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mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/__init__.py

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+from .main import minimize
+from .utils import show_versions
+
+# PEP0440 compatible formatted version, see:
+# https://www.python.org/dev/peps/pep-0440/
+#
+# Final release markers:
+#   X.Y.0   # For first release after an increment in Y
+#   X.Y.Z   # For bugfix releases
+#
+# Admissible pre-release markers:
+#   X.YaN   # Alpha release
+#   X.YbN   # Beta release
+#   X.YrcN  # Release Candidate
+#
+# Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
+# 'X.Y.dev0' is the canonical version of 'X.Y.dev'.
+__version__ = "1.1.2"
+
+__all__ = ["minimize", "show_versions"]

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/framework.py

@@ -0,0 +1,1240 @@
+import warnings
+
+import numpy as np
+from scipy.optimize import lsq_linear
+
+from .models import Models, Quadratic
+from .settings import Options, Constants
+from .subsolvers import (
+    cauchy_geometry,
+    spider_geometry,
+    normal_byrd_omojokun,
+    tangential_byrd_omojokun,
+    constrained_tangential_byrd_omojokun,
+)
+from .subsolvers.optim import qr_tangential_byrd_omojokun
+from .utils import get_arrays_tol
+
+
+TINY = np.finfo(float).tiny
+EPS = np.finfo(float).eps
+
+
+class TrustRegion:
+    """
+    Trust-region framework.
+    """
+
+    def __init__(self, pb, options, constants):
+        """
+        Initialize the trust-region framework.
+
+        Parameters
+        ----------
+        pb : `cobyqa.problem.Problem`
+            Problem to solve.
+        options : dict
+            Options of the solver.
+        constants : dict
+            Constants of the solver.
+
+        Raises
+        ------
+        `cobyqa.utils.MaxEvalError`
+            If the maximum number of evaluations is reached.
+        `cobyqa.utils.TargetSuccess`
+            If a nearly feasible point has been found with an objective
+            function value below the target.
+        `cobyqa.utils.FeasibleSuccess`
+            If a feasible point has been found for a feasibility problem.
+        `numpy.linalg.LinAlgError`
+            If the initial interpolation system is ill-defined.
+        """
+        # Set the initial penalty parameter.
+        self._penalty = 0.0
+
+        # Initialize the models.
+        self._pb = pb
+        self._models = Models(self._pb, options, self.penalty)
+        self._constants = constants
+
+        # Set the index of the best interpolation point.
+        self._best_index = 0
+        self.set_best_index()
+
+        # Set the initial Lagrange multipliers.
+        self._lm_linear_ub = np.zeros(self.m_linear_ub)
+        self._lm_linear_eq = np.zeros(self.m_linear_eq)
+        self._lm_nonlinear_ub = np.zeros(self.m_nonlinear_ub)
+        self._lm_nonlinear_eq = np.zeros(self.m_nonlinear_eq)
+        self.set_multipliers(self.x_best)
+
+        # Set the initial trust-region radius and the resolution.
+        self._resolution = options[Options.RHOBEG]
+        self._radius = self.resolution
+
+    @property
+    def n(self):
+        """
+        Number of variables.
+
+        Returns
+        -------
+        int
+            Number of variables.
+        """
+        return self._pb.n
+
+    @property
+    def m_linear_ub(self):
+        """
+        Number of linear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of linear inequality constraints.
+        """
+        return self._pb.m_linear_ub
+
+    @property
+    def m_linear_eq(self):
+        """
+        Number of linear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of linear equality constraints.
+        """
+        return self._pb.m_linear_eq
+
+    @property
+    def m_nonlinear_ub(self):
+        """
+        Number of nonlinear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear inequality constraints.
+        """
+        return self._pb.m_nonlinear_ub
+
+    @property
+    def m_nonlinear_eq(self):
+        """
+        Number of nonlinear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear equality constraints.
+        """
+        return self._pb.m_nonlinear_eq
+
+    @property
+    def radius(self):
+        """
+        Trust-region radius.
+
+        Returns
+        -------
+        float
+            Trust-region radius.
+        """
+        return self._radius
+
+    @radius.setter
+    def radius(self, radius):
+        """
+        Set the trust-region radius.
+
+        Parameters
+        ----------
+        radius : float
+            New trust-region radius.
+        """
+        self._radius = radius
+        if (
+            self.radius
+            <= self._constants[Constants.DECREASE_RADIUS_THRESHOLD]
+            * self.resolution
+        ):
+            self._radius = self.resolution
+
+    @property
+    def resolution(self):
+        """
+        Resolution of the trust-region framework.
+
+        The resolution is a lower bound on the trust-region radius.
+
+        Returns
+        -------
+        float
+            Resolution of the trust-region framework.
+        """
+        return self._resolution
+
+    @resolution.setter
+    def resolution(self, resolution):
+        """
+        Set the resolution of the trust-region framework.
+
+        Parameters
+        ----------
+        resolution : float
+            New resolution of the trust-region framework.
+        """
+        self._resolution = resolution
+
+    @property
+    def penalty(self):
+        """
+        Penalty parameter.
+
+        Returns
+        -------
+        float
+            Penalty parameter.
+        """
+        return self._penalty
+
+    @property
+    def models(self):
+        """
+        Models of the objective function and constraints.
+
+        Returns
+        -------
+        `cobyqa.models.Models`
+            Models of the objective function and constraints.
+        """
+        return self._models
+
+    @property
+    def best_index(self):
+        """
+        Index of the best interpolation point.
+
+        Returns
+        -------
+        int
+            Index of the best interpolation point.
+        """
+        return self._best_index
+
+    @property
+    def x_best(self):
+        """
+        Best interpolation point.
+
+        Its value is interpreted as relative to the origin, not the base point.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Best interpolation point.
+        """
+        return self.models.interpolation.point(self.best_index)
+
+    @property
+    def fun_best(self):
+        """
+        Value of the objective function at `x_best`.
+
+        Returns
+        -------
+        float
+            Value of the objective function at `x_best`.
+        """
+        return self.models.fun_val[self.best_index]
+
+    @property
+    def cub_best(self):
+        """
+        Values of the nonlinear inequality constraints at `x_best`.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Values of the nonlinear inequality constraints at `x_best`.
+        """
+        return self.models.cub_val[self.best_index, :]
+
+    @property
+    def ceq_best(self):
+        """
+        Values of the nonlinear equality constraints at `x_best`.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m_nonlinear_eq,)
+            Values of the nonlinear equality constraints at `x_best`.
+        """
+        return self.models.ceq_val[self.best_index, :]
+
+    def lag_model(self, x):
+        """
+        Evaluate the Lagrangian model at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the Lagrangian model is evaluated.
+
+        Returns
+        -------
+        float
+            Value of the Lagrangian model at `x`.
+        """
+        return (
+            self.models.fun(x)
+            + self._lm_linear_ub
+            @ (self._pb.linear.a_ub @ x - self._pb.linear.b_ub)
+            + self._lm_linear_eq
+            @ (self._pb.linear.a_eq @ x - self._pb.linear.b_eq)
+            + self._lm_nonlinear_ub @ self.models.cub(x)
+            + self._lm_nonlinear_eq @ self.models.ceq(x)
+        )
+
+    def lag_model_grad(self, x):
+        """
+        Evaluate the gradient of the Lagrangian model at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the gradient of the Lagrangian model is evaluated.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Gradient of the Lagrangian model at `x`.
+        """
+        return (
+            self.models.fun_grad(x)
+            + self._lm_linear_ub @ self._pb.linear.a_ub
+            + self._lm_linear_eq @ self._pb.linear.a_eq
+            + self._lm_nonlinear_ub @ self.models.cub_grad(x)
+            + self._lm_nonlinear_eq @ self.models.ceq_grad(x)
+        )
+
+    def lag_model_hess(self):
+        """
+        Evaluate the Hessian matrix of the Lagrangian model at a given point.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n, n)
+            Hessian matrix of the Lagrangian model at `x`.
+        """
+        hess = self.models.fun_hess()
+        if self.m_nonlinear_ub > 0:
+            hess += self._lm_nonlinear_ub @ self.models.cub_hess()
+        if self.m_nonlinear_eq > 0:
+            hess += self._lm_nonlinear_eq @ self.models.ceq_hess()
+        return hess
+
+    def lag_model_hess_prod(self, v):
+        """
+        Evaluate the right product of the Hessian matrix of the Lagrangian
+        model with a given vector.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Vector with which the Hessian matrix of the Lagrangian model is
+            multiplied from the right.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Right product of the Hessian matrix of the Lagrangian model with
+            `v`.
+        """
+        return (
+            self.models.fun_hess_prod(v)
+            + self._lm_nonlinear_ub @ self.models.cub_hess_prod(v)
+            + self._lm_nonlinear_eq @ self.models.ceq_hess_prod(v)
+        )
+
+    def lag_model_curv(self, v):
+        """
+        Evaluate the curvature of the Lagrangian model along a given direction.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Direction along which the curvature of the Lagrangian model is
+            evaluated.
+
+        Returns
+        -------
+        float
+            Curvature of the Lagrangian model along `v`.
+        """
+        return (
+            self.models.fun_curv(v)
+            + self._lm_nonlinear_ub @ self.models.cub_curv(v)
+            + self._lm_nonlinear_eq @ self.models.ceq_curv(v)
+        )
+
+    def sqp_fun(self, step):
+        """
+        Evaluate the objective function of the SQP subproblem.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Step along which the objective function of the SQP subproblem is
+            evaluated.
+
+        Returns
+        -------
+        float
+            Value of the objective function of the SQP subproblem along `step`.
+        """
+        return step @ (
+            self.models.fun_grad(self.x_best)
+            + 0.5 * self.lag_model_hess_prod(step)
+        )
+
+    def sqp_cub(self, step):
+        """
+        Evaluate the linearization of the nonlinear inequality constraints.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Step along which the linearization of the nonlinear inequality
+            constraints is evaluated.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Value of the linearization of the nonlinear inequality constraints
+            along `step`.
+        """
+        return (
+            self.models.cub(self.x_best)
+            + self.models.cub_grad(self.x_best) @ step
+        )
+
+    def sqp_ceq(self, step):
+        """
+        Evaluate the linearization of the nonlinear equality constraints.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Step along which the linearization of the nonlinear equality
+            constraints is evaluated.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Value of the linearization of the nonlinear equality constraints
+            along `step`.
+        """
+        return (
+            self.models.ceq(self.x_best)
+            + self.models.ceq_grad(self.x_best) @ step
+        )
+
+    def merit(self, x, fun_val=None, cub_val=None, ceq_val=None):
+        """
+        Evaluate the merit function at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the merit function is evaluated.
+        fun_val : float, optional
+            Value of the objective function at `x`. If not provided, the
+            objective function is evaluated at `x`.
+        cub_val : `numpy.ndarray`, shape (m_nonlinear_ub,), optional
+            Values of the nonlinear inequality constraints. If not provided,
+            the nonlinear inequality constraints are evaluated at `x`.
+        ceq_val : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Values of the nonlinear equality constraints. If not provided,
+            the nonlinear equality constraints are evaluated at `x`.
+
+        Returns
+        -------
+        float
+            Value of the merit function at `x`.
+        """
+        if fun_val is None or cub_val is None or ceq_val is None:
+            fun_val, cub_val, ceq_val = self._pb(x, self.penalty)
+        m_val = fun_val
+        if self._penalty > 0.0:
+            c_val = self._pb.violation(x, cub_val=cub_val, ceq_val=ceq_val)
+            if np.count_nonzero(c_val):
+                m_val += self._penalty * np.linalg.norm(c_val)
+        return m_val
+
+    def get_constraint_linearizations(self, x):
+        """
+        Get the linearizations of the constraints at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the linearizations of the constraints are evaluated.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m_linear_ub + m_nonlinear_ub, n)
+            Left-hand side matrix of the linearized inequality constraints.
+        `numpy.ndarray`, shape (m_linear_ub + m_nonlinear_ub,)
+            Right-hand side vector of the linearized inequality constraints.
+        `numpy.ndarray`, shape (m_linear_eq + m_nonlinear_eq, n)
+            Left-hand side matrix of the linearized equality constraints.
+        `numpy.ndarray`, shape (m_linear_eq + m_nonlinear_eq,)
+            Right-hand side vector of the linearized equality constraints.
+        """
+        aub = np.block(
+            [
+                [self._pb.linear.a_ub],
+                [self.models.cub_grad(x)],
+            ]
+        )
+        bub = np.block(
+            [
+                self._pb.linear.b_ub - self._pb.linear.a_ub @ x,
+                -self.models.cub(x),
+            ]
+        )
+        aeq = np.block(
+            [
+                [self._pb.linear.a_eq],
+                [self.models.ceq_grad(x)],
+            ]
+        )
+        beq = np.block(
+            [
+                self._pb.linear.b_eq - self._pb.linear.a_eq @ x,
+                -self.models.ceq(x),
+            ]
+        )
+        return aub, bub, aeq, beq
+
+    def get_trust_region_step(self, options):
+        """
+        Get the trust-region step.
+
+        The trust-region step is computed by solving the derivative-free
+        trust-region SQP subproblem using a Byrd-Omojokun composite-step
+        approach. For more details, see Section 5.2.3 of [1]_.
+
+        Parameters
+        ----------
+        options : dict
+            Options of the solver.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Normal step.
+        `numpy.ndarray`, shape (n,)
+            Tangential step.
+
+        References
+        ----------
+        .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization
+           Methods and Software*. PhD thesis, Department of Applied
+           Mathematics, The Hong Kong Polytechnic University, Hong Kong, China,
+           2022. URL: https://theses.lib.polyu.edu.hk/handle/200/12294.
+        """
+        # Evaluate the linearizations of the constraints.
+        aub, bub, aeq, beq = self.get_constraint_linearizations(self.x_best)
+        xl = self._pb.bounds.xl - self.x_best
+        xu = self._pb.bounds.xu - self.x_best
+
+        # Evaluate the normal step.
+        radius = self._constants[Constants.BYRD_OMOJOKUN_FACTOR] * self.radius
+        normal_step = normal_byrd_omojokun(
+            aub,
+            bub,
+            aeq,
+            beq,
+            xl,
+            xu,
+            radius,
+            options[Options.DEBUG],
+            **self._constants,
+        )
+        if options[Options.DEBUG]:
+            tol = get_arrays_tol(xl, xu)
+            if (np.any(normal_step + tol < xl)
+                    or np.any(xu < normal_step - tol)):
+                warnings.warn(
+                    "the normal step does not respect the bound constraint.",
+                    RuntimeWarning,
+                    2,
+                )
+            if np.linalg.norm(normal_step) > 1.1 * radius:
+                warnings.warn(
+                    "the normal step does not respect the trust-region "
+                    "constraint.",
+                    RuntimeWarning,
+                    2,
+                )
+
+        # Evaluate the tangential step.
+        radius = np.sqrt(self.radius**2.0 - normal_step @ normal_step)
+        xl -= normal_step
+        xu -= normal_step
+        bub = np.maximum(bub - aub @ normal_step, 0.0)
+        g_best = self.models.fun_grad(self.x_best) + self.lag_model_hess_prod(
+            normal_step
+        )
+        if self._pb.type in ["unconstrained", "bound-constrained"]:
+            tangential_step = tangential_byrd_omojokun(
+                g_best,
+                self.lag_model_hess_prod,
+                xl,
+                xu,
+                radius,
+                options[Options.DEBUG],
+                **self._constants,
+            )
+        else:
+            tangential_step = constrained_tangential_byrd_omojokun(
+                g_best,
+                self.lag_model_hess_prod,
+                xl,
+                xu,
+                aub,
+                bub,
+                aeq,
+                radius,
+                options["debug"],
+                **self._constants,
+            )
+        if options[Options.DEBUG]:
+            tol = get_arrays_tol(xl, xu)
+            if np.any(tangential_step + tol < xl) or np.any(
+                xu < tangential_step - tol
+            ):
+                warnings.warn(
+                    "The tangential step does not respect the bound "
+                    "constraints.",
+                    RuntimeWarning,
+                    2,
+                )
+            if (
+                np.linalg.norm(normal_step + tangential_step)
+                > 1.1 * np.sqrt(2.0) * self.radius
+            ):
+                warnings.warn(
+                    "The trial step does not respect the trust-region "
+                    "constraint.",
+                    RuntimeWarning,
+                    2,
+                )
+        return normal_step, tangential_step
+
+    def get_geometry_step(self, k_new, options):
+        """
+        Get the geometry-improving step.
