems. "
+                         "Use 'trf' or 'dogbox' instead.")
+
+    if check_finite is None:
+        check_finite = True if nan_policy is None else False
+
+    # optimization may produce garbage for float32 inputs, cast them to float64
+    if check_finite:
+        ydata = np.asarray_chkfinite(ydata, float)
+    else:
+        ydata = np.asarray(ydata, float)
+
+    if isinstance(xdata, (list, tuple, np.ndarray)):
+        # `xdata` is passed straight to the user-defined `f`, so allow
+        # non-array_like `xdata`.
+        if check_finite:
+            xdata = np.asarray_chkfinite(xdata, float)
+        else:
+            xdata = np.asarray(xdata, float)
+
+    if ydata.size == 0:
+        raise ValueError("`ydata` must not be empty!")
+
+    # nan handling is needed only if check_finite is False because if True,
+    # the x-y data are already checked, and they don't contain nans.
+    if not check_finite and nan_policy is not None:
+        if nan_policy == "propagate":
+            raise ValueError("`nan_policy='propagate'` is not supported "
+                             "by this function.")
+
+        policies = [None, 'raise', 'omit']
+        x_contains_nan, nan_policy = _contains_nan(xdata, nan_policy,
+                                                   policies=policies)
+        y_contains_nan, nan_policy = _contains_nan(ydata, nan_policy,
+                                                   policies=policies)
+
+        if (x_contains_nan or y_contains_nan) and nan_policy == 'omit':
+            # ignore NaNs for N dimensional arrays
+            has_nan = np.isnan(xdata)
+            has_nan = has_nan.any(axis=tuple(range(has_nan.ndim-1)))
+            has_nan |= np.isnan(ydata)
+
+            xdata = xdata[..., ~has_nan]
+            ydata = ydata[~has_nan]
+
+    # Determine type of sigma
+    if sigma is not None:
+        sigma = np.asarray(sigma)
+
+        # if 1-D or a scalar, sigma are errors, define transform = 1/sigma
+        if sigma.size == 1 or sigma.shape == (ydata.size, ):
+            transform = 1.0 / sigma
+        # if 2-D, sigma is the covariance matrix,
+        # define transform = L such that L L^T = C
+        elif sigma.shape == (ydata.size, ydata.size):
+            try:
+                # scipy.linalg.cholesky requires lower=True to return L L^T = A
+                transform = cholesky(sigma, lower=True)
+            except LinAlgError as e:
+                raise ValueError("`sigma` must be positive definite.") from e
+        else:
+            raise ValueError("`sigma` has incorrect shape.")
+    else:
+        transform = None
+
+    func = _lightweight_memoizer(_wrap_func(f, xdata, ydata, transform))
+
+    if callable(jac):
+        jac = _lightweight_memoizer(_wrap_jac(jac, xdata, transform))
+    elif jac is None and method != 'lm':
+        jac = '2-point'
+
+    if 'args' in kwargs:
+        # The specification for the model function `f` does not support
+        # additional arguments. Refer to the `curve_fit` docstring for
+        # acceptable call signatures of `f`.
+        raise ValueError("'args' is not a supported keyword argument.")
+
+    if method == 'lm':
+        # if ydata.size == 1, this might be used for broadcast.
+        if ydata.size != 1 and n > ydata.size:
+            raise TypeError(f"The number of func parameters={n} must not"
+                            f" exceed the number of data points={ydata.size}")
+        res = leastsq(func, p0, Dfun=jac, full_output=1, **kwargs)
+        popt, pcov, infodict, errmsg, ier = res
+        ysize = len(infodict['fvec'])
+        cost = np.sum(infodict['fvec'] ** 2)
+        if ier not in [1, 2, 3, 4]:
+            raise RuntimeError("Optimal parameters not found: " + errmsg)
+    else:
+        # Rename maxfev (leastsq) to max_nfev (least_squares), if specified.
+        if 'max_nfev' not in kwargs:
+            kwargs['max_nfev'] = kwargs.pop('maxfev', None)
+
+        res = least_squares(func, p0, jac=jac, bounds=bounds, method=method,
+                            **kwargs)
+
+        if not res.success:
+            raise RuntimeError("Optimal parameters not found: " + res.message)
+
+        infodict = dict(nfev=res.nfev, fvec=res.fun)
+        ier = res.status
+        errmsg = res.message
+
+        ysize = len(res.fun)
+        cost = 2 * res.cost  # res.cost is half sum of squares!
+        popt = res.x
+
+        # Do Moore-Penrose inverse discarding zero singular values.
+        _, s, VT = svd(res.jac, full_matrices=False)
+        threshold = np.finfo(float).eps * max(res.jac.shape) * s[0]
+        s = s[s > threshold]
+        VT = VT[:s.size]
+        pcov = np.dot(VT.T / s**2, VT)
+
+    warn_cov = False
+    if pcov is None or np.isnan(pcov).any():
+        # indeterminate covariance
+        pcov = zeros((len(popt), len(popt)), dtype=float)
+        pcov.fill(inf)
+        warn_cov = True
+    elif not absolute_sigma:
+        if ysize > p0.size:
+            s_sq = cost / (ysize - p0.size)
+            pcov = pcov * s_sq
+        else:
+            pcov.fill(inf)
+            warn_cov = True
+
+    if warn_cov:
+        warnings.warn('Covariance of the parameters could not be estimated',
+                      category=OptimizeWarning, stacklevel=2)
+
+    if full_output:
+        return popt, pcov, infodict, errmsg, ier
+    else:
+        return popt, pcov
+
+
+def check_gradient(fcn, Dfcn, x0, args=(), col_deriv=0):
+    """Perform a simple check on the gradient for correctness.
+
+    """
+
+    x = atleast_1d(x0)
+    n = len(x)
+    x = x.reshape((n,))
+    fvec = atleast_1d(fcn(x, *args))
+    m = len(fvec)
+    fvec = fvec.reshape((m,))
+    ldfjac = m
+    fjac = atleast_1d(Dfcn(x, *args))
+    fjac = fjac.reshape((m, n))
+    if col_deriv == 0:
+        fjac = transpose(fjac)
+
+    xp = zeros((n,), float)
+    err = zeros((m,), float)
+    fvecp = None
+    _minpack._chkder(m, n, x, fvec, fjac, ldfjac, xp, fvecp, 1, err)
+
+    fvecp = atleast_1d(fcn(xp, *args))
+    fvecp = fvecp.reshape((m,))
+    _minpack._chkder(m, n, x, fvec, fjac, ldfjac, xp, fvecp, 2, err)
+
+    good = (prod(greater(err, 0.5), axis=0))
+
+    return (good, err)
+
+
+def _del2(p0, p1, d):
+    return p0 - np.square(p1 - p0) / d
+
+
+def _relerr(actual, desired):
+    return (actual - desired) / desired
+
+
+def _fixed_point_helper(func, x0, args, xtol, maxiter, use_accel):
+    p0 = x0
+    for i in range(maxiter):
+        p1 = func(p0, *args)
+        if use_accel:
+            p2 = func(p1, *args)
+            d = p2 - 2.0 * p1 + p0
+            p = _lazywhere(d != 0, (p0, p1, d), f=_del2, fillvalue=p2)
+        else:
+            p = p1
+        relerr = _lazywhere(p0 != 0, (p, p0), f=_relerr, fillvalue=p)
+        if np.all(np.abs(relerr) < xtol):
+            return p
+        p0 = p
+    msg = "Failed to converge after %d iterations, value is %s" % (maxiter, p)
+    raise RuntimeError(msg)
+
+
+def fixed_point(func, x0, args=(), xtol=1e-8, maxiter=500, method='del2'):
+    """
+    Find a fixed point of the function.
+
+    Given a function of one or more variables and a starting point, find a
+    fixed point of the function: i.e., where ``func(x0) == x0``.
+
+    Parameters
+    ----------
+    func : function
+        Function to evaluate.
+    x0 : array_like
+        Fixed point of function.
+    args : tuple, optional
+        Extra arguments to `func`.
+    xtol : float, optional
+        Convergence tolerance, defaults to 1e-08.
+    maxiter : int, optional
+        Maximum number of iterations, defaults to 500.
+    method : {"del2", "iteration"}, optional
+        Method of finding the fixed-point, defaults to "del2",
+        which uses Steffensen's Method with Aitken's ``Del^2``
+        convergence acceleration [1]_. The "iteration" method simply iterates
+        the function until convergence is detected, without attempting to
+        accelerate the convergence.
+
+    References
+    ----------
+    .. [1] Burden, Faires, "Numerical Analysis", 5th edition, pg. 80
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import optimize
+    >>> def func(x, c1, c2):
+    ...    return np.sqrt(c1/(x+c2))
+    >>> c1 = np.array([10,12.])
+    >>> c2 = np.array([3, 5.])
+    >>> optimize.fixed_point(func, [1.2, 1.3], args=(c1,c2))
+    array([ 1.4920333 ,  1.37228132])
+
+    """
+    use_accel = {'del2': True, 'iteration': False}[method]
+    x0 = _asarray_validated(x0, as_inexact=True)
+    return _fixed_point_helper(func, x0, args, xtol, maxiter, use_accel)

vila/lib/python3.10/site-packages/scipy/optimize/_moduleTNC.cpython-310-x86_64-linux-gnu.so

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d7584b3d74b2c7f2804c049af2291355762236b8a294520a6c7a83085ac11544
+size 152168

vila/lib/python3.10/site-packages/scipy/optimize/_nnls.py

@@ -0,0 +1,164 @@
+import numpy as np
+from scipy.linalg import solve, LinAlgWarning
+import warnings
+
+__all__ = ['nnls']
+
+
+def nnls(A, b, maxiter=None, *, atol=None):
+    """
+    Solve ``argmin_x || Ax - b ||_2`` for ``x>=0``.
+
+    This problem, often called as NonNegative Least Squares, is a convex
+    optimization problem with convex constraints. It typically arises when
+    the ``x`` models quantities for which only nonnegative values are
+    attainable; weight of ingredients, component costs and so on.
+
+    Parameters
+    ----------
+    A : (m, n) ndarray
+        Coefficient array
+    b : (m,) ndarray, float
+        Right-hand side vector.
+    maxiter: int, optional
+        Maximum number of iterations, optional. Default value is ``3 * n``.
+    atol: float
+        Tolerance value used in the algorithm to assess closeness to zero in
+        the projected residual ``(A.T @ (A x - b)`` entries. Increasing this
+        value relaxes the solution constraints. A typical relaxation value can
+        be selected as ``max(m, n) * np.linalg.norm(a, 1) * np.spacing(1.)``.
+        This value is not set as default since the norm operation becomes
+        expensive for large problems hence can be used only when necessary.
+
+    Returns
+    -------
+    x : ndarray
+        Solution vector.
+    rnorm : float
+        The 2-norm of the residual, ``|| Ax-b ||_2``.
+
+    See Also
+    --------
+    lsq_linear : Linear least squares with bounds on the variables
+
+    Notes
+    -----
+    The code is based on [2]_ which is an improved version of the classical
+    algorithm of [1]_. It utilizes an active set method and solves the KKT
+    (Karush-Kuhn-Tucker) conditions for the non-negative least squares problem.
+
+    References
+    ----------
+    .. [1] : Lawson C., Hanson R.J., "Solving Least Squares Problems", SIAM,
+       1995, :doi:`10.1137/1.9781611971217`
+    .. [2] : Bro, Rasmus and de Jong, Sijmen, "A Fast Non-Negativity-
+       Constrained Least Squares Algorithm", Journal Of Chemometrics, 1997,
+       :doi:`10.1002/(SICI)1099-128X(199709/10)11:5<393::AID-CEM483>3.0.CO;2-L`
+
+     Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.optimize import nnls
+    ...
+    >>> A = np.array([[1, 0], [1, 0], [0, 1]])
+    >>> b = np.array([2, 1, 1])
+    >>> nnls(A, b)
+    (array([1.5, 1. ]), 0.7071067811865475)
+
+    >>> b = np.array([-1, -1, -1])
+    >>> nnls(A, b)
+    (array([0., 0.]), 1.7320508075688772)
+
+    """
+
+    A = np.asarray_chkfinite(A)
+    b = np.asarray_chkfinite(b)
+
+    if len(A.shape) != 2:
+        raise ValueError("Expected a two-dimensional array (matrix)" +
+                         f", but the shape of A is {A.shape}")
+    if len(b.shape) != 1:
+        raise ValueError("Expected a one-dimensional array (vector)" +
+                         f", but the shape of b is {b.shape}")
+
+    m, n = A.shape
+
+    if m != b.shape[0]:
+        raise ValueError(
+                "Incompatible dimensions. The first dimension of " +
+                f"A is {m}, while the shape of b is {(b.shape[0], )}")
+
+    x, rnorm, mode = _nnls(A, b, maxiter, tol=atol)
+    if mode != 1:
+        raise RuntimeError("Maximum number of iterations reached.")
+
+    return x, rnorm
+
+
+def _nnls(A, b, maxiter=None, tol=None):
+    """
+    This is a single RHS algorithm from ref [2] above. For multiple RHS
+    support, the algorithm is given in  :doi:`10.1002/cem.889`
+    """
+    m, n = A.shape
+
+    AtA = A.T @ A
+    Atb = b @ A  # Result is 1D - let NumPy figure it out
+
+    if not maxiter:
+        maxiter = 3*n
+    if tol is None:
+        tol = 10 * max(m, n) * np.spacing(1.)
+
+    # Initialize vars
+    x = np.zeros(n, dtype=np.float64)
+    s = np.zeros(n, dtype=np.float64)
+    # Inactive constraint switches
+    P = np.zeros(n, dtype=bool)
+
+    # Projected residual
+    w = Atb.copy().astype(np.float64)  # x=0. Skip (-AtA @ x) term
+
+    # Overall iteration counter
+    # Outer loop is not counted, inner iter is counted across outer spins
+    iter = 0
+
+    while (not P.all()) and (w[~P] > tol).any():  # B
+        # Get the "most" active coeff index and move to inactive set
+        k = np.argmax(w * (~P))  # B.2
+        P[k] = True  # B.3
+
+        # Iteration solution
+        s[:] = 0.
+        # B.4
+        with warnings.catch_warnings():
+            warnings.filterwarnings('ignore', message='Ill-conditioned matrix',
+                                    category=LinAlgWarning)
+            s[P] = solve(AtA[np.ix_(P, P)], Atb[P], assume_a='sym', check_finite=False)
+
+        # Inner loop
+        while (iter < maxiter) and (s[P].min() < 0):  # C.1
+            iter += 1
+            inds = P * (s < 0)
+            alpha = (x[inds] / (x[inds] - s[inds])).min()  # C.2
+            x *= (1 - alpha)
+            x += alpha*s
+            P[x <= tol] = False
+            with warnings.catch_warnings():
+                warnings.filterwarnings('ignore', message='Ill-conditioned matrix',
+                                        category=LinAlgWarning)
+                s[P] = solve(AtA[np.ix_(P, P)], Atb[P], assume_a='sym',
+                             check_finite=False)
+            s[~P] = 0  # C.6
+
+        x[:] = s[:]
+        w[:] = Atb - AtA @ x
+
+        if iter == maxiter:
+            # Typically following line should return
+            # return x, np.linalg.norm(A@x - b), -1
+            # however at the top level, -1 raises an exception wasting norm
+            # Instead return dummy number 0.
+            return x, 0., -1
+
+    return x, np.linalg.norm(A@x - b), 1