+
+        Three different geometry-improving steps are computed and the best one
+        is returned. For more details, see Section 5.2.7 of [1]_.
+
+        Parameters
+        ----------
+        k_new : int
+            Index of the interpolation point to be modified.
+        options : dict
+            Options of the solver.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Geometry-improving step.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the computation of a determinant fails.
+
+        References
+        ----------
+        .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization
+           Methods and Software*. PhD thesis, Department of Applied
+           Mathematics, The Hong Kong Polytechnic University, Hong Kong, China,
+           2022. URL: https://theses.lib.polyu.edu.hk/handle/200/12294.
+        """
+        if options[Options.DEBUG]:
+            assert (
+                k_new != self.best_index
+            ), "The index `k_new` must be different from the best index."
+
+        # Build the k_new-th Lagrange polynomial.
+        coord_vec = np.squeeze(np.eye(1, self.models.npt, k_new))
+        lag = Quadratic(
+            self.models.interpolation,
+            coord_vec,
+            options[Options.DEBUG],
+        )
+        g_lag = lag.grad(self.x_best, self.models.interpolation)
+
+        # Compute a simple constrained Cauchy step.
+        xl = self._pb.bounds.xl - self.x_best
+        xu = self._pb.bounds.xu - self.x_best
+        step = cauchy_geometry(
+            0.0,
+            g_lag,
+            lambda v: lag.curv(v, self.models.interpolation),
+            xl,
+            xu,
+            self.radius,
+            options[Options.DEBUG],
+        )
+        sigma = self.models.determinants(self.x_best + step, k_new)
+
+        # Compute the solution on the straight lines joining the interpolation
+        # points to the k-th one, and choose it if it provides a larger value
+        # of the determinant of the interpolation system in absolute value.
+        xpt = (
+            self.models.interpolation.xpt
+            - self.models.interpolation.xpt[:, self.best_index, np.newaxis]
+        )
+        xpt[:, [0, self.best_index]] = xpt[:, [self.best_index, 0]]
+        step_alt = spider_geometry(
+            0.0,
+            g_lag,
+            lambda v: lag.curv(v, self.models.interpolation),
+            xpt[:, 1:],
+            xl,
+            xu,
+            self.radius,
+            options[Options.DEBUG],
+        )
+        sigma_alt = self.models.determinants(self.x_best + step_alt, k_new)
+        if abs(sigma_alt) > abs(sigma):
+            step = step_alt
+            sigma = sigma_alt
+
+        # Compute a Cauchy step on the tangent space of the active constraints.
+        if self._pb.type in [
+            "linearly constrained",
+            "nonlinearly constrained",
+        ]:
+            aub, bub, aeq, beq = (
+                self.get_constraint_linearizations(self.x_best))
+            tol_bd = get_arrays_tol(xl, xu)
+            tol_ub = get_arrays_tol(bub)
+            free_xl = xl <= -tol_bd
+            free_xu = xu >= tol_bd
+            free_ub = bub >= tol_ub
+
+            # Compute the Cauchy step.
+            n_act, q = qr_tangential_byrd_omojokun(
+                aub,
+                aeq,
+                free_xl,
+                free_xu,
+                free_ub,
+            )
+            g_lag_proj = q[:, n_act:] @ (q[:, n_act:].T @ g_lag)
+            norm_g_lag_proj = np.linalg.norm(g_lag_proj)
+            if 0 < n_act < self._pb.n and norm_g_lag_proj > TINY * self.radius:
+                step_alt = (self.radius / norm_g_lag_proj) * g_lag_proj
+                if lag.curv(step_alt, self.models.interpolation) < 0.0:
+                    step_alt = -step_alt
+
+                # Evaluate the constraint violation at the Cauchy step.
+                cbd = np.block([xl - step_alt, step_alt - xu])
+                cub = aub @ step_alt - bub
+                ceq = aeq @ step_alt - beq
+                maxcv_val = max(
+                    np.max(array, initial=0.0)
+                    for array in [cbd, cub, np.abs(ceq)]
+                )
+
+                # Accept the new step if it is nearly feasible and do not
+                # drastically worsen the determinant of the interpolation
+                # system in absolute value.
+                tol = np.max(np.abs(step_alt[~free_xl]), initial=0.0)
+                tol = np.max(np.abs(step_alt[~free_xu]), initial=tol)
+                tol = np.max(np.abs(aub[~free_ub, :] @ step_alt), initial=tol)
+                tol = min(10.0 * tol, 1e-2 * np.linalg.norm(step_alt))
+                if maxcv_val <= tol:
+                    sigma_alt = self.models.determinants(
+                        self.x_best + step_alt, k_new
+                    )
+                    if abs(sigma_alt) >= 0.1 * abs(sigma):
+                        step = np.clip(step_alt, xl, xu)
+
+        if options[Options.DEBUG]:
+            tol = get_arrays_tol(xl, xu)
+            if np.any(step + tol < xl) or np.any(xu < step - tol):
+                warnings.warn(
+                    "The geometry step does not respect the bound "
+                    "constraints.",
+                    RuntimeWarning,
+                    2,
+                )
+            if np.linalg.norm(step) > 1.1 * self.radius:
+                warnings.warn(
+                    "The geometry step does not respect the "
+                    "trust-region constraint.",
+                    RuntimeWarning,
+                    2,
+                )
+        return step
+
+    def get_second_order_correction_step(self, step, options):
+        """
+        Get the second-order correction step.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Trust-region step.
+        options : dict
+            Options of the solver.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Second-order correction step.
+        """
+        # Evaluate the linearizations of the constraints.
+        aub, bub, aeq, beq = self.get_constraint_linearizations(self.x_best)
+        xl = self._pb.bounds.xl - self.x_best
+        xu = self._pb.bounds.xu - self.x_best
+        radius = np.linalg.norm(step)
+        soc_step = normal_byrd_omojokun(
+            aub,
+            bub,
+            aeq,
+            beq,
+            xl,
+            xu,
+            radius,
+            options[Options.DEBUG],
+            **self._constants,
+        )
+        if options[Options.DEBUG]:
+            tol = get_arrays_tol(xl, xu)
+            if np.any(soc_step + tol < xl) or np.any(xu < soc_step - tol):
+                warnings.warn(
+                    "The second-order correction step does not "
+                    "respect the bound constraints.",
+                    RuntimeWarning,
+                    2,
+                )
+            if np.linalg.norm(soc_step) > 1.1 * radius:
+                warnings.warn(
+                    "The second-order correction step does not "
+                    "respect the trust-region constraint.",
+                    RuntimeWarning,
+                    2,
+                )
+        return soc_step
+
+    def get_reduction_ratio(self, step, fun_val, cub_val, ceq_val):
+        """
+        Get the reduction ratio.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Trust-region step.
+        fun_val : float
+            Objective function value at the trial point.
+        cub_val : `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Nonlinear inequality constraint values at the trial point.
+        ceq_val : `numpy.ndarray`, shape (m_nonlinear_eq,)
+            Nonlinear equality constraint values at the trial point.
+
+        Returns
+        -------
+        float
+            Reduction ratio.
+        """
+        merit_old = self.merit(
+            self.x_best,
+            self.fun_best,
+            self.cub_best,
+            self.ceq_best,
+        )
+        merit_new = self.merit(self.x_best + step, fun_val, cub_val, ceq_val)
+        merit_model_old = self.merit(
+            self.x_best,
+            0.0,
+            self.models.cub(self.x_best),
+            self.models.ceq(self.x_best),
+        )
+        merit_model_new = self.merit(
+            self.x_best + step,
+            self.sqp_fun(step),
+            self.sqp_cub(step),
+            self.sqp_ceq(step),
+        )
+        if abs(merit_model_old - merit_model_new) > TINY * abs(
+            merit_old - merit_new
+        ):
+            return (merit_old - merit_new) / abs(
+                merit_model_old - merit_model_new
+            )
+        else:
+            return -1.0
+
+    def increase_penalty(self, step):
+        """
+        Increase the penalty parameter.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Trust-region step.
+        """
+        aub, bub, aeq, beq = self.get_constraint_linearizations(self.x_best)
+        viol_diff = max(
+            np.linalg.norm(
+                np.block(
+                    [
+                        np.maximum(0.0, -bub),
+                        beq,
+                    ]
+                )
+            )
+            - np.linalg.norm(
+                np.block(
+                    [
+                        np.maximum(0.0, aub @ step - bub),
+                        aeq @ step - beq,
+                    ]
+                )
+            ),
+            0.0,
+        )
+        sqp_val = self.sqp_fun(step)
+
+        threshold = np.linalg.norm(
+            np.block(
+                [
+                    self._lm_linear_ub,
+                    self._lm_linear_eq,
+                    self._lm_nonlinear_ub,
+                    self._lm_nonlinear_eq,
+                ]
+            )
+        )
+        if abs(viol_diff) > TINY * abs(sqp_val):
+            threshold = max(threshold, sqp_val / viol_diff)
+        best_index_save = self.best_index
+        if (
+            self._penalty
+            <= self._constants[Constants.PENALTY_INCREASE_THRESHOLD]
+                * threshold
+        ):
+            self._penalty = max(
+                self._constants[Constants.PENALTY_INCREASE_FACTOR] * threshold,
+                1.0,
+            )
+            self.set_best_index()
+        return best_index_save == self.best_index
+
+    def decrease_penalty(self):
+        """
+        Decrease the penalty parameter.
+        """
+        self._penalty = min(self._penalty, self._get_low_penalty())
+        self.set_best_index()
+
+    def set_best_index(self):
+        """
+        Set the index of the best point.
+        """
+        best_index = self.best_index
+        m_best = self.merit(
+            self.x_best,
+            self.models.fun_val[best_index],
+            self.models.cub_val[best_index, :],
+            self.models.ceq_val[best_index, :],
+        )
+        r_best = self._pb.maxcv(
+            self.x_best,
+            self.models.cub_val[best_index, :],
+            self.models.ceq_val[best_index, :],
+        )
+        tol = (
+            10.0
+            * EPS
+            * max(self.models.n, self.models.npt)
+            * max(abs(m_best), 1.0)
+        )
+        for k in range(self.models.npt):
+            if k != self.best_index:
+                x_val = self.models.interpolation.point(k)
+                m_val = self.merit(
+                    x_val,
+                    self.models.fun_val[k],
+                    self.models.cub_val[k, :],
+                    self.models.ceq_val[k, :],
+                )
+                r_val = self._pb.maxcv(
+                    x_val,
+                    self.models.cub_val[k, :],
+                    self.models.ceq_val[k, :],
+                )
+                if m_val < m_best or (m_val < m_best + tol and r_val < r_best):
+                    best_index = k
+                    m_best = m_val
+                    r_best = r_val
+        self._best_index = best_index
+
+    def get_index_to_remove(self, x_new=None):
+        """
+        Get the index of the interpolation point to remove.
+
+        If `x_new` is not provided, the index returned should be used during
+        the geometry-improvement phase. Otherwise, the index returned is the
+        best index for included `x_new` in the interpolation set.
+
+        Parameters
+        ----------
+        x_new : `numpy.ndarray`, shape (n,), optional
+            New point to be included in the interpolation set.
+
+        Returns
+        -------
+        int
+            Index of the interpolation point to remove.
+        float
+            Distance between `x_best` and the removed point.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the computation of a determinant fails.
+        """
+        dist_sq = np.sum(
+            (
+                self.models.interpolation.xpt
+                - self.models.interpolation.xpt[:, self.best_index, np.newaxis]
+            )
+            ** 2.0,
+            axis=0,
+        )
+        if x_new is None:
+            sigma = 1.0
+            weights = dist_sq
+        else:
+            sigma = self.models.determinants(x_new)
+            weights = (
+                np.maximum(
+                    1.0,
+                    dist_sq
+                    / max(
+                        self._constants[Constants.LOW_RADIUS_FACTOR]
+                        * self.radius,
+                        self.resolution,
+                    )
+                    ** 2.0,
+                )
+                ** 3.0
+            )
+            weights[self.best_index] = -1.0  # do not remove the best point
+        k_max = np.argmax(weights * np.abs(sigma))
+        return k_max, np.sqrt(dist_sq[k_max])
+
+    def update_radius(self, step, ratio):
+        """
+        Update the trust-region radius.
+
+        Parameters
+        ----------
+        step : `numpy.ndarray`, shape (n,)
+            Trust-region step.
+        ratio : float
+            Reduction ratio.
+        """
+        s_norm = np.linalg.norm(step)
+        if ratio <= self._constants[Constants.LOW_RATIO]:
+            self.radius *= self._constants[Constants.DECREASE_RADIUS_FACTOR]
+        elif ratio <= self._constants[Constants.HIGH_RATIO]:
+            self.radius = max(
+                self._constants[Constants.DECREASE_RADIUS_FACTOR]
+                * self.radius,
+                s_norm,
+            )
+        else:
+            self.radius = min(
+                self._constants[Constants.INCREASE_RADIUS_FACTOR]
+                * self.radius,
+                max(
+                    self._constants[Constants.DECREASE_RADIUS_FACTOR]
+                    * self.radius,
+                    self._constants[Constants.INCREASE_RADIUS_THRESHOLD]
+                    * s_norm,
+                ),
+            )
+
+    def enhance_resolution(self, options):
+        """
+        Enhance the resolution of the trust-region framework.
+
+        Parameters
+        ----------
+        options : dict
+            Options of the solver.
+        """
+        if (
+            self._constants[Constants.LARGE_RESOLUTION_THRESHOLD]
+            * options[Options.RHOEND]
+            < self.resolution
+        ):
+            self.resolution *= self._constants[
+                Constants.DECREASE_RESOLUTION_FACTOR
+            ]
+        elif (
+            self._constants[Constants.MODERATE_RESOLUTION_THRESHOLD]
+            * options[Options.RHOEND]
+            < self.resolution
+        ):
+            self.resolution = np.sqrt(self.resolution
+                                      * options[Options.RHOEND])
+        else:
+            self.resolution = options[Options.RHOEND]
+
+        # Reduce the trust-region radius.
+        self._radius = max(
+            self._constants[Constants.DECREASE_RADIUS_FACTOR] * self._radius,
+            self.resolution,
+        )
+
+    def shift_x_base(self, options):
+        """
+        Shift the base point to `x_best`.
+
+        Parameters
+        ----------
+        options : dict
+            Options of the solver.
+        """
+        self.models.shift_x_base(np.copy(self.x_best), options)
+
+    def set_multipliers(self, x):
+        """
+        Set the Lagrange multipliers.
+
+        This method computes and set the Lagrange multipliers of the linear and
+        nonlinear constraints to be the QP multipliers.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the Lagrange multipliers are computed.
+        """
+        # Build the constraints of the least-squares problem.
+        incl_linear_ub = self._pb.linear.a_ub @ x >= self._pb.linear.b_ub
+        incl_nonlinear_ub = self.cub_best >= 0.0
+        incl_xl = self._pb.bounds.xl >= x
+        incl_xu = self._pb.bounds.xu <= x
+        m_linear_ub = np.count_nonzero(incl_linear_ub)
+        m_nonlinear_ub = np.count_nonzero(incl_nonlinear_ub)
+        m_xl = np.count_nonzero(incl_xl)
+        m_xu = np.count_nonzero(incl_xu)
+
+        if (
+            m_linear_ub + m_nonlinear_ub + self.m_linear_eq
+                + self.m_nonlinear_eq > 0
+        ):
+            identity = np.eye(self._pb.n)
+            c_jac = np.r_[
+                -identity[incl_xl, :],
+                identity[incl_xu, :],
+                self._pb.linear.a_ub[incl_linear_ub, :],
+                self.models.cub_grad(x, incl_nonlinear_ub),
+                self._pb.linear.a_eq,
+                self.models.ceq_grad(x),
+            ]
+
+            # Solve the least-squares problem.
+            g_best = self.models.fun_grad(x)
+            xl_lm = np.full(c_jac.shape[0], -np.inf)
+            xl_lm[: m_xl + m_xu + m_linear_ub + m_nonlinear_ub] = 0.0
+            res = lsq_linear(
+                c_jac.T,
+                -g_best,
+                bounds=(xl_lm, np.inf),
+                method="bvls",
+            )
+
+            # Extract the Lagrange multipliers.
+            self._lm_linear_ub[incl_linear_ub] = res.x[
+                m_xl + m_xu:m_xl + m_xu + m_linear_ub
+            ]
+            self._lm_linear_ub[~incl_linear_ub] = 0.0
+            self._lm_nonlinear_ub[incl_nonlinear_ub] = res.x[
+                m_xl
+                + m_xu
+                + m_linear_ub:m_xl
+                + m_xu
+                + m_linear_ub
+                + m_nonlinear_ub
+            ]
+            self._lm_nonlinear_ub[~incl_nonlinear_ub] = 0.0
+            self._lm_linear_eq[:] = res.x[
+                m_xl
+                + m_xu
+                + m_linear_ub
+                + m_nonlinear_ub:m_xl
+                + m_xu
+                + m_linear_ub
+                + m_nonlinear_ub
+                + self.m_linear_eq
+            ]
+            self._lm_nonlinear_eq[:] = res.x[
+                m_xl + m_xu + m_linear_ub + m_nonlinear_ub + self.m_linear_eq:
+            ]
+
+    def _get_low_penalty(self):
+        r_val_ub = np.c_[
+            (
+                self.models.interpolation.x_base[np.newaxis, :]
+                + self.models.interpolation.xpt.T
+            )
+            @ self._pb.linear.a_ub.T
+            - self._pb.linear.b_ub[np.newaxis, :],
+            self.models.cub_val,
+        ]
+        r_val_eq = (
+            self.models.interpolation.x_base[np.newaxis, :]
+            + self.models.interpolation.xpt.T
+        ) @ self._pb.linear.a_eq.T - self._pb.linear.b_eq[np.newaxis, :]
+        r_val_eq = np.block(
+            [
+                r_val_eq,
+                -r_val_eq,
+                self.models.ceq_val,
+                -self.models.ceq_val,
+            ]
+        )
+        r_val = np.block([r_val_ub, r_val_eq])
+        c_min = np.nanmin(r_val, axis=0)
+        c_max = np.nanmax(r_val, axis=0)
+        indices = (
+            c_min
+            < self._constants[Constants.THRESHOLD_RATIO_CONSTRAINTS] * c_max
+        )
+        if np.any(indices):
+            f_min = np.nanmin(self.models.fun_val)
+            f_max = np.nanmax(self.models.fun_val)
+            c_min_neg = np.minimum(0.0, c_min[indices])
+            c_diff = np.min(c_max[indices] - c_min_neg)
+            if c_diff > TINY * (f_max - f_min):
+                penalty = (f_max - f_min) / c_diff
+            else:
+                penalty = np.inf
+        else:
+            penalty = 0.0
+        return penalty

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/main.py

@@ -0,0 +1,1506 @@
+import warnings
+
+import numpy as np
+from scipy.optimize import (
+    Bounds,
+    LinearConstraint,
+    NonlinearConstraint,
+    OptimizeResult,
+)
+
+from .framework import TrustRegion
+from .problem import (
+    ObjectiveFunction,
+    BoundConstraints,
+    LinearConstraints,
+    NonlinearConstraints,
+    Problem,
+)
+from .utils import (
+    MaxEvalError,
+    TargetSuccess,
+    CallbackSuccess,
+    FeasibleSuccess,
+    exact_1d_array,
+)
+from .settings import (
+    ExitStatus,
+    Options,
+    Constants,
+    DEFAULT_OPTIONS,
+    DEFAULT_CONSTANTS,
+    PRINT_OPTIONS,
+)
+
+
+def minimize(
+    fun,
+    x0,
+    args=(),
+    bounds=None,
+    constraints=(),
+    callback=None,
+    options=None,
+    **kwargs,
+):
+    r"""
+    Minimize a scalar function using the COBYQA method.
+
+    The Constrained Optimization BY Quadratic Approximations (COBYQA) method is
+    a derivative-free optimization method designed to solve general nonlinear
+    optimization problems. A complete description of COBYQA is given in [3]_.
+
+    Parameters
+    ----------
+    fun : {callable, None}
+        Objective function to be minimized.
+
+            ``fun(x, *args) -> float``
+
+        where ``x`` is an array with shape (n,) and `args` is a tuple. If `fun`
+        is ``None``, the objective function is assumed to be the zero function,
+        resulting in a feasibility problem.
+    x0 : array_like, shape (n,)
+        Initial guess.
+    args : tuple, optional
+        Extra arguments passed to the objective function.
+    bounds : {`scipy.optimize.Bounds`, array_like, shape (n, 2)}, optional
+        Bound constraints of the problem. It can be one of the cases below.
+
+        #. An instance of `scipy.optimize.Bounds`. For the time being, the
+           argument ``keep_feasible`` is disregarded, and all the constraints
+           are considered unrelaxable and will be enforced.
+        #. An array with shape (n, 2). The bound constraints for ``x[i]`` are
+           ``bounds[i][0] <= x[i] <= bounds[i][1]``. Set ``bounds[i][0]`` to
+           :math:`-\infty` if there is no lower bound, and set ``bounds[i][1]``
+           to :math:`\infty` if there is no upper bound.
+
+        The COBYQA method always respect the bound constraints.
+    constraints : {Constraint, list}, optional
+        General constraints of the problem. It can be one of the cases below.
+
+        #. An instance of `scipy.optimize.LinearConstraint`. The argument
+           ``keep_feasible`` is disregarded.
+        #. An instance of `scipy.optimize.NonlinearConstraint`. The arguments
+           ``jac``, ``hess``, ``keep_feasible``, ``finite_diff_rel_step``, and
+           ``finite_diff_jac_sparsity`` are disregarded.
+
+        #. A list, each of whose elements are described in the cases above.
+
+    callback : callable, optional
+        A callback executed at each objective function evaluation. The method
+        terminates if a ``StopIteration`` exception is raised by the callback
+        function. Its signature can be one of the following:
+
+            ``callback(intermediate_result)``
+
+        where ``intermediate_result`` is a keyword parameter that contains an
+        instance of `scipy.optimize.OptimizeResult`, with attributes ``x``
+        and ``fun``, being the point at which the objective function is
+        evaluated and the value of the objective function, respectively. The
+        name of the parameter must be ``intermediate_result`` for the callback
+        to be passed an instance of `scipy.optimize.OptimizeResult`.
+
+        Alternatively, the callback function can have the signature:
+
+            ``callback(xk)``
+
+        where ``xk`` is the point at which the objective function is evaluated.
+        Introspection is used to determine which of the signatures to invoke.
+    options : dict, optional
+        Options passed to the solver. Accepted keys are:
+
+            disp : bool, optional
+                Whether to print information about the optimization procedure.
+                Default is ``False``.
+            maxfev : int, optional
+                Maximum number of function evaluations. Default is ``500 * n``.
+            maxiter : int, optional
+                Maximum number of iterations. Default is ``1000 * n``.
+            target : float, optional
+                Target on the objective function value. The optimization
+                procedure is terminated when the objective function value of a
+                feasible point is less than or equal to this target. Default is
+                ``-numpy.inf``.
+            feasibility_tol : float, optional
+                Tolerance on the constraint violation. If the maximum
+                constraint violation at a point is less than or equal to this
+                tolerance, the point is considered feasible. Default is
+                ``numpy.sqrt(numpy.finfo(float).eps)``.
+            radius_init : float, optional
+                Initial trust-region radius. Typically, this value should be in
+                the order of one tenth of the greatest expected change to `x0`.
+                Default is ``1.0``.
+            radius_final : float, optional
+                Final trust-region radius. It should indicate the accuracy
+                required in the final values of the variables. Default is
+                ``1e-6``.
+            nb_points : int, optional
+                Number of interpolation points used to build the quadratic
+                models of the objective and constraint functions. Default is
+                ``2 * n + 1``.
+            scale : bool, optional
+                Whether to scale the variables according to the bounds. Default
+                is ``False``.
+            filter_size : int, optional
+                Maximum number of points in the filter. The filter is used to
+                select the best point returned by the optimization procedure.
+                Default is ``sys.maxsize``.
+            store_history : bool, optional
+                Whether to store the history of the function evaluations.
+                Default is ``False``.
+            history_size : int, optional
+                Maximum number of function evaluations to store in the history.
+                Default is ``sys.maxsize``.
+            debug : bool, optional
+                Whether to perform additional checks during the optimization
+                procedure. This option should be used only for debugging
+                purposes and is highly discouraged to general users. Default is
+                ``False``.
+
+        Other constants (from the keyword arguments) are described below. They
+        are not intended to be changed by general users. They should only be
+        changed by users with a deep understanding of the algorithm, who want
+        to experiment with different settings.
+
+    Returns
+    -------
+    `scipy.optimize.OptimizeResult`
+        Result of the optimization procedure, with the following fields:
+
+            message : str
+                Description of the cause of the termination.
+            success : bool
+                Whether the optimization procedure terminated successfully.
+            status : int
+                Termination status of the optimization procedure.
+            x : `numpy.ndarray`, shape (n,)
+                Solution point.
+            fun : float
+                Objective function value at the solution point.
+            maxcv : float
+                Maximum constraint violation at the solution point.
+            nfev : int
+                Number of function evaluations.
+            nit : int
+                Number of iterations.
+
+        If ``store_history`` is True, the result also has the following fields:
+
+            fun_history : `numpy.ndarray`, shape (nfev,)
+                History of the objective function values.
+            maxcv_history : `numpy.ndarray`, shape (nfev,)
+                History of the maximum constraint violations.
+
+        A description of the termination statuses is given below.
+
+        .. list-table::
+            :widths: 25 75
+            :header-rows: 1
+
+            * - Exit status
+              - Description
+            * - 0
+              - The lower bound for the trust-region radius has been reached.
+            * - 1
+              - The target objective function value has been reached.
+            * - 2
+              - All variables are fixed by the bound constraints.
+            * - 3
+              - The callback requested to stop the optimization procedure.
+            * - 4
+              - The feasibility problem received has been solved successfully.
+            * - 5
+              - The maximum number of function evaluations has been exceeded.
+            * - 6
+              - The maximum number of iterations has been exceeded.
+            * - -1
+              - The bound constraints are infeasible.
+            * - -2
+              - A linear algebra error occurred.
+
+    Other Parameters
+    ----------------
+    decrease_radius_factor : float, optional
+        Factor by which the trust-region radius is reduced when the reduction
+        ratio is low or negative. Default is ``0.5``.
+    increase_radius_factor : float, optional
+        Factor by which the trust-region radius is increased when the reduction
+        ratio is large. Default is ``numpy.sqrt(2.0)``.
+    increase_radius_threshold : float, optional
+        Threshold that controls the increase of the trust-region radius when
+        the reduction ratio is large. Default is ``2.0``.
+    decrease_radius_threshold : float, optional
+        Threshold used to determine whether the trust-region radius should be
+        reduced to the resolution. Default is ``1.4``.
+    decrease_resolution_factor : float, optional
+        Factor by which the resolution is reduced when the current value is far
+        from its final value. Default is ``0.1``.
+    large_resolution_threshold : float, optional
+        Threshold used to determine whether the resolution is far from its
+        final value. Default is ``250.0``.
+    moderate_resolution_threshold : float, optional
+        Threshold used to determine whether the resolution is close to its
+        final value. Default is ``16.0``.
+    low_ratio : float, optional
+        Threshold used to determine whether the reduction ratio is low. Default
+        is ``0.1``.
+    high_ratio : float, optional
+        Threshold used to determine whether the reduction ratio is high.
+        Default is ``0.7``.
+    very_low_ratio : float, optional
+        Threshold used to determine whether the reduction ratio is very low.
+        This is used to determine whether the models should be reset. Default
+        is ``0.01``.
+    penalty_increase_threshold : float, optional
+        Threshold used to determine whether the penalty parameter should be
+        increased. Default is ``1.5``.
+    penalty_increase_factor : float, optional
+        Factor by which the penalty parameter is increased. Default is ``2.0``.
+    short_step_threshold : float, optional
+        Factor used to determine whether the trial step is too short. Default
+        is ``0.5``.
+    low_radius_factor : float, optional
+        Factor used to determine which interpolation point should be removed
+        from the interpolation set at each iteration. Default is ``0.1``.
+    byrd_omojokun_factor : float, optional
+        Factor by which the trust-region radius is reduced for the computations
+        of the normal step in the Byrd-Omojokun composite-step approach.
+        Default is ``0.8``.
+    threshold_ratio_constraints : float, optional
+        Threshold used to determine which constraints should be taken into
+        account when decreasing the penalty parameter. Default is ``2.0``.
+    large_shift_factor : float, optional
+        Factor used to determine whether the point around which the quadratic
+        models are built should be updated. Default is ``10.0``.
+    large_gradient_factor : float, optional
+        Factor used to determine whether the models should be reset. Default is
+        ``10.0``.
+    resolution_factor : float, optional
+        Factor by which the resolution is decreased. Default is ``2.0``.
+    improve_tcg : bool, optional
+        Whether to improve the steps computed by the truncated conjugate
+        gradient method when the trust-region boundary is reached. Default is
+        ``True``.
+
+    References
+    ----------
+    .. [1] J. Nocedal and S. J. Wright. *Numerical Optimization*. Springer Ser.
+       Oper. Res. Financ. Eng. Springer, New York, NY, USA, second edition,
+       2006. `doi:10.1007/978-0-387-40065-5
+       <https://doi.org/10.1007/978-0-387-40065-5>`_.
+    .. [2] M. J. D. Powell. A direct search optimization method that models the
+       objective and constraint functions by linear interpolation. In S. Gomez
+       and J.-P. Hennart, editors, *Advances in Optimization and Numerical
+       Analysis*, volume 275 of Math. Appl., pages 51--67. Springer, Dordrecht,
+       Netherlands, 1994. `doi:10.1007/978-94-015-8330-5_4
+       <https://doi.org/10.1007/978-94-015-8330-5_4>`_.
+    .. [3] T. M. Ragonneau. *Model-Based Derivative-Free Optimization Methods
+       and Software*. PhD thesis, Department of Applied Mathematics, The Hong
+       Kong Polytechnic University, Hong Kong, China, 2022. URL:
+       https://theses.lib.polyu.edu.hk/handle/200/12294.
+
+    Examples
+    --------
+    To demonstrate how to use `minimize`, we first minimize the Rosenbrock
+    function implemented in `scipy.optimize` in an unconstrained setting.
+
+    .. testsetup::
+
+        import numpy as np
+        np.set_printoptions(precision=3, suppress=True)
+
+    >>> from cobyqa import minimize
+    >>> from scipy.optimize import rosen
+
+    To solve the problem using COBYQA, run:
+
+    >>> x0 = [1.3, 0.7, 0.8, 1.9, 1.2]
+    >>> res = minimize(rosen, x0)
+    >>> res.x
+    array([1., 1., 1., 1., 1.])
+
+    To see how bound and constraints are handled using `minimize`, we solve
+    Example 16.4 of [1]_, defined as
+
+    .. math::
+
+        \begin{aligned}
+            \min_{x \in \mathbb{R}^2}   & \quad (x_1 - 1)^2 + (x_2 - 2.5)^2\\
+            \text{s.t.}                 & \quad -x_1 + 2x_2 \le 2,\\
+                                        & \quad x_1 + 2x_2 \le 6,\\
+                                        & \quad x_1 - 2x_2 \le 2,\\
+                                        & \quad x_1 \ge 0,\\
+                                        & \quad x_2 \ge 0.
+        \end{aligned}
+
+    >>> import numpy as np
+    >>> from scipy.optimize import Bounds, LinearConstraint
+
+    Its objective function can be implemented as:
+
+    >>> def fun(x):
+    ...     return (x[0] - 1.0)**2 + (x[1] - 2.5)**2
+
+    This problem can be solved using `minimize` as:
+
+    >>> x0 = [2.0, 0.0]
+    >>> bounds = Bounds([0.0, 0.0], np.inf)
+    >>> constraints = LinearConstraint([
+    ...     [-1.0, 2.0],
+    ...     [1.0, 2.0],
+    ...     [1.0, -2.0],
+    ... ], -np.inf, [2.0, 6.0, 2.0])
+    >>> res = minimize(fun, x0, bounds=bounds, constraints=constraints)
+    >>> res.x
+    array([1.4, 1.7])
+
+    To see how nonlinear constraints are handled, we solve Problem (F) of [2]_,
+    defined as
+
+    .. math::
+
+        \begin{aligned}
+            \min_{x \in \mathbb{R}^2}   & \quad -x_1 - x_2\\
+            \text{s.t.}                 & \quad x_1^2 - x_2 \le 0,\\
+                                        & \quad x_1^2 + x_2^2 \le 1.