vila/lib/python3.10/site-packages/scipy/optimize/_nonlin.py

@@ -0,0 +1,1585 @@
+# Copyright (C) 2009, Pauli Virtanen <pav@iki.fi>
+# Distributed under the same license as SciPy.
+
+import inspect
+import sys
+import warnings
+
+import numpy as np
+from numpy import asarray, dot, vdot
+
+from scipy.linalg import norm, solve, inv, qr, svd, LinAlgError
+import scipy.sparse.linalg
+import scipy.sparse
+from scipy.linalg import get_blas_funcs
+from scipy._lib._util import copy_if_needed
+from scipy._lib._util import getfullargspec_no_self as _getfullargspec
+from ._linesearch import scalar_search_wolfe1, scalar_search_armijo
+
+
+__all__ = [
+    'broyden1', 'broyden2', 'anderson', 'linearmixing',
+    'diagbroyden', 'excitingmixing', 'newton_krylov',
+    'BroydenFirst', 'KrylovJacobian', 'InverseJacobian', 'NoConvergence']
+
+#------------------------------------------------------------------------------
+# Utility functions
+#------------------------------------------------------------------------------
+
+
+class NoConvergence(Exception):
+    """Exception raised when nonlinear solver fails to converge within the specified
+    `maxiter`."""
+    pass
+
+
+def maxnorm(x):
+    return np.absolute(x).max()
+
+
+def _as_inexact(x):
+    """Return `x` as an array, of either floats or complex floats"""
+    x = asarray(x)
+    if not np.issubdtype(x.dtype, np.inexact):
+        return asarray(x, dtype=np.float64)
+    return x
+
+
+def _array_like(x, x0):
+    """Return ndarray `x` as same array subclass and shape as `x0`"""
+    x = np.reshape(x, np.shape(x0))
+    wrap = getattr(x0, '__array_wrap__', x.__array_wrap__)
+    return wrap(x)
+
+
+def _safe_norm(v):
+    if not np.isfinite(v).all():
+        return np.array(np.inf)
+    return norm(v)
+
+#------------------------------------------------------------------------------
+# Generic nonlinear solver machinery
+#------------------------------------------------------------------------------
+
+
+_doc_parts = dict(
+    params_basic="""
+    F : function(x) -> f
+        Function whose root to find; should take and return an array-like
+        object.
+    xin : array_like
+        Initial guess for the solution
+    """.strip(),
+    params_extra="""
+    iter : int, optional
+        Number of iterations to make. If omitted (default), make as many
+        as required to meet tolerances.
+    verbose : bool, optional
+        Print status to stdout on every iteration.
+    maxiter : int, optional
+        Maximum number of iterations to make. If more are needed to
+        meet convergence, `NoConvergence` is raised.
+    f_tol : float, optional
+        Absolute tolerance (in max-norm) for the residual.
+        If omitted, default is 6e-6.
+    f_rtol : float, optional
+        Relative tolerance for the residual. If omitted, not used.
+    x_tol : float, optional
+        Absolute minimum step size, as determined from the Jacobian
+        approximation. If the step size is smaller than this, optimization
+        is terminated as successful. If omitted, not used.
+    x_rtol : float, optional
+        Relative minimum step size. If omitted, not used.
+    tol_norm : function(vector) -> scalar, optional
+        Norm to use in convergence check. Default is the maximum norm.
+    line_search : {None, 'armijo' (default), 'wolfe'}, optional
+        Which type of a line search to use to determine the step size in the
+        direction given by the Jacobian approximation. Defaults to 'armijo'.
+    callback : function, optional
+        Optional callback function. It is called on every iteration as
+        ``callback(x, f)`` where `x` is the current solution and `f`
+        the corresponding residual.
+
+    Returns
+    -------
+    sol : ndarray
+        An array (of similar array type as `x0`) containing the final solution.
+
+    Raises
+    ------
+    NoConvergence
+        When a solution was not found.
+
+    """.strip()
+)
+
+
+def _set_doc(obj):
+    if obj.__doc__:
+        obj.__doc__ = obj.__doc__ % _doc_parts
+
+
+def nonlin_solve(F, x0, jacobian='krylov', iter=None, verbose=False,
+                 maxiter=None, f_tol=None, f_rtol=None, x_tol=None, x_rtol=None,
+                 tol_norm=None, line_search='armijo', callback=None,
+                 full_output=False, raise_exception=True):
+    """
+    Find a root of a function, in a way suitable for large-scale problems.
+
+    Parameters
+    ----------
+    %(params_basic)s
+    jacobian : Jacobian
+        A Jacobian approximation: `Jacobian` object or something that
+        `asjacobian` can transform to one. Alternatively, a string specifying
+        which of the builtin Jacobian approximations to use:
+
+            krylov, broyden1, broyden2, anderson
+            diagbroyden, linearmixing, excitingmixing
+
+    %(params_extra)s
+    full_output : bool
+        If true, returns a dictionary `info` containing convergence
+        information.
+    raise_exception : bool
+        If True, a `NoConvergence` exception is raise if no solution is found.
+
+    See Also
+    --------
+    asjacobian, Jacobian
+
+    Notes
+    -----
+    This algorithm implements the inexact Newton method, with
+    backtracking or full line searches. Several Jacobian
+    approximations are available, including Krylov and Quasi-Newton
+    methods.
+
+    References
+    ----------
+    .. [KIM] C. T. Kelley, \"Iterative Methods for Linear and Nonlinear
+       Equations\". Society for Industrial and Applied Mathematics. (1995)
+       https://archive.siam.org/books/kelley/fr16/
+
+    """
+    # Can't use default parameters because it's being explicitly passed as None
+    # from the calling function, so we need to set it here.
+    tol_norm = maxnorm if tol_norm is None else tol_norm
+    condition = TerminationCondition(f_tol=f_tol, f_rtol=f_rtol,
+                                     x_tol=x_tol, x_rtol=x_rtol,
+                                     iter=iter, norm=tol_norm)
+
+    x0 = _as_inexact(x0)
+    def func(z):
+        return _as_inexact(F(_array_like(z, x0))).flatten()
+    x = x0.flatten()
+
+    dx = np.full_like(x, np.inf)
+    Fx = func(x)
+    Fx_norm = norm(Fx)
+
+    jacobian = asjacobian(jacobian)
+    jacobian.setup(x.copy(), Fx, func)
+
+    if maxiter is None:
+        if iter is not None:
+            maxiter = iter + 1
+        else:
+            maxiter = 100*(x.size+1)
+
+    if line_search is True:
+        line_search = 'armijo'
+    elif line_search is False:
+        line_search = None
+
+    if line_search not in (None, 'armijo', 'wolfe'):
+        raise ValueError("Invalid line search")
+
+    # Solver tolerance selection
+    gamma = 0.9
+    eta_max = 0.9999
+    eta_treshold = 0.1
+    eta = 1e-3
+
+    for n in range(maxiter):
+        status = condition.check(Fx, x, dx)
+        if status:
+            break
+
+        # The tolerance, as computed for scipy.sparse.linalg.* routines
+        tol = min(eta, eta*Fx_norm)
+        dx = -jacobian.solve(Fx, tol=tol)
+
+        if norm(dx) == 0:
+            raise ValueError("Jacobian inversion yielded zero vector. "
+                             "This indicates a bug in the Jacobian "
+                             "approximation.")
+
+        # Line search, or Newton step
+        if line_search:
+            s, x, Fx, Fx_norm_new = _nonlin_line_search(func, x, Fx, dx,
+                                                        line_search)
+        else:
+            s = 1.0
+            x = x + dx
+            Fx = func(x)
+            Fx_norm_new = norm(Fx)
+
+        jacobian.update(x.copy(), Fx)
+
+        if callback:
+            callback(x, Fx)
+
+        # Adjust forcing parameters for inexact methods
+        eta_A = gamma * Fx_norm_new**2 / Fx_norm**2
+        if gamma * eta**2 < eta_treshold:
+            eta = min(eta_max, eta_A)
+        else:
+            eta = min(eta_max, max(eta_A, gamma*eta**2))
+
+        Fx_norm = Fx_norm_new
+
+        # Print status
+        if verbose:
+            sys.stdout.write("%d:  |F(x)| = %g; step %g\n" % (
+                n, tol_norm(Fx), s))
+            sys.stdout.flush()
+    else:
+        if raise_exception:
+            raise NoConvergence(_array_like(x, x0))
+        else:
+            status = 2
+
+    if full_output:
+        info = {'nit': condition.iteration,
+                'fun': Fx,
+                'status': status,
+                'success': status == 1,
+                'message': {1: 'A solution was found at the specified '
+                               'tolerance.',
+                            2: 'The maximum number of iterations allowed '
+                               'has been reached.'
+                            }[status]
+                }
+        return _array_like(x, x0), info
+    else:
+        return _array_like(x, x0)
+
+
+_set_doc(nonlin_solve)
+
+
+def _nonlin_line_search(func, x, Fx, dx, search_type='armijo', rdiff=1e-8,
+                        smin=1e-2):
+    tmp_s = [0]
+    tmp_Fx = [Fx]
+    tmp_phi = [norm(Fx)**2]
+    s_norm = norm(x) / norm(dx)
+
+    def phi(s, store=True):
+        if s == tmp_s[0]:
+            return tmp_phi[0]
+        xt = x + s*dx
+        v = func(xt)
+        p = _safe_norm(v)**2
+        if store:
+            tmp_s[0] = s
+            tmp_phi[0] = p
+            tmp_Fx[0] = v
+        return p
+
+    def derphi(s):
+        ds = (abs(s) + s_norm + 1) * rdiff
+        return (phi(s+ds, store=False) - phi(s)) / ds
+
+    if search_type == 'wolfe':
+        s, phi1, phi0 = scalar_search_wolfe1(phi, derphi, tmp_phi[0],
+                                             xtol=1e-2, amin=smin)
+    elif search_type == 'armijo':
+        s, phi1 = scalar_search_armijo(phi, tmp_phi[0], -tmp_phi[0],
+                                       amin=smin)
+
+    if s is None:
+        # XXX: No suitable step length found. Take the full Newton step,
+        #      and hope for the best.
+        s = 1.0
+
+    x = x + s*dx
+    if s == tmp_s[0]:
+        Fx = tmp_Fx[0]
+    else:
+        Fx = func(x)
+    Fx_norm = norm(Fx)
+
+    return s, x, Fx, Fx_norm
+
+
+class TerminationCondition:
+    """
+    Termination condition for an iteration. It is terminated if
+
+    - |F| < f_rtol*|F_0|, AND
+    - |F| < f_tol
+
+    AND
+
+    - |dx| < x_rtol*|x|, AND
+    - |dx| < x_tol
+
+    """
+    def __init__(self, f_tol=None, f_rtol=None, x_tol=None, x_rtol=None,
+                 iter=None, norm=maxnorm):
+
+        if f_tol is None:
+            f_tol = np.finfo(np.float64).eps ** (1./3)
+        if f_rtol is None:
+            f_rtol = np.inf
+        if x_tol is None:
+            x_tol = np.inf
+        if x_rtol is None:
+            x_rtol = np.inf
+
+        self.x_tol = x_tol
+        self.x_rtol = x_rtol
+        self.f_tol = f_tol
+        self.f_rtol = f_rtol
+
+        self.norm = norm
+
+        self.iter = iter
+
+        self.f0_norm = None
+        self.iteration = 0
+
+    def check(self, f, x, dx):
+        self.iteration += 1
+        f_norm = self.norm(f)
+        x_norm = self.norm(x)
+        dx_norm = self.norm(dx)
+
+        if self.f0_norm is None:
+            self.f0_norm = f_norm
+
+        if f_norm == 0:
+            return 1
+
+        if self.iter is not None:
+            # backwards compatibility with SciPy 0.6.0
+            return 2 * (self.iteration > self.iter)
+
+        # NB: condition must succeed for rtol=inf even if norm == 0
+        return int((f_norm <= self.f_tol
+                    and f_norm/self.f_rtol <= self.f0_norm)
+                   and (dx_norm <= self.x_tol
+                        and dx_norm/self.x_rtol <= x_norm))
+
+
+#------------------------------------------------------------------------------
+# Generic Jacobian approximation
+#------------------------------------------------------------------------------
+
+class Jacobian:
+    """
+    Common interface for Jacobians or Jacobian approximations.
+
+    The optional methods come useful when implementing trust region
+    etc., algorithms that often require evaluating transposes of the
+    Jacobian.
+
+    Methods
+    -------
+    solve
+        Returns J^-1 * v
+    update
+        Updates Jacobian to point `x` (where the function has residual `Fx`)
+
+    matvec : optional
+        Returns J * v
+    rmatvec : optional
+        Returns A^H * v
+    rsolve : optional
+        Returns A^-H * v
+    matmat : optional
+        Returns A * V, where V is a dense matrix with dimensions (N,K).
+    todense : optional
+        Form the dense Jacobian matrix. Necessary for dense trust region
+        algorithms, and useful for testing.
+
+    Attributes
+    ----------
+    shape
+        Matrix dimensions (M, N)
+    dtype
+        Data type of the matrix.
+    func : callable, optional
+        Function the Jacobian corresponds to
+
+    """
+
+    def __init__(self, **kw):
+        names = ["solve", "update", "matvec", "rmatvec", "rsolve",
+                 "matmat", "todense", "shape", "dtype"]
+        for name, value in kw.items():
+            if name not in names:
+                raise ValueError("Unknown keyword argument %s" % name)
+            if value is not None:
+                setattr(self, name, kw[name])
+
+
+        if hasattr(self, "todense"):
+            def __array__(self, dtype=None, copy=None):
+                if dtype is not None:
+                    raise ValueError(f"`dtype` must be None, was {dtype}")
+                return self.todense()
+
+    def aspreconditioner(self):
+        return InverseJacobian(self)
+
+    def solve(self, v, tol=0):
+        raise NotImplementedError
+
+    def update(self, x, F):
+        pass
+
+    def setup(self, x, F, func):
+        self.func = func
+        self.shape = (F.size, x.size)
+        self.dtype = F.dtype
+        if self.__class__.setup is Jacobian.setup:
+            # Call on the first point unless overridden
+            self.update(x, F)
+
+
+class InverseJacobian:
+    def __init__(self, jacobian):
+        self.jacobian = jacobian
+        self.matvec = jacobian.solve
+        self.update = jacobian.update
+        if hasattr(jacobian, 'setup'):
+            self.setup = jacobian.setup
+        if hasattr(jacobian, 'rsolve'):
+            self.rmatvec = jacobian.rsolve
+
+    @property
+    def shape(self):
+        return self.jacobian.shape
+
+    @property
+    def dtype(self):
+        return self.jacobian.dtype
+
+
+def asjacobian(J):
+    """
+    Convert given object to one suitable for use as a Jacobian.
+    """
+    spsolve = scipy.sparse.linalg.spsolve
+    if isinstance(J, Jacobian):
+        return J
+    elif inspect.isclass(J) and issubclass(J, Jacobian):
+        return J()
+    elif isinstance(J, np.ndarray):
+        if J.ndim > 2:
+            raise ValueError('array must have rank <= 2')
+        J = np.atleast_2d(np.asarray(J))
+        if J.shape[0] != J.shape[1]:
+            raise ValueError('array must be square')
+
+        return Jacobian(matvec=lambda v: dot(J, v),
+                        rmatvec=lambda v: dot(J.conj().T, v),
+                        solve=lambda v, tol=0: solve(J, v),
+                        rsolve=lambda v, tol=0: solve(J.conj().T, v),
+                        dtype=J.dtype, shape=J.shape)
+    elif scipy.sparse.issparse(J):
+        if J.shape[0] != J.shape[1]:
+            raise ValueError('matrix must be square')
+        return Jacobian(matvec=lambda v: J @ v,
+                        rmatvec=lambda v: J.conj().T @ v,
+                        solve=lambda v, tol=0: spsolve(J, v),
+                        rsolve=lambda v, tol=0: spsolve(J.conj().T, v),
+                        dtype=J.dtype, shape=J.shape)
+    elif hasattr(J, 'shape') and hasattr(J, 'dtype') and hasattr(J, 'solve'):
+        return Jacobian(matvec=getattr(J, 'matvec'),
+                        rmatvec=getattr(J, 'rmatvec'),
+                        solve=J.solve,
+                        rsolve=getattr(J, 'rsolve'),
+                        update=getattr(J, 'update'),
+                        setup=getattr(J, 'setup'),
+                        dtype=J.dtype,
+                        shape=J.shape)
+    elif callable(J):
+        # Assume it's a function J(x) that returns the Jacobian
+        class Jac(Jacobian):
+            def update(self, x, F):
+                self.x = x
+
+            def solve(self, v, tol=0):
+                m = J(self.x)
+                if isinstance(m, np.ndarray):
+                    return solve(m, v)
+                elif scipy.sparse.issparse(m):
+                    return spsolve(m, v)
+                else:
+                    raise ValueError("Unknown matrix type")
+
+            def matvec(self, v):
+                m = J(self.x)
+                if isinstance(m, np.ndarray):
+                    return dot(m, v)
+                elif scipy.sparse.issparse(m):
+                    return m @ v
+                else:
+                    raise ValueError("Unknown matrix type")
+
+            def rsolve(self, v, tol=0):
+                m = J(self.x)
+                if isinstance(m, np.ndarray):
+                    return solve(m.conj().T, v)
+                elif scipy.sparse.issparse(m):
+                    return spsolve(m.conj().T, v)
+                else:
+                    raise ValueError("Unknown matrix type")
+
+            def rmatvec(self, v):
+                m = J(self.x)
+                if isinstance(m, np.ndarray):
+                    return dot(m.conj().T, v)
+                elif scipy.sparse.issparse(m):
+                    return m.conj().T @ v
+                else:
+                    raise ValueError("Unknown matrix type")
+        return Jac()
+    elif isinstance(J, str):
+        return dict(broyden1=BroydenFirst,
+                    broyden2=BroydenSecond,
+                    anderson=Anderson,
+                    diagbroyden=DiagBroyden,
+                    linearmixing=LinearMixing,
+                    excitingmixing=ExcitingMixing,
+                    krylov=KrylovJacobian)[J]()
+    else:
+        raise TypeError('Cannot convert object to a Jacobian')
+
+
+#------------------------------------------------------------------------------
+# Broyden
+#------------------------------------------------------------------------------
+
+class GenericBroyden(Jacobian):
+    def setup(self, x0, f0, func):
+        Jacobian.setup(self, x0, f0, func)
+        self.last_f = f0
+        self.last_x = x0
+
+        if hasattr(self, 'alpha') and self.alpha is None:
+            # Autoscale the initial Jacobian parameter
+            # unless we have already guessed the solution.
+            normf0 = norm(f0)
+            if normf0:
+                self.alpha = 0.5*max(norm(x0), 1) / normf0
+            else:
+                self.alpha = 1.0
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        raise NotImplementedError
+
+    def update(self, x, f):
+        df = f - self.last_f
+        dx = x - self.last_x
+        self._update(x, f, dx, df, norm(dx), norm(df))
+        self.last_f = f
+        self.last_x = x
+
+
+class LowRankMatrix:
+    r"""
+    A matrix represented as
+
+    .. math:: \alpha I + \sum_{n=0}^{n=M} c_n d_n^\dagger
+
+    However, if the rank of the matrix reaches the dimension of the vectors,
+    full matrix representation will be used thereon.
+
+    """
+
+    def __init__(self, alpha, n, dtype):
+        self.alpha = alpha
+        self.cs = []
+        self.ds = []
+        self.n = n
+        self.dtype = dtype
+        self.collapsed = None
+
+    @staticmethod
+    def _matvec(v, alpha, cs, ds):
+        axpy, scal, dotc = get_blas_funcs(['axpy', 'scal', 'dotc'],
+                                          cs[:1] + [v])
+        w = alpha * v
+        for c, d in zip(cs, ds):
+            a = dotc(d, v)
+            w = axpy(c, w, w.size, a)
+        return w
+
+    @staticmethod
+    def _solve(v, alpha, cs, ds):
+        """Evaluate w = M^-1 v"""
+        if len(cs) == 0:
+            return v/alpha
+
+        # (B + C D^H)^-1 = B^-1 - B^-1 C (I + D^H B^-1 C)^-1 D^H B^-1
+
+        axpy, dotc = get_blas_funcs(['axpy', 'dotc'], cs[:1] + [v])
+
+        c0 = cs[0]
+        A = alpha * np.identity(len(cs), dtype=c0.dtype)
+        for i, d in enumerate(ds):
+            for j, c in enumerate(cs):
+                A[i,j] += dotc(d, c)
+
+        q = np.zeros(len(cs), dtype=c0.dtype)
+        for j, d in enumerate(ds):
+            q[j] = dotc(d, v)
+        q /= alpha
+        q = solve(A, q)
+
+        w = v/alpha
+        for c, qc in zip(cs, q):
+            w = axpy(c, w, w.size, -qc)
+
+        return w
+
+    def matvec(self, v):
+        """Evaluate w = M v"""
+        if self.collapsed is not None:
+            return np.dot(self.collapsed, v)
+        return LowRankMatrix._matvec(v, self.alpha, self.cs, self.ds)
+
+    def rmatvec(self, v):
+        """Evaluate w = M^H v"""
+        if self.collapsed is not None:
+            return np.dot(self.collapsed.T.conj(), v)
+        return LowRankMatrix._matvec(v, np.conj(self.alpha), self.ds, self.cs)
+
+    def solve(self, v, tol=0):
+        """Evaluate w = M^-1 v"""
+        if self.collapsed is not None:
+            return solve(self.collapsed, v)
+        return LowRankMatrix._solve(v, self.alpha, self.cs, self.ds)
+
+    def rsolve(self, v, tol=0):
+        """Evaluate w = M^-H v"""
+        if self.collapsed is not None:
+            return solve(self.collapsed.T.conj(), v)
+        return LowRankMatrix._solve(v, np.conj(self.alpha), self.ds, self.cs)
+
+    def append(self, c, d):
+        if self.collapsed is not None:
+            self.collapsed += c[:,None] * d[None,:].conj()
+            return
+
+        self.cs.append(c)
+        self.ds.append(d)
+
+        if len(self.cs) > c.size:
+            self.collapse()
+
+    def __array__(self, dtype=None, copy=None):
+        if dtype is not None:
+            warnings.warn("LowRankMatrix is scipy-internal code, `dtype` "
+                          f"should only be None but was {dtype} (not handled)",
+                          stacklevel=3)
+        if copy is not None:
+            warnings.warn("LowRankMatrix is scipy-internal code, `copy` "
+                          f"should only be None but was {copy} (not handled)",
+                          stacklevel=3)
+        if self.collapsed is not None:
+            return self.collapsed
+
+        Gm = self.alpha*np.identity(self.n, dtype=self.dtype)
+        for c, d in zip(self.cs, self.ds):
+            Gm += c[:,None]*d[None,:].conj()
+        return Gm
+
+    def collapse(self):
+        """Collapse the low-rank matrix to a full-rank one."""
+        self.collapsed = np.array(self, copy=copy_if_needed)
+        self.cs = None
+        self.ds = None
+        self.alpha = None
+
+    def restart_reduce(self, rank):
+        """
+        Reduce the rank of the matrix by dropping all vectors.
+        """
+        if self.collapsed is not None:
+            return
+        assert rank > 0
+        if len(self.cs) > rank:
+            del self.cs[:]
+            del self.ds[:]
+
+    def simple_reduce(self, rank):
+        """
+        Reduce the rank of the matrix by dropping oldest vectors.
+        """
+        if self.collapsed is not None:
+            return
+        assert rank > 0
+        while len(self.cs) > rank:
+            del self.cs[0]
+            del self.ds[0]
+
+    def svd_reduce(self, max_rank, to_retain=None):
+        """
+        Reduce the rank of the matrix by retaining some SVD components.
+
+        This corresponds to the \"Broyden Rank Reduction Inverse\"
+        algorithm described in [1]_.
+
+        Note that the SVD decomposition can be done by solving only a
+        problem whose size is the effective rank of this matrix, which
+        is viable even for large problems.
+
+        Parameters
+        ----------
+        max_rank : int
+            Maximum rank of this matrix after reduction.
+        to_retain : int, optional
+            Number of SVD components to retain when reduction is done
+            (ie. rank > max_rank). Default is ``max_rank - 2``.
+
+        References
+        ----------
+        .. [1] B.A. van der Rotten, PhD thesis,
+           \"A limited memory Broyden method to solve high-dimensional
+           systems of nonlinear equations\". Mathematisch Instituut,
+           Universiteit Leiden, The Netherlands (2003).
+
+           https://web.archive.org/web/20161022015821/http://www.math.leidenuniv.nl/scripties/Rotten.pdf
+
+        """
+        if self.collapsed is not None:
+            return
+
+        p = max_rank
+        if to_retain is not None:
+            q = to_retain
+        else:
+            q = p - 2
+
+        if self.cs:
+            p = min(p, len(self.cs[0]))
+        q = max(0, min(q, p-1))
+
+        m = len(self.cs)
+        if m < p:
+            # nothing to do
+            return
+
+        C = np.array(self.cs).T
+        D = np.array(self.ds).T
+
+        D, R = qr(D, mode='economic')
+        C = dot(C, R.T.conj())
+
+        U, S, WH = svd(C, full_matrices=False)
+
+        C = dot(C, inv(WH))
+        D = dot(D, WH.T.conj())
+
+        for k in range(q):
+            self.cs[k] = C[:,k].copy()
+            self.ds[k] = D[:,k].copy()
+
+        del self.cs[q:]
+        del self.ds[q:]
+
+
+_doc_parts['broyden_params'] = """
+    alpha : float, optional