+        \end{aligned}
+
+    >>> from scipy.optimize import NonlinearConstraint
+
+    Its objective and constraint functions can be implemented as:
+
+    >>> def fun(x):
+    ...     return -x[0] - x[1]
+    >>>
+    >>> def cub(x):
+    ...     return [x[0]**2 - x[1], x[0]**2 + x[1]**2]
+
+    This problem can be solved using `minimize` as:
+
+    >>> x0 = [1.0, 1.0]
+    >>> constraints = NonlinearConstraint(cub, -np.inf, [0.0, 1.0])
+    >>> res = minimize(fun, x0, constraints=constraints)
+    >>> res.x
+    array([0.707, 0.707])
+
+    Finally, to see how to supply linear and nonlinear constraints
+    simultaneously, we solve Problem (G) of [2]_, defined as
+
+    .. math::
+
+        \begin{aligned}
+            \min_{x \in \mathbb{R}^3}   & \quad x_3\\
+            \text{s.t.}                 & \quad 5x_1 - x_2 + x_3 \ge 0,\\
+                                        & \quad -5x_1 - x_2 + x_3 \ge 0,\\
+                                        & \quad x_1^2 + x_2^2 + 4x_2 \le x_3.
+        \end{aligned}
+
+    Its objective and nonlinear constraint functions can be implemented as:
+
+    >>> def fun(x):
+    ...     return x[2]
+    >>>
+    >>> def cub(x):
+    ...     return x[0]**2 + x[1]**2 + 4.0*x[1] - x[2]
+
+    This problem can be solved using `minimize` as:
+
+    >>> x0 = [1.0, 1.0, 1.0]
+    >>> constraints = [
+    ...     LinearConstraint(
+    ...         [[5.0, -1.0, 1.0], [-5.0, -1.0, 1.0]],
+    ...         [0.0, 0.0],
+    ...         np.inf,
+    ...     ),
+    ...     NonlinearConstraint(cub, -np.inf, 0.0),
+    ... ]
+    >>> res = minimize(fun, x0, constraints=constraints)
+    >>> res.x
+    array([ 0., -3., -3.])
+    """
+    # Get basic options that are needed for the initialization.
+    if options is None:
+        options = {}
+    else:
+        options = dict(options)
+    verbose = options.get(Options.VERBOSE, DEFAULT_OPTIONS[Options.VERBOSE])
+    verbose = bool(verbose)
+    feasibility_tol = options.get(
+        Options.FEASIBILITY_TOL,
+        DEFAULT_OPTIONS[Options.FEASIBILITY_TOL],
+    )
+    feasibility_tol = float(feasibility_tol)
+    scale = options.get(Options.SCALE, DEFAULT_OPTIONS[Options.SCALE])
+    scale = bool(scale)
+    store_history = options.get(
+        Options.STORE_HISTORY,
+        DEFAULT_OPTIONS[Options.STORE_HISTORY],
+    )
+    store_history = bool(store_history)
+    if Options.HISTORY_SIZE in options and options[Options.HISTORY_SIZE] <= 0:
+        raise ValueError("The size of the history must be positive.")
+    history_size = options.get(
+        Options.HISTORY_SIZE,
+        DEFAULT_OPTIONS[Options.HISTORY_SIZE],
+    )
+    history_size = int(history_size)
+    if Options.FILTER_SIZE in options and options[Options.FILTER_SIZE] <= 0:
+        raise ValueError("The size of the filter must be positive.")
+    filter_size = options.get(
+        Options.FILTER_SIZE,
+        DEFAULT_OPTIONS[Options.FILTER_SIZE],
+    )
+    filter_size = int(filter_size)
+    debug = options.get(Options.DEBUG, DEFAULT_OPTIONS[Options.DEBUG])
+    debug = bool(debug)
+
+    # Initialize the objective function.
+    if not isinstance(args, tuple):
+        args = (args,)
+    obj = ObjectiveFunction(fun, verbose, debug, *args)
+
+    # Initialize the bound constraints.
+    if not hasattr(x0, "__len__"):
+        x0 = [x0]
+    n_orig = len(x0)
+    bounds = BoundConstraints(_get_bounds(bounds, n_orig))
+
+    # Initialize the constraints.
+    linear_constraints, nonlinear_constraints = _get_constraints(constraints)
+    linear = LinearConstraints(linear_constraints, n_orig, debug)
+    nonlinear = NonlinearConstraints(nonlinear_constraints, verbose, debug)
+
+    # Initialize the problem (and remove the fixed variables).
+    pb = Problem(
+        obj,
+        x0,
+        bounds,
+        linear,
+        nonlinear,
+        callback,
+        feasibility_tol,
+        scale,
+        store_history,
+        history_size,
+        filter_size,
+        debug,
+    )
+
+    # Set the default options.
+    _set_default_options(options, pb.n)
+    constants = _set_default_constants(**kwargs)
+
+    # Initialize the models and skip the computations whenever possible.
+    if not pb.bounds.is_feasible:
+        # The bound constraints are infeasible.
+        return _build_result(
+            pb,
+            0.0,
+            False,
+            ExitStatus.INFEASIBLE_ERROR,
+            0,
+            options,
+        )
+    elif pb.n == 0:
+        # All variables are fixed by the bound constraints.
+        return _build_result(
+            pb,
+            0.0,
+            True,
+            ExitStatus.FIXED_SUCCESS,
+            0,
+            options,
+        )
+    if verbose:
+        print("Starting the optimization procedure.")
+        print(f"Initial trust-region radius: {options[Options.RHOBEG]}.")
+        print(f"Final trust-region radius: {options[Options.RHOEND]}.")
+        print(
+            f"Maximum number of function evaluations: "
+            f"{options[Options.MAX_EVAL]}."
+        )
+        print(f"Maximum number of iterations: {options[Options.MAX_ITER]}.")
+        print()
+    try:
+        framework = TrustRegion(pb, options, constants)
+    except TargetSuccess:
+        # The target on the objective function value has been reached
+        return _build_result(
+            pb,
+            0.0,
+            True,
+            ExitStatus.TARGET_SUCCESS,
+            0,
+            options,
+        )
+    except CallbackSuccess:
+        # The callback raised a StopIteration exception.
+        return _build_result(
+            pb,
+            0.0,
+            True,
+            ExitStatus.CALLBACK_SUCCESS,
+            0,
+            options,
+        )
+    except FeasibleSuccess:
+        # The feasibility problem has been solved successfully.
+        return _build_result(
+            pb,
+            0.0,
+            True,
+            ExitStatus.FEASIBLE_SUCCESS,
+            0,
+            options,
+        )
+    except MaxEvalError:
+        # The maximum number of function evaluations has been exceeded.
+        return _build_result(
+            pb,
+            0.0,
+            False,
+            ExitStatus.MAX_ITER_WARNING,
+            0,
+            options,
+        )
+    except np.linalg.LinAlgError:
+        # The construction of the initial interpolation set failed.
+        return _build_result(
+            pb,
+            0.0,
+            False,
+            ExitStatus.LINALG_ERROR,
+            0,
+            options,
+        )
+
+    # Start the optimization procedure.
+    success = False
+    n_iter = 0
+    k_new = None
+    n_short_steps = 0
+    n_very_short_steps = 0
+    n_alt_models = 0
+    while True:
+        # Stop the optimization procedure if the maximum number of iterations
+        # has been exceeded. We do not write the main loop as a for loop
+        # because we want to access the number of iterations outside the loop.
+        if n_iter >= options[Options.MAX_ITER]:
+            status = ExitStatus.MAX_ITER_WARNING
+            break
+        n_iter += 1
+
+        # Update the point around which the quadratic models are built.
+        if (
+            np.linalg.norm(
+                framework.x_best - framework.models.interpolation.x_base
+            )
+            >= constants[Constants.LARGE_SHIFT_FACTOR] * framework.radius
+        ):
+            framework.shift_x_base(options)
+
+        # Evaluate the trial step.
+        radius_save = framework.radius
+        normal_step, tangential_step = framework.get_trust_region_step(options)
+        step = normal_step + tangential_step
+        s_norm = np.linalg.norm(step)
+
+        # If the trial step is too short, we do not attempt to evaluate the
+        # objective and constraint functions. Instead, we reduce the
+        # trust-region radius and check whether the resolution should be
+        # enhanced and whether the geometry of the interpolation set should be
+        # improved. Otherwise, we entertain a classical iteration. The
+        # criterion for performing an exceptional jump is taken from NEWUOA.
+        if (
+            s_norm
+            <= constants[Constants.SHORT_STEP_THRESHOLD] * framework.resolution
+        ):
+            framework.radius *= constants[Constants.DECREASE_RESOLUTION_FACTOR]
+            if radius_save > framework.resolution:
+                n_short_steps = 0
+                n_very_short_steps = 0
+            else:
+                n_short_steps += 1
+                n_very_short_steps += 1
+                if s_norm > 0.1 * framework.resolution:
+                    n_very_short_steps = 0
+            enhance_resolution = n_short_steps >= 5 or n_very_short_steps >= 3
+            if enhance_resolution:
+                n_short_steps = 0
+                n_very_short_steps = 0
+                improve_geometry = False
+            else:
+                try:
+                    k_new, dist_new = framework.get_index_to_remove()
+                except np.linalg.LinAlgError:
+                    status = ExitStatus.LINALG_ERROR
+                    break
+                improve_geometry = dist_new > max(
+                    framework.radius,
+                    constants[Constants.RESOLUTION_FACTOR]
+                    * framework.resolution,
+                )
+        else:
+            # Increase the penalty parameter if necessary.
+            same_best_point = framework.increase_penalty(step)
+            if same_best_point:
+                # Evaluate the objective and constraint functions.
+                try:
+                    fun_val, cub_val, ceq_val = _eval(
+                        pb,
+                        framework,
+                        step,
+                        options,
+                    )
+                except TargetSuccess:
+                    status = ExitStatus.TARGET_SUCCESS
+                    success = True
+                    break
+                except FeasibleSuccess:
+                    status = ExitStatus.FEASIBLE_SUCCESS
+                    success = True
+                    break
+                except CallbackSuccess:
+                    status = ExitStatus.CALLBACK_SUCCESS
+                    success = True
+                    break
+                except MaxEvalError:
+                    status = ExitStatus.MAX_EVAL_WARNING
+                    break
+
+                # Perform a second-order correction step if necessary.
+                merit_old = framework.merit(
+                    framework.x_best,
+                    framework.fun_best,
+                    framework.cub_best,
+                    framework.ceq_best,
+                )
+                merit_new = framework.merit(
+                    framework.x_best + step, fun_val, cub_val, ceq_val
+                )
+                if (
+                    pb.type == "nonlinearly constrained"
+                    and merit_new > merit_old
+                    and np.linalg.norm(normal_step)
+                    > constants[Constants.BYRD_OMOJOKUN_FACTOR] ** 2.0
+                    * framework.radius
+                ):
+                    soc_step = framework.get_second_order_correction_step(
+                        step, options
+                    )
+                    if np.linalg.norm(soc_step) > 0.0:
+                        step += soc_step
+
+                        # Evaluate the objective and constraint functions.
+                        try:
+                            fun_val, cub_val, ceq_val = _eval(
+                                pb,
+                                framework,
+                                step,
+                                options,
+                            )
+                        except TargetSuccess:
+                            status = ExitStatus.TARGET_SUCCESS
+                            success = True
+                            break
+                        except FeasibleSuccess:
+                            status = ExitStatus.FEASIBLE_SUCCESS
+                            success = True
+                            break
+                        except CallbackSuccess:
+                            status = ExitStatus.CALLBACK_SUCCESS
+                            success = True
+                            break
+                        except MaxEvalError:
+                            status = ExitStatus.MAX_EVAL_WARNING
+                            break
+
+                # Calculate the reduction ratio.
+                ratio = framework.get_reduction_ratio(
+                    step,
+                    fun_val,
+                    cub_val,
+                    ceq_val,
+                )
+
+                # Choose an interpolation point to remove.
+                try:
+                    k_new = framework.get_index_to_remove(
+                        framework.x_best + step
+                    )[0]
+                except np.linalg.LinAlgError:
+                    status = ExitStatus.LINALG_ERROR
+                    break
+
+                # Update the interpolation set.
+                try:
+                    ill_conditioned = framework.models.update_interpolation(
+                        k_new, framework.x_best + step, fun_val, cub_val,
+                        ceq_val
+                    )
+                except np.linalg.LinAlgError:
+                    status = ExitStatus.LINALG_ERROR
+                    break
+                framework.set_best_index()
+
+                # Update the trust-region radius.
+                framework.update_radius(step, ratio)
+
+                # Attempt to replace the models by the alternative ones.
+                if framework.radius <= framework.resolution:
+                    if ratio >= constants[Constants.VERY_LOW_RATIO]:
+                        n_alt_models = 0
+                    else:
+                        n_alt_models += 1
+                        grad = framework.models.fun_grad(framework.x_best)
+                        try:
+                            grad_alt = framework.models.fun_alt_grad(
+                                framework.x_best
+                            )
+                        except np.linalg.LinAlgError:
+                            status = ExitStatus.LINALG_ERROR
+                            break
+                        if np.linalg.norm(grad) < constants[
+                            Constants.LARGE_GRADIENT_FACTOR
+                        ] * np.linalg.norm(grad_alt):
+                            n_alt_models = 0
+                        if n_alt_models >= 3:
+                            try:
+                                framework.models.reset_models()
+                            except np.linalg.LinAlgError:
+                                status = ExitStatus.LINALG_ERROR
+                                break
+                            n_alt_models = 0
+
+                # Update the Lagrange multipliers.
+                framework.set_multipliers(framework.x_best + step)
+
+                # Check whether the resolution should be enhanced.
+                try:
+                    k_new, dist_new = framework.get_index_to_remove()
+                except np.linalg.LinAlgError:
+                    status = ExitStatus.LINALG_ERROR
+                    break
+                improve_geometry = (
+                    ill_conditioned
+                    or ratio <= constants[Constants.LOW_RATIO]
+                    and dist_new
+                    > max(
+                        framework.radius,
+                        constants[Constants.RESOLUTION_FACTOR]
+                        * framework.resolution,
+                    )
+                )
+                enhance_resolution = (
+                    radius_save <= framework.resolution
+                    and ratio <= constants[Constants.LOW_RATIO]
+                    and not improve_geometry
+                )
+            else:
+                # When increasing the penalty parameter, the best point so far
+                # may change. In this case, we restart the iteration.
+                enhance_resolution = False
+                improve_geometry = False
+
+        # Reduce the resolution if necessary.
+        if enhance_resolution:
+            if framework.resolution <= options[Options.RHOEND]:
+                success = True
+                status = ExitStatus.RADIUS_SUCCESS
+                break
+            framework.enhance_resolution(options)
+            framework.decrease_penalty()
+
+            if verbose:
+                maxcv_val = pb.maxcv(
+                    framework.x_best, framework.cub_best, framework.ceq_best
+                )
+                _print_step(
+                    f"New trust-region radius: {framework.resolution}",
+                    pb,
+                    pb.build_x(framework.x_best),
+                    framework.fun_best,
+                    maxcv_val,
+                    pb.n_eval,
+                    n_iter,
+                )
+                print()
+
+        # Improve the geometry of the interpolation set if necessary.
+        if improve_geometry:
+            try:
+                step = framework.get_geometry_step(k_new, options)
+            except np.linalg.LinAlgError:
+                status = ExitStatus.LINALG_ERROR
+                break
+
+            # Evaluate the objective and constraint functions.
+            try:
+                fun_val, cub_val, ceq_val = _eval(pb, framework, step, options)
+            except TargetSuccess:
+                status = ExitStatus.TARGET_SUCCESS
+                success = True
+                break
+            except FeasibleSuccess:
+                status = ExitStatus.FEASIBLE_SUCCESS
+                success = True
+                break
+            except CallbackSuccess:
+                status = ExitStatus.CALLBACK_SUCCESS
+                success = True
+                break
+            except MaxEvalError:
+                status = ExitStatus.MAX_EVAL_WARNING
+                break
+
+            # Update the interpolation set.
+            try:
+                framework.models.update_interpolation(
+                    k_new,
+                    framework.x_best + step,
+                    fun_val,
+                    cub_val,
+                    ceq_val,
+                )
+            except np.linalg.LinAlgError:
+                status = ExitStatus.LINALG_ERROR
+                break
+            framework.set_best_index()
+
+    return _build_result(
+        pb,
+        framework.penalty,
+        success,
+        status,
+        n_iter,
+        options,
+    )
+
+
+def _get_bounds(bounds, n):
+    """
+    Uniformize the bounds.
+    """
+    if bounds is None:
+        return Bounds(np.full(n, -np.inf), np.full(n, np.inf))
+    elif isinstance(bounds, Bounds):
+        if bounds.lb.shape != (n,) or bounds.ub.shape != (n,):
+            raise ValueError(f"The bounds must have {n} elements.")
+        return Bounds(bounds.lb, bounds.ub)
+    elif hasattr(bounds, "__len__"):
+        bounds = np.asarray(bounds)
+        if bounds.shape != (n, 2):
+            raise ValueError(
+                "The shape of the bounds is not compatible with "
+                "the number of variables."
+            )
+        return Bounds(bounds[:, 0], bounds[:, 1])
+    else:
+        raise TypeError(
+            "The bounds must be an instance of "
+            "scipy.optimize.Bounds or an array-like object."
+        )
+
+
+def _get_constraints(constraints):
+    """
+    Extract the linear and nonlinear constraints.
+    """
+    if isinstance(constraints, dict) or not hasattr(constraints, "__len__"):
+        constraints = (constraints,)
+
+    # Extract the linear and nonlinear constraints.
+    linear_constraints = []
+    nonlinear_constraints = []
+    for constraint in constraints:
+        if isinstance(constraint, LinearConstraint):
+            lb = exact_1d_array(
+                constraint.lb,
+                "The lower bound of the linear constraints must be a vector.",
+            )
+            ub = exact_1d_array(
+                constraint.ub,
+                "The upper bound of the linear constraints must be a vector.",
+            )
+            linear_constraints.append(
+                LinearConstraint(
+                    constraint.A,
+                    *np.broadcast_arrays(lb, ub),
+                )
+            )
+        elif isinstance(constraint, NonlinearConstraint):
+            lb = exact_1d_array(
+                constraint.lb,
+                "The lower bound of the "
+                "nonlinear constraints must be a "
+                "vector.",
+            )
+            ub = exact_1d_array(
+                constraint.ub,
+                "The upper bound of the "
+                "nonlinear constraints must be a "
+                "vector.",
+            )
+            nonlinear_constraints.append(
+                NonlinearConstraint(
+                    constraint.fun,
+                    *np.broadcast_arrays(lb, ub),
+                )
+            )
+        elif isinstance(constraint, dict):
+            if "type" not in constraint or constraint["type"] not in (
+                "eq",
+                "ineq",
+            ):
+                raise ValueError('The constraint type must be "eq" or "ineq".')
+            if "fun" not in constraint or not callable(constraint["fun"]):
+                raise ValueError("The constraint function must be callable.")
+            nonlinear_constraints.append(
+                {
+                    "fun": constraint["fun"],
+                    "type": constraint["type"],
+                    "args": constraint.get("args", ()),
+                }
+            )
+        else:
+            raise TypeError(
+                "The constraints must be instances of "
+                "scipy.optimize.LinearConstraint, "
+                "scipy.optimize.NonlinearConstraint, or dict."
+            )
+    return linear_constraints, nonlinear_constraints
+
+
+def _set_default_options(options, n):
+    """
+    Set the default options.
+    """
+    if Options.RHOBEG in options and options[Options.RHOBEG] <= 0.0:
+        raise ValueError("The initial trust-region radius must be positive.")
+    if Options.RHOEND in options and options[Options.RHOEND] < 0.0:
+        raise ValueError("The final trust-region radius must be nonnegative.")
+    if Options.RHOBEG in options and Options.RHOEND in options:
+        if options[Options.RHOBEG] < options[Options.RHOEND]:
+            raise ValueError(
+                "The initial trust-region radius must be greater "
+                "than or equal to the final trust-region radius."
+            )
+    elif Options.RHOBEG in options:
+        options[Options.RHOEND.value] = np.min(
+            [
+                DEFAULT_OPTIONS[Options.RHOEND],
+                options[Options.RHOBEG],
+            ]
+        )
+    elif Options.RHOEND in options:
+        options[Options.RHOBEG.value] = np.max(
+            [
+                DEFAULT_OPTIONS[Options.RHOBEG],
+                options[Options.RHOEND],
+            ]
+        )
+    else:
+        options[Options.RHOBEG.value] = DEFAULT_OPTIONS[Options.RHOBEG]
+        options[Options.RHOEND.value] = DEFAULT_OPTIONS[Options.RHOEND]
+    options[Options.RHOBEG.value] = float(options[Options.RHOBEG])
+    options[Options.RHOEND.value] = float(options[Options.RHOEND])
+    if Options.NPT in options and options[Options.NPT] <= 0:
+        raise ValueError("The number of interpolation points must be "
+                         "positive.")
+    if (
+        Options.NPT in options
+        and options[Options.NPT] > ((n + 1) * (n + 2)) // 2
+    ):
+        raise ValueError(
+            f"The number of interpolation points must be at most "
+            f"{((n + 1) * (n + 2)) // 2}."
+        )
+    options.setdefault(Options.NPT.value, DEFAULT_OPTIONS[Options.NPT](n))
+    options[Options.NPT.value] = int(options[Options.NPT])
+    if Options.MAX_EVAL in options and options[Options.MAX_EVAL] <= 0:
+        raise ValueError(
+            "The maximum number of function evaluations must be positive."
+        )
+    options.setdefault(
+        Options.MAX_EVAL.value,
+        np.max(
+            [
+                DEFAULT_OPTIONS[Options.MAX_EVAL](n),
+                options[Options.NPT] + 1,
+            ]
+        ),
+    )
+    options[Options.MAX_EVAL.value] = int(options[Options.MAX_EVAL])
+    if Options.MAX_ITER in options and options[Options.MAX_ITER] <= 0:
+        raise ValueError("The maximum number of iterations must be positive.")
+    options.setdefault(
+        Options.MAX_ITER.value,
+        DEFAULT_OPTIONS[Options.MAX_ITER](n),
+    )
+    options[Options.MAX_ITER.value] = int(options[Options.MAX_ITER])
+    options.setdefault(Options.TARGET.value, DEFAULT_OPTIONS[Options.TARGET])
+    options[Options.TARGET.value] = float(options[Options.TARGET])
+    options.setdefault(
+        Options.FEASIBILITY_TOL.value,
+        DEFAULT_OPTIONS[Options.FEASIBILITY_TOL],
+    )
+    options[Options.FEASIBILITY_TOL.value] = float(
+        options[Options.FEASIBILITY_TOL]
+    )
+    options.setdefault(Options.VERBOSE.value, DEFAULT_OPTIONS[Options.VERBOSE])
+    options[Options.VERBOSE.value] = bool(options[Options.VERBOSE])
+    options.setdefault(Options.SCALE.value, DEFAULT_OPTIONS[Options.SCALE])
+    options[Options.SCALE.value] = bool(options[Options.SCALE])
+    options.setdefault(
+        Options.FILTER_SIZE.value,
+        DEFAULT_OPTIONS[Options.FILTER_SIZE],
+    )
+    options[Options.FILTER_SIZE.value] = int(options[Options.FILTER_SIZE])
+    options.setdefault(
+        Options.STORE_HISTORY.value,
+        DEFAULT_OPTIONS[Options.STORE_HISTORY],
+    )
+    options[Options.STORE_HISTORY.value] = bool(options[Options.STORE_HISTORY])
+    options.setdefault(
+        Options.HISTORY_SIZE.value,
+        DEFAULT_OPTIONS[Options.HISTORY_SIZE],
+    )
+    options[Options.HISTORY_SIZE.value] = int(options[Options.HISTORY_SIZE])
+    options.setdefault(Options.DEBUG.value, DEFAULT_OPTIONS[Options.DEBUG])
+    options[Options.DEBUG.value] = bool(options[Options.DEBUG])
+
+    # Check whether they are any unknown options.
+    for key in options:
+        if key not in Options.__members__.values():
+            warnings.warn(f"Unknown option: {key}.", RuntimeWarning, 3)
+
+
+def _set_default_constants(**kwargs):
+    """
+    Set the default constants.
+    """
+    constants = dict(kwargs)
+    constants.setdefault(
+        Constants.DECREASE_RADIUS_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.DECREASE_RADIUS_FACTOR],
+    )
+    constants[Constants.DECREASE_RADIUS_FACTOR.value] = float(
+        constants[Constants.DECREASE_RADIUS_FACTOR]
+    )
+    if (
+        constants[Constants.DECREASE_RADIUS_FACTOR] <= 0.0
+        or constants[Constants.DECREASE_RADIUS_FACTOR] >= 1.0
+    ):
+        raise ValueError(
+            "The constant decrease_radius_factor must be in the interval "
+            "(0, 1)."
+        )
+    constants.setdefault(
+        Constants.INCREASE_RADIUS_THRESHOLD.value,
+        DEFAULT_CONSTANTS[Constants.INCREASE_RADIUS_THRESHOLD],
+    )
+    constants[Constants.INCREASE_RADIUS_THRESHOLD.value] = float(
+        constants[Constants.INCREASE_RADIUS_THRESHOLD]
+    )
+    if constants[Constants.INCREASE_RADIUS_THRESHOLD] <= 1.0:
+        raise ValueError(
+            "The constant increase_radius_threshold must be greater than 1."
+        )
+    if (
+        Constants.INCREASE_RADIUS_FACTOR in constants
+        and constants[Constants.INCREASE_RADIUS_FACTOR] <= 1.0
+    ):
+        raise ValueError(
+            "The constant increase_radius_factor must be greater than 1."
+        )
+    if (
+        Constants.DECREASE_RADIUS_THRESHOLD in constants
+        and constants[Constants.DECREASE_RADIUS_THRESHOLD] <= 1.0
+    ):
+        raise ValueError(
+            "The constant decrease_radius_threshold must be greater than 1."
+        )
+    if (
+        Constants.INCREASE_RADIUS_FACTOR in constants
+        and Constants.DECREASE_RADIUS_THRESHOLD in constants
+    ):
+        if (
+            constants[Constants.DECREASE_RADIUS_THRESHOLD]
+            >= constants[Constants.INCREASE_RADIUS_FACTOR]
+        ):
+            raise ValueError(
+                "The constant decrease_radius_threshold must be "
+                "less than increase_radius_factor."
+            )
+    elif Constants.INCREASE_RADIUS_FACTOR in constants:
+        constants[Constants.DECREASE_RADIUS_THRESHOLD.value] = np.min(
+            [
+                DEFAULT_CONSTANTS[Constants.DECREASE_RADIUS_THRESHOLD],
+                0.5 * (1.0 + constants[Constants.INCREASE_RADIUS_FACTOR]),
+            ]
+        )
+    elif Constants.DECREASE_RADIUS_THRESHOLD in constants:
+        constants[Constants.INCREASE_RADIUS_FACTOR.value] = np.max(
+            [
+                DEFAULT_CONSTANTS[Constants.INCREASE_RADIUS_FACTOR],
+                2.0 * constants[Constants.DECREASE_RADIUS_THRESHOLD],
+            ]
+        )
+    else:
+        constants[Constants.INCREASE_RADIUS_FACTOR.value] = DEFAULT_CONSTANTS[
+            Constants.INCREASE_RADIUS_FACTOR
+        ]
+        constants[Constants.DECREASE_RADIUS_THRESHOLD.value] = (
+            DEFAULT_CONSTANTS[Constants.DECREASE_RADIUS_THRESHOLD])
+    constants.setdefault(
+        Constants.DECREASE_RESOLUTION_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.DECREASE_RESOLUTION_FACTOR],
+    )
+    constants[Constants.DECREASE_RESOLUTION_FACTOR.value] = float(
+        constants[Constants.DECREASE_RESOLUTION_FACTOR]
+    )
+    if (
+        constants[Constants.DECREASE_RESOLUTION_FACTOR] <= 0.0
+        or constants[Constants.DECREASE_RESOLUTION_FACTOR] >= 1.0
+    ):
+        raise ValueError(
+            "The constant decrease_resolution_factor must be in the interval "
+            "(0, 1)."
+        )
+    if (
+        Constants.LARGE_RESOLUTION_THRESHOLD in constants
+        and constants[Constants.LARGE_RESOLUTION_THRESHOLD] <= 1.0
+    ):
+        raise ValueError(
+            "The constant large_resolution_threshold must be greater than 1."
+        )
+    if (
+        Constants.MODERATE_RESOLUTION_THRESHOLD in constants
+        and constants[Constants.MODERATE_RESOLUTION_THRESHOLD] <= 1.0
+    ):
+        raise ValueError(
+            "The constant moderate_resolution_threshold must be greater than "
+            "1."
+        )
+    if (
+        Constants.LARGE_RESOLUTION_THRESHOLD in constants
+        and Constants.MODERATE_RESOLUTION_THRESHOLD in constants
+    ):
+        if (
+            constants[Constants.MODERATE_RESOLUTION_THRESHOLD]
+            > constants[Constants.LARGE_RESOLUTION_THRESHOLD]
+        ):
+            raise ValueError(
+                "The constant moderate_resolution_threshold "
+                "must be at most large_resolution_threshold."
+            )
+    elif Constants.LARGE_RESOLUTION_THRESHOLD in constants:
+        constants[Constants.MODERATE_RESOLUTION_THRESHOLD.value] = np.min(
+            [
+                DEFAULT_CONSTANTS[Constants.MODERATE_RESOLUTION_THRESHOLD],
+                constants[Constants.LARGE_RESOLUTION_THRESHOLD],
+            ]
+        )
+    elif Constants.MODERATE_RESOLUTION_THRESHOLD in constants:
+        constants[Constants.LARGE_RESOLUTION_THRESHOLD.value] = np.max(
+            [
+                DEFAULT_CONSTANTS[Constants.LARGE_RESOLUTION_THRESHOLD],
+                constants[Constants.MODERATE_RESOLUTION_THRESHOLD],
+            ]
+        )
+    else:
+        constants[Constants.LARGE_RESOLUTION_THRESHOLD.value] = (
+            DEFAULT_CONSTANTS[Constants.LARGE_RESOLUTION_THRESHOLD]
+        )
+        constants[Constants.MODERATE_RESOLUTION_THRESHOLD.value] = (
+            DEFAULT_CONSTANTS[Constants.MODERATE_RESOLUTION_THRESHOLD]
+        )
+    if Constants.LOW_RATIO in constants and (
+        constants[Constants.LOW_RATIO] <= 0.0
+        or constants[Constants.LOW_RATIO] >= 1.0
+    ):
+        raise ValueError(
+            "The constant low_ratio must be in the interval (0, 1)."
+        )
+    if Constants.HIGH_RATIO in constants and (
+        constants[Constants.HIGH_RATIO] <= 0.0
+        or constants[Constants.HIGH_RATIO] >= 1.0
+    ):
+        raise ValueError(
+            "The constant high_ratio must be in the interval (0, 1)."
+        )
+    if Constants.LOW_RATIO in constants and Constants.HIGH_RATIO in constants:
+        if constants[Constants.LOW_RATIO] > constants[Constants.HIGH_RATIO]:
+            raise ValueError(
+                "The constant low_ratio must be at most high_ratio."
+            )
+    elif Constants.LOW_RATIO in constants:
+        constants[Constants.HIGH_RATIO.value] = np.max(
+            [
+                DEFAULT_CONSTANTS[Constants.HIGH_RATIO],
+                constants[Constants.LOW_RATIO],
+            ]
+        )
+    elif Constants.HIGH_RATIO in constants:
+        constants[Constants.LOW_RATIO.value] = np.min(
+            [
+                DEFAULT_CONSTANTS[Constants.LOW_RATIO],
+                constants[Constants.HIGH_RATIO],
+            ]
+        )
+    else:
+        constants[Constants.LOW_RATIO.value] = DEFAULT_CONSTANTS[
+            Constants.LOW_RATIO
+        ]
+        constants[Constants.HIGH_RATIO.value] = DEFAULT_CONSTANTS[
+            Constants.HIGH_RATIO
+        ]
+    constants.setdefault(
+        Constants.VERY_LOW_RATIO.value,
+        DEFAULT_CONSTANTS[Constants.VERY_LOW_RATIO],
+    )
+    constants[Constants.VERY_LOW_RATIO.value] = float(
+        constants[Constants.VERY_LOW_RATIO]
+    )
+    if (
+        constants[Constants.VERY_LOW_RATIO] <= 0.0
+        or constants[Constants.VERY_LOW_RATIO] >= 1.0
+    ):
+        raise ValueError(
+            "The constant very_low_ratio must be in the interval (0, 1)."