+        Initial guess for the Jacobian is ``(-1/alpha)``.
+    reduction_method : str or tuple, optional
+        Method used in ensuring that the rank of the Broyden matrix
+        stays low. Can either be a string giving the name of the method,
+        or a tuple of the form ``(method, param1, param2, ...)``
+        that gives the name of the method and values for additional parameters.
+
+        Methods available:
+
+            - ``restart``: drop all matrix columns. Has no extra parameters.
+            - ``simple``: drop oldest matrix column. Has no extra parameters.
+            - ``svd``: keep only the most significant SVD components.
+              Takes an extra parameter, ``to_retain``, which determines the
+              number of SVD components to retain when rank reduction is done.
+              Default is ``max_rank - 2``.
+
+    max_rank : int, optional
+        Maximum rank for the Broyden matrix.
+        Default is infinity (i.e., no rank reduction).
+    """.strip()
+
+
+class BroydenFirst(GenericBroyden):
+    r"""
+    Find a root of a function, using Broyden's first Jacobian approximation.
+
+    This method is also known as \"Broyden's good method\".
+
+    Parameters
+    ----------
+    %(params_basic)s
+    %(broyden_params)s
+    %(params_extra)s
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='broyden1'`` in particular.
+
+    Notes
+    -----
+    This algorithm implements the inverse Jacobian Quasi-Newton update
+
+    .. math:: H_+ = H + (dx - H df) dx^\dagger H / ( dx^\dagger H df)
+
+    which corresponds to Broyden's first Jacobian update
+
+    .. math:: J_+ = J + (df - J dx) dx^\dagger / dx^\dagger dx
+
+
+    References
+    ----------
+    .. [1] B.A. van der Rotten, PhD thesis,
+       \"A limited memory Broyden method to solve high-dimensional
+       systems of nonlinear equations\". Mathematisch Instituut,
+       Universiteit Leiden, The Netherlands (2003).
+
+       https://web.archive.org/web/20161022015821/http://www.math.leidenuniv.nl/scripties/Rotten.pdf
+
+    Examples
+    --------
+    The following functions define a system of nonlinear equations
+
+    >>> def fun(x):
+    ...     return [x[0]  + 0.5 * (x[0] - x[1])**3 - 1.0,
+    ...             0.5 * (x[1] - x[0])**3 + x[1]]
+
+    A solution can be obtained as follows.
+
+    >>> from scipy import optimize
+    >>> sol = optimize.broyden1(fun, [0, 0])
+    >>> sol
+    array([0.84116396, 0.15883641])
+
+    """
+
+    def __init__(self, alpha=None, reduction_method='restart', max_rank=None):
+        GenericBroyden.__init__(self)
+        self.alpha = alpha
+        self.Gm = None
+
+        if max_rank is None:
+            max_rank = np.inf
+        self.max_rank = max_rank
+
+        if isinstance(reduction_method, str):
+            reduce_params = ()
+        else:
+            reduce_params = reduction_method[1:]
+            reduction_method = reduction_method[0]
+        reduce_params = (max_rank - 1,) + reduce_params
+
+        if reduction_method == 'svd':
+            self._reduce = lambda: self.Gm.svd_reduce(*reduce_params)
+        elif reduction_method == 'simple':
+            self._reduce = lambda: self.Gm.simple_reduce(*reduce_params)
+        elif reduction_method == 'restart':
+            self._reduce = lambda: self.Gm.restart_reduce(*reduce_params)
+        else:
+            raise ValueError("Unknown rank reduction method '%s'" %
+                             reduction_method)
+
+    def setup(self, x, F, func):
+        GenericBroyden.setup(self, x, F, func)
+        self.Gm = LowRankMatrix(-self.alpha, self.shape[0], self.dtype)
+
+    def todense(self):
+        return inv(self.Gm)
+
+    def solve(self, f, tol=0):
+        r = self.Gm.matvec(f)
+        if not np.isfinite(r).all():
+            # singular; reset the Jacobian approximation
+            self.setup(self.last_x, self.last_f, self.func)
+            return self.Gm.matvec(f)
+        return r
+
+    def matvec(self, f):
+        return self.Gm.solve(f)
+
+    def rsolve(self, f, tol=0):
+        return self.Gm.rmatvec(f)
+
+    def rmatvec(self, f):
+        return self.Gm.rsolve(f)
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        self._reduce()  # reduce first to preserve secant condition
+
+        v = self.Gm.rmatvec(dx)
+        c = dx - self.Gm.matvec(df)
+        d = v / vdot(df, v)
+
+        self.Gm.append(c, d)
+
+
+class BroydenSecond(BroydenFirst):
+    """
+    Find a root of a function, using Broyden\'s second Jacobian approximation.
+
+    This method is also known as \"Broyden's bad method\".
+
+    Parameters
+    ----------
+    %(params_basic)s
+    %(broyden_params)s
+    %(params_extra)s
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='broyden2'`` in particular.
+
+    Notes
+    -----
+    This algorithm implements the inverse Jacobian Quasi-Newton update
+
+    .. math:: H_+ = H + (dx - H df) df^\\dagger / ( df^\\dagger df)
+
+    corresponding to Broyden's second method.
+
+    References
+    ----------
+    .. [1] B.A. van der Rotten, PhD thesis,
+       \"A limited memory Broyden method to solve high-dimensional
+       systems of nonlinear equations\". Mathematisch Instituut,
+       Universiteit Leiden, The Netherlands (2003).
+
+       https://web.archive.org/web/20161022015821/http://www.math.leidenuniv.nl/scripties/Rotten.pdf
+
+    Examples
+    --------
+    The following functions define a system of nonlinear equations
+
+    >>> def fun(x):
+    ...     return [x[0]  + 0.5 * (x[0] - x[1])**3 - 1.0,
+    ...             0.5 * (x[1] - x[0])**3 + x[1]]
+
+    A solution can be obtained as follows.
+
+    >>> from scipy import optimize
+    >>> sol = optimize.broyden2(fun, [0, 0])
+    >>> sol
+    array([0.84116365, 0.15883529])
+
+    """
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        self._reduce()  # reduce first to preserve secant condition
+
+        v = df
+        c = dx - self.Gm.matvec(df)
+        d = v / df_norm**2
+        self.Gm.append(c, d)
+
+
+#------------------------------------------------------------------------------
+# Broyden-like (restricted memory)
+#------------------------------------------------------------------------------
+
+class Anderson(GenericBroyden):
+    """
+    Find a root of a function, using (extended) Anderson mixing.
+
+    The Jacobian is formed by for a 'best' solution in the space
+    spanned by last `M` vectors. As a result, only a MxM matrix
+    inversions and MxN multiplications are required. [Ey]_
+
+    Parameters
+    ----------
+    %(params_basic)s
+    alpha : float, optional
+        Initial guess for the Jacobian is (-1/alpha).
+    M : float, optional
+        Number of previous vectors to retain. Defaults to 5.
+    w0 : float, optional
+        Regularization parameter for numerical stability.
+        Compared to unity, good values of the order of 0.01.
+    %(params_extra)s
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='anderson'`` in particular.
+
+    References
+    ----------
+    .. [Ey] V. Eyert, J. Comp. Phys., 124, 271 (1996).
+
+    Examples
+    --------
+    The following functions define a system of nonlinear equations
+
+    >>> def fun(x):
+    ...     return [x[0]  + 0.5 * (x[0] - x[1])**3 - 1.0,
+    ...             0.5 * (x[1] - x[0])**3 + x[1]]
+
+    A solution can be obtained as follows.
+
+    >>> from scipy import optimize
+    >>> sol = optimize.anderson(fun, [0, 0])
+    >>> sol
+    array([0.84116588, 0.15883789])
+
+    """
+
+    # Note:
+    #
+    # Anderson method maintains a rank M approximation of the inverse Jacobian,
+    #
+    #     J^-1 v ~ -v*alpha + (dX + alpha dF) A^-1 dF^H v
+    #     A      = W + dF^H dF
+    #     W      = w0^2 diag(dF^H dF)
+    #
+    # so that for w0 = 0 the secant condition applies for last M iterates, i.e.,
+    #
+    #     J^-1 df_j = dx_j
+    #
+    # for all j = 0 ... M-1.
+    #
+    # Moreover, (from Sherman-Morrison-Woodbury formula)
+    #
+    #    J v ~ [ b I - b^2 C (I + b dF^H A^-1 C)^-1 dF^H ] v
+    #    C   = (dX + alpha dF) A^-1
+    #    b   = -1/alpha
+    #
+    # and after simplification
+    #
+    #    J v ~ -v/alpha + (dX/alpha + dF) (dF^H dX - alpha W)^-1 dF^H v
+    #
+
+    def __init__(self, alpha=None, w0=0.01, M=5):
+        GenericBroyden.__init__(self)
+        self.alpha = alpha
+        self.M = M
+        self.dx = []
+        self.df = []
+        self.gamma = None
+        self.w0 = w0
+
+    def solve(self, f, tol=0):
+        dx = -self.alpha*f
+
+        n = len(self.dx)
+        if n == 0:
+            return dx
+
+        df_f = np.empty(n, dtype=f.dtype)
+        for k in range(n):
+            df_f[k] = vdot(self.df[k], f)
+
+        try:
+            gamma = solve(self.a, df_f)
+        except LinAlgError:
+            # singular; reset the Jacobian approximation
+            del self.dx[:]
+            del self.df[:]
+            return dx
+
+        for m in range(n):
+            dx += gamma[m]*(self.dx[m] + self.alpha*self.df[m])
+        return dx
+
+    def matvec(self, f):
+        dx = -f/self.alpha
+
+        n = len(self.dx)
+        if n == 0:
+            return dx
+
+        df_f = np.empty(n, dtype=f.dtype)
+        for k in range(n):
+            df_f[k] = vdot(self.df[k], f)
+
+        b = np.empty((n, n), dtype=f.dtype)
+        for i in range(n):
+            for j in range(n):
+                b[i,j] = vdot(self.df[i], self.dx[j])
+                if i == j and self.w0 != 0:
+                    b[i,j] -= vdot(self.df[i], self.df[i])*self.w0**2*self.alpha
+        gamma = solve(b, df_f)
+
+        for m in range(n):
+            dx += gamma[m]*(self.df[m] + self.dx[m]/self.alpha)
+        return dx
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        if self.M == 0:
+            return
+
+        self.dx.append(dx)
+        self.df.append(df)
+
+        while len(self.dx) > self.M:
+            self.dx.pop(0)
+            self.df.pop(0)
+
+        n = len(self.dx)
+        a = np.zeros((n, n), dtype=f.dtype)
+
+        for i in range(n):
+            for j in range(i, n):
+                if i == j:
+                    wd = self.w0**2
+                else:
+                    wd = 0
+                a[i,j] = (1+wd)*vdot(self.df[i], self.df[j])
+
+        a += np.triu(a, 1).T.conj()
+        self.a = a
+
+#------------------------------------------------------------------------------
+# Simple iterations
+#------------------------------------------------------------------------------
+
+
+class DiagBroyden(GenericBroyden):
+    """
+    Find a root of a function, using diagonal Broyden Jacobian approximation.
+
+    The Jacobian approximation is derived from previous iterations, by
+    retaining only the diagonal of Broyden matrices.
+
+    .. warning::
+
+       This algorithm may be useful for specific problems, but whether
+       it will work may depend strongly on the problem.
+
+    Parameters
+    ----------
+    %(params_basic)s
+    alpha : float, optional
+        Initial guess for the Jacobian is (-1/alpha).
+    %(params_extra)s
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='diagbroyden'`` in particular.
+
+    Examples
+    --------
+    The following functions define a system of nonlinear equations
+
+    >>> def fun(x):
+    ...     return [x[0]  + 0.5 * (x[0] - x[1])**3 - 1.0,
+    ...             0.5 * (x[1] - x[0])**3 + x[1]]
+
+    A solution can be obtained as follows.
+
+    >>> from scipy import optimize
+    >>> sol = optimize.diagbroyden(fun, [0, 0])
+    >>> sol
+    array([0.84116403, 0.15883384])
+
+    """
+
+    def __init__(self, alpha=None):
+        GenericBroyden.__init__(self)
+        self.alpha = alpha
+
+    def setup(self, x, F, func):
+        GenericBroyden.setup(self, x, F, func)
+        self.d = np.full((self.shape[0],), 1 / self.alpha, dtype=self.dtype)
+
+    def solve(self, f, tol=0):
+        return -f / self.d
+
+    def matvec(self, f):
+        return -f * self.d
+
+    def rsolve(self, f, tol=0):
+        return -f / self.d.conj()
+
+    def rmatvec(self, f):
+        return -f * self.d.conj()
+
+    def todense(self):
+        return np.diag(-self.d)
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        self.d -= (df + self.d*dx)*dx/dx_norm**2
+
+
+class LinearMixing(GenericBroyden):
+    """
+    Find a root of a function, using a scalar Jacobian approximation.
+
+    .. warning::
+
+       This algorithm may be useful for specific problems, but whether
+       it will work may depend strongly on the problem.
+
+    Parameters
+    ----------
+    %(params_basic)s
+    alpha : float, optional
+        The Jacobian approximation is (-1/alpha).
+    %(params_extra)s
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='linearmixing'`` in particular.
+
+    """
+
+    def __init__(self, alpha=None):
+        GenericBroyden.__init__(self)
+        self.alpha = alpha
+
+    def solve(self, f, tol=0):
+        return -f*self.alpha
+
+    def matvec(self, f):
+        return -f/self.alpha
+
+    def rsolve(self, f, tol=0):
+        return -f*np.conj(self.alpha)
+
+    def rmatvec(self, f):
+        return -f/np.conj(self.alpha)
+
+    def todense(self):
+        return np.diag(np.full(self.shape[0], -1/self.alpha))
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        pass
+
+
+class ExcitingMixing(GenericBroyden):
+    """
+    Find a root of a function, using a tuned diagonal Jacobian approximation.
+
+    The Jacobian matrix is diagonal and is tuned on each iteration.
+
+    .. warning::
+
+       This algorithm may be useful for specific problems, but whether
+       it will work may depend strongly on the problem.
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='excitingmixing'`` in particular.
+
+    Parameters
+    ----------
+    %(params_basic)s
+    alpha : float, optional
+        Initial Jacobian approximation is (-1/alpha).
+    alphamax : float, optional
+        The entries of the diagonal Jacobian are kept in the range
+        ``[alpha, alphamax]``.
+    %(params_extra)s
+    """
+
+    def __init__(self, alpha=None, alphamax=1.0):
+        GenericBroyden.__init__(self)
+        self.alpha = alpha
+        self.alphamax = alphamax
+        self.beta = None
+
+    def setup(self, x, F, func):
+        GenericBroyden.setup(self, x, F, func)
+        self.beta = np.full((self.shape[0],), self.alpha, dtype=self.dtype)
+
+    def solve(self, f, tol=0):
+        return -f*self.beta
+
+    def matvec(self, f):
+        return -f/self.beta
+
+    def rsolve(self, f, tol=0):
+        return -f*self.beta.conj()
+
+    def rmatvec(self, f):
+        return -f/self.beta.conj()
+
+    def todense(self):
+        return np.diag(-1/self.beta)
+
+    def _update(self, x, f, dx, df, dx_norm, df_norm):
+        incr = f*self.last_f > 0
+        self.beta[incr] += self.alpha
+        self.beta[~incr] = self.alpha
+        np.clip(self.beta, 0, self.alphamax, out=self.beta)
+
+
+#------------------------------------------------------------------------------
+# Iterative/Krylov approximated Jacobians
+#------------------------------------------------------------------------------
+
+class KrylovJacobian(Jacobian):
+    r"""
+    Find a root of a function, using Krylov approximation for inverse Jacobian.
+
+    This method is suitable for solving large-scale problems.
+
+    Parameters
+    ----------
+    %(params_basic)s
+    rdiff : float, optional
+        Relative step size to use in numerical differentiation.
+    method : str or callable, optional
+        Krylov method to use to approximate the Jacobian.  Can be a string,
+        or a function implementing the same interface as the iterative
+        solvers in `scipy.sparse.linalg`. If a string, needs to be one of:
+        ``'lgmres'``, ``'gmres'``, ``'bicgstab'``, ``'cgs'``, ``'minres'``,
+        ``'tfqmr'``.
+
+        The default is `scipy.sparse.linalg.lgmres`.
+    inner_maxiter : int, optional
+        Parameter to pass to the "inner" Krylov solver: maximum number of
+        iterations. Iteration will stop after maxiter steps even if the
+        specified tolerance has not been achieved.
+    inner_M : LinearOperator or InverseJacobian
+        Preconditioner for the inner Krylov iteration.
+        Note that you can use also inverse Jacobians as (adaptive)
+        preconditioners. For example,
+
+        >>> from scipy.optimize import BroydenFirst, KrylovJacobian
+        >>> from scipy.optimize import InverseJacobian
+        >>> jac = BroydenFirst()
+        >>> kjac = KrylovJacobian(inner_M=InverseJacobian(jac))
+
+        If the preconditioner has a method named 'update', it will be called
+        as ``update(x, f)`` after each nonlinear step, with ``x`` giving
+        the current point, and ``f`` the current function value.
+    outer_k : int, optional
+        Size of the subspace kept across LGMRES nonlinear iterations.
+        See `scipy.sparse.linalg.lgmres` for details.
+    inner_kwargs : kwargs
+        Keyword parameters for the "inner" Krylov solver
+        (defined with `method`). Parameter names must start with
+        the `inner_` prefix which will be stripped before passing on
+        the inner method. See, e.g., `scipy.sparse.linalg.gmres` for details.
+    %(params_extra)s
+
+    See Also
+    --------
+    root : Interface to root finding algorithms for multivariate
+           functions. See ``method='krylov'`` in particular.
+    scipy.sparse.linalg.gmres
+    scipy.sparse.linalg.lgmres
+
+    Notes
+    -----
+    This function implements a Newton-Krylov solver. The basic idea is
+    to compute the inverse of the Jacobian with an iterative Krylov
+    method. These methods require only evaluating the Jacobian-vector
+    products, which are conveniently approximated by a finite difference:
+
+    .. math:: J v \approx (f(x + \omega*v/|v|) - f(x)) / \omega
+
+    Due to the use of iterative matrix inverses, these methods can
+    deal with large nonlinear problems.
+
+    SciPy's `scipy.sparse.linalg` module offers a selection of Krylov
+    solvers to choose from. The default here is `lgmres`, which is a
+    variant of restarted GMRES iteration that reuses some of the
+    information obtained in the previous Newton steps to invert
+    Jacobians in subsequent steps.
+
+    For a review on Newton-Krylov methods, see for example [1]_,
+    and for the LGMRES sparse inverse method, see [2]_.
+
+    References
+    ----------
+    .. [1] C. T. Kelley, Solving Nonlinear Equations with Newton's Method,
+           SIAM, pp.57-83, 2003.
+           :doi:`10.1137/1.9780898718898.ch3`
+    .. [2] D.A. Knoll and D.E. Keyes, J. Comp. Phys. 193, 357 (2004).
+           :doi:`10.1016/j.jcp.2003.08.010`
+    .. [3] A.H. Baker and E.R. Jessup and T. Manteuffel,
+           SIAM J. Matrix Anal. Appl. 26, 962 (2005).
+           :doi:`10.1137/S0895479803422014`
+
+    Examples
+    --------
+    The following functions define a system of nonlinear equations
+
+    >>> def fun(x):
+    ...     return [x[0] + 0.5 * x[1] - 1.0,
+    ...             0.5 * (x[1] - x[0]) ** 2]
+
+    A solution can be obtained as follows.
+
+    >>> from scipy import optimize
+    >>> sol = optimize.newton_krylov(fun, [0, 0])
+    >>> sol
+    array([0.66731771, 0.66536458])
+
+    """
+
+    def __init__(self, rdiff=None, method='lgmres', inner_maxiter=20,
+                 inner_M=None, outer_k=10, **kw):
+        self.preconditioner = inner_M
+        self.rdiff = rdiff
+        # Note that this retrieves one of the named functions, or otherwise
+        # uses `method` as is (i.e., for a user-provided callable).
+        self.method = dict(
+            bicgstab=scipy.sparse.linalg.bicgstab,
+            gmres=scipy.sparse.linalg.gmres,
+            lgmres=scipy.sparse.linalg.lgmres,
+            cgs=scipy.sparse.linalg.cgs,
+            minres=scipy.sparse.linalg.minres,
+            tfqmr=scipy.sparse.linalg.tfqmr,
+            ).get(method, method)
+
+        self.method_kw = dict(maxiter=inner_maxiter, M=self.preconditioner)
+
+        if self.method is scipy.sparse.linalg.gmres:
+            # Replace GMRES's outer iteration with Newton steps
+            self.method_kw['restart'] = inner_maxiter
+            self.method_kw['maxiter'] = 1
+            self.method_kw.setdefault('atol', 0)
+        elif self.method in (scipy.sparse.linalg.gcrotmk,
+                             scipy.sparse.linalg.bicgstab,
+                             scipy.sparse.linalg.cgs):
+            self.method_kw.setdefault('atol', 0)
+        elif self.method is scipy.sparse.linalg.lgmres:
+            self.method_kw['outer_k'] = outer_k
+            # Replace LGMRES's outer iteration with Newton steps
+            self.method_kw['maxiter'] = 1
+            # Carry LGMRES's `outer_v` vectors across nonlinear iterations
+            self.method_kw.setdefault('outer_v', [])
+            self.method_kw.setdefault('prepend_outer_v', True)
+            # But don't carry the corresponding Jacobian*v products, in case
+            # the Jacobian changes a lot in the nonlinear step
+            #
+            # XXX: some trust-region inspired ideas might be more efficient...
+            #      See e.g., Brown & Saad. But needs to be implemented separately
+            #      since it's not an inexact Newton method.
+            self.method_kw.setdefault('store_outer_Av', False)
+            self.method_kw.setdefault('atol', 0)
+
+        for key, value in kw.items():
+            if not key.startswith('inner_'):
+                raise ValueError("Unknown parameter %s" % key)
+            self.method_kw[key[6:]] = value
+
+    def _update_diff_step(self):
+        mx = abs(self.x0).max()
+        mf = abs(self.f0).max()
+        self.omega = self.rdiff * max(1, mx) / max(1, mf)
+
+    def matvec(self, v):
+        nv = norm(v)
+        if nv == 0:
+            return 0*v
+        sc = self.omega / nv
+        r = (self.func(self.x0 + sc*v) - self.f0) / sc
+        if not np.all(np.isfinite(r)) and np.all(np.isfinite(v)):
+            raise ValueError('Function returned non-finite results')
+        return r
+
+    def solve(self, rhs, tol=0):
+        if 'rtol' in self.method_kw:
+            sol, info = self.method(self.op, rhs, **self.method_kw)
+        else:
+            sol, info = self.method(self.op, rhs, rtol=tol, **self.method_kw)
+        return sol
+
+    def update(self, x, f):
+        self.x0 = x
+        self.f0 = f
+        self._update_diff_step()
+
+        # Update also the preconditioner, if possible
+        if self.preconditioner is not None:
+            if hasattr(self.preconditioner, 'update'):
+                self.preconditioner.update(x, f)
+
+    def setup(self, x, f, func):
+        Jacobian.setup(self, x, f, func)
+        self.x0 = x
+        self.f0 = f
+        self.op = scipy.sparse.linalg.aslinearoperator(self)
+
+        if self.rdiff is None:
+            self.rdiff = np.finfo(x.dtype).eps ** (1./2)
+
+        self._update_diff_step()
+
+        # Setup also the preconditioner, if possible
+        if self.preconditioner is not None:
+            if hasattr(self.preconditioner, 'setup'):
+                self.preconditioner.setup(x, f, func)
+
+
+#------------------------------------------------------------------------------
+# Wrapper functions
+#------------------------------------------------------------------------------
+
+def _nonlin_wrapper(name, jac):
+    """
+    Construct a solver wrapper with given name and Jacobian approx.
+
+    It inspects the keyword arguments of ``jac.__init__``, and allows to
+    use the same arguments in the wrapper function, in addition to the
+    keyword arguments of `nonlin_solve`
+
+    """
+    signature = _getfullargspec(jac.__init__)
+    args, varargs, varkw, defaults, kwonlyargs, kwdefaults, _ = signature
+    kwargs = list(zip(args[-len(defaults):], defaults))
+    kw_str = ", ".join([f"{k}={v!r}" for k, v in kwargs])
+    if kw_str:
+        kw_str = ", " + kw_str
+    kwkw_str = ", ".join([f"{k}={k}" for k, v in kwargs])
+    if kwkw_str:
+        kwkw_str = kwkw_str + ", "
+    if kwonlyargs:
+        raise ValueError('Unexpected signature %s' % signature)
+
+    # Construct the wrapper function so that its keyword arguments
+    # are visible in pydoc.help etc.
+    wrapper = """
+def %(name)s(F, xin, iter=None %(kw)s, verbose=False, maxiter=None,
+             f_tol=None, f_rtol=None, x_tol=None, x_rtol=None,
+             tol_norm=None, line_search='armijo', callback=None, **kw):
+    jac = %(jac)s(%(kwkw)s **kw)
+    return nonlin_solve(F, xin, jac, iter, verbose, maxiter,
+                        f_tol, f_rtol, x_tol, x_rtol, tol_norm, line_search,
+                        callback)
+"""
+
+    wrapper = wrapper % dict(name=name, kw=kw_str, jac=jac.__name__,
+                             kwkw=kwkw_str)
+    ns = {}
+    ns.update(globals())
+    exec(wrapper, ns)
+    func = ns[name]
+    func.__doc__ = jac.__doc__
+    _set_doc(func)
+    return func
+
+
+broyden1 = _nonlin_wrapper('broyden1', BroydenFirst)
+broyden2 = _nonlin_wrapper('broyden2', BroydenSecond)
+anderson = _nonlin_wrapper('anderson', Anderson)
+linearmixing = _nonlin_wrapper('linearmixing', LinearMixing)
+diagbroyden = _nonlin_wrapper('diagbroyden', DiagBroyden)
+excitingmixing = _nonlin_wrapper('excitingmixing', ExcitingMixing)
+newton_krylov = _nonlin_wrapper('newton_krylov', KrylovJacobian)

vila/lib/python3.10/site-packages/scipy/optimize/_numdiff.py

@@ -0,0 +1,779 @@
+"""Routines for numerical differentiation."""
+import functools
+import numpy as np
+from numpy.linalg import norm
+
+from scipy.sparse.linalg import LinearOperator
+from ..sparse import issparse, csc_matrix, csr_matrix, coo_matrix, find
+from ._group_columns import group_dense, group_sparse
+from scipy._lib._array_api import atleast_nd, array_namespace
+
+
+def _adjust_scheme_to_bounds(x0, h, num_steps, scheme, lb, ub):
+    """Adjust final difference scheme to the presence of bounds.
+
+    Parameters
+    ----------
+    x0 : ndarray, shape (n,)
+        Point at which we wish to estimate derivative.
+    h : ndarray, shape (n,)
+        Desired absolute finite difference steps.
+    num_steps : int
+        Number of `h` steps in one direction required to implement finite
+        difference scheme. For example, 2 means that we need to evaluate
+        f(x0 + 2 * h) or f(x0 - 2 * h)
+    scheme : {'1-sided', '2-sided'}
+        Whether steps in one or both directions are required. In other
+        words '1-sided' applies to forward and backward schemes, '2-sided'
+        applies to center schemes.
+    lb : ndarray, shape (n,)
+        Lower bounds on independent variables.
+    ub : ndarray, shape (n,)
+        Upper bounds on independent variables.
+
+    Returns
+    -------
+    h_adjusted : ndarray, shape (n,)
+        Adjusted absolute step sizes. Step size decreases only if a sign flip
+        or switching to one-sided scheme doesn't allow to take a full step.
+    use_one_sided : ndarray of bool, shape (n,)
+        Whether to switch to one-sided scheme. Informative only for
+        ``scheme='2-sided'``.
+    """
+    if scheme == '1-sided':
+        use_one_sided = np.ones_like(h, dtype=bool)
+    elif scheme == '2-sided':
+        h = np.abs(h)
+        use_one_sided = np.zeros_like(h, dtype=bool)
+    else:
+        raise ValueError("`scheme` must be '1-sided' or '2-sided'.")
+
+    if np.all((lb == -np.inf) & (ub == np.inf)):
+        return h, use_one_sided
+
+    h_total = h * num_steps
+    h_adjusted = h.copy()
+
+    lower_dist = x0 - lb
+    upper_dist = ub - x0
+
+    if scheme == '1-sided':
+        x = x0 + h_total
+        violated = (x < lb) | (x > ub)
+        fitting = np.abs(h_total) <= np.maximum(lower_dist, upper_dist)
+        h_adjusted[violated & fitting] *= -1
+
+        forward = (upper_dist >= lower_dist) & ~fitting
+        h_adjusted[forward] = upper_dist[forward] / num_steps
+        backward = (upper_dist < lower_dist) & ~fitting
+        h_adjusted[backward] = -lower_dist[backward] / num_steps
+    elif scheme == '2-sided':
+        central = (lower_dist >= h_total) & (upper_dist >= h_total)
+
+        forward = (upper_dist >= lower_dist) & ~central
+        h_adjusted[forward] = np.minimum(
+            h[forward], 0.5 * upper_dist[forward] / num_steps)
+        use_one_sided[forward] = True
+
+        backward = (upper_dist < lower_dist) & ~central
+        h_adjusted[backward] = -np.minimum(
+            h[backward], 0.5 * lower_dist[backward] / num_steps)
+        use_one_sided[backward] = True
+
+        min_dist = np.minimum(upper_dist, lower_dist) / num_steps
+        adjusted_central = (~central & (np.abs(h_adjusted) <= min_dist))
+        h_adjusted[adjusted_central] = min_dist[adjusted_central]
+        use_one_sided[adjusted_central] = False
+
+    return h_adjusted, use_one_sided
+
+
+@functools.lru_cache
+def _eps_for_method(x0_dtype, f0_dtype, method):
+    """
+    Calculates relative EPS step to use for a given data type
+    and numdiff step method.
+
+    Progressively smaller steps are used for larger floating point types.
+
+    Parameters
+    ----------
+    f0_dtype: np.dtype
+        dtype of function evaluation
+
+    x0_dtype: np.dtype
+        dtype of parameter vector
+
+    method: {'2-point', '3-point', 'cs'}
+
+    Returns
+    -------
+    EPS: float
+        relative step size. May be np.float16, np.float32, np.float64
+
+    Notes
+    -----
+    The default relative step will be np.float64. However, if x0 or f0 are
+    smaller floating point types (np.float16, np.float32), then the smallest
+    floating point type is chosen.
+    """
+    # the default EPS value
+    EPS = np.finfo(np.float64).eps
+
+    x0_is_fp = False
+    if np.issubdtype(x0_dtype, np.inexact):
+        # if you're a floating point type then over-ride the default EPS
+        EPS = np.finfo(x0_dtype).eps
+        x0_itemsize = np.dtype(x0_dtype).itemsize
+        x0_is_fp = True
+
+    if np.issubdtype(f0_dtype, np.inexact):
+        f0_itemsize = np.dtype(f0_dtype).itemsize
+        # choose the smallest itemsize between x0 and f0
+        if x0_is_fp and f0_itemsize < x0_itemsize:
+            EPS = np.finfo(f0_dtype).eps
+
+    if method in ["2-point", "cs"]:
+        return EPS**0.5
+    elif method in ["3-point"]:
+        return EPS**(1/3)
+    else:
+        raise RuntimeError("Unknown step method, should be one of "
+                           "{'2-point', '3-point', 'cs'}")
+
+
+def _compute_absolute_step(rel_step, x0, f0, method):
+    """
+    Computes an absolute step from a relative step for finite difference
+    calculation.
+
+    Parameters
+    ----------
+    rel_step: None or array-like
+        Relative step for the finite difference calculation
+    x0 : np.ndarray
+        Parameter vector
+    f0 : np.ndarray or scalar
+    method : {'2-point', '3-point', 'cs'}
+
+    Returns
+    -------
+    h : float
+        The absolute step size
+
+    Notes
+    -----
+    `h` will always be np.float64. However, if `x0` or `f0` are
+    smaller floating point dtypes (e.g. np.float32), then the absolute
+    step size will be calculated from the smallest floating point size.
+    """
+    # this is used instead of np.sign(x0) because we need
+    # sign_x0 to be 1 when x0 == 0.
+    sign_x0 = (x0 >= 0).astype(float) * 2 - 1
+
+    rstep = _eps_for_method(x0.dtype, f0.dtype, method)
+
+    if rel_step is None:
+        abs_step = rstep * sign_x0 * np.maximum(1.0, np.abs(x0))
+    else:
+        # User has requested specific relative steps.
+        # Don't multiply by max(1, abs(x0) because if x0 < 1 then their
+        # requested step is not used.
+        abs_step = rel_step * sign_x0 * np.abs(x0)
+
+        # however we don't want an abs_step of 0, which can happen if
+        # rel_step is 0, or x0 is 0. Instead, substitute a realistic step
+        dx = ((x0 + abs_step) - x0)
+        abs_step = np.where(dx == 0,
+                            rstep * sign_x0 * np.maximum(1.0, np.abs(x0)),
+                            abs_step)
+
+    return abs_step
+
+
+def _prepare_bounds(bounds, x0):
+    """
+    Prepares new-style bounds from a two-tuple specifying the lower and upper
+    limits for values in x0. If a value is not bound then the lower/upper bound
+    will be expected to be -np.inf/np.inf.
+
+    Examples
+    --------
+    >>> _prepare_bounds([(0, 1, 2), (1, 2, np.inf)], [0.5, 1.5, 2.5])
+    (array([0., 1., 2.]), array([ 1.,  2., inf]))
+    """
+    lb, ub = (np.asarray(b, dtype=float) for b in bounds)
+    if lb.ndim == 0:
+        lb = np.resize(lb, x0.shape)
+
+    if ub.ndim == 0:
+        ub = np.resize(ub, x0.shape)
+
+    return lb, ub
+
+
+def group_columns(A, order=0):
+    """Group columns of a 2-D matrix for sparse finite differencing [1]_.
+
+    Two columns are in the same group if in each row at least one of them
+    has zero. A greedy sequential algorithm is used to construct groups.
+
+    Parameters
+    ----------
+    A : array_like or sparse matrix, shape (m, n)
+        Matrix of which to group columns.
+    order : int, iterable of int with shape (n,) or None
+        Permutation array which defines the order of columns enumeration.
+        If int or None, a random permutation is used with `order` used as
+        a random seed. Default is 0, that is use a random permutation but
+        guarantee repeatability.
+
+    Returns
+    -------
+    groups : ndarray of int, shape (n,)
+        Contains values from 0 to n_groups-1, where n_groups is the number
+        of found groups. Each value ``groups[i]`` is an index of a group to
+        which ith column assigned. The procedure was helpful only if
+        n_groups is significantly less than n.
+
+    References
+    ----------
+    .. [1] A. Curtis, M. J. D. Powell, and J. Reid, "On the estimation of
+           sparse Jacobian matrices", Journal of the Institute of Mathematics
+           and its Applications, 13 (1974), pp. 117-120.
+    """
+    if issparse(A):
+        A = csc_matrix(A)
+    else:
+        A = np.atleast_2d(A)
+        A = (A != 0).astype(np.int32)
+
+    if A.ndim != 2:
+        raise ValueError("`A` must be 2-dimensional.")
+
+    m, n = A.shape
+
+    if order is None or np.isscalar(order):
+        rng = np.random.RandomState(order)
+        order = rng.permutation(n)
+    else:
+        order = np.asarray(order)
+        if order.shape != (n,):
+            raise ValueError("`order` has incorrect shape.")
+
+    A = A[:, order]
+
+    if issparse(A):
+        groups = group_sparse(m, n, A.indices, A.indptr)
+    else:
+        groups = group_dense(m, n, A)
+
+    groups[order] = groups.copy()
+
+    return groups
+
+
+def approx_derivative(fun, x0, method='3-point', rel_step=None, abs_step=None,
+                      f0=None, bounds=(-np.inf, np.inf), sparsity=None,
+                      as_linear_operator=False, args=(), kwargs={}):
+    """Compute finite difference approximation of the derivatives of a
+    vector-valued function.
+
+    If a function maps from R^n to R^m, its derivatives form m-by-n matrix
+    called the Jacobian, where an element (i, j) is a partial derivative of
+    f[i] with respect to x[j].
+
+    Parameters
+    ----------
+    fun : callable
+        Function of which to estimate the derivatives. The argument x
+        passed to this function is ndarray of shape (n,) (never a scalar
+        even if n=1). It must return 1-D array_like of shape (m,) or a scalar.
+    x0 : array_like of shape (n,) or float
+        Point at which to estimate the derivatives. Float will be converted
+        to a 1-D array.
+    method : {'3-point', '2-point', 'cs'}, optional
+        Finite difference method to use:
+            - '2-point' - use the first order accuracy forward or backward
+                          difference.
+            - '3-point' - use central difference in interior points and the
+                          second order accuracy forward or backward difference
+                          near the boundary.
+            - 'cs' - use a complex-step finite difference scheme. This assumes
+                     that the user function is real-valued and can be
+                     analytically continued to the complex plane. Otherwise,
+                     produces bogus results.
+    rel_step : None or array_like, optional
+        Relative step size to use. If None (default) the absolute step size is
+        computed as ``h = rel_step * sign(x0) * max(1, abs(x0))``, with
+        `rel_step` being selected automatically, see Notes. Otherwise
+        ``h = rel_step * sign(x0) * abs(x0)``. For ``method='3-point'`` the
+        sign of `h` is ignored. The calculated step size is possibly adjusted
+        to fit into the bounds.
+    abs_step : array_like, optional
+        Absolute step size to use, possibly adjusted to fit into the bounds.
+        For ``method='3-point'`` the sign of `abs_step` is ignored. By default
+        relative steps are used, only if ``abs_step is not None`` are absolute
+        steps used.
+    f0 : None or array_like, optional
+        If not None it is assumed to be equal to ``fun(x0)``, in this case
+        the ``fun(x0)`` is not called. Default is None.
+    bounds : tuple of array_like, optional
+        Lower and upper bounds on independent variables. Defaults to no bounds.
+        Each bound must match the size of `x0` or be a scalar, in the latter
+        case the bound will be the same for all variables. Use it to limit the
+        range of function evaluation. Bounds checking is not implemented
+        when `as_linear_operator` is True.
+    sparsity : {None, array_like, sparse matrix, 2-tuple}, optional
+        Defines a sparsity structure of the Jacobian matrix. If the Jacobian
+        matrix is known to have only few non-zero elements in each row, then
+        it's possible to estimate its several columns by a single function
+        evaluation [3]_. To perform such economic computations two ingredients
+        are required:
+
+        * structure : array_like or sparse matrix of shape (m, n). A zero
+          element means that a corresponding element of the Jacobian
+          identically equals to zero.
+        * groups : array_like of shape (n,). A column grouping for a given
+          sparsity structure, use `group_columns` to obtain it.
+
+        A single array or a sparse matrix is interpreted as a sparsity
+        structure, and groups are computed inside the function. A tuple is
+        interpreted as (structure, groups). If None (default), a standard
+        dense differencing will be used.
+
+        Note, that sparse differencing makes sense only for large Jacobian
+        matrices where each row contains few non-zero elements.
+    as_linear_operator : bool, optional
+        When True the function returns an `scipy.sparse.linalg.LinearOperator`.
+        Otherwise it returns a dense array or a sparse matrix depending on
+        `sparsity`. The linear operator provides an efficient way of computing
+        ``J.dot(p)`` for any vector ``p`` of shape (n,), but does not allow
+        direct access to individual elements of the matrix. By default
+        `as_linear_operator` is False.
+    args, kwargs : tuple and dict, optional
+        Additional arguments passed to `fun`. Both empty by default.
+        The calling signature is ``fun(x, *args, **kwargs)``.
+
+    Returns
+    -------
+    J : {ndarray, sparse matrix, LinearOperator}
+        Finite difference approximation of the Jacobian matrix.
+        If `as_linear_operator` is True returns a LinearOperator
+        with shape (m, n). Otherwise it returns a dense array or sparse
+        matrix depending on how `sparsity` is defined. If `sparsity`
+        is None then a ndarray with shape (m, n) is returned. If
+        `sparsity` is not None returns a csr_matrix with shape (m, n).
+        For sparse matrices and linear operators it is always returned as
+        a 2-D structure, for ndarrays, if m=1 it is returned
+        as a 1-D gradient array with shape (n,).
+
+    See Also
+    --------
+    check_derivative : Check correctness of a function computing derivatives.
+
+    Notes
+    -----
+    If `rel_step` is not provided, it assigned as ``EPS**(1/s)``, where EPS is
+    determined from the smallest floating point dtype of `x0` or `fun(x0)`,
+    ``np.finfo(x0.dtype).eps``, s=2 for '2-point' method and
+    s=3 for '3-point' method. Such relative step approximately minimizes a sum
+    of truncation and round-off errors, see [1]_. Relative steps are used by
+    default. However, absolute steps are used when ``abs_step is not None``.
+    If any of the absolute or relative steps produces an indistinguishable
+    difference from the original `x0`, ``(x0 + dx) - x0 == 0``, then a
+    automatic step size is substituted for that particular entry.
+
+    A finite difference scheme for '3-point' method is selected automatically.
+    The well-known central difference scheme is used for points sufficiently
+    far from the boundary, and 3-point forward or backward scheme is used for
+    points near the boundary. Both schemes have the second-order accuracy in
+    terms of Taylor expansion. Refer to [2]_ for the formulas of 3-point
+    forward and backward difference schemes.
+
+    For dense differencing when m=1 Jacobian is returned with a shape (n,),
+    on the other hand when n=1 Jacobian is returned with a shape (m, 1).
+    Our motivation is the following: a) It handles a case of gradient
+    computation (m=1) in a conventional way. b) It clearly separates these two
+    different cases. b) In all cases np.atleast_2d can be called to get 2-D
+    Jacobian with correct dimensions.
+
+    References
+    ----------
+    .. [1] W. H. Press et. al. "Numerical Recipes. The Art of Scientific
+           Computing. 3rd edition", sec. 5.7.
+
+    .. [2] A. Curtis, M. J. D. Powell, and J. Reid, "On the estimation of
+           sparse Jacobian matrices", Journal of the Institute of Mathematics
+           and its Applications, 13 (1974), pp. 117-120.
+
+    .. [3] B. Fornberg, "Generation of Finite Difference Formulas on
+           Arbitrarily Spaced Grids", Mathematics of Computation 51, 1988.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.optimize._numdiff import approx_derivative
+    >>>
+    >>> def f(x, c1, c2):
+    ...     return np.array([x[0] * np.sin(c1 * x[1]),
+    ...                      x[0] * np.cos(c2 * x[1])])
+    ...
+    >>> x0 = np.array([1.0, 0.5 * np.pi])
+    >>> approx_derivative(f, x0, args=(1, 2))
+    array([[ 1.,  0.],
+           [-1.,  0.]])
+
+    Bounds can be used to limit the region of function evaluation.
+    In the example below we compute left and right derivative at point 1.0.
+
+    >>> def g(x):
+    ...     return x**2 if x >= 1 else x
+    ...
+    >>> x0 = 1.0
+    >>> approx_derivative(g, x0, bounds=(-np.inf, 1.0))
+    array([ 1.])
+    >>> approx_derivative(g, x0, bounds=(1.0, np.inf))
+    array([ 2.])
+    """
+    if method not in ['2-point', '3-point', 'cs']:
+        raise ValueError("Unknown method '%s'. " % method)
+
+    xp = array_namespace(x0)
+    _x = atleast_nd(x0, ndim=1, xp=xp)
+    _dtype = xp.float64
+    if xp.isdtype(_x.dtype, "real floating"):
+        _dtype = _x.dtype
+
+    # promotes to floating
+    x0 = xp.astype(_x, _dtype)
+
+    if x0.ndim > 1:
+        raise ValueError("`x0` must have at most 1 dimension.")
+
+    lb, ub = _prepare_bounds(bounds, x0)
+
+    if lb.shape != x0.shape or ub.shape != x0.shape:
+        raise ValueError("Inconsistent shapes between bounds and `x0`.")
+
+    if as_linear_operator and not (np.all(np.isinf(lb))
+                                   and np.all(np.isinf(ub))):
+        raise ValueError("Bounds not supported when "
+                         "`as_linear_operator` is True.")
+
+    def fun_wrapped(x):
+        # send user function same fp type as x0. (but only if cs is not being
+        # used
+        if xp.isdtype(x.dtype, "real floating"):
+            x = xp.astype(x, x0.dtype)
+
+        f = np.atleast_1d(fun(x, *args, **kwargs))
+        if f.ndim > 1:
+            raise RuntimeError("`fun` return value has "
+                               "more than 1 dimension.")
+        return f
+
+    if f0 is None:
+        f0 = fun_wrapped(x0)
+    else:
+        f0 = np.atleast_1d(f0)
+        if f0.ndim > 1:
+            raise ValueError("`f0` passed has more than 1 dimension.")
+
+    if np.any((x0 < lb) | (x0 > ub)):
+        raise ValueError("`x0` violates bound constraints.")
+
+    if as_linear_operator:
+        if rel_step is None:
+            rel_step = _eps_for_method(x0.dtype, f0.dtype, method)
+
+        return _linear_operator_difference(fun_wrapped, x0,
+                                           f0, rel_step, method)
+    else:
+        # by default we use rel_step
+        if abs_step is None:
+            h = _compute_absolute_step(rel_step, x0, f0, method)
+        else:
+            # user specifies an absolute step
+            sign_x0 = (x0 >= 0).astype(float) * 2 - 1
+            h = abs_step
+
+            # cannot have a zero step. This might happen if x0 is very large
+            # or small. In which case fall back to relative step.
+            dx = ((x0 + h) - x0)
+            h = np.where(dx == 0,
+                         _eps_for_method(x0.dtype, f0.dtype, method) *
+                         sign_x0 * np.maximum(1.0, np.abs(x0)),
+                         h)
+
+        if method == '2-point':
+            h, use_one_sided = _adjust_scheme_to_bounds(
+                x0, h, 1, '1-sided', lb, ub)
+        elif method == '3-point':
+            h, use_one_sided = _adjust_scheme_to_bounds(
+                x0, h, 1, '2-sided', lb, ub)
+        elif method == 'cs':
+            use_one_sided = False
+
+        if sparsity is None:
+            return _dense_difference(fun_wrapped, x0, f0, h,
+                                     use_one_sided, method)
+        else:
+            if not issparse(sparsity) and len(sparsity) == 2:
+                structure, groups = sparsity
+            else:
+                structure = sparsity
+                groups = group_columns(sparsity)
+
+            if issparse(structure):
+                structure = csc_matrix(structure)
+            else:
+                structure = np.atleast_2d(structure)
+
+            groups = np.atleast_1d(groups)
+            return _sparse_difference(fun_wrapped, x0, f0, h,
+                                      use_one_sided, structure,
+                                      groups, method)
+
+
+def _linear_operator_difference(fun, x0, f0, h, method):
+    m = f0.size
+    n = x0.size
+
+    if method == '2-point':
+        def matvec(p):
+            if np.array_equal(p, np.zeros_like(p)):
+                return np.zeros(m)
+            dx = h / norm(p)
+            x = x0 + dx*p
+            df = fun(x) - f0
+            return df / dx
+
+    elif method == '3-point':
+        def matvec(p):
+            if np.array_equal(p, np.zeros_like(p)):
+                return np.zeros(m)
+            dx = 2*h / norm(p)
+            x1 = x0 - (dx/2)*p
+            x2 = x0 + (dx/2)*p
+            f1 = fun(x1)
+            f2 = fun(x2)
+            df = f2 - f1
+            return df / dx
+
+    elif method == 'cs':
+        def matvec(p):
+            if np.array_equal(p, np.zeros_like(p)):
+                return np.zeros(m)
+            dx = h / norm(p)
+            x = x0 + dx*p*1.j
+            f1 = fun(x)
+            df = f1.imag
+            return df / dx
+
+    else:
+        raise RuntimeError("Never be here.")
+
+    return LinearOperator((m, n), matvec)
+
+
+def _dense_difference(fun, x0, f0, h, use_one_sided, method):
+    m = f0.size
+    n = x0.size
+    J_transposed = np.empty((n, m))
+    x1 = x0.copy()
+    x2 = x0.copy()
+    xc = x0.astype(complex, copy=True)
+
+    for i in range(h.size):
+        if method == '2-point':
+            x1[i] += h[i]
+            dx = x1[i] - x0[i]  # Recompute dx as exactly representable number.
+            df = fun(x1) - f0
+        elif method == '3-point' and use_one_sided[i]:
+            x1[i] += h[i]
+            x2[i] += 2 * h[i]
+            dx = x2[i] - x0[i]
+            f1 = fun(x1)
+            f2 = fun(x2)
+            df = -3.0 * f0 + 4 * f1 - f2
+        elif method == '3-point' and not use_one_sided[i]:
+            x1[i] -= h[i]
+            x2[i] += h[i]
+            dx = x2[i] - x1[i]
+            f1 = fun(x1)
+            f2 = fun(x2)
+            df = f2 - f1
+        elif method == 'cs':
+            xc[i] += h[i] * 1.j
+            f1 = fun(xc)
+            df = f1.imag
+            dx = h[i]
+        else:
+            raise RuntimeError("Never be here.")
+
+        J_transposed[i] = df / dx
+        x1[i] = x2[i] = xc[i] = x0[i]
+
+    if m == 1:
+        J_transposed = np.ravel(J_transposed)
+
+    return J_transposed.T
+
+
+def _sparse_difference(fun, x0, f0, h, use_one_sided,
+                       structure, groups, method):
+    m = f0.size
+    n = x0.size
+    row_indices = []
+    col_indices = []
+    fractions = []
+
+    n_groups = np.max(groups) + 1
+    for group in range(n_groups):
+        # Perturb variables which are in the same group simultaneously.
+        e = np.equal(group, groups)
+        h_vec = h * e
+        if method == '2-point':
+            x = x0 + h_vec
+            dx = x - x0
+            df = fun(x) - f0
+            # The result is  written to columns which correspond to perturbed
+            # variables.
+            cols, = np.nonzero(e)
+            # Find all non-zero elements in selected columns of Jacobian.
+            i, j, _ = find(structure[:, cols])
+            # Restore column indices in the full array.
+            j = cols[j]
+        elif method == '3-point':
+            # Here we do conceptually the same but separate one-sided
+            # and two-sided schemes.
+            x1 = x0.copy()
+            x2 = x0.copy()
+
+            mask_1 = use_one_sided & e
+            x1[mask_1] += h_vec[mask_1]
+            x2[mask_1] += 2 * h_vec[mask_1]
+
+            mask_2 = ~use_one_sided & e
+            x1[mask_2] -= h_vec[mask_2]
+            x2[mask_2] += h_vec[mask_2]
+
+            dx = np.zeros(n)
+            dx[mask_1] = x2[mask_1] - x0[mask_1]
+            dx[mask_2] = x2[mask_2] - x1[mask_2]
+
+            f1 = fun(x1)
+            f2 = fun(x2)
+
+            cols, = np.nonzero(e)
+            i, j, _ = find(structure[:, cols])
+            j = cols[j]
+
+            mask = use_one_sided[j]
+            df = np.empty(m)
+
+            rows = i[mask]
+            df[rows] = -3 * f0[rows] + 4 * f1[rows] - f2[rows]
+
+            rows = i[~mask]
+            df[rows] = f2[rows] - f1[rows]
+        elif method == 'cs':
+            f1 = fun(x0 + h_vec*1.j)
+            df = f1.imag
+            dx = h_vec
+            cols, = np.nonzero(e)
+            i, j, _ = find(structure[:, cols])
+            j = cols[j]
+        else:
+            raise ValueError("Never be here.")
+
+        # All that's left is to compute the fraction. We store i, j and
+        # fractions as separate arrays and later construct coo_matrix.
+        row_indices.append(i)
+        col_indices.append(j)
+        fractions.append(df[i] / dx[j])
+
+    row_indices = np.hstack(row_indices)
+    col_indices = np.hstack(col_indices)
+    fractions = np.hstack(fractions)
+    J = coo_matrix((fractions, (row_indices, col_indices)), shape=(m, n))
+    return csr_matrix(J)
+
+
+def check_derivative(fun, jac, x0, bounds=(-np.inf, np.inf), args=(),
+                     kwargs={}):
+    """Check correctness of a function computing derivatives (Jacobian or
+    gradient) by comparison with a finite difference approximation.
+
+    Parameters
+    ----------
+    fun : callable
+        Function of which to estimate the derivatives. The argument x
+        passed to this function is ndarray of shape (n,) (never a scalar
+        even if n=1). It must return 1-D array_like of shape (m,) or a scalar.
+    jac : callable
+        Function which computes Jacobian matrix of `fun`. It must work with
+        argument x the same way as `fun`. The return value must be array_like
+        or sparse matrix with an appropriate shape.
+    x0 : array_like of shape (n,) or float
+        Point at which to estimate the derivatives. Float will be converted
+        to 1-D array.
+    bounds : 2-tuple of array_like, optional
+        Lower and upper bounds on independent variables. Defaults to no bounds.
+        Each bound must match the size of `x0` or be a scalar, in the latter
+        case the bound will be the same for all variables. Use it to limit the
+        range of function evaluation.
+    args, kwargs : tuple and dict, optional
+        Additional arguments passed to `fun` and `jac`. Both empty by default.
+        The calling signature is ``fun(x, *args, **kwargs)`` and the same
+        for `jac`.
+
+    Returns
+    -------
+    accuracy : float
+        The maximum among all relative errors for elements with absolute values
+        higher than 1 and absolute errors for elements with absolute values
+        less or equal than 1. If `accuracy` is on the order of 1e-6 or lower,
+        then it is likely that your `jac` implementation is correct.
+
+    See Also
+    --------
+    approx_derivative : Compute finite difference approximation of derivative.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.optimize._numdiff import check_derivative
+    >>>
+    >>>
+    >>> def f(x, c1, c2):
+    ...     return np.array([x[0] * np.sin(c1 * x[1]),
+    ...                      x[0] * np.cos(c2 * x[1])])
+    ...
+    >>> def jac(x, c1, c2):
+    ...     return np.array([
+    ...         [np.sin(c1 * x[1]),  c1 * x[0] * np.cos(c1 * x[1])],
+    ...         [np.cos(c2 * x[1]), -c2 * x[0] * np.sin(c2 * x[1])]
+    ...     ])
+    ...
+    >>>
+    >>> x0 = np.array([1.0, 0.5 * np.pi])
+    >>> check_derivative(f, jac, x0, args=(1, 2))
+    2.4492935982947064e-16
+    """
+    J_to_test = jac(x0, *args, **kwargs)
+    if issparse(J_to_test):
+        J_diff = approx_derivative(fun, x0, bounds=bounds, sparsity=J_to_test,
+                                   args=args, kwargs=kwargs)
+        J_to_test = csr_matrix(J_to_test)
+        abs_err = J_to_test - J_diff
+        i, j, abs_err_data = find(abs_err)
+        J_diff_data = np.asarray(J_diff[i, j]).ravel()
+        return np.max(np.abs(abs_err_data) /
+                      np.maximum(1, np.abs(J_diff_data)))
+    else:
+        J_diff = approx_derivative(fun, x0, bounds=bounds,
+                                   args=args, kwargs=kwargs)
+        abs_err = np.abs(J_to_test - J_diff)
+        return np.max(abs_err / np.maximum(1, np.abs(J_diff)))

vila/lib/python3.10/site-packages/scipy/optimize/_pava_pybind.cpython-310-x86_64-linux-gnu.so