+        )
+    if (
+        Constants.PENALTY_INCREASE_THRESHOLD in constants
+        and constants[Constants.PENALTY_INCREASE_THRESHOLD] < 1.0
+    ):
+        raise ValueError(
+            "The constant penalty_increase_threshold must be "
+            "greater than or equal to 1."
+        )
+    if (
+        Constants.PENALTY_INCREASE_FACTOR in constants
+        and constants[Constants.PENALTY_INCREASE_FACTOR] <= 1.0
+    ):
+        raise ValueError(
+            "The constant penalty_increase_factor must be greater than 1."
+        )
+    if (
+        Constants.PENALTY_INCREASE_THRESHOLD in constants
+        and Constants.PENALTY_INCREASE_FACTOR in constants
+    ):
+        if (
+            constants[Constants.PENALTY_INCREASE_FACTOR]
+            < constants[Constants.PENALTY_INCREASE_THRESHOLD]
+        ):
+            raise ValueError(
+                "The constant penalty_increase_factor must be "
+                "greater than or equal to "
+                "penalty_increase_threshold."
+            )
+    elif Constants.PENALTY_INCREASE_THRESHOLD in constants:
+        constants[Constants.PENALTY_INCREASE_FACTOR.value] = np.max(
+            [
+                DEFAULT_CONSTANTS[Constants.PENALTY_INCREASE_FACTOR],
+                constants[Constants.PENALTY_INCREASE_THRESHOLD],
+            ]
+        )
+    elif Constants.PENALTY_INCREASE_FACTOR in constants:
+        constants[Constants.PENALTY_INCREASE_THRESHOLD.value] = np.min(
+            [
+                DEFAULT_CONSTANTS[Constants.PENALTY_INCREASE_THRESHOLD],
+                constants[Constants.PENALTY_INCREASE_FACTOR],
+            ]
+        )
+    else:
+        constants[Constants.PENALTY_INCREASE_THRESHOLD.value] = (
+            DEFAULT_CONSTANTS[Constants.PENALTY_INCREASE_THRESHOLD]
+        )
+        constants[Constants.PENALTY_INCREASE_FACTOR.value] = DEFAULT_CONSTANTS[
+            Constants.PENALTY_INCREASE_FACTOR
+        ]
+    constants.setdefault(
+        Constants.SHORT_STEP_THRESHOLD.value,
+        DEFAULT_CONSTANTS[Constants.SHORT_STEP_THRESHOLD],
+    )
+    constants[Constants.SHORT_STEP_THRESHOLD.value] = float(
+        constants[Constants.SHORT_STEP_THRESHOLD]
+    )
+    if (
+        constants[Constants.SHORT_STEP_THRESHOLD] <= 0.0
+        or constants[Constants.SHORT_STEP_THRESHOLD] >= 1.0
+    ):
+        raise ValueError(
+            "The constant short_step_threshold must be in the interval (0, 1)."
+        )
+    constants.setdefault(
+        Constants.LOW_RADIUS_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.LOW_RADIUS_FACTOR],
+    )
+    constants[Constants.LOW_RADIUS_FACTOR.value] = float(
+        constants[Constants.LOW_RADIUS_FACTOR]
+    )
+    if (
+        constants[Constants.LOW_RADIUS_FACTOR] <= 0.0
+        or constants[Constants.LOW_RADIUS_FACTOR] >= 1.0
+    ):
+        raise ValueError(
+            "The constant low_radius_factor must be in the interval (0, 1)."
+        )
+    constants.setdefault(
+        Constants.BYRD_OMOJOKUN_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.BYRD_OMOJOKUN_FACTOR],
+    )
+    constants[Constants.BYRD_OMOJOKUN_FACTOR.value] = float(
+        constants[Constants.BYRD_OMOJOKUN_FACTOR]
+    )
+    if (
+        constants[Constants.BYRD_OMOJOKUN_FACTOR] <= 0.0
+        or constants[Constants.BYRD_OMOJOKUN_FACTOR] >= 1.0
+    ):
+        raise ValueError(
+            "The constant byrd_omojokun_factor must be in the interval (0, 1)."
+        )
+    constants.setdefault(
+        Constants.THRESHOLD_RATIO_CONSTRAINTS.value,
+        DEFAULT_CONSTANTS[Constants.THRESHOLD_RATIO_CONSTRAINTS],
+    )
+    constants[Constants.THRESHOLD_RATIO_CONSTRAINTS.value] = float(
+        constants[Constants.THRESHOLD_RATIO_CONSTRAINTS]
+    )
+    if constants[Constants.THRESHOLD_RATIO_CONSTRAINTS] <= 1.0:
+        raise ValueError(
+            "The constant threshold_ratio_constraints must be greater than 1."
+        )
+    constants.setdefault(
+        Constants.LARGE_SHIFT_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.LARGE_SHIFT_FACTOR],
+    )
+    constants[Constants.LARGE_SHIFT_FACTOR.value] = float(
+        constants[Constants.LARGE_SHIFT_FACTOR]
+    )
+    if constants[Constants.LARGE_SHIFT_FACTOR] < 0.0:
+        raise ValueError("The constant large_shift_factor must be "
+                         "nonnegative.")
+    constants.setdefault(
+        Constants.LARGE_GRADIENT_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.LARGE_GRADIENT_FACTOR],
+    )
+    constants[Constants.LARGE_GRADIENT_FACTOR.value] = float(
+        constants[Constants.LARGE_GRADIENT_FACTOR]
+    )
+    if constants[Constants.LARGE_GRADIENT_FACTOR] <= 1.0:
+        raise ValueError(
+            "The constant large_gradient_factor must be greater than 1."
+        )
+    constants.setdefault(
+        Constants.RESOLUTION_FACTOR.value,
+        DEFAULT_CONSTANTS[Constants.RESOLUTION_FACTOR],
+    )
+    constants[Constants.RESOLUTION_FACTOR.value] = float(
+        constants[Constants.RESOLUTION_FACTOR]
+    )
+    if constants[Constants.RESOLUTION_FACTOR] <= 1.0:
+        raise ValueError(
+            "The constant resolution_factor must be greater than 1."
+        )
+    constants.setdefault(
+        Constants.IMPROVE_TCG.value,
+        DEFAULT_CONSTANTS[Constants.IMPROVE_TCG],
+    )
+    constants[Constants.IMPROVE_TCG.value] = bool(
+        constants[Constants.IMPROVE_TCG]
+    )
+
+    # Check whether they are any unknown options.
+    for key in kwargs:
+        if key not in Constants.__members__.values():
+            warnings.warn(f"Unknown constant: {key}.", RuntimeWarning, 3)
+    return constants
+
+
+def _eval(pb, framework, step, options):
+    """
+    Evaluate the objective and constraint functions.
+    """
+    if pb.n_eval >= options[Options.MAX_EVAL]:
+        raise MaxEvalError
+    x_eval = framework.x_best + step
+    fun_val, cub_val, ceq_val = pb(x_eval, framework.penalty)
+    r_val = pb.maxcv(x_eval, cub_val, ceq_val)
+    if (
+        fun_val <= options[Options.TARGET]
+        and r_val <= options[Options.FEASIBILITY_TOL]
+    ):
+        raise TargetSuccess
+    if pb.is_feasibility and r_val <= options[Options.FEASIBILITY_TOL]:
+        raise FeasibleSuccess
+    return fun_val, cub_val, ceq_val
+
+
+def _build_result(pb, penalty, success, status, n_iter, options):
+    """
+    Build the result of the optimization process.
+    """
+    # Build the result.
+    x, fun, maxcv = pb.best_eval(penalty)
+    success = success and np.isfinite(fun) and np.isfinite(maxcv)
+    if status not in [ExitStatus.TARGET_SUCCESS, ExitStatus.FEASIBLE_SUCCESS]:
+        success = success and maxcv <= options[Options.FEASIBILITY_TOL]
+    result = OptimizeResult()
+    result.message = {
+        ExitStatus.RADIUS_SUCCESS: "The lower bound for the trust-region "
+                                   "radius has been reached",
+        ExitStatus.TARGET_SUCCESS: "The target objective function value has "
+                                   "been reached",
+        ExitStatus.FIXED_SUCCESS: "All variables are fixed by the bound "
+                                  "constraints",
+        ExitStatus.CALLBACK_SUCCESS: "The callback requested to stop the "
+                                     "optimization procedure",
+        ExitStatus.FEASIBLE_SUCCESS: "The feasibility problem received has "
+                                     "been solved successfully",
+        ExitStatus.MAX_EVAL_WARNING: "The maximum number of function "
+                                     "evaluations has been exceeded",
+        ExitStatus.MAX_ITER_WARNING: "The maximum number of iterations has "
+                                     "been exceeded",
+        ExitStatus.INFEASIBLE_ERROR: "The bound constraints are infeasible",
+        ExitStatus.LINALG_ERROR: "A linear algebra error occurred",
+    }.get(status, "Unknown exit status")
+    result.success = success
+    result.status = status.value
+    result.x = pb.build_x(x)
+    result.fun = fun
+    result.maxcv = maxcv
+    result.nfev = pb.n_eval
+    result.nit = n_iter
+    if options[Options.STORE_HISTORY]:
+        result.fun_history = pb.fun_history
+        result.maxcv_history = pb.maxcv_history
+
+    # Print the result if requested.
+    if options[Options.VERBOSE]:
+        _print_step(
+            result.message,
+            pb,
+            result.x,
+            result.fun,
+            result.maxcv,
+            result.nfev,
+            result.nit,
+        )
+    return result
+
+
+def _print_step(message, pb, x, fun_val, r_val, n_eval, n_iter):
+    """
+    Print information about the current state of the optimization process.
+    """
+    print()
+    print(f"{message}.")
+    print(f"Number of function evaluations: {n_eval}.")
+    print(f"Number of iterations: {n_iter}.")
+    if not pb.is_feasibility:
+        print(f"Least value of {pb.fun_name}: {fun_val}.")
+    print(f"Maximum constraint violation: {r_val}.")
+    with np.printoptions(**PRINT_OPTIONS):
+        print(f"Corresponding point: {x}.")

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/models.py

@@ -0,0 +1,1529 @@
+import warnings
+
+import numpy as np
+from scipy.linalg import eigh
+
+from .settings import Options
+from .utils import MaxEvalError, TargetSuccess, FeasibleSuccess
+
+
+EPS = np.finfo(float).eps
+
+
+class Interpolation:
+    """
+    Interpolation set.
+
+    This class stores a base point around which the models are expanded and the
+    interpolation points. The coordinates of the interpolation points are
+    relative to the base point.
+    """
+
+    def __init__(self, pb, options):
+        """
+        Initialize the interpolation set.
+
+        Parameters
+        ----------
+        pb : `cobyqa.problem.Problem`
+            Problem to be solved.
+        options : dict
+            Options of the solver.
+        """
+        # Reduce the initial trust-region radius if necessary.
+        self._debug = options[Options.DEBUG]
+        max_radius = 0.5 * np.min(pb.bounds.xu - pb.bounds.xl)
+        if options[Options.RHOBEG] > max_radius:
+            options[Options.RHOBEG.value] = max_radius
+            options[Options.RHOEND.value] = np.min(
+                [
+                    options[Options.RHOEND],
+                    max_radius,
+                ]
+            )
+
+        # Set the initial point around which the models are expanded.
+        self._x_base = np.copy(pb.x0)
+        very_close_xl_idx = (
+            self.x_base <= pb.bounds.xl + 0.5 * options[Options.RHOBEG]
+        )
+        self.x_base[very_close_xl_idx] = pb.bounds.xl[very_close_xl_idx]
+        close_xl_idx = (
+            pb.bounds.xl + 0.5 * options[Options.RHOBEG] < self.x_base
+        ) & (self.x_base <= pb.bounds.xl + options[Options.RHOBEG])
+        self.x_base[close_xl_idx] = np.minimum(
+            pb.bounds.xl[close_xl_idx] + options[Options.RHOBEG],
+            pb.bounds.xu[close_xl_idx],
+        )
+        very_close_xu_idx = (
+            self.x_base >= pb.bounds.xu - 0.5 * options[Options.RHOBEG]
+        )
+        self.x_base[very_close_xu_idx] = pb.bounds.xu[very_close_xu_idx]
+        close_xu_idx = (
+            self.x_base < pb.bounds.xu - 0.5 * options[Options.RHOBEG]
+        ) & (pb.bounds.xu - options[Options.RHOBEG] <= self.x_base)
+        self.x_base[close_xu_idx] = np.maximum(
+            pb.bounds.xu[close_xu_idx] - options[Options.RHOBEG],
+            pb.bounds.xl[close_xu_idx],
+        )
+
+        # Set the initial interpolation set.
+        self._xpt = np.zeros((pb.n, options[Options.NPT]))
+        for k in range(1, options[Options.NPT]):
+            if k <= pb.n:
+                if very_close_xu_idx[k - 1]:
+                    self.xpt[k - 1, k] = -options[Options.RHOBEG]
+                else:
+                    self.xpt[k - 1, k] = options[Options.RHOBEG]
+            elif k <= 2 * pb.n:
+                if very_close_xl_idx[k - pb.n - 1]:
+                    self.xpt[k - pb.n - 1, k] = 2.0 * options[Options.RHOBEG]
+                elif very_close_xu_idx[k - pb.n - 1]:
+                    self.xpt[k - pb.n - 1, k] = -2.0 * options[Options.RHOBEG]
+                else:
+                    self.xpt[k - pb.n - 1, k] = -options[Options.RHOBEG]
+            else:
+                spread = (k - pb.n - 1) // pb.n
+                k1 = k - (1 + spread) * pb.n - 1
+                k2 = (k1 + spread) % pb.n
+                self.xpt[k1, k] = self.xpt[k1, k1 + 1]
+                self.xpt[k2, k] = self.xpt[k2, k2 + 1]
+
+    @property
+    def n(self):
+        """
+        Number of variables.
+
+        Returns
+        -------
+        int
+            Number of variables.
+        """
+        return self.xpt.shape[0]
+
+    @property
+    def npt(self):
+        """
+        Number of interpolation points.
+
+        Returns
+        -------
+        int
+            Number of interpolation points.
+        """
+        return self.xpt.shape[1]
+
+    @property
+    def xpt(self):
+        """
+        Interpolation points.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n, npt)
+            Interpolation points.
+        """
+        return self._xpt
+
+    @xpt.setter
+    def xpt(self, xpt):
+        """
+        Set the interpolation points.
+
+        Parameters
+        ----------
+        xpt : `numpy.ndarray`, shape (n, npt)
+            New interpolation points.
+        """
+        if self._debug:
+            assert xpt.shape == (
+                self.n,
+                self.npt,
+            ), "The shape of `xpt` is not valid."
+        self._xpt = xpt
+
+    @property
+    def x_base(self):
+        """
+        Base point around which the models are expanded.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Base point around which the models are expanded.
+        """
+        return self._x_base
+
+    @x_base.setter
+    def x_base(self, x_base):
+        """
+        Set the base point around which the models are expanded.
+
+        Parameters
+        ----------
+        x_base : `numpy.ndarray`, shape (n,)
+            New base point around which the models are expanded.
+        """
+        if self._debug:
+            assert x_base.shape == (
+                self.n,
+            ), "The shape of `x_base` is not valid."
+        self._x_base = x_base
+
+    def point(self, k):
+        """
+        Get the `k`-th interpolation point.
+
+        The return point is relative to the origin.
+
+        Parameters
+        ----------
+        k : int
+            Index of the interpolation point.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            `k`-th interpolation point.
+        """
+        if self._debug:
+            assert 0 <= k < self.npt, "The index `k` is not valid."
+        return self.x_base + self.xpt[:, k]
+
+
+_cache = {"xpt": None, "a": None, "right_scaling": None, "eigh": None}
+
+
+def build_system(interpolation):
+    """
+    Build the left-hand side matrix of the interpolation system. The
+    matrix below stores W * diag(right_scaling),
+    where W is the theoretical matrix of the interpolation system. The
+    right scaling matrices is chosen to keep the elements in
+    the matrix well-balanced.
+
+    Parameters
+    ----------
+    interpolation : `cobyqa.models.Interpolation`
+        Interpolation set.
+    """
+
+    # Compute the scaled directions from the base point to the
+    # interpolation points. We scale the directions to avoid numerical
+    # difficulties.
+    if _cache["xpt"] is not None and np.array_equal(
+        interpolation.xpt, _cache["xpt"]
+    ):
+        return _cache["a"], _cache["right_scaling"], _cache["eigh"]
+
+    scale = np.max(np.linalg.norm(interpolation.xpt, axis=0), initial=EPS)
+    xpt_scale = interpolation.xpt / scale
+
+    n, npt = xpt_scale.shape
+    a = np.zeros((npt + n + 1, npt + n + 1))
+    a[:npt, :npt] = 0.5 * (xpt_scale.T @ xpt_scale) ** 2.0
+    a[:npt, npt] = 1.0
+    a[:npt, npt + 1:] = xpt_scale.T
+    a[npt, :npt] = 1.0
+    a[npt + 1:, :npt] = xpt_scale
+
+    # Build the left and right scaling diagonal matrices.
+    right_scaling = np.empty(npt + n + 1)
+    right_scaling[:npt] = 1.0 / scale**2.0
+    right_scaling[npt] = scale**2.0
+    right_scaling[npt + 1:] = scale
+
+    eig_values, eig_vectors = eigh(a, check_finite=False)
+
+    _cache["xpt"] = np.copy(interpolation.xpt)
+    _cache["a"] = np.copy(a)
+    _cache["right_scaling"] = np.copy(right_scaling)
+    _cache["eigh"] = (eig_values, eig_vectors)
+
+    return a, right_scaling, (eig_values, eig_vectors)
+
+
+class Quadratic:
+    """
+    Quadratic model.
+
+    This class stores the Hessian matrix of the quadratic model using the
+    implicit/explicit representation designed by Powell for NEWUOA [1]_.
+
+    References
+    ----------
+    .. [1] M. J. D. Powell. The NEWUOA software for unconstrained optimization
+       without derivatives. In G. Di Pillo and M. Roma, editors, *Large-Scale
+       Nonlinear Optimization*, volume 83 of Nonconvex Optim. Appl., pages
+       255--297. Springer, Boston, MA, USA, 2006. `doi:10.1007/0-387-30065-1_16
+       <https://doi.org/10.1007/0-387-30065-1_16>`_.
+    """
+
+    def __init__(self, interpolation, values, debug):
+        """
+        Initialize the quadratic model.
+
+        Parameters
+        ----------
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+        values : `numpy.ndarray`, shape (npt,)
+            Values of the interpolated function at the interpolation points.
+        debug : bool
+            Whether to make debugging tests during the execution.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        self._debug = debug
+        if self._debug:
+            assert values.shape == (
+                interpolation.npt,
+            ), "The shape of `values` is not valid."
+        if interpolation.npt < interpolation.n + 1:
+            raise ValueError(
+                f"The number of interpolation points must be at least "
+                f"{interpolation.n + 1}."
+            )
+        self._const, self._grad, self._i_hess, _ = self._get_model(
+            interpolation,
+            values,
+        )
+        self._e_hess = np.zeros((self.n, self.n))
+
+    def __call__(self, x, interpolation):
+        """
+        Evaluate the quadratic model at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the quadratic model is evaluated.
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+
+        Returns
+        -------
+        float
+            Value of the quadratic model at `x`.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+        x_diff = x - interpolation.x_base
+        return (
+            self._const
+            + self._grad @ x_diff
+            + 0.5
+            * (
+                self._i_hess @ (interpolation.xpt.T @ x_diff) ** 2.0
+                + x_diff @ self._e_hess @ x_diff
+            )
+        )
+
+    @property
+    def n(self):
+        """
+        Number of variables.
+
+        Returns
+        -------
+        int
+            Number of variables.
+        """
+        return self._grad.size
+
+    @property
+    def npt(self):
+        """
+        Number of interpolation points used to define the quadratic model.
+
+        Returns
+        -------
+        int
+            Number of interpolation points used to define the quadratic model.
+        """
+        return self._i_hess.size
+
+    def grad(self, x, interpolation):
+        """
+        Evaluate the gradient of the quadratic model at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which the gradient of the quadratic model is evaluated.
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Gradient of the quadratic model at `x`.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+        x_diff = x - interpolation.x_base
+        return self._grad + self.hess_prod(x_diff, interpolation)
+
+    def hess(self, interpolation):
+        """
+        Evaluate the Hessian matrix of the quadratic model.
+
+        Parameters
+        ----------
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n, n)
+            Hessian matrix of the quadratic model.
+        """
+        return self._e_hess + interpolation.xpt @ (
+            self._i_hess[:, np.newaxis] * interpolation.xpt.T
+        )
+
+    def hess_prod(self, v, interpolation):
+        """
+        Evaluate the right product of the Hessian matrix of the quadratic model
+        with a given vector.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Vector with which the Hessian matrix of the quadratic model is
+            multiplied from the right.
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Right product of the Hessian matrix of the quadratic model with
+            `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+        return self._e_hess @ v + interpolation.xpt @ (
+            self._i_hess * (interpolation.xpt.T @ v)
+        )
+
+    def curv(self, v, interpolation):
+        """
+        Evaluate the curvature of the quadratic model along a given direction.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Direction along which the curvature of the quadratic model is
+            evaluated.
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+
+        Returns
+        -------
+        float
+            Curvature of the quadratic model along `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+        return (
+            v @ self._e_hess @ v
+            + self._i_hess @ (interpolation.xpt.T @ v) ** 2.0
+        )
+
+    def update(self, interpolation, k_new, dir_old, values_diff):
+        """
+        Update the quadratic model.
+
+        This method applies the derivative-free symmetric Broyden update to the
+        quadratic model. The `knew`-th interpolation point must be updated
+        before calling this method.
+
+        Parameters
+        ----------
+        interpolation : `cobyqa.models.Interpolation`
+            Updated interpolation set.
+        k_new : int
+            Index of the updated interpolation point.
+        dir_old : `numpy.ndarray`, shape (n,)
+            Value of ``interpolation.xpt[:, k_new]`` before the update.
+        values_diff : `numpy.ndarray`, shape (npt,)
+            Differences between the values of the interpolated nonlinear
+            function and the previous quadratic model at the updated
+            interpolation points.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        if self._debug:
+            assert 0 <= k_new < self.npt, "The index `k_new` is not valid."
+            assert dir_old.shape == (
+                self.n,
+            ), "The shape of `dir_old` is not valid."
+            assert values_diff.shape == (
+                self.npt,
+            ), "The shape of `values_diff` is not valid."
+
+        # Forward the k_new-th element of the implicit Hessian matrix to the
+        # explicit Hessian matrix. This must be done because the implicit
+        # Hessian matrix is related to the interpolation points, and the
+        # k_new-th interpolation point is modified.
+        self._e_hess += self._i_hess[k_new] * np.outer(dir_old, dir_old)
+        self._i_hess[k_new] = 0.0
+
+        # Update the quadratic model.
+        const, grad, i_hess, ill_conditioned = self._get_model(
+            interpolation,
+            values_diff,
+        )
+        self._const += const
+        self._grad += grad
+        self._i_hess += i_hess
+        return ill_conditioned
+
+    def shift_x_base(self, interpolation, new_x_base):
+        """
+        Shift the point around which the quadratic model is defined.
+
+        Parameters
+        ----------
+        interpolation : `cobyqa.models.Interpolation`
+            Previous interpolation set.
+        new_x_base : `numpy.ndarray`, shape (n,)
+            Point that will replace ``interpolation.x_base``.
+        """
+        if self._debug:
+            assert new_x_base.shape == (
+                self.n,
+            ), "The shape of `new_x_base` is not valid."
+        self._const = self(new_x_base, interpolation)
+        self._grad = self.grad(new_x_base, interpolation)
+        shift = new_x_base - interpolation.x_base
+        update = np.outer(
+            shift,
+            (interpolation.xpt - 0.5 * shift[:, np.newaxis]) @ self._i_hess,
+        )
+        self._e_hess += update + update.T
+
+    @staticmethod
+    def solve_systems(interpolation, rhs):
+        """
+        Solve the interpolation systems.
+
+        Parameters
+        ----------
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+        rhs : `numpy.ndarray`, shape (npt + n + 1, m)
+            Right-hand side vectors of the ``m`` interpolation systems.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (npt + n + 1, m)
+            Solutions of the interpolation systems.
+        `numpy.ndarray`, shape (m, )
+            Whether the interpolation systems are ill-conditioned.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation systems are ill-defined.
+        """
+        n, npt = interpolation.xpt.shape
+        assert (
+            rhs.ndim == 2 and rhs.shape[0] == npt + n + 1
+        ), "The shape of `rhs` is not valid."
+
+        # Build the left-hand side matrix of the interpolation system. The
+        # matrix below stores diag(left_scaling) * W * diag(right_scaling),
+        # where W is the theoretical matrix of the interpolation system. The
+        # left and right scaling matrices are chosen to keep the elements in
+        # the matrix well-balanced.
+        a, right_scaling, eig = build_system(interpolation)
+
+        # Build the solution. After a discussion with Mike Saunders and Alexis
+        # Montoison during their visit to the Hong Kong Polytechnic University
+        # in 2024, we decided to use the eigendecomposition of the symmetric
+        # matrix a. This is more stable than the previously employed LBL
+        # decomposition, and allows us to directly detect ill-conditioning of
+        # the system and to build the least-squares solution if necessary.
+        # Numerical experiments have shown that this strategy improves the
+        # performance of the solver.
+        rhs_scaled = rhs * right_scaling[:, np.newaxis]
+        if not (np.all(np.isfinite(a)) and np.all(np.isfinite(rhs_scaled))):
+            raise np.linalg.LinAlgError(
+                "The interpolation system is ill-defined."
+            )
+
+        # calculated in build_system
+        eig_values, eig_vectors = eig
+
+        large_eig_values = np.abs(eig_values) > EPS
+        eig_vectors = eig_vectors[:, large_eig_values]
+        inv_eig_values = 1.0 / eig_values[large_eig_values]
+        ill_conditioned = ~np.all(large_eig_values, 0)
+        left_scaled_solutions = eig_vectors @ (
+            (eig_vectors.T @ rhs_scaled) * inv_eig_values[:, np.newaxis]
+        )
+        return (
+            left_scaled_solutions * right_scaling[:, np.newaxis],
+            ill_conditioned,
+        )
+
+    @staticmethod
+    def _get_model(interpolation, values):
+        """
+        Solve the interpolation system.
+
+        Parameters
+        ----------
+        interpolation : `cobyqa.models.Interpolation`
+            Interpolation set.
+        values : `numpy.ndarray`, shape (npt,)
+            Values of the interpolated function at the interpolation points.
+
+        Returns
+        -------
+        float
+            Constant term of the quadratic model.
+        `numpy.ndarray`, shape (n,)
+            Gradient of the quadratic model at ``interpolation.x_base``.
+        `numpy.ndarray`, shape (npt,)
+            Implicit Hessian matrix of the quadratic model.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        assert values.shape == (
+            interpolation.npt,
+        ), "The shape of `values` is not valid."
+        n, npt = interpolation.xpt.shape
+        x, ill_conditioned = Quadratic.solve_systems(
+            interpolation,
+            np.block(
+                [
+                    [
+                        values,
+                        np.zeros(n + 1),
+                    ]
+                ]
+            ).T,
+        )
+        return x[npt, 0], x[npt + 1:, 0], x[:npt, 0], ill_conditioned
+
+
+class Models:
+    """
+    Models for a nonlinear optimization problem.
+    """
+
+    def __init__(self, pb, options, penalty):
+        """
+        Initialize the models.
+
+        Parameters
+        ----------
+        pb : `cobyqa.problem.Problem`
+            Problem to be solved.
+        options : dict
+            Options of the solver.
+        penalty : float
+            Penalty parameter used to select the point in the filter to forward
+            to the callback function.
+
+        Raises
+        ------
+        `cobyqa.utils.MaxEvalError`
+            If the maximum number of evaluations is reached.
+        `cobyqa.utils.TargetSuccess`
+            If a nearly feasible point has been found with an objective
+            function value below the target.
+        `cobyqa.utils.FeasibleSuccess`
+            If a feasible point has been found for a feasibility problem.
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        # Set the initial interpolation set.
+        self._debug = options[Options.DEBUG]
+        self._interpolation = Interpolation(pb, options)
+
+        # Evaluate the nonlinear functions at the initial interpolation points.
+        x_eval = self.interpolation.point(0)
+        fun_init, cub_init, ceq_init = pb(x_eval, penalty)
+        self._fun_val = np.full(options[Options.NPT], np.nan)
+        self._cub_val = np.full((options[Options.NPT], cub_init.size), np.nan)
+        self._ceq_val = np.full((options[Options.NPT], ceq_init.size), np.nan)
+        for k in range(options[Options.NPT]):
+            if k >= options[Options.MAX_EVAL]:
+                raise MaxEvalError
+            if k == 0:
+                self.fun_val[k] = fun_init
+                self.cub_val[k, :] = cub_init
+                self.ceq_val[k, :] = ceq_init
+            else:
+                x_eval = self.interpolation.point(k)
+                self.fun_val[k], self.cub_val[k, :], self.ceq_val[k, :] = pb(
+                    x_eval,
+                    penalty,
+                )
+
+            # Stop the iterations if the problem is a feasibility problem and
+            # the current interpolation point is feasible.
+            if (
+                pb.is_feasibility
+                and pb.maxcv(
+                    self.interpolation.point(k),
+                    self.cub_val[k, :],
+                    self.ceq_val[k, :],
+                )
+                <= options[Options.FEASIBILITY_TOL]
+            ):
+                raise FeasibleSuccess
+
+            # Stop the iterations if the current interpolation point is nearly
+            # feasible and has an objective function value below the target.
+            if (
+                self._fun_val[k] <= options[Options.TARGET]
+                and pb.maxcv(
+                    self.interpolation.point(k),
+                    self.cub_val[k, :],
+                    self.ceq_val[k, :],
+                )
+                <= options[Options.FEASIBILITY_TOL]
+            ):
+                raise TargetSuccess
+
+        # Build the initial quadratic models.
+        self._fun = Quadratic(
+            self.interpolation,
+            self._fun_val,
+            options[Options.DEBUG],
+        )
+        self._cub = np.empty(self.m_nonlinear_ub, dtype=Quadratic)
+        self._ceq = np.empty(self.m_nonlinear_eq, dtype=Quadratic)
+        for i in range(self.m_nonlinear_ub):
+            self._cub[i] = Quadratic(
+                self.interpolation,
+                self.cub_val[:, i],
+                options[Options.DEBUG],
+            )
+        for i in range(self.m_nonlinear_eq):
+            self._ceq[i] = Quadratic(
+                self.interpolation,
+                self.ceq_val[:, i],
+                options[Options.DEBUG],
+            )
+        if self._debug:
+            self._check_interpolation_conditions()
+
+    @property
+    def n(self):
+        """
+        Dimension of the problem.
+
+        Returns
+        -------
+        int
+            Dimension of the problem.
+        """
+        return self.interpolation.n
+
+    @property
+    def npt(self):
+        """
+        Number of interpolation points.
+
+        Returns
+        -------
+        int
+            Number of interpolation points.
+        """
+        return self.interpolation.npt
+
+    @property
+    def m_nonlinear_ub(self):
+        """
+        Number of nonlinear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear inequality constraints.
+        """
+        return self.cub_val.shape[1]
+
+    @property
+    def m_nonlinear_eq(self):
+        """
+        Number of nonlinear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear equality constraints.
+        """
+        return self.ceq_val.shape[1]
+
+    @property
+    def interpolation(self):
+        """
+        Interpolation set.
+
+        Returns
+        -------
+        `cobyqa.models.Interpolation`
+            Interpolation set.
+        """
+        return self._interpolation
+
+    @property
+    def fun_val(self):
+        """
+        Values of the objective function at the interpolation points.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (npt,)
+            Values of the objective function at the interpolation points.
+        """
+        return self._fun_val
+
+    @property
+    def cub_val(self):
+        """
+        Values of the nonlinear inequality constraint functions at the
+        interpolation points.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (npt, m_nonlinear_ub)
+            Values of the nonlinear inequality constraint functions at the
+            interpolation points.