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eea00160871368c5807d7825188089b3fdb35c1373133b5b4c504be8a5dc9d2c
+size 223832

vila/lib/python3.10/site-packages/scipy/optimize/_root_scalar.py

@@ -0,0 +1,525 @@
+"""
+Unified interfaces to root finding algorithms for real or complex
+scalar functions.
+
+Functions
+---------
+- root : find a root of a scalar function.
+"""
+import numpy as np
+
+from . import _zeros_py as optzeros
+from ._numdiff import approx_derivative
+
+__all__ = ['root_scalar']
+
+ROOT_SCALAR_METHODS = ['bisect', 'brentq', 'brenth', 'ridder', 'toms748',
+                       'newton', 'secant', 'halley']
+
+
+class MemoizeDer:
+    """Decorator that caches the value and derivative(s) of function each
+    time it is called.
+
+    This is a simplistic memoizer that calls and caches a single value
+    of `f(x, *args)`.
+    It assumes that `args` does not change between invocations.
+    It supports the use case of a root-finder where `args` is fixed,
+    `x` changes, and only rarely, if at all, does x assume the same value
+    more than once."""
+    def __init__(self, fun):
+        self.fun = fun
+        self.vals = None
+        self.x = None
+        self.n_calls = 0
+
+    def __call__(self, x, *args):
+        r"""Calculate f or use cached value if available"""
+        # Derivative may be requested before the function itself, always check
+        if self.vals is None or x != self.x:
+            fg = self.fun(x, *args)
+            self.x = x
+            self.n_calls += 1
+            self.vals = fg[:]
+        return self.vals[0]
+
+    def fprime(self, x, *args):
+        r"""Calculate f' or use a cached value if available"""
+        if self.vals is None or x != self.x:
+            self(x, *args)
+        return self.vals[1]
+
+    def fprime2(self, x, *args):
+        r"""Calculate f'' or use a cached value if available"""
+        if self.vals is None or x != self.x:
+            self(x, *args)
+        return self.vals[2]
+
+    def ncalls(self):
+        return self.n_calls
+
+
+def root_scalar(f, args=(), method=None, bracket=None,
+                fprime=None, fprime2=None,
+                x0=None, x1=None,
+                xtol=None, rtol=None, maxiter=None,
+                options=None):
+    """
+    Find a root of a scalar function.
+
+    Parameters
+    ----------
+    f : callable
+        A function to find a root of.
+    args : tuple, optional
+        Extra arguments passed to the objective function and its derivative(s).
+    method : str, optional
+        Type of solver.  Should be one of
+
+            - 'bisect'    :ref:`(see here) <optimize.root_scalar-bisect>`
+            - 'brentq'    :ref:`(see here) <optimize.root_scalar-brentq>`
+            - 'brenth'    :ref:`(see here) <optimize.root_scalar-brenth>`
+            - 'ridder'    :ref:`(see here) <optimize.root_scalar-ridder>`
+            - 'toms748'    :ref:`(see here) <optimize.root_scalar-toms748>`
+            - 'newton'    :ref:`(see here) <optimize.root_scalar-newton>`
+            - 'secant'    :ref:`(see here) <optimize.root_scalar-secant>`
+            - 'halley'    :ref:`(see here) <optimize.root_scalar-halley>`
+
+    bracket: A sequence of 2 floats, optional
+        An interval bracketing a root.  `f(x, *args)` must have different
+        signs at the two endpoints.
+    x0 : float, optional
+        Initial guess.
+    x1 : float, optional
+        A second guess.
+    fprime : bool or callable, optional
+        If `fprime` is a boolean and is True, `f` is assumed to return the
+        value of the objective function and of the derivative.
+        `fprime` can also be a callable returning the derivative of `f`. In
+        this case, it must accept the same arguments as `f`.
+    fprime2 : bool or callable, optional
+        If `fprime2` is a boolean and is True, `f` is assumed to return the
+        value of the objective function and of the
+        first and second derivatives.
+        `fprime2` can also be a callable returning the second derivative of `f`.
+        In this case, it must accept the same arguments as `f`.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    options : dict, optional
+        A dictionary of solver options. E.g., ``k``, see
+        :obj:`show_options()` for details.
+
+    Returns
+    -------
+    sol : RootResults
+        The solution represented as a ``RootResults`` object.
+        Important attributes are: ``root`` the solution , ``converged`` a
+        boolean flag indicating if the algorithm exited successfully and
+        ``flag`` which describes the cause of the termination. See
+        `RootResults` for a description of other attributes.
+
+    See also
+    --------
+    show_options : Additional options accepted by the solvers
+    root : Find a root of a vector function.
+
+    Notes
+    -----
+    This section describes the available solvers that can be selected by the
+    'method' parameter.
+
+    The default is to use the best method available for the situation
+    presented.
+    If a bracket is provided, it may use one of the bracketing methods.
+    If a derivative and an initial value are specified, it may
+    select one of the derivative-based methods.
+    If no method is judged applicable, it will raise an Exception.
+
+    Arguments for each method are as follows (x=required, o=optional).
+
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    |                    method                     | f | args | bracket | x0 | x1 | fprime | fprime2 | xtol | rtol | maxiter | options |
+    +===============================================+===+======+=========+====+====+========+=========+======+======+=========+=========+
+    | :ref:`bisect <optimize.root_scalar-bisect>`   | x |  o   |    x    |    |    |        |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`brentq <optimize.root_scalar-brentq>`   | x |  o   |    x    |    |    |        |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`brenth <optimize.root_scalar-brenth>`   | x |  o   |    x    |    |    |        |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`ridder <optimize.root_scalar-ridder>`   | x |  o   |    x    |    |    |        |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`toms748 <optimize.root_scalar-toms748>` | x |  o   |    x    |    |    |        |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`secant <optimize.root_scalar-secant>`   | x |  o   |         | x  | o  |        |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`newton <optimize.root_scalar-newton>`   | x |  o   |         | x  |    |   o    |         |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+    | :ref:`halley <optimize.root_scalar-halley>`   | x |  o   |         | x  |    |   x    |    x    |  o   |  o   |    o    |   o     |
+    +-----------------------------------------------+---+------+---------+----+----+--------+---------+------+------+---------+---------+
+
+    Examples
+    --------
+
+    Find the root of a simple cubic
+
+    >>> from scipy import optimize
+    >>> def f(x):
+    ...     return (x**3 - 1)  # only one real root at x = 1
+
+    >>> def fprime(x):
+    ...     return 3*x**2
+
+    The `brentq` method takes as input a bracket
+
+    >>> sol = optimize.root_scalar(f, bracket=[0, 3], method='brentq')
+    >>> sol.root, sol.iterations, sol.function_calls
+    (1.0, 10, 11)
+
+    The `newton` method takes as input a single point and uses the
+    derivative(s).
+
+    >>> sol = optimize.root_scalar(f, x0=0.2, fprime=fprime, method='newton')
+    >>> sol.root, sol.iterations, sol.function_calls
+    (1.0, 11, 22)
+
+    The function can provide the value and derivative(s) in a single call.
+
+    >>> def f_p_pp(x):
+    ...     return (x**3 - 1), 3*x**2, 6*x
+
+    >>> sol = optimize.root_scalar(
+    ...     f_p_pp, x0=0.2, fprime=True, method='newton'
+    ... )
+    >>> sol.root, sol.iterations, sol.function_calls
+    (1.0, 11, 11)
+
+    >>> sol = optimize.root_scalar(
+    ...     f_p_pp, x0=0.2, fprime=True, fprime2=True, method='halley'
+    ... )
+    >>> sol.root, sol.iterations, sol.function_calls
+    (1.0, 7, 8)
+
+
+    """  # noqa: E501
+    if not isinstance(args, tuple):
+        args = (args,)
+
+    if options is None:
+        options = {}
+
+    # fun also returns the derivative(s)
+    is_memoized = False
+    if fprime2 is not None and not callable(fprime2):
+        if bool(fprime2):
+            f = MemoizeDer(f)
+            is_memoized = True
+            fprime2 = f.fprime2
+            fprime = f.fprime
+        else:
+            fprime2 = None
+    if fprime is not None and not callable(fprime):
+        if bool(fprime):
+            f = MemoizeDer(f)
+            is_memoized = True
+            fprime = f.fprime
+        else:
+            fprime = None
+
+    # respect solver-specific default tolerances - only pass in if actually set
+    kwargs = {}
+    for k in ['xtol', 'rtol', 'maxiter']:
+        v = locals().get(k)
+        if v is not None:
+            kwargs[k] = v
+
+    # Set any solver-specific options
+    if options:
+        kwargs.update(options)
+    # Always request full_output from the underlying method as _root_scalar
+    # always returns a RootResults object
+    kwargs.update(full_output=True, disp=False)
+
+    # Pick a method if not specified.
+    # Use the "best" method available for the situation.
+    if not method:
+        if bracket:
+            method = 'brentq'
+        elif x0 is not None:
+            if fprime:
+                if fprime2:
+                    method = 'halley'
+                else:
+                    method = 'newton'
+            elif x1 is not None:
+                method = 'secant'
+            else:
+                method = 'newton'
+    if not method:
+        raise ValueError('Unable to select a solver as neither bracket '
+                         'nor starting point provided.')
+
+    meth = method.lower()
+    map2underlying = {'halley': 'newton', 'secant': 'newton'}
+
+    try:
+        methodc = getattr(optzeros, map2underlying.get(meth, meth))
+    except AttributeError as e:
+        raise ValueError('Unknown solver %s' % meth) from e
+
+    if meth in ['bisect', 'ridder', 'brentq', 'brenth', 'toms748']:
+        if not isinstance(bracket, (list, tuple, np.ndarray)):
+            raise ValueError('Bracket needed for %s' % method)
+
+        a, b = bracket[:2]
+        try:
+            r, sol = methodc(f, a, b, args=args, **kwargs)
+        except ValueError as e:
+            # gh-17622 fixed some bugs in low-level solvers by raising an error
+            # (rather than returning incorrect results) when the callable
+            # returns a NaN. It did so by wrapping the callable rather than
+            # modifying compiled code, so the iteration count is not available.
+            if hasattr(e, "_x"):
+                sol = optzeros.RootResults(root=e._x,
+                                           iterations=np.nan,
+                                           function_calls=e._function_calls,
+                                           flag=str(e), method=method)
+            else:
+                raise
+
+    elif meth in ['secant']:
+        if x0 is None:
+            raise ValueError('x0 must not be None for %s' % method)
+        if 'xtol' in kwargs:
+            kwargs['tol'] = kwargs.pop('xtol')
+        r, sol = methodc(f, x0, args=args, fprime=None, fprime2=None,
+                         x1=x1, **kwargs)
+    elif meth in ['newton']:
+        if x0 is None:
+            raise ValueError('x0 must not be None for %s' % method)
+        if not fprime:
+            # approximate fprime with finite differences
+
+            def fprime(x, *args):
+                # `root_scalar` doesn't actually seem to support vectorized
+                # use of `newton`. In that case, `approx_derivative` will
+                # always get scalar input. Nonetheless, it always returns an
+                # array, so we extract the element to produce scalar output.
+                return approx_derivative(f, x, method='2-point', args=args)[0]
+
+        if 'xtol' in kwargs:
+            kwargs['tol'] = kwargs.pop('xtol')
+        r, sol = methodc(f, x0, args=args, fprime=fprime, fprime2=None,
+                         **kwargs)
+    elif meth in ['halley']:
+        if x0 is None:
+            raise ValueError('x0 must not be None for %s' % method)
+        if not fprime:
+            raise ValueError('fprime must be specified for %s' % method)
+        if not fprime2:
+            raise ValueError('fprime2 must be specified for %s' % method)
+        if 'xtol' in kwargs:
+            kwargs['tol'] = kwargs.pop('xtol')
+        r, sol = methodc(f, x0, args=args, fprime=fprime, fprime2=fprime2, **kwargs)
+    else:
+        raise ValueError('Unknown solver %s' % method)
+
+    if is_memoized:
+        # Replace the function_calls count with the memoized count.
+        # Avoids double and triple-counting.
+        n_calls = f.n_calls
+        sol.function_calls = n_calls
+
+    return sol
+
+
+def _root_scalar_brentq_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    bracket: A sequence of 2 floats, optional
+        An interval bracketing a root.  `f(x, *args)` must have different
+        signs at the two endpoints.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    options: dict, optional
+        Specifies any method-specific options not covered above
+
+    """
+    pass
+
+
+def _root_scalar_brenth_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    bracket: A sequence of 2 floats, optional
+        An interval bracketing a root.  `f(x, *args)` must have different
+        signs at the two endpoints.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass
+
+def _root_scalar_toms748_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    bracket: A sequence of 2 floats, optional
+        An interval bracketing a root.  `f(x, *args)` must have different
+        signs at the two endpoints.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass
+
+
+def _root_scalar_secant_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    x0 : float, required
+        Initial guess.
+    x1 : float, required
+        A second guess.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass
+
+
+def _root_scalar_newton_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function and its derivative.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    x0 : float, required
+        Initial guess.
+    fprime : bool or callable, optional
+        If `fprime` is a boolean and is True, `f` is assumed to return the
+        value of derivative along with the objective function.
+        `fprime` can also be a callable returning the derivative of `f`. In
+        this case, it must accept the same arguments as `f`.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass
+
+
+def _root_scalar_halley_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function and its derivatives.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    x0 : float, required
+        Initial guess.
+    fprime : bool or callable, required
+        If `fprime` is a boolean and is True, `f` is assumed to return the
+        value of derivative along with the objective function.
+        `fprime` can also be a callable returning the derivative of `f`. In
+        this case, it must accept the same arguments as `f`.
+    fprime2 : bool or callable, required
+        If `fprime2` is a boolean and is True, `f` is assumed to return the
+        value of 1st and 2nd derivatives along with the objective function.
+        `fprime2` can also be a callable returning the 2nd derivative of `f`.
+        In this case, it must accept the same arguments as `f`.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass
+
+
+def _root_scalar_ridder_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    bracket: A sequence of 2 floats, optional
+        An interval bracketing a root.  `f(x, *args)` must have different
+        signs at the two endpoints.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass
+
+
+def _root_scalar_bisect_doc():
+    r"""
+    Options
+    -------
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    bracket: A sequence of 2 floats, optional
+        An interval bracketing a root.  `f(x, *args)` must have different
+        signs at the two endpoints.
+    xtol : float, optional
+        Tolerance (absolute) for termination.
+    rtol : float, optional
+        Tolerance (relative) for termination.
+    maxiter : int, optional
+        Maximum number of iterations.
+    options: dict, optional
+        Specifies any method-specific options not covered above.
+
+    """
+    pass

vila/lib/python3.10/site-packages/scipy/optimize/_shgo_lib/_complex.py

@@ -0,0 +1,1225 @@
+"""Base classes for low memory simplicial complex structures."""
+import copy
+import logging
+import itertools
+import decimal
+from functools import cache
+
+import numpy as np
+
+from ._vertex import (VertexCacheField, VertexCacheIndex)
+
+
+class Complex:
+    """
+    Base class for a simplicial complex described as a cache of vertices
+    together with their connections.
+
+    Important methods:
+        Domain triangulation:
+                Complex.triangulate, Complex.split_generation
+        Triangulating arbitrary points (must be traingulable,
+            may exist outside domain):
+                Complex.triangulate(sample_set)
+        Converting another simplicial complex structure data type to the
+            structure used in Complex (ex. OBJ wavefront)
+                Complex.convert(datatype, data)
+
+    Important objects:
+        HC.V: The cache of vertices and their connection
+        HC.H: Storage structure of all vertex groups
+
+    Parameters
+    ----------
+    dim : int
+        Spatial dimensionality of the complex R^dim
+    domain : list of tuples, optional
+        The bounds [x_l, x_u]^dim of the hyperrectangle space
+        ex. The default domain is the hyperrectangle [0, 1]^dim
+        Note: The domain must be convex, non-convex spaces can be cut
+              away from this domain using the non-linear
+              g_cons functions to define any arbitrary domain
+              (these domains may also be disconnected from each other)
+    sfield :
+        A scalar function defined in the associated domain f: R^dim --> R
+    sfield_args : tuple
+        Additional arguments to be passed to `sfield`
+    vfield :
+        A scalar function defined in the associated domain
+                       f: R^dim --> R^m
+                   (for example a gradient function of the scalar field)
+    vfield_args : tuple
+        Additional arguments to be passed to vfield
+    symmetry : None or list
+            Specify if the objective function contains symmetric variables.
+            The search space (and therefore performance) is decreased by up to
+            O(n!) times in the fully symmetric case.
+
+            E.g.  f(x) = (x_1 + x_2 + x_3) + (x_4)**2 + (x_5)**2 + (x_6)**2
+
+            In this equation x_2 and x_3 are symmetric to x_1, while x_5 and
+             x_6 are symmetric to x_4, this can be specified to the solver as:
+
+            symmetry = [0,  # Variable 1
+                        0,  # symmetric to variable 1
+                        0,  # symmetric to variable 1
+                        3,  # Variable 4
+                        3,  # symmetric to variable 4
+                        3,  # symmetric to variable 4
+                        ]
+
+    constraints : dict or sequence of dict, optional
+        Constraints definition.
+        Function(s) ``R**n`` in the form::
+
+            g(x) <= 0 applied as g : R^n -> R^m
+            h(x) == 0 applied as h : R^n -> R^p
+
+        Each constraint is defined in a dictionary with fields:
+
+            type : str
+                Constraint type: 'eq' for equality, 'ineq' for inequality.
+            fun : callable
+                The function defining the constraint.
+            jac : callable, optional
+                The Jacobian of `fun` (only for SLSQP).
+            args : sequence, optional
+                Extra arguments to be passed to the function and Jacobian.
+
+        Equality constraint means that the constraint function result is to
+        be zero whereas inequality means that it is to be
+        non-negative.constraints : dict or sequence of dict, optional
+        Constraints definition.
+        Function(s) ``R**n`` in the form::
+
+            g(x) <= 0 applied as g : R^n -> R^m
+            h(x) == 0 applied as h : R^n -> R^p
+
+        Each constraint is defined in a dictionary with fields:
+
+            type : str
+                Constraint type: 'eq' for equality, 'ineq' for inequality.
+            fun : callable
+                The function defining the constraint.
+            jac : callable, optional
+                The Jacobian of `fun` (unused).
+            args : sequence, optional
+                Extra arguments to be passed to the function and Jacobian.
+
+        Equality constraint means that the constraint function result is to
+        be zero whereas inequality means that it is to be non-negative.
+
+    workers : int  optional
+        Uses `multiprocessing.Pool <multiprocessing>`) to compute the field
+         functions in parallel.
+    """
+    def __init__(self, dim, domain=None, sfield=None, sfield_args=(),
+                 symmetry=None, constraints=None, workers=1):
+        self.dim = dim
+
+        # Domains
+        self.domain = domain
+        if domain is None:
+            self.bounds = [(0.0, 1.0), ] * dim
+        else:
+            self.bounds = domain
+        self.symmetry = symmetry
+        #      here in init to avoid if checks
+
+        # Field functions
+        self.sfield = sfield
+        self.sfield_args = sfield_args
+
+        # Process constraints
+        # Constraints
+        # Process constraint dict sequence:
+        if constraints is not None:
+            self.min_cons = constraints
+            self.g_cons = []
+            self.g_args = []
+            if not isinstance(constraints, (tuple, list)):
+                constraints = (constraints,)
+
+            for cons in constraints:
+                if cons['type'] in ('ineq'):
+                    self.g_cons.append(cons['fun'])
+                    try:
+                        self.g_args.append(cons['args'])
+                    except KeyError:
+                        self.g_args.append(())
+            self.g_cons = tuple(self.g_cons)
+            self.g_args = tuple(self.g_args)
+        else:
+            self.g_cons = None
+            self.g_args = None
+
+        # Homology properties
+        self.gen = 0
+        self.perm_cycle = 0
+
+        # Every cell is stored in a list of its generation,
+        # ex. the initial cell is stored in self.H[0]
+        # 1st get new cells are stored in self.H[1] etc.
+        # When a cell is sub-generated it is removed from this list
+
+        self.H = []  # Storage structure of vertex groups
+
+        # Cache of all vertices
+        if (sfield is not None) or (self.g_cons is not None):
+            # Initiate a vertex cache and an associated field cache, note that
+            # the field case is always initiated inside the vertex cache if an
+            # associated field scalar field is defined:
+            if sfield is not None:
+                self.V = VertexCacheField(field=sfield, field_args=sfield_args,
+                                          g_cons=self.g_cons,
+                                          g_cons_args=self.g_args,
+                                          workers=workers)
+            elif self.g_cons is not None:
+                self.V = VertexCacheField(field=sfield, field_args=sfield_args,
+                                          g_cons=self.g_cons,
+                                          g_cons_args=self.g_args,
+                                          workers=workers)
+        else:
+            self.V = VertexCacheIndex()
+
+        self.V_non_symm = []  # List of non-symmetric vertices
+
+    def __call__(self):
+        return self.H
+
+    # %% Triangulation methods
+    def cyclic_product(self, bounds, origin, supremum, centroid=True):
+        """Generate initial triangulation using cyclic product"""
+        # Define current hyperrectangle
+        vot = tuple(origin)
+        vut = tuple(supremum)  # Hyperrectangle supremum
+        self.V[vot]
+        vo = self.V[vot]
+        yield vo.x
+        self.V[vut].connect(self.V[vot])
+        yield vut
+        # Cyclic group approach with second x_l --- x_u operation.
+
+        # These containers store the "lower" and "upper" vertices
+        # corresponding to the origin or supremum of every C2 group.
+        # It has the structure of `dim` times embedded lists each containing
+        # these vertices as the entire complex grows. Bounds[0] has to be done
+        # outside the loops before we have symmetric containers.
+        # NOTE: This means that bounds[0][1] must always exist
+        C0x = [[self.V[vot]]]
+        a_vo = copy.copy(list(origin))
+        a_vo[0] = vut[0]  # Update aN Origin
+        a_vo = self.V[tuple(a_vo)]
+        # self.V[vot].connect(self.V[tuple(a_vo)])
+        self.V[vot].connect(a_vo)
+        yield a_vo.x
+        C1x = [[a_vo]]
+        # C1x = [[self.V[tuple(a_vo)]]]
+        ab_C = []  # Container for a + b operations
+
+        # Loop over remaining bounds
+        for i, x in enumerate(bounds[1:]):
+            # Update lower and upper containers
+            C0x.append([])
+            C1x.append([])
+            # try to access a second bound (if not, C1 is symmetric)
+            try:
+                # Early try so that we don't have to copy the cache before
+                # moving on to next C1/C2: Try to add the operation of a new
+                # C2 product by accessing the upper bound
+                x[1]
+                # Copy lists for iteration
+                cC0x = [x[:] for x in C0x[:i + 1]]
+                cC1x = [x[:] for x in C1x[:i + 1]]
+                for j, (VL, VU) in enumerate(zip(cC0x, cC1x)):
+                    for k, (vl, vu) in enumerate(zip(VL, VU)):
+                        # Build aN vertices for each lower-upper pair in N:
+                        a_vl = list(vl.x)
+                        a_vu = list(vu.x)
+                        a_vl[i + 1] = vut[i + 1]
+                        a_vu[i + 1] = vut[i + 1]
+                        a_vl = self.V[tuple(a_vl)]
+
+                        # Connect vertices in N to corresponding vertices
+                        # in aN:
+                        vl.connect(a_vl)
+
+                        yield a_vl.x
+
+                        a_vu = self.V[tuple(a_vu)]
+                        # Connect vertices in N to corresponding vertices
+                        # in aN:
+                        vu.connect(a_vu)
+
+                        # Connect new vertex pair in aN:
+                        a_vl.connect(a_vu)
+
+                        # Connect lower pair to upper (triangulation
+                        # operation of a + b (two arbitrary operations):
+                        vl.connect(a_vu)
+                        ab_C.append((vl, a_vu))
+
+                        # Update the containers
+                        C0x[i + 1].append(vl)
+                        C0x[i + 1].append(vu)
+                        C1x[i + 1].append(a_vl)
+                        C1x[i + 1].append(a_vu)
+
+                        # Update old containers
+                        C0x[j].append(a_vl)
+                        C1x[j].append(a_vu)
+
+                        # Yield new points
+                        yield a_vu.x
+
+                # Try to connect aN lower source of previous a + b
+                # operation with a aN vertex
+                ab_Cc = copy.copy(ab_C)
+
+                for vp in ab_Cc:
+                    b_v = list(vp[0].x)
+                    ab_v = list(vp[1].x)
+                    b_v[i + 1] = vut[i + 1]
+                    ab_v[i + 1] = vut[i + 1]
+                    b_v = self.V[tuple(b_v)]  # b + vl
+                    ab_v = self.V[tuple(ab_v)]  # b + a_vl
+                    # Note o---o is already connected
+                    vp[0].connect(ab_v)  # o-s
+                    b_v.connect(ab_v)  # s-s
+
+                    # Add new list of cross pairs
+                    ab_C.append((vp[0], ab_v))
+                    ab_C.append((b_v, ab_v))
+
+            except IndexError:
+                cC0x = C0x[i]
+                cC1x = C1x[i]
+                VL, VU = cC0x, cC1x
+                for k, (vl, vu) in enumerate(zip(VL, VU)):
+                    # Build aN vertices for each lower-upper pair in N:
+                    a_vu = list(vu.x)
+                    a_vu[i + 1] = vut[i + 1]
+                    # Connect vertices in N to corresponding vertices
+                    # in aN:
+                    a_vu = self.V[tuple(a_vu)]
+                    # Connect vertices in N to corresponding vertices
+                    # in aN:
+                    vu.connect(a_vu)
+                    # Connect new vertex pair in aN:
+                    # a_vl.connect(a_vu)
+                    # Connect lower pair to upper (triangulation
+                    # operation of a + b (two arbitrary operations):
+                    vl.connect(a_vu)
+                    ab_C.append((vl, a_vu))
+                    C0x[i + 1].append(vu)
+                    C1x[i + 1].append(a_vu)
+                    # Yield new points
+                    a_vu.connect(self.V[vut])
+                    yield a_vu.x
+                    ab_Cc = copy.copy(ab_C)
+                    for vp in ab_Cc:
+                        if vp[1].x[i] == vut[i]:
+                            ab_v = list(vp[1].x)
+                            ab_v[i + 1] = vut[i + 1]
+                            ab_v = self.V[tuple(ab_v)]  # b + a_vl
+                            # Note o---o is already connected
+                            vp[0].connect(ab_v)  # o-s
+
+                            # Add new list of cross pairs
+                            ab_C.append((vp[0], ab_v))
+
+        # Clean class trash
+        try:
+            del C0x
+            del cC0x
+            del C1x
+            del cC1x
+            del ab_C
+            del ab_Cc
+        except UnboundLocalError:
+            pass
+
+        # Extra yield to ensure that the triangulation is completed
+        if centroid:
+            vo = self.V[vot]
+            vs = self.V[vut]
+            # Disconnect the origin and supremum
+            vo.disconnect(vs)
+            # Build centroid
+            vc = self.split_edge(vot, vut)
+            for v in vo.nn:
+                v.connect(vc)
+            yield vc.x
+            return vc.x
+        else:
+            yield vut
+            return vut
+
+    def triangulate(self, n=None, symmetry=None, centroid=True,
+                    printout=False):
+        """
+        Triangulate the initial domain, if n is not None then a limited number
+        of points will be generated
+
+        Parameters
+        ----------
+        n : int, Number of points to be sampled.
+        symmetry :
+
+            Ex. Dictionary/hashtable
+            f(x) = (x_1 + x_2 + x_3) + (x_4)**2 + (x_5)**2 + (x_6)**2
+
+            symmetry = symmetry[0]: 0,  # Variable 1
+                       symmetry[1]: 0,  # symmetric to variable 1
+                       symmetry[2]: 0,  # symmetric to variable 1
+                       symmetry[3]: 3,  # Variable 4
+                       symmetry[4]: 3,  # symmetric to variable 4
+                       symmetry[5]: 3,  # symmetric to variable 4
+                        }
+        centroid : bool, if True add a central point to the hypercube
+        printout : bool, if True print out results
+
+        NOTES:
+        ------
+        Rather than using the combinatorial algorithm to connect vertices we
+        make the following observation:
+
+        The bound pairs are similar a C2 cyclic group and the structure is
+        formed using the cartesian product:
+
+        H = C2 x C2 x C2 ... x C2 (dim times)
+
+        So construct any normal subgroup N and consider H/N first, we connect
+        all vertices within N (ex. N is C2 (the first dimension), then we move
+        to a left coset aN (an operation moving around the defined H/N group by
+        for example moving from the lower bound in C2 (dimension 2) to the
+        higher bound in C2. During this operation connection all the vertices.
+        Now repeat the N connections. Note that these elements can be connected
+        in parallel.
+        """
+        # Inherit class arguments
+        if symmetry is None:
+            symmetry = self.symmetry
+        # Build origin and supremum vectors
+        origin = [i[0] for i in self.bounds]
+        self.origin = origin
+        supremum = [i[1] for i in self.bounds]
+
+        self.supremum = supremum
+
+        if symmetry is None:
+            cbounds = self.bounds
+        else:
+            cbounds = copy.copy(self.bounds)
+            for i, j in enumerate(symmetry):
+                if i is not j:
+                    # pop second entry on second symmetry vars
+                    cbounds[i] = [self.bounds[symmetry[i]][0]]
+                    # Sole (first) entry is the sup value and there is no
+                    # origin:
+                    cbounds[i] = [self.bounds[symmetry[i]][1]]
+                    if (self.bounds[symmetry[i]] is not
+                            self.bounds[symmetry[j]]):
+                        logging.warning(f"Variable {i} was specified as "
+                                        f"symmetetric to variable {j}, however"
+                                        f", the bounds {i} ="
+                                        f" {self.bounds[symmetry[i]]} and {j}"
+                                        f" ="
+                                        f" {self.bounds[symmetry[j]]} do not "
+                                        f"match, the mismatch was ignored in "
+                                        f"the initial triangulation.")
+                        cbounds[i] = self.bounds[symmetry[j]]
+
+        if n is None:
+            # Build generator
+            self.cp = self.cyclic_product(cbounds, origin, supremum, centroid)
+            for i in self.cp:
+                i
+
+            try:
+                self.triangulated_vectors.append((tuple(self.origin),
+                                                  tuple(self.supremum)))
+            except (AttributeError, KeyError):
+                self.triangulated_vectors = [(tuple(self.origin),
+                                              tuple(self.supremum))]
+
+        else:
+            # Check if generator already exists
+            try:
+                self.cp
+            except (AttributeError, KeyError):
+                self.cp = self.cyclic_product(cbounds, origin, supremum,
+                                              centroid)
+
+            try:
+                while len(self.V.cache) < n:
+                    next(self.cp)
+            except StopIteration:
+                try:
+                    self.triangulated_vectors.append((tuple(self.origin),
+                                                      tuple(self.supremum)))
+                except (AttributeError, KeyError):
+                    self.triangulated_vectors = [(tuple(self.origin),
+                                                  tuple(self.supremum))]
+
+        if printout:
+            # for v in self.C0():
+            #   v.print_out()
+            for v in self.V.cache:
+                self.V[v].print_out()
+
+        return
+
+    def refine(self, n=1):
+        if n is None:
+            try:
+                self.triangulated_vectors
+                self.refine_all()
+                return
+            except AttributeError as ae:
+                if str(ae) == "'Complex' object has no attribute " \
+                              "'triangulated_vectors'":
+                    self.triangulate(symmetry=self.symmetry)
+                    return
+                else:
+                    raise
+
+        nt = len(self.V.cache) + n  # Target number of total vertices
+        # In the outer while loop we iterate until we have added an extra `n`
+        # vertices to the complex:
+        while len(self.V.cache) < nt:  # while loop 1
+            try:  # try 1
+                # Try to access triangulated_vectors, this should only be
+                # defined if an initial triangulation has already been
+                # performed:
+                self.triangulated_vectors
+                # Try a usual iteration of the current generator, if it
+                # does not exist or is exhausted then produce a new generator
+                try:  # try 2
+                    next(self.rls)
+                except (AttributeError, StopIteration, KeyError):
+                    vp = self.triangulated_vectors[0]
+                    self.rls = self.refine_local_space(*vp, bounds=self.bounds)
+                    next(self.rls)
+
+            except (AttributeError, KeyError):
+                # If an initial triangulation has not been completed, then
+                # we start/continue the initial triangulation targeting `nt`
+                # vertices, if nt is greater than the initial number of
+                # vertices then the `refine` routine will move back to try 1.
+                self.triangulate(nt, self.symmetry)
+        return
+
+    def refine_all(self, centroids=True):
+        """Refine the entire domain of the current complex."""
+        try:
+            self.triangulated_vectors
+            tvs = copy.copy(self.triangulated_vectors)
+            for i, vp in enumerate(tvs):
+                self.rls = self.refine_local_space(*vp, bounds=self.bounds)
+                for i in self.rls:
+                    i
+        except AttributeError as ae:
+            if str(ae) == "'Complex' object has no attribute " \
+                          "'triangulated_vectors'":
+                self.triangulate(symmetry=self.symmetry, centroid=centroids)
+            else:
+                raise
+
+        # This adds a centroid to every new sub-domain generated and defined
+        # by self.triangulated_vectors, in addition the vertices ! to complete
+        # the triangulation
+        return
+
+    def refine_local_space(self, origin, supremum, bounds, centroid=1):
+        # Copy for later removal
+        origin_c = copy.copy(origin)
+        supremum_c = copy.copy(supremum)
+
+        # Initiate local variables redefined in later inner `for` loop:
+        vl, vu, a_vu = None, None, None
+
+        # Change the vector orientation so that it is only increasing
+        s_ov = list(origin)
+        s_origin = list(origin)
+        s_sv = list(supremum)
+        s_supremum = list(supremum)
+        for i, vi in enumerate(s_origin):
+            if s_ov[i] > s_sv[i]:
+                s_origin[i] = s_sv[i]
+                s_supremum[i] = s_ov[i]
+
+        vot = tuple(s_origin)
+        vut = tuple(s_supremum)  # Hyperrectangle supremum
+
+        vo = self.V[vot]  # initiate if doesn't exist yet
+        vs = self.V[vut]
+        # Start by finding the old centroid of the new space:
+        vco = self.split_edge(vo.x, vs.x)  # Split in case not centroid arg
+
+        # Find set of extreme vertices in current local space
+        sup_set = copy.copy(vco.nn)
+        # Cyclic group approach with second x_l --- x_u operation.
+
+        # These containers store the "lower" and "upper" vertices
+        # corresponding to the origin or supremum of every C2 group.
+        # It has the structure of `dim` times embedded lists each containing
+        # these vertices as the entire complex grows. Bounds[0] has to be done
+        # outside the loops before we have symmetric containers.
+        # NOTE: This means that bounds[0][1] must always exist
+
+        a_vl = copy.copy(list(vot))
+        a_vl[0] = vut[0]  # Update aN Origin
+        if tuple(a_vl) not in self.V.cache:
+            vo = self.V[vot]  # initiate if doesn't exist yet
+            vs = self.V[vut]
+            # Start by finding the old centroid of the new space:
+            vco = self.split_edge(vo.x, vs.x)  # Split in case not centroid arg
+
+            # Find set of extreme vertices in current local space
+            sup_set = copy.copy(vco.nn)
+            a_vl = copy.copy(list(vot))
+            a_vl[0] = vut[0]  # Update aN Origin
+            a_vl = self.V[tuple(a_vl)]
+        else:
+            a_vl = self.V[tuple(a_vl)]
+
+        c_v = self.split_edge(vo.x, a_vl.x)
+        c_v.connect(vco)
+        yield c_v.x
+        Cox = [[vo]]
+        Ccx = [[c_v]]
+        Cux = [[a_vl]]
+        ab_C = []  # Container for a + b operations
+        s_ab_C = []  # Container for symmetric a + b operations
+
+        # Loop over remaining bounds
+        for i, x in enumerate(bounds[1:]):
+            # Update lower and upper containers
+            Cox.append([])
+            Ccx.append([])
+            Cux.append([])
+            # try to access a second bound (if not, C1 is symmetric)
+            try:
+                t_a_vl = list(vot)
+                t_a_vl[i + 1] = vut[i + 1]
+
+                # New: lists are used anyway, so copy all
+                # %%
+                # Copy lists for iteration
+                cCox = [x[:] for x in Cox[:i + 1]]
+                cCcx = [x[:] for x in Ccx[:i + 1]]
+                cCux = [x[:] for x in Cux[:i + 1]]
+                # Try to connect aN lower source of previous a + b
+                # operation with a aN vertex
+                ab_Cc = copy.copy(ab_C)  # NOTE: We append ab_C in the
+                # (VL, VC, VU) for-loop, but we use the copy of the list in the
+                # ab_Cc for-loop.
+                s_ab_Cc = copy.copy(s_ab_C)
+
+                # Early try so that we don't have to copy the cache before
+                # moving on to next C1/C2: Try to add the operation of a new
+                # C2 product by accessing the upper bound
+                if tuple(t_a_vl) not in self.V.cache:
+                    # Raise error to continue symmetric refine
+                    raise IndexError
+                t_a_vu = list(vut)
+                t_a_vu[i + 1] = vut[i + 1]
+                if tuple(t_a_vu) not in self.V.cache:
+                    # Raise error to continue symmetric refine:
+                    raise IndexError
+
+                for vectors in s_ab_Cc:
+                    # s_ab_C.append([c_vc, vl, vu, a_vu])
+                    bc_vc = list(vectors[0].x)
+                    b_vl = list(vectors[1].x)
+                    b_vu = list(vectors[2].x)
+                    ba_vu = list(vectors[3].x)
+
+                    bc_vc[i + 1] = vut[i + 1]
+                    b_vl[i + 1] = vut[i + 1]
+                    b_vu[i + 1] = vut[i + 1]
+                    ba_vu[i + 1] = vut[i + 1]
+
+                    bc_vc = self.V[tuple(bc_vc)]
+                    bc_vc.connect(vco)  # NOTE: Unneeded?
+                    yield bc_vc
+
+                    # Split to centre, call this centre group "d = 0.5*a"
+                    d_bc_vc = self.split_edge(vectors[0].x, bc_vc.x)
+                    d_bc_vc.connect(bc_vc)
+                    d_bc_vc.connect(vectors[1])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[2])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[3])  # Connect all to centroid
+                    yield d_bc_vc.x
+                    b_vl = self.V[tuple(b_vl)]
+                    bc_vc.connect(b_vl)  # Connect aN cross pairs
+                    d_bc_vc.connect(b_vl)  # Connect all to centroid
+
+                    yield b_vl
+                    b_vu = self.V[tuple(b_vu)]
+                    bc_vc.connect(b_vu)  # Connect aN cross pairs
+                    d_bc_vc.connect(b_vu)  # Connect all to centroid
+
+                    b_vl_c = self.split_edge(b_vu.x, b_vl.x)
+                    bc_vc.connect(b_vl_c)
+
+                    yield b_vu
+                    ba_vu = self.V[tuple(ba_vu)]
+                    bc_vc.connect(ba_vu)  # Connect aN cross pairs
+                    d_bc_vc.connect(ba_vu)  # Connect all to centroid
+
+                    # Split the a + b edge of the initial triangulation:
+                    os_v = self.split_edge(vectors[1].x, ba_vu.x)  # o-s
+                    ss_v = self.split_edge(b_vl.x, ba_vu.x)  # s-s
+                    b_vu_c = self.split_edge(b_vu.x, ba_vu.x)
+                    bc_vc.connect(b_vu_c)
+                    yield os_v.x  # often equal to vco, but not always
+                    yield ss_v.x  # often equal to bc_vu, but not always
+                    yield ba_vu
+                    # Split remaining to centre, call this centre group
+                    # "d = 0.5*a"
+                    d_bc_vc = self.split_edge(vectors[0].x, bc_vc.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    yield d_bc_vc.x
+                    d_b_vl = self.split_edge(vectors[1].x, b_vl.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_b_vl)  # Connect dN cross pairs
+                    yield d_b_vl.x
+                    d_b_vu = self.split_edge(vectors[2].x, b_vu.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_b_vu)  # Connect dN cross pairs
+                    yield d_b_vu.x
+                    d_ba_vu = self.split_edge(vectors[3].x, ba_vu.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_ba_vu)  # Connect dN cross pairs
+                    yield d_ba_vu
+
+                    # comb = [c_vc, vl, vu, a_vl, a_vu,
+                    #       bc_vc, b_vl, b_vu, ba_vl, ba_vu]
+                    comb = [vl, vu, a_vu,
+                            b_vl, b_vu, ba_vu]
+                    comb_iter = itertools.combinations(comb, 2)
+                    for vecs in comb_iter:
+                        self.split_edge(vecs[0].x, vecs[1].x)
+                    # Add new list of cross pairs
+                    ab_C.append((d_bc_vc, vectors[1], b_vl, a_vu, ba_vu))
+                    ab_C.append((d_bc_vc, vl, b_vl, a_vu, ba_vu))  # = prev
+
+                for vectors in ab_Cc:
+                    bc_vc = list(vectors[0].x)
+                    b_vl = list(vectors[1].x)
+                    b_vu = list(vectors[2].x)
+                    ba_vl = list(vectors[3].x)
+                    ba_vu = list(vectors[4].x)
+                    bc_vc[i + 1] = vut[i + 1]
+                    b_vl[i + 1] = vut[i + 1]
+                    b_vu[i + 1] = vut[i + 1]
+                    ba_vl[i + 1] = vut[i + 1]
+                    ba_vu[i + 1] = vut[i + 1]
+                    bc_vc = self.V[tuple(bc_vc)]
+                    bc_vc.connect(vco)  # NOTE: Unneeded?
+                    yield bc_vc
+
+                    # Split to centre, call this centre group "d = 0.5*a"
+                    d_bc_vc = self.split_edge(vectors[0].x, bc_vc.x)
+                    d_bc_vc.connect(bc_vc)
+                    d_bc_vc.connect(vectors[1])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[2])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[3])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[4])  # Connect all to centroid
+                    yield d_bc_vc.x
+                    b_vl = self.V[tuple(b_vl)]
+                    bc_vc.connect(b_vl)  # Connect aN cross pairs
+                    d_bc_vc.connect(b_vl)  # Connect all to centroid
+                    yield b_vl
+                    b_vu = self.V[tuple(b_vu)]
+                    bc_vc.connect(b_vu)  # Connect aN cross pairs
+                    d_bc_vc.connect(b_vu)  # Connect all to centroid
+                    yield b_vu
+                    ba_vl = self.V[tuple(ba_vl)]
+                    bc_vc.connect(ba_vl)  # Connect aN cross pairs
+                    d_bc_vc.connect(ba_vl)  # Connect all to centroid
+                    self.split_edge(b_vu.x, ba_vl.x)
+                    yield ba_vl
+                    ba_vu = self.V[tuple(ba_vu)]
+                    bc_vc.connect(ba_vu)  # Connect aN cross pairs
+                    d_bc_vc.connect(ba_vu)  # Connect all to centroid
+                    # Split the a + b edge of the initial triangulation:
+                    os_v = self.split_edge(vectors[1].x, ba_vu.x)  # o-s
+                    ss_v = self.split_edge(b_vl.x, ba_vu.x)  # s-s
+                    yield os_v.x  # often equal to vco, but not always
+                    yield ss_v.x  # often equal to bc_vu, but not always
+                    yield ba_vu
+                    # Split remaining to centre, call this centre group
+                    # "d = 0.5*a"
+                    d_bc_vc = self.split_edge(vectors[0].x, bc_vc.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    yield d_bc_vc.x
+                    d_b_vl = self.split_edge(vectors[1].x, b_vl.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_b_vl)  # Connect dN cross pairs
+                    yield d_b_vl.x
+                    d_b_vu = self.split_edge(vectors[2].x, b_vu.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_b_vu)  # Connect dN cross pairs
+                    yield d_b_vu.x
+                    d_ba_vl = self.split_edge(vectors[3].x, ba_vl.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_ba_vl)  # Connect dN cross pairs
+                    yield d_ba_vl
+                    d_ba_vu = self.split_edge(vectors[4].x, ba_vu.x)
+                    d_bc_vc.connect(vco)  # NOTE: Unneeded?
+                    d_bc_vc.connect(d_ba_vu)  # Connect dN cross pairs
+                    yield d_ba_vu
+                    c_vc, vl, vu, a_vl, a_vu = vectors
+
+                    comb = [vl, vu, a_vl, a_vu,
+                            b_vl, b_vu, ba_vl, ba_vu]
+                    comb_iter = itertools.combinations(comb, 2)
+                    for vecs in comb_iter:
+                        self.split_edge(vecs[0].x, vecs[1].x)
+
+                    # Add new list of cross pairs
+                    ab_C.append((bc_vc, b_vl, b_vu, ba_vl, ba_vu))
+                    ab_C.append((d_bc_vc, d_b_vl, d_b_vu, d_ba_vl, d_ba_vu))
+                    ab_C.append((d_bc_vc, vectors[1], b_vl, a_vu, ba_vu))
+                    ab_C.append((d_bc_vc, vu, b_vu, a_vl, ba_vl))
+
+                for j, (VL, VC, VU) in enumerate(zip(cCox, cCcx, cCux)):
+                    for k, (vl, vc, vu) in enumerate(zip(VL, VC, VU)):
+                        # Build aN vertices for each lower-upper C3 group in N:
+                        a_vl = list(vl.x)
+                        a_vu = list(vu.x)
+                        a_vl[i + 1] = vut[i + 1]
+                        a_vu[i + 1] = vut[i + 1]
+                        a_vl = self.V[tuple(a_vl)]
+                        a_vu = self.V[tuple(a_vu)]
+                        # Note, build (a + vc) later for consistent yields
+                        # Split the a + b edge of the initial triangulation:
+                        c_vc = self.split_edge(vl.x, a_vu.x)
+                        self.split_edge(vl.x, vu.x)  # Equal to vc
+                        # Build cN vertices for each lower-upper C3 group in N:
+                        c_vc.connect(vco)
+                        c_vc.connect(vc)
+                        c_vc.connect(vl)  # Connect c + ac operations
+                        c_vc.connect(vu)  # Connect c + ac operations
+                        c_vc.connect(a_vl)  # Connect c + ac operations
+                        c_vc.connect(a_vu)  # Connect c + ac operations
+                        yield c_vc.x
+                        c_vl = self.split_edge(vl.x, a_vl.x)
+                        c_vl.connect(vco)
+                        c_vc.connect(c_vl)  # Connect cN group vertices
+                        yield c_vl.x
+                        # yield at end of loop:
+                        c_vu = self.split_edge(vu.x, a_vu.x)
+                        c_vu.connect(vco)
+                        # Connect remaining cN group vertices
+                        c_vc.connect(c_vu)  # Connect cN group vertices
+                        yield c_vu.x
+
+                        a_vc = self.split_edge(a_vl.x, a_vu.x)  # is (a + vc) ?
+                        a_vc.connect(vco)
+                        a_vc.connect(c_vc)
+
+                        # Storage for connecting c + ac operations:
+                        ab_C.append((c_vc, vl, vu, a_vl, a_vu))
+
+                        # Update the containers
+                        Cox[i + 1].append(vl)
+                        Cox[i + 1].append(vc)
+                        Cox[i + 1].append(vu)
+                        Ccx[i + 1].append(c_vl)
+                        Ccx[i + 1].append(c_vc)
+                        Ccx[i + 1].append(c_vu)
+                        Cux[i + 1].append(a_vl)
+                        Cux[i + 1].append(a_vc)
+                        Cux[i + 1].append(a_vu)
+
+                        # Update old containers
+                        Cox[j].append(c_vl)  # !
+                        Cox[j].append(a_vl)
+                        Ccx[j].append(c_vc)  # !
+                        Ccx[j].append(a_vc)  # !
+                        Cux[j].append(c_vu)  # !
+                        Cux[j].append(a_vu)
+
+                        # Yield new points
+                        yield a_vc.x
+
+            except IndexError:
+                for vectors in ab_Cc:
+                    ba_vl = list(vectors[3].x)
+                    ba_vu = list(vectors[4].x)
+                    ba_vl[i + 1] = vut[i + 1]
+                    ba_vu[i + 1] = vut[i + 1]
+                    ba_vu = self.V[tuple(ba_vu)]
+                    yield ba_vu
+                    d_bc_vc = self.split_edge(vectors[1].x, ba_vu.x)  # o-s
+                    yield ba_vu
+                    d_bc_vc.connect(vectors[1])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[2])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[3])  # Connect all to centroid
+                    d_bc_vc.connect(vectors[4])  # Connect all to centroid
+                    yield d_bc_vc.x
+                    ba_vl = self.V[tuple(ba_vl)]
+                    yield ba_vl
+                    d_ba_vl = self.split_edge(vectors[3].x, ba_vl.x)
+                    d_ba_vu = self.split_edge(vectors[4].x, ba_vu.x)
+                    d_ba_vc = self.split_edge(d_ba_vl.x, d_ba_vu.x)
+                    yield d_ba_vl
+                    yield d_ba_vu
+                    yield d_ba_vc
+                    c_vc, vl, vu, a_vl, a_vu = vectors
+                    comb = [vl, vu, a_vl, a_vu,
+                            ba_vl,
+                            ba_vu]
+                    comb_iter = itertools.combinations(comb, 2)
+                    for vecs in comb_iter:
+                        self.split_edge(vecs[0].x, vecs[1].x)
+
+                # Copy lists for iteration
+                cCox = Cox[i]
+                cCcx = Ccx[i]
+                cCux = Cux[i]
+                VL, VC, VU = cCox, cCcx, cCux
+                for k, (vl, vc, vu) in enumerate(zip(VL, VC, VU)):
+                    # Build aN vertices for each lower-upper pair in N:
+                    a_vu = list(vu.x)
+                    a_vu[i + 1] = vut[i + 1]
+
+                    # Connect vertices in N to corresponding vertices
+                    # in aN:
+                    a_vu = self.V[tuple(a_vu)]
+                    yield a_vl.x
+                    # Split the a + b edge of the initial triangulation:
+                    c_vc = self.split_edge(vl.x, a_vu.x)
+                    self.split_edge(vl.x, vu.x)  # Equal to vc
+                    c_vc.connect(vco)
+                    c_vc.connect(vc)
+                    c_vc.connect(vl)  # Connect c + ac operations
+                    c_vc.connect(vu)  # Connect c + ac operations
+                    c_vc.connect(a_vu)  # Connect c + ac operations
+                    yield (c_vc.x)
+                    c_vu = self.split_edge(vu.x,
+                                           a_vu.x)  # yield at end of loop
+                    c_vu.connect(vco)
+                    # Connect remaining cN group vertices
+                    c_vc.connect(c_vu)  # Connect cN group vertices
+                    yield (c_vu.x)
+
+                    # Update the containers
+                    Cox[i + 1].append(vu)
+                    Ccx[i + 1].append(c_vu)
+                    Cux[i + 1].append(a_vu)
+
+                    # Update old containers
+                    s_ab_C.append([c_vc, vl, vu, a_vu])
+
+                    yield a_vu.x
+
+        # Clean class trash
+        try:
+            del Cox
+            del Ccx
+            del Cux
+            del ab_C
+            del ab_Cc
+        except UnboundLocalError:
+            pass
+
+        try:
+            self.triangulated_vectors.remove((tuple(origin_c),
+                                              tuple(supremum_c)))
+        except ValueError:
+            # Turn this into a logging warning?
+            pass
+        # Add newly triangulated vectors:
+        for vs in sup_set:
+            self.triangulated_vectors.append((tuple(vco.x), tuple(vs.x)))
+
+        # Extra yield to ensure that the triangulation is completed
+        if centroid:
+            vcn_set = set()
+            c_nn_lists = []
+            for vs in sup_set:
+                # Build centroid
+                c_nn = self.vpool(vco.x, vs.x)
+                try:
+                    c_nn.remove(vcn_set)
+                except KeyError:
+                    pass
+                c_nn_lists.append(c_nn)
+
+            for c_nn in c_nn_lists:
+                try:
+                    c_nn.remove(vcn_set)
+                except KeyError:
+                    pass
+
+            for vs, c_nn in zip(sup_set, c_nn_lists):
+                # Build centroid
+                vcn = self.split_edge(vco.x, vs.x)
+                vcn_set.add(vcn)
+                try:  # Shouldn't be needed?
+                    c_nn.remove(vcn_set)
+                except KeyError:
+                    pass
+                for vnn in c_nn:
+                    vcn.connect(vnn)
+                yield vcn.x
+        else:
+            pass
+
+        yield vut
+        return
+
+    def refine_star(self, v):
+        """Refine the star domain of a vertex `v`."""
+        # Copy lists before iteration
+        vnn = copy.copy(v.nn)
+        v1nn = []
+        d_v0v1_set = set()
+        for v1 in vnn:
+            v1nn.append(copy.copy(v1.nn))
+
+        for v1, v1nn in zip(vnn, v1nn):
+            vnnu = v1nn.intersection(vnn)
+
+            d_v0v1 = self.split_edge(v.x, v1.x)
+            for o_d_v0v1 in d_v0v1_set:
+                d_v0v1.connect(o_d_v0v1)
+            d_v0v1_set.add(d_v0v1)
+            for v2 in vnnu:
+                d_v1v2 = self.split_edge(v1.x, v2.x)
+                d_v0v1.connect(d_v1v2)
+        return
+
+    @cache
+    def split_edge(self, v1, v2):
+        v1 = self.V[v1]
+        v2 = self.V[v2]
+        # Destroy original edge, if it exists:
+        v1.disconnect(v2)
+        # Compute vertex on centre of edge:
+        try:
+            vct = (v2.x_a - v1.x_a) / 2.0 + v1.x_a
+        except TypeError:  # Allow for decimal operations
+            vct = (v2.x_a - v1.x_a) / decimal.Decimal(2.0) + v1.x_a
+
+        vc = self.V[tuple(vct)]
+        # Connect to original 2 vertices to the new centre vertex
+        vc.connect(v1)
+        vc.connect(v2)
+        return vc
+
+    def vpool(self, origin, supremum):
+        vot = tuple(origin)
+        vst = tuple(supremum)
+        # Initiate vertices in case they don't exist
+        vo = self.V[vot]
+        vs = self.V[vst]
+
+        # Remove origin - supremum disconnect
+
+        # Find the lower/upper bounds of the refinement hyperrectangle
+        bl = list(vot)
+        bu = list(vst)
+        for i, (voi, vsi) in enumerate(zip(vot, vst)):
+            if bl[i] > vsi:
+                bl[i] = vsi
+            if bu[i] < voi:
+                bu[i] = voi
+
+        #      NOTE: This is mostly done with sets/lists because we aren't sure
+        #            how well the numpy arrays will scale to thousands of
+        #             dimensions.
+        vn_pool = set()
+        vn_pool.update(vo.nn)
+        vn_pool.update(vs.nn)
+        cvn_pool = copy.copy(vn_pool)
+        for vn in cvn_pool:
+            for i, xi in enumerate(vn.x):
+                if bl[i] <= xi <= bu[i]:
+                    pass
+                else:
+                    try:
+                        vn_pool.remove(vn)
+                    except KeyError:
+                        pass  # NOTE: Not all neigbouds are in initial pool
+        return vn_pool
+
+    def vf_to_vv(self, vertices, simplices):
+        """
+        Convert a vertex-face mesh to a vertex-vertex mesh used by this class
+
+        Parameters
+        ----------
+        vertices : list
+            Vertices
+        simplices : list
+            Simplices
+        """
+        if self.dim > 1:
+            for s in simplices:
+                edges = itertools.combinations(s, self.dim)
+                for e in edges:
+                    self.V[tuple(vertices[e[0]])].connect(
+                        self.V[tuple(vertices[e[1]])])
+        else:
+            for e in simplices:
+                self.V[tuple(vertices[e[0]])].connect(
+                    self.V[tuple(vertices[e[1]])])
+        return
+
+    def connect_vertex_non_symm(self, v_x, near=None):
+        """
+        Adds a vertex at coords v_x to the complex that is not symmetric to the
+        initial triangulation and sub-triangulation.
+
+        If near is specified (for example; a star domain or collections of
+        cells known to contain v) then only those simplices containd in near
+        will be searched, this greatly speeds up the process.
+
+        If near is not specified this method will search the entire simplicial
+        complex structure.
+
+        Parameters
+        ----------
+        v_x : tuple
+            Coordinates of non-symmetric vertex
+        near : set or list
+            List of vertices, these are points near v to check for
+        """
+        if near is None:
+            star = self.V
+        else:
+            star = near
+        # Create the vertex origin
+        if tuple(v_x) in self.V.cache:
+            if self.V[v_x] in self.V_non_symm:
+                pass
+            else:
+                return
+
+        self.V[v_x]
+        found_nn = False
+        S_rows = []
+        for v in star:
+            S_rows.append(v.x)
+
+        S_rows = np.array(S_rows)
+        A = np.array(S_rows) - np.array(v_x)
+        # Iterate through all the possible simplices of S_rows
+        for s_i in itertools.combinations(range(S_rows.shape[0]),
+                                          r=self.dim + 1):
+            # Check if connected, else s_i is not a simplex
+            valid_simplex = True
+            for i in itertools.combinations(s_i, r=2):
+                # Every combination of vertices must be connected, we check of
+                # the current iteration of all combinations of s_i are
+                # connected we break the loop if it is not.
+                if ((self.V[tuple(S_rows[i[1]])] not in
+                        self.V[tuple(S_rows[i[0]])].nn)
+                    and (self.V[tuple(S_rows[i[0]])] not in
+                         self.V[tuple(S_rows[i[1]])].nn)):
+                    valid_simplex = False
+                    break
+
+            S = S_rows[tuple([s_i])]
+            if valid_simplex:
+                if self.deg_simplex(S, proj=None):
+                    valid_simplex = False
+
+            # If s_i is a valid simplex we can test if v_x is inside si
+            if valid_simplex:
+                # Find the A_j0 value from the precalculated values
+                A_j0 = A[tuple([s_i])]
+                if self.in_simplex(S, v_x, A_j0):
+                    found_nn = True
+                    # breaks the main for loop, s_i is the target simplex:
+                    break
+
+        # Connect the simplex to point
+        if found_nn:
+            for i in s_i:
+                self.V[v_x].connect(self.V[tuple(S_rows[i])])
+        # Attached the simplex to storage for all non-symmetric vertices
+        self.V_non_symm.append(self.V[v_x])
+        # this bool value indicates a successful connection if True:
+        return found_nn
+
+    def in_simplex(self, S, v_x, A_j0=None):
+        """Check if a vector v_x is in simplex `S`.
+
+        Parameters
+        ----------
+        S : array_like
+            Array containing simplex entries of vertices as rows
+        v_x :
+            A candidate vertex
+        A_j0 : array, optional,
+            Allows for A_j0 to be pre-calculated
+
+        Returns
+        -------
+        res : boolean
+            True if `v_x` is in `S`
+        """
+        A_11 = np.delete(S, 0, 0) - S[0]
+
+        sign_det_A_11 = np.sign(np.linalg.det(A_11))
+        if sign_det_A_11 == 0:
+            # NOTE: We keep the variable A_11, but we loop through A_jj
+            # ind=
+            # while sign_det_A_11 == 0:
+            #    A_11 = np.delete(S, ind, 0) - S[ind]
+            #    sign_det_A_11 = np.sign(np.linalg.det(A_11))
+
+            sign_det_A_11 = -1  # TODO: Choose another det of j instead?
+            # TODO: Unlikely to work in many cases
+
+        if A_j0 is None:
+            A_j0 = S - v_x
+
+        for d in range(self.dim + 1):
+            det_A_jj = (-1)**d * sign_det_A_11
+            # TODO: Note that scipy might be faster to add as an optional
+            #       dependency
+            sign_det_A_j0 = np.sign(np.linalg.det(np.delete(A_j0, d,
+                                                                     0)))
+            # TODO: Note if sign_det_A_j0 == then the point is coplanar to the
+            #       current simplex facet, so perhaps return True and attach?
+            if det_A_jj == sign_det_A_j0:
+                continue
+            else:
+                return False
+
+        return True
+
+    def deg_simplex(self, S, proj=None):
+        """Test a simplex S for degeneracy (linear dependence in R^dim).
+
+        Parameters
+        ----------
+        S : np.array
+            Simplex with rows as vertex vectors
+        proj : array, optional,
+            If the projection S[1:] - S[0] is already
+            computed it can be added as an optional argument.
+        """
+        # Strategy: we test all combination of faces, if any of the
+        # determinants are zero then the vectors lie on the same face and is
+        # therefore linearly dependent in the space of R^dim
+        if proj is None:
+            proj = S[1:] - S[0]
+
+        # TODO: Is checking the projection of one vertex against faces of other
+        #       vertices sufficient? Or do we need to check more vertices in
+        #       dimensions higher than 2?
+        # TODO: Literature seems to suggest using proj.T, but why is this
+        #       needed?
+        if np.linalg.det(proj) == 0.0:  # TODO: Repalace with tolerance?
+            return True  # Simplex is degenerate
+        else:
+            return False  # Simplex is not degenerate

vila/lib/python3.10/site-packages/scipy/optimize/_shgo_lib/_vertex.py

@@ -0,0 +1,460 @@
+import collections
+from abc import ABC, abstractmethod
+
+import numpy as np
+
+from scipy._lib._util import MapWrapper
+
+
+class VertexBase(ABC):
+    """
+    Base class for a vertex.
+    """
+    def __init__(self, x, nn=None, index=None):
+        """
+        Initiation of a vertex object.
+
+        Parameters
+        ----------
+        x : tuple or vector
+            The geometric location (domain).
+        nn : list, optional
+            Nearest neighbour list.
+        index : int, optional
+            Index of vertex.
+        """
+        self.x = x
+        self.hash = hash(self.x)  # Save precomputed hash
+
+        if nn is not None:
+            self.nn = set(nn)  # can use .indexupdate to add a new list
+        else:
+            self.nn = set()
+
+        self.index = index
+
+    def __hash__(self):
+        return self.hash
+
+    def __getattr__(self, item):
+        if item not in ['x_a']:
+            raise AttributeError(f"{type(self)} object has no attribute "
+                                 f"'{item}'")
+        if item == 'x_a':
+            self.x_a = np.array(self.x)
+            return self.x_a
+
+    @abstractmethod
+    def connect(self, v):
+        raise NotImplementedError("This method is only implemented with an "
+                                  "associated child of the base class.")
+
+    @abstractmethod
+    def disconnect(self, v):
+        raise NotImplementedError("This method is only implemented with an "
+                                  "associated child of the base class.")
+
+    def star(self):
+        """Returns the star domain ``st(v)`` of the vertex.
+
+        Parameters
+        ----------
+        v :
+            The vertex ``v`` in ``st(v)``
+
+        Returns
+        -------
+        st : set
+            A set containing all the vertices in ``st(v)``
+        """
+        self.st = self.nn
+        self.st.add(self)
+        return self.st
+
+
+class VertexScalarField(VertexBase):
+    """
+    Add homology properties of a scalar field f: R^n --> R associated with
+    the geometry built from the VertexBase class
+    """
+
+    def __init__(self, x, field=None, nn=None, index=None, field_args=(),
+                 g_cons=None, g_cons_args=()):
+        """
+        Parameters
+        ----------
+        x : tuple,
+            vector of vertex coordinates
+        field : callable, optional
+            a scalar field f: R^n --> R associated with the geometry
+        nn : list, optional
+            list of nearest neighbours
+        index : int, optional
+            index of the vertex
+        field_args : tuple, optional
+            additional arguments to be passed to field
+        g_cons : callable, optional
+            constraints on the vertex
+        g_cons_args : tuple, optional
+            additional arguments to be passed to g_cons
+
+        """
+        super().__init__(x, nn=nn, index=index)
+
+        # Note Vertex is only initiated once for all x so only
+        # evaluated once
+        # self.feasible = None
+
+        # self.f is externally defined by the cache to allow parallel
+        # processing
+        # None type that will break arithmetic operations unless defined
+        # self.f = None
+
+        self.check_min = True
+        self.check_max = True
+
+    def connect(self, v):
+        """Connects self to another vertex object v.
+
+        Parameters
+        ----------
+        v : VertexBase or VertexScalarField object
+        """
+        if v is not self and v not in self.nn:
+            self.nn.add(v)
+            v.nn.add(self)
+
+            # Flags for checking homology properties:
+            self.check_min = True
+            self.check_max = True
+            v.check_min = True
+            v.check_max = True
+
+    def disconnect(self, v):
+        if v in self.nn:
+            self.nn.remove(v)
+            v.nn.remove(self)
+
+            # Flags for checking homology properties:
+            self.check_min = True
+            self.check_max = True
+            v.check_min = True
+            v.check_max = True
+
+    def minimiser(self):
+        """Check whether this vertex is strictly less than all its
+           neighbours"""
+        if self.check_min:
+            self._min = all(self.f < v.f for v in self.nn)
+            self.check_min = False
+
+        return self._min
+
+    def maximiser(self):
+        """
+        Check whether this vertex is strictly greater than all its
+        neighbours.
+        """
+        if self.check_max:
+            self._max = all(self.f > v.f for v in self.nn)
+            self.check_max = False
+
+        return self._max
+
+
+class VertexVectorField(VertexBase):
+    """
+    Add homology properties of a scalar field f: R^n --> R^m associated with
+    the geometry built from the VertexBase class.
+    """
+
+    def __init__(self, x, sfield=None, vfield=None, field_args=(),
+                 vfield_args=(), g_cons=None,
+                 g_cons_args=(), nn=None, index=None):
+        super().__init__(x, nn=nn, index=index)
+
+        raise NotImplementedError("This class is still a work in progress")
+
+
+class VertexCacheBase:
+    """Base class for a vertex cache for a simplicial complex."""
+    def __init__(self):
+
+        self.cache = collections.OrderedDict()
+        self.nfev = 0  # Feasible points
+        self.index = -1
+
+    def __iter__(self):
+        for v in self.cache:
+            yield self.cache[v]
+        return
+
+    def size(self):
+        """Returns the size of the vertex cache."""
+        return self.index + 1
+
+    def print_out(self):
+        headlen = len(f"Vertex cache of size: {len(self.cache)}:")
+        print('=' * headlen)
+        print(f"Vertex cache of size: {len(self.cache)}:")
+        print('=' * headlen)
+        for v in self.cache:
+            self.cache[v].print_out()
+
+
+class VertexCube(VertexBase):
+    """Vertex class to be used for a pure simplicial complex with no associated
+    differential geometry (single level domain that exists in R^n)"""
+    def __init__(self, x, nn=None, index=None):
+        super().__init__(x, nn=nn, index=index)
+
+    def connect(self, v):
+        if v is not self and v not in self.nn:
+            self.nn.add(v)
+            v.nn.add(self)
+
+    def disconnect(self, v):
+        if v in self.nn:
+            self.nn.remove(v)
+            v.nn.remove(self)
+
+
+class VertexCacheIndex(VertexCacheBase):
+    def __init__(self):
+        """
+        Class for a vertex cache for a simplicial complex without an associated
+        field. Useful only for building and visualising a domain complex.
+
+        Parameters
+        ----------
+        """
+        super().__init__()
+        self.Vertex = VertexCube
+
+    def __getitem__(self, x, nn=None):
+        try:
+            return self.cache[x]
+        except KeyError:
+            self.index += 1
+            xval = self.Vertex(x, index=self.index)
+            # logging.info("New generated vertex at x = {}".format(x))
+            # NOTE: Surprisingly high performance increase if logging
+            # is commented out
+            self.cache[x] = xval
+            return self.cache[x]
+
+
+class VertexCacheField(VertexCacheBase):
+    def __init__(self, field=None, field_args=(), g_cons=None, g_cons_args=(),
+                 workers=1):
+        """
+        Class for a vertex cache for a simplicial complex with an associated
+        field.
+
+        Parameters
+        ----------
+        field : callable
+            Scalar or vector field callable.
+        field_args : tuple, optional
+            Any additional fixed parameters needed to completely specify the
+            field function
+        g_cons : dict or sequence of dict, optional
+            Constraints definition.
+            Function(s) ``R**n`` in the form::
+        g_cons_args : tuple, optional
+            Any additional fixed parameters needed to completely specify the
+            constraint functions
+        workers : int  optional
+            Uses `multiprocessing.Pool <multiprocessing>`) to compute the field
+             functions in parallel.
+
+        """
+        super().__init__()
+        self.index = -1
+        self.Vertex = VertexScalarField
+        self.field = field
+        self.field_args = field_args
+        self.wfield = FieldWrapper(field, field_args)  # if workers is not 1
+
+        self.g_cons = g_cons
+        self.g_cons_args = g_cons_args
+        self.wgcons = ConstraintWrapper(g_cons, g_cons_args)
+        self.gpool = set()  # A set of tuples to process for feasibility
+
+        # Field processing objects
+        self.fpool = set()  # A set of tuples to process for scalar function
+        self.sfc_lock = False  # True if self.fpool is non-Empty
+
+        self.workers = workers
+        self._mapwrapper = MapWrapper(workers)
+
+        if workers == 1:
+            self.process_gpool = self.proc_gpool
+            if g_cons is None:
+                self.process_fpool = self.proc_fpool_nog
+            else:
+                self.process_fpool = self.proc_fpool_g
+        else:
+            self.process_gpool = self.pproc_gpool
+            if g_cons is None:
+                self.process_fpool = self.pproc_fpool_nog
+            else:
+                self.process_fpool = self.pproc_fpool_g
+
+    def __getitem__(self, x, nn=None):
+        try:
+            return self.cache[x]
+        except KeyError:
+            self.index += 1
+            xval = self.Vertex(x, field=self.field, nn=nn, index=self.index,
+                               field_args=self.field_args,
+                               g_cons=self.g_cons,
+                               g_cons_args=self.g_cons_args)
+
+            self.cache[x] = xval  # Define in cache
+            self.gpool.add(xval)  # Add to pool for processing feasibility
+            self.fpool.add(xval)  # Add to pool for processing field values
+            return self.cache[x]
+
+    def __getstate__(self):
+        self_dict = self.__dict__.copy()
+        del self_dict['pool']
+        return self_dict
+
+    def process_pools(self):
+        if self.g_cons is not None:
+            self.process_gpool()
+        self.process_fpool()
+        self.proc_minimisers()
+
+    def feasibility_check(self, v):
+        v.feasible = True
+        for g, args in zip(self.g_cons, self.g_cons_args):
+            # constraint may return more than 1 value.
+            if np.any(g(v.x_a, *args) < 0.0):
+                v.f = np.inf
+                v.feasible = False
+                break
+
+    def compute_sfield(self, v):
+        """Compute the scalar field values of a vertex object `v`.
+
+        Parameters
+        ----------
+        v : VertexBase or VertexScalarField object
+        """
+        try:
+            v.f = self.field(v.x_a, *self.field_args)
+            self.nfev += 1
+        except AttributeError:
+            v.f = np.inf
+            # logging.warning(f"Field function not found at x = {self.x_a}")
+        if np.isnan(v.f):
+            v.f = np.inf
+
+    def proc_gpool(self):
+        """Process all constraints."""
+        if self.g_cons is not None:
+            for v in self.gpool:
+                self.feasibility_check(v)
+        # Clean the pool
+        self.gpool = set()
+
+    def pproc_gpool(self):
+        """Process all constraints in parallel."""
+        gpool_l = []
+        for v in self.gpool:
+            gpool_l.append(v.x_a)
+
+        G = self._mapwrapper(self.wgcons.gcons, gpool_l)
+        for v, g in zip(self.gpool, G):
+            v.feasible = g  # set vertex object attribute v.feasible = g (bool)
+
+    def proc_fpool_g(self):
+        """Process all field functions with constraints supplied."""
+        for v in self.fpool:
+            if v.feasible:
+                self.compute_sfield(v)
+        # Clean the pool
+        self.fpool = set()
+
+    def proc_fpool_nog(self):
+        """Process all field functions with no constraints supplied."""
+        for v in self.fpool:
+            self.compute_sfield(v)
+        # Clean the pool
+        self.fpool = set()
+
+    def pproc_fpool_g(self):
+        """
+        Process all field functions with constraints supplied in parallel.
+        """
+        self.wfield.func
+        fpool_l = []
+        for v in self.fpool:
+            if v.feasible:
+                fpool_l.append(v.x_a)
+            else:
+                v.f = np.inf
+        F = self._mapwrapper(self.wfield.func, fpool_l)
+        for va, f in zip(fpool_l, F):
+            vt = tuple(va)
+            self[vt].f = f  # set vertex object attribute v.f = f
+            self.nfev += 1
+        # Clean the pool
+        self.fpool = set()
+
+    def pproc_fpool_nog(self):
+        """
+        Process all field functions with no constraints supplied in parallel.
+        """
+        self.wfield.func
+        fpool_l = []
+        for v in self.fpool:
+            fpool_l.append(v.x_a)
+        F = self._mapwrapper(self.wfield.func, fpool_l)
+        for va, f in zip(fpool_l, F):
+            vt = tuple(va)
+            self[vt].f = f  # set vertex object attribute v.f = f
+            self.nfev += 1
+        # Clean the pool
+        self.fpool = set()
+
+    def proc_minimisers(self):
+        """Check for minimisers."""
+        for v in self:
+            v.minimiser()
+            v.maximiser()
+
+
+class ConstraintWrapper:
+    """Object to wrap constraints to pass to `multiprocessing.Pool`."""
+    def __init__(self, g_cons, g_cons_args):
+        self.g_cons = g_cons
+        self.g_cons_args = g_cons_args
+
+    def gcons(self, v_x_a):
+        vfeasible = True
+        for g, args in zip(self.g_cons, self.g_cons_args):
+            # constraint may return more than 1 value.
+            if np.any(g(v_x_a, *args) < 0.0):
+                vfeasible = False
+                break
+        return vfeasible
+
+
+class FieldWrapper:
+    """Object to wrap field to pass to `multiprocessing.Pool`."""
+    def __init__(self, field, field_args):
+        self.field = field
+        self.field_args = field_args
+
+    def func(self, v_x_a):
+        try:
+            v_f = self.field(v_x_a, *self.field_args)
+        except Exception:
+            v_f = np.inf
+        if np.isnan(v_f):
+            v_f = np.inf
+
+        return v_f

vila/lib/python3.10/site-packages/scipy/optimize/_tnc.py

@@ -0,0 +1,430 @@
+# TNC Python interface
+# @(#) $Jeannot: tnc.py,v 1.11 2005/01/28 18:27:31 js Exp $
+
+# Copyright (c) 2004-2005, Jean-Sebastien Roy (js@jeannot.org)
+
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+"""
+TNC: A Python interface to the TNC non-linear optimizer
+
+TNC is a non-linear optimizer. To use it, you must provide a function to
+minimize. The function must take one argument: the list of coordinates where to
+evaluate the function; and it must return either a tuple, whose first element is the
+value of the function, and whose second argument is the gradient of the function
+(as a list of values); or None, to abort the minimization.
+"""
+
+from scipy.optimize import _moduleTNC as moduleTNC
+from ._optimize import (MemoizeJac, OptimizeResult, _check_unknown_options,
+                       _prepare_scalar_function)
+from ._constraints import old_bound_to_new
+from scipy._lib._array_api import atleast_nd, array_namespace
+
+from numpy import inf, array, zeros
+
+__all__ = ['fmin_tnc']
+
+
+MSG_NONE = 0  # No messages
+MSG_ITER = 1  # One line per iteration
+MSG_INFO = 2  # Informational messages
+MSG_VERS = 4  # Version info
+MSG_EXIT = 8  # Exit reasons
+MSG_ALL = MSG_ITER + MSG_INFO + MSG_VERS + MSG_EXIT
+
+MSGS = {
+        MSG_NONE: "No messages",
+        MSG_ITER: "One line per iteration",
+        MSG_INFO: "Informational messages",
+        MSG_VERS: "Version info",
+        MSG_EXIT: "Exit reasons",
+        MSG_ALL: "All messages"
+}
+
+INFEASIBLE = -1  # Infeasible (lower bound > upper bound)
+LOCALMINIMUM = 0  # Local minimum reached (|pg| ~= 0)
+FCONVERGED = 1  # Converged (|f_n-f_(n-1)| ~= 0)
+XCONVERGED = 2  # Converged (|x_n-x_(n-1)| ~= 0)
+MAXFUN = 3  # Max. number of function evaluations reached
+LSFAIL = 4  # Linear search failed
+CONSTANT = 5  # All lower bounds are equal to the upper bounds
+NOPROGRESS = 6  # Unable to progress
+USERABORT = 7  # User requested end of minimization
+
+RCSTRINGS = {
+        INFEASIBLE: "Infeasible (lower bound > upper bound)",
+        LOCALMINIMUM: "Local minimum reached (|pg| ~= 0)",
+        FCONVERGED: "Converged (|f_n-f_(n-1)| ~= 0)",
+        XCONVERGED: "Converged (|x_n-x_(n-1)| ~= 0)",
+        MAXFUN: "Max. number of function evaluations reached",
+        LSFAIL: "Linear search failed",
+        CONSTANT: "All lower bounds are equal to the upper bounds",
+        NOPROGRESS: "Unable to progress",
+        USERABORT: "User requested end of minimization"
+}
+
+# Changes to interface made by Travis Oliphant, Apr. 2004 for inclusion in
+#  SciPy
+
+
+def fmin_tnc(func, x0, fprime=None, args=(), approx_grad=0,
+             bounds=None, epsilon=1e-8, scale=None, offset=None,
+             messages=MSG_ALL, maxCGit=-1, maxfun=None, eta=-1,
+             stepmx=0, accuracy=0, fmin=0, ftol=-1, xtol=-1, pgtol=-1,
+             rescale=-1, disp=None, callback=None):
+    """
+    Minimize a function with variables subject to bounds, using
+    gradient information in a truncated Newton algorithm. This
+    method wraps a C implementation of the algorithm.
+
+    Parameters
+    ----------
+    func : callable ``func(x, *args)``
+        Function to minimize.  Must do one of:
+
+        1. Return f and g, where f is the value of the function and g its
+           gradient (a list of floats).
+
+        2. Return the function value but supply gradient function
+           separately as `fprime`.
+
+        3. Return the function value and set ``approx_grad=True``.
+
+        If the function returns None, the minimization
+        is aborted.
+    x0 : array_like
+        Initial estimate of minimum.
+    fprime : callable ``fprime(x, *args)``, optional
+        Gradient of `func`. If None, then either `func` must return the
+        function value and the gradient (``f,g = func(x, *args)``)
+        or `approx_grad` must be True.
+    args : tuple, optional
+        Arguments to pass to function.
+    approx_grad : bool, optional
+        If true, approximate the gradient numerically.
+    bounds : list, optional
+        (min, max) pairs for each element in x0, defining the
+        bounds on that parameter. Use None or +/-inf for one of
+        min or max when there is no bound in that direction.
+    epsilon : float, optional
+        Used if approx_grad is True. The stepsize in a finite
+        difference approximation for fprime.
+    scale : array_like, optional
+        Scaling factors to apply to each variable. If None, the
+        factors are up-low for interval bounded variables and
+        1+|x| for the others. Defaults to None.
+    offset : array_like, optional
+        Value to subtract from each variable. If None, the
+        offsets are (up+low)/2 for interval bounded variables
+        and x for the others.
+    messages : int, optional
+        Bit mask used to select messages display during
+        minimization values defined in the MSGS dict. Defaults to
+        MGS_ALL.
+    disp : int, optional
+        Integer interface to messages. 0 = no message, 5 = all messages
+    maxCGit : int, optional
+        Maximum number of hessian*vector evaluations per main
+        iteration. If maxCGit == 0, the direction chosen is
+        -gradient if maxCGit < 0, maxCGit is set to
+        max(1,min(50,n/2)). Defaults to -1.
+    maxfun : int, optional
+        Maximum number of function evaluation. If None, maxfun is
+        set to max(100, 10*len(x0)). Defaults to None. Note that this function
+        may violate the limit because of evaluating gradients by numerical
+        differentiation.
+    eta : float, optional
+        Severity of the line search. If < 0 or > 1, set to 0.25.
+        Defaults to -1.
+    stepmx : float, optional
+        Maximum step for the line search. May be increased during
+        call. If too small, it will be set to 10.0. Defaults to 0.
+    accuracy : float, optional
+        Relative precision for finite difference calculations. If
+        <= machine_precision, set to sqrt(machine_precision).
+        Defaults to 0.
+    fmin : float, optional
+        Minimum function value estimate. Defaults to 0.
+    ftol : float, optional
+        Precision goal for the value of f in the stopping criterion.
+        If ftol < 0.0, ftol is set to 0.0 defaults to -1.
+    xtol : float, optional
+        Precision goal for the value of x in the stopping
+        criterion (after applying x scaling factors). If xtol <
+        0.0, xtol is set to sqrt(machine_precision). Defaults to
+        -1.
+    pgtol : float, optional
+        Precision goal for the value of the projected gradient in
+        the stopping criterion (after applying x scaling factors).
+        If pgtol < 0.0, pgtol is set to 1e-2 * sqrt(accuracy).
+        Setting it to 0.0 is not recommended. Defaults to -1.
+    rescale : float, optional
+        Scaling factor (in log10) used to trigger f value
+        rescaling. If 0, rescale at each iteration. If a large
+        value, never rescale. If < 0, rescale is set to 1.3.
+    callback : callable, optional
+        Called after each iteration, as callback(xk), where xk is the
+        current parameter vector.
+
+    Returns
+    -------
+    x : ndarray
+        The solution.
+    nfeval : int
+        The number of function evaluations.
+    rc : int
+        Return code, see below
+
+    See also
+    --------
+    minimize: Interface to minimization algorithms for multivariate
+        functions. See the 'TNC' `method` in particular.
+
+    Notes
+    -----
+    The underlying algorithm is truncated Newton, also called
+    Newton Conjugate-Gradient. This method differs from
+    scipy.optimize.fmin_ncg in that
+
+    1. it wraps a C implementation of the algorithm
+    2. it allows each variable to be given an upper and lower bound.
+
+    The algorithm incorporates the bound constraints by determining
+    the descent direction as in an unconstrained truncated Newton,
+    but never taking a step-size large enough to leave the space
+    of feasible x's. The algorithm keeps track of a set of
+    currently active constraints, and ignores them when computing
+    the minimum allowable step size. (The x's associated with the
+    active constraint are kept fixed.) If the maximum allowable
+    step size is zero then a new constraint is added. At the end
+    of each iteration one of the constraints may be deemed no
+    longer active and removed. A constraint is considered
+    no longer active is if it is currently active
+    but the gradient for that variable points inward from the
+    constraint. The specific constraint removed is the one
+    associated with the variable of largest index whose
+    constraint is no longer active.
+
+    Return codes are defined as follows::
+
+        -1 : Infeasible (lower bound > upper bound)
+         0 : Local minimum reached (|pg| ~= 0)
+         1 : Converged (|f_n-f_(n-1)| ~= 0)
+         2 : Converged (|x_n-x_(n-1)| ~= 0)
+         3 : Max. number of function evaluations reached
+         4 : Linear search failed
+         5 : All lower bounds are equal to the upper bounds
+         6 : Unable to progress
+         7 : User requested end of minimization
+
+    References
+    ----------
+    Wright S., Nocedal J. (2006), 'Numerical Optimization'
+
+    Nash S.G. (1984), "Newton-Type Minimization Via the Lanczos Method",
+    SIAM Journal of Numerical Analysis 21, pp. 770-778
+
+    """
+    # handle fprime/approx_grad
+    if approx_grad:
+        fun = func
+        jac = None
+    elif fprime is None:
+        fun = MemoizeJac(func)
+        jac = fun.derivative
+    else:
+        fun = func
+        jac = fprime
+
+    if disp is not None:  # disp takes precedence over messages
+        mesg_num = disp
+    else:
+        mesg_num = {0:MSG_NONE, 1:MSG_ITER, 2:MSG_INFO, 3:MSG_VERS,
+                    4:MSG_EXIT, 5:MSG_ALL}.get(messages, MSG_ALL)
+    # build options
+    opts = {'eps': epsilon,
+            'scale': scale,
+            'offset': offset,
+            'mesg_num': mesg_num,
+            'maxCGit': maxCGit,
+            'maxfun': maxfun,
+            'eta': eta,
+            'stepmx': stepmx,
+            'accuracy': accuracy,
+            'minfev': fmin,
+            'ftol': ftol,
+            'xtol': xtol,
+            'gtol': pgtol,
+            'rescale': rescale,
+            'disp': False}
+
+    res = _minimize_tnc(fun, x0, args, jac, bounds, callback=callback, **opts)
+
+    return res['x'], res['nfev'], res['status']
+
+
+def _minimize_tnc(fun, x0, args=(), jac=None, bounds=None,
+                  eps=1e-8, scale=None, offset=None, mesg_num=None,
+                  maxCGit=-1, eta=-1, stepmx=0, accuracy=0,
+                  minfev=0, ftol=-1, xtol=-1, gtol=-1, rescale=-1, disp=False,
+                  callback=None, finite_diff_rel_step=None, maxfun=None,
+                  **unknown_options):
+    """
+    Minimize a scalar function of one or more variables using a truncated
+    Newton (TNC) algorithm.
+
+    Options
+    -------
+    eps : float or ndarray
+        If `jac is None` the absolute step size used for numerical
+        approximation of the jacobian via forward differences.
+    scale : list of floats
+        Scaling factors to apply to each variable. If None, the
+        factors are up-low for interval bounded variables and
+        1+|x] for the others. Defaults to None.
+    offset : float
+        Value to subtract from each variable. If None, the
+        offsets are (up+low)/2 for interval bounded variables
+        and x for the others.
+    disp : bool
+       Set to True to print convergence messages.
+    maxCGit : int
+        Maximum number of hessian*vector evaluations per main
+        iteration. If maxCGit == 0, the direction chosen is
+        -gradient if maxCGit < 0, maxCGit is set to
+        max(1,min(50,n/2)). Defaults to -1.
+    eta : float
+        Severity of the line search. If < 0 or > 1, set to 0.25.
+        Defaults to -1.
+    stepmx : float
+        Maximum step for the line search. May be increased during
+        call. If too small, it will be set to 10.0. Defaults to 0.
+    accuracy : float
+        Relative precision for finite difference calculations. If
+        <= machine_precision, set to sqrt(machine_precision).
+        Defaults to 0.
+    minfev : float
+        Minimum function value estimate. Defaults to 0.
+    ftol : float
+        Precision goal for the value of f in the stopping criterion.
+        If ftol < 0.0, ftol is set to 0.0 defaults to -1.
+    xtol : float
+        Precision goal for the value of x in the stopping
+        criterion (after applying x scaling factors). If xtol <
+        0.0, xtol is set to sqrt(machine_precision). Defaults to
+        -1.
+    gtol : float
+        Precision goal for the value of the projected gradient in
+        the stopping criterion (after applying x scaling factors).
+        If gtol < 0.0, gtol is set to 1e-2 * sqrt(accuracy).
+        Setting it to 0.0 is not recommended. Defaults to -1.
+    rescale : float
+        Scaling factor (in log10) used to trigger f value
+        rescaling.  If 0, rescale at each iteration.  If a large
+        value, never rescale.  If < 0, rescale is set to 1.3.
+    finite_diff_rel_step : None or array_like, optional
+        If `jac in ['2-point', '3-point', 'cs']` the relative step size to
+        use for numerical approximation of the jacobian. The absolute step
+        size is computed as ``h = rel_step * sign(x) * max(1, abs(x))``,
+        possibly adjusted to fit into the bounds. For ``method='3-point'``
+        the sign of `h` is ignored. If None (default) then step is selected
+        automatically.
+    maxfun : int
+        Maximum number of function evaluations. If None, `maxfun` is
+        set to max(100, 10*len(x0)). Defaults to None.
+    """
+    _check_unknown_options(unknown_options)
+    fmin = minfev
+    pgtol = gtol
+
+    xp = array_namespace(x0)
+    x0 = atleast_nd(x0, ndim=1, xp=xp)
+    dtype = xp.float64
+    if xp.isdtype(x0.dtype, "real floating"):
+        dtype = x0.dtype
+    x0 = xp.reshape(xp.astype(x0, dtype), -1)
+
+    n = len(x0)
+
+    if bounds is None:
+        bounds = [(None,None)] * n
+    if len(bounds) != n:
+        raise ValueError('length of x0 != length of bounds')
+    new_bounds = old_bound_to_new(bounds)
+
+    if mesg_num is not None:
+        messages = {0:MSG_NONE, 1:MSG_ITER, 2:MSG_INFO, 3:MSG_VERS,
+                    4:MSG_EXIT, 5:MSG_ALL}.get(mesg_num, MSG_ALL)
+    elif disp:
+        messages = MSG_ALL
+    else:
+        messages = MSG_NONE
+
+    sf = _prepare_scalar_function(fun, x0, jac=jac, args=args, epsilon=eps,
+                                  finite_diff_rel_step=finite_diff_rel_step,
+                                  bounds=new_bounds)
+    func_and_grad = sf.fun_and_grad
+
+    """
+    low, up   : the bounds (lists of floats)
+                if low is None, the lower bounds are removed.
+                if up is None, the upper bounds are removed.
+                low and up defaults to None
+    """
+    low = zeros(n)
+    up = zeros(n)
+    for i in range(n):
+        if bounds[i] is None:
+            l, u = -inf, inf
+        else:
+            l,u = bounds[i]
+            if l is None:
+                low[i] = -inf
+            else:
+                low[i] = l
+            if u is None:
+                up[i] = inf
+            else:
+                up[i] = u
+
+    if scale is None:
+        scale = array([])
+
+    if offset is None:
+        offset = array([])
+
+    if maxfun is None:
+        maxfun = max(100, 10*len(x0))
+
+    rc, nf, nit, x, funv, jacv = moduleTNC.tnc_minimize(
+        func_and_grad, x0, low, up, scale,
+        offset, messages, maxCGit, maxfun,
+        eta, stepmx, accuracy, fmin, ftol,
+        xtol, pgtol, rescale, callback
+    )
+    # the TNC documentation states: "On output, x, f and g may be very
+    # slightly out of sync because of scaling". Therefore re-evaluate
+    # func_and_grad so they are synced.
+    funv, jacv = func_and_grad(x)
+
+    return OptimizeResult(x=x, fun=funv, jac=jacv, nfev=sf.nfev,
+                          nit=nit, status=rc, message=RCSTRINGS[rc],
+                          success=(-1 < rc < 3))

vila/lib/python3.10/site-packages/scipy/optimize/_trustregion_constr/__init__.py

@@ -0,0 +1,6 @@
+"""This module contains the equality constrained SQP solver."""
+
+
+from .minimize_trustregion_constr import _minimize_trustregion_constr
+
+__all__ = ['_minimize_trustregion_constr']