+        """
+        return self._cub_val
+
+    @property
+    def ceq_val(self):
+        """
+        Values of the nonlinear equality constraint functions at the
+        interpolation points.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (npt, m_nonlinear_eq)
+            Values of the nonlinear equality constraint functions at the
+            interpolation points.
+        """
+        return self._ceq_val
+
+    def fun(self, x):
+        """
+        Evaluate the quadratic model of the objective function at a given
+        point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the quadratic model of the objective
+            function.
+
+        Returns
+        -------
+        float
+            Value of the quadratic model of the objective function at `x`.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+        return self._fun(x, self.interpolation)
+
+    def fun_grad(self, x):
+        """
+        Evaluate the gradient of the quadratic model of the objective function
+        at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the gradient of the quadratic model of
+            the objective function.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Gradient of the quadratic model of the objective function at `x`.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+        return self._fun.grad(x, self.interpolation)
+
+    def fun_hess(self):
+        """
+        Evaluate the Hessian matrix of the quadratic model of the objective
+        function.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n, n)
+            Hessian matrix of the quadratic model of the objective function.
+        """
+        return self._fun.hess(self.interpolation)
+
+    def fun_hess_prod(self, v):
+        """
+        Evaluate the right product of the Hessian matrix of the quadratic model
+        of the objective function with a given vector.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Vector with which the Hessian matrix of the quadratic model of the
+            objective function is multiplied from the right.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Right product of the Hessian matrix of the quadratic model of the
+            objective function with `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+        return self._fun.hess_prod(v, self.interpolation)
+
+    def fun_curv(self, v):
+        """
+        Evaluate the curvature of the quadratic model of the objective function
+        along a given direction.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Direction along which the curvature of the quadratic model of the
+            objective function is evaluated.
+
+        Returns
+        -------
+        float
+            Curvature of the quadratic model of the objective function along
+            `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+        return self._fun.curv(v, self.interpolation)
+
+    def fun_alt_grad(self, x):
+        """
+        Evaluate the gradient of the alternative quadratic model of the
+        objective function at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the gradient of the alternative
+            quadratic model of the objective function.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Gradient of the alternative quadratic model of the objective
+            function at `x`.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+        model = Quadratic(self.interpolation, self.fun_val, self._debug)
+        return model.grad(x, self.interpolation)
+
+    def cub(self, x, mask=None):
+        """
+        Evaluate the quadratic models of the nonlinear inequality functions at
+        a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the quadratic models of the nonlinear
+            inequality functions.
+        mask : `numpy.ndarray`, shape (m_nonlinear_ub,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Values of the quadratic model of the nonlinear inequality
+            functions.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_ub,
+            ), "The shape of `mask` is not valid."
+        return np.array(
+            [model(x, self.interpolation) for model in self._get_cub(mask)]
+        )
+
+    def cub_grad(self, x, mask=None):
+        """
+        Evaluate the gradients of the quadratic models of the nonlinear
+        inequality functions at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the gradients of the quadratic models of
+            the nonlinear inequality functions.
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Gradients of the quadratic model of the nonlinear inequality
+            functions.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_ub,
+            ), "The shape of `mask` is not valid."
+        return np.reshape(
+            [model.grad(x, self.interpolation)
+             for model in self._get_cub(mask)],
+            (-1, self.n),
+        )
+
+    def cub_hess(self, mask=None):
+        """
+        Evaluate the Hessian matrices of the quadratic models of the nonlinear
+        inequality functions.
+
+        Parameters
+        ----------
+        mask : `numpy.ndarray`, shape (m_nonlinear_ub,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Hessian matrices of the quadratic models of the nonlinear
+            inequality functions.
+        """
+        if self._debug:
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_ub,
+            ), "The shape of `mask` is not valid."
+        return np.reshape(
+            [model.hess(self.interpolation) for model in self._get_cub(mask)],
+            (-1, self.n, self.n),
+        )
+
+    def cub_hess_prod(self, v, mask=None):
+        """
+        Evaluate the right product of the Hessian matrices of the quadratic
+        models of the nonlinear inequality functions with a given vector.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Vector with which the Hessian matrices of the quadratic models of
+            the nonlinear inequality functions are multiplied from the right.
+        mask : `numpy.ndarray`, shape (m_nonlinear_ub,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Right products of the Hessian matrices of the quadratic models of
+            the nonlinear inequality functions with `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_ub,
+            ), "The shape of `mask` is not valid."
+        return np.reshape(
+            [
+                model.hess_prod(v, self.interpolation)
+                for model in self._get_cub(mask)
+            ],
+            (-1, self.n),
+        )
+
+    def cub_curv(self, v, mask=None):
+        """
+        Evaluate the curvature of the quadratic models of the nonlinear
+        inequality functions along a given direction.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Direction along which the curvature of the quadratic models of the
+            nonlinear inequality functions is evaluated.
+        mask : `numpy.ndarray`, shape (m_nonlinear_ub,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Curvature of the quadratic models of the nonlinear inequality
+            functions along `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_ub,
+            ), "The shape of `mask` is not valid."
+        return np.array(
+            [model.curv(v, self.interpolation)
+             for model in self._get_cub(mask)]
+        )
+
+    def ceq(self, x, mask=None):
+        """
+        Evaluate the quadratic models of the nonlinear equality functions at a
+        given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the quadratic models of the nonlinear
+            equality functions.
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Values of the quadratic model of the nonlinear equality functions.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_eq,
+            ), "The shape of `mask` is not valid."
+        return np.array(
+            [model(x, self.interpolation) for model in self._get_ceq(mask)]
+        )
+
+    def ceq_grad(self, x, mask=None):
+        """
+        Evaluate the gradients of the quadratic models of the nonlinear
+        equality functions at a given point.
+
+        Parameters
+        ----------
+        x : `numpy.ndarray`, shape (n,)
+            Point at which to evaluate the gradients of the quadratic models of
+            the nonlinear equality functions.
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Gradients of the quadratic model of the nonlinear equality
+            functions.
+        """
+        if self._debug:
+            assert x.shape == (self.n,), "The shape of `x` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_eq,
+            ), "The shape of `mask` is not valid."
+        return np.reshape(
+            [model.grad(x, self.interpolation)
+             for model in self._get_ceq(mask)],
+            (-1, self.n),
+        )
+
+    def ceq_hess(self, mask=None):
+        """
+        Evaluate the Hessian matrices of the quadratic models of the nonlinear
+        equality functions.
+
+        Parameters
+        ----------
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Hessian matrices of the quadratic models of the nonlinear equality
+            functions.
+        """
+        if self._debug:
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_eq,
+            ), "The shape of `mask` is not valid."
+        return np.reshape(
+            [model.hess(self.interpolation) for model in self._get_ceq(mask)],
+            (-1, self.n, self.n),
+        )
+
+    def ceq_hess_prod(self, v, mask=None):
+        """
+        Evaluate the right product of the Hessian matrices of the quadratic
+        models of the nonlinear equality functions with a given vector.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Vector with which the Hessian matrices of the quadratic models of
+            the nonlinear equality functions are multiplied from the right.
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Right products of the Hessian matrices of the quadratic models of
+            the nonlinear equality functions with `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_eq,
+            ), "The shape of `mask` is not valid."
+        return np.reshape(
+            [
+                model.hess_prod(v, self.interpolation)
+                for model in self._get_ceq(mask)
+            ],
+            (-1, self.n),
+        )
+
+    def ceq_curv(self, v, mask=None):
+        """
+        Evaluate the curvature of the quadratic models of the nonlinear
+        equality functions along a given direction.
+
+        Parameters
+        ----------
+        v : `numpy.ndarray`, shape (n,)
+            Direction along which the curvature of the quadratic models of the
+            nonlinear equality functions is evaluated.
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to consider.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Curvature of the quadratic models of the nonlinear equality
+            functions along `v`.
+        """
+        if self._debug:
+            assert v.shape == (self.n,), "The shape of `v` is not valid."
+            assert mask is None or mask.shape == (
+                self.m_nonlinear_eq,
+            ), "The shape of `mask` is not valid."
+        return np.array(
+            [model.curv(v, self.interpolation)
+             for model in self._get_ceq(mask)]
+        )
+
+    def reset_models(self):
+        """
+        Set the quadratic models of the objective function, nonlinear
+        inequality constraints, and nonlinear equality constraints to the
+        alternative quadratic models.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        self._fun = Quadratic(self.interpolation, self.fun_val, self._debug)
+        for i in range(self.m_nonlinear_ub):
+            self._cub[i] = Quadratic(
+                self.interpolation,
+                self.cub_val[:, i],
+                self._debug,
+            )
+        for i in range(self.m_nonlinear_eq):
+            self._ceq[i] = Quadratic(
+                self.interpolation,
+                self.ceq_val[:, i],
+                self._debug,
+            )
+        if self._debug:
+            self._check_interpolation_conditions()
+
+    def update_interpolation(self, k_new, x_new, fun_val, cub_val, ceq_val):
+        """
+        Update the interpolation set.
+
+        This method updates the interpolation set by replacing the `knew`-th
+        interpolation point with `xnew`. It also updates the function values
+        and the quadratic models.
+
+        Parameters
+        ----------
+        k_new : int
+            Index of the updated interpolation point.
+        x_new : `numpy.ndarray`, shape (n,)
+            New interpolation point. Its value is interpreted as relative to
+            the origin, not the base point.
+        fun_val : float
+            Value of the objective function at `x_new`.
+            Objective function value at `x_new`.
+        cub_val : `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Values of the nonlinear inequality constraints at `x_new`.
+        ceq_val : `numpy.ndarray`, shape (m_nonlinear_eq,)
+            Values of the nonlinear equality constraints at `x_new`.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+        """
+        if self._debug:
+            assert 0 <= k_new < self.npt, "The index `k_new` is not valid."
+            assert x_new.shape == (self.n,), \
+                "The shape of `x_new` is not valid."
+            assert isinstance(fun_val, float), \
+                "The function value is not valid."
+            assert cub_val.shape == (
+                self.m_nonlinear_ub,
+            ), "The shape of `cub_val` is not valid."
+            assert ceq_val.shape == (
+                self.m_nonlinear_eq,
+            ), "The shape of `ceq_val` is not valid."
+
+        # Compute the updates in the interpolation conditions.
+        fun_diff = np.zeros(self.npt)
+        cub_diff = np.zeros(self.cub_val.shape)
+        ceq_diff = np.zeros(self.ceq_val.shape)
+        fun_diff[k_new] = fun_val - self.fun(x_new)
+        cub_diff[k_new, :] = cub_val - self.cub(x_new)
+        ceq_diff[k_new, :] = ceq_val - self.ceq(x_new)
+
+        # Update the function values.
+        self.fun_val[k_new] = fun_val
+        self.cub_val[k_new, :] = cub_val
+        self.ceq_val[k_new, :] = ceq_val
+
+        # Update the interpolation set.
+        dir_old = np.copy(self.interpolation.xpt[:, k_new])
+        self.interpolation.xpt[:, k_new] = x_new - self.interpolation.x_base
+
+        # Update the quadratic models.
+        ill_conditioned = self._fun.update(
+            self.interpolation,
+            k_new,
+            dir_old,
+            fun_diff,
+        )
+        for i in range(self.m_nonlinear_ub):
+            ill_conditioned = ill_conditioned or self._cub[i].update(
+                self.interpolation,
+                k_new,
+                dir_old,
+                cub_diff[:, i],
+            )
+        for i in range(self.m_nonlinear_eq):
+            ill_conditioned = ill_conditioned or self._ceq[i].update(
+                self.interpolation,
+                k_new,
+                dir_old,
+                ceq_diff[:, i],
+            )
+        if self._debug:
+            self._check_interpolation_conditions()
+        return ill_conditioned
+
+    def determinants(self, x_new, k_new=None):
+        """
+        Compute the normalized determinants of the new interpolation systems.
+
+        Parameters
+        ----------
+        x_new : `numpy.ndarray`, shape (n,)
+            New interpolation point. Its value is interpreted as relative to
+            the origin, not the base point.
+        k_new : int, optional
+            Index of the updated interpolation point. If `k_new` is not
+            specified, all the possible determinants are computed.
+
+        Returns
+        -------
+        {float, `numpy.ndarray`, shape (npt,)}
+            Determinant(s) of the new interpolation system.
+
+        Raises
+        ------
+        `numpy.linalg.LinAlgError`
+            If the interpolation system is ill-defined.
+
+        Notes
+        -----
+        The determinants are normalized by the determinant of the current
+        interpolation system. For stability reasons, the calculations are done
+        using the formula (2.12) in [1]_.
+
+        References
+        ----------
+        .. [1] M. J. D. Powell. On updating the inverse of a KKT matrix.
+           Technical Report DAMTP 2004/NA01, Department of Applied Mathematics
+           and Theoretical Physics, University of Cambridge, Cambridge, UK,
+           2004.
+        """
+        if self._debug:
+            assert x_new.shape == (self.n,), \
+                "The shape of `x_new` is not valid."
+            assert (
+                k_new is None or 0 <= k_new < self.npt
+            ), "The index `k_new` is not valid."
+
+        # Compute the values independent of k_new.
+        shift = x_new - self.interpolation.x_base
+        new_col = np.empty((self.npt + self.n + 1, 1))
+        new_col[: self.npt, 0] = (
+                0.5 * (self.interpolation.xpt.T @ shift) ** 2.0)
+        new_col[self.npt, 0] = 1.0
+        new_col[self.npt + 1:, 0] = shift
+        inv_new_col = Quadratic.solve_systems(self.interpolation, new_col)[0]
+        beta = 0.5 * (shift @ shift) ** 2.0 - new_col[:, 0] @ inv_new_col[:, 0]
+
+        # Compute the values that depend on k.
+        if k_new is None:
+            coord_vec = np.eye(self.npt + self.n + 1, self.npt)
+            alpha = np.diag(
+                Quadratic.solve_systems(
+                    self.interpolation,
+                    coord_vec,
+                )[0]
+            )
+            tau = inv_new_col[: self.npt, 0]
+        else:
+            coord_vec = np.eye(self.npt + self.n + 1, 1, -k_new)
+            alpha = Quadratic.solve_systems(
+                self.interpolation,
+                coord_vec,
+            )[
+                0
+            ][k_new, 0]
+            tau = inv_new_col[k_new, 0]
+        return alpha * beta + tau**2.0
+
+    def shift_x_base(self, new_x_base, options):
+        """
+        Shift the base point without changing the interpolation set.
+
+        Parameters
+        ----------
+        new_x_base : `numpy.ndarray`, shape (n,)
+            New base point.
+        options : dict
+            Options of the solver.
+        """
+        if self._debug:
+            assert new_x_base.shape == (
+                self.n,
+            ), "The shape of `new_x_base` is not valid."
+
+        # Update the models.
+        self._fun.shift_x_base(self.interpolation, new_x_base)
+        for model in self._cub:
+            model.shift_x_base(self.interpolation, new_x_base)
+        for model in self._ceq:
+            model.shift_x_base(self.interpolation, new_x_base)
+
+        # Update the base point and the interpolation points.
+        shift = new_x_base - self.interpolation.x_base
+        self.interpolation.x_base += shift
+        self.interpolation.xpt -= shift[:, np.newaxis]
+        if options[Options.DEBUG]:
+            self._check_interpolation_conditions()
+
+    def _get_cub(self, mask=None):
+        """
+        Get the quadratic models of the nonlinear inequality constraints.
+
+        Parameters
+        ----------
+        mask : `numpy.ndarray`, shape (m_nonlinear_ub,), optional
+            Mask of the quadratic models to return.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Quadratic models of the nonlinear inequality constraints.
+        """
+        return self._cub if mask is None else self._cub[mask]
+
+    def _get_ceq(self, mask=None):
+        """
+        Get the quadratic models of the nonlinear equality constraints.
+
+        Parameters
+        ----------
+        mask : `numpy.ndarray`, shape (m_nonlinear_eq,), optional
+            Mask of the quadratic models to return.
+
+        Returns
+        -------
+        `numpy.ndarray`
+            Quadratic models of the nonlinear equality constraints.
+        """
+        return self._ceq if mask is None else self._ceq[mask]
+
+    def _check_interpolation_conditions(self):
+        """
+        Check the interpolation conditions of all quadratic models.
+        """
+        error_fun = 0.0
+        error_cub = 0.0
+        error_ceq = 0.0
+        for k in range(self.npt):
+            error_fun = np.max(
+                [
+                    error_fun,
+                    np.abs(
+                        self.fun(self.interpolation.point(k)) - self.fun_val[k]
+                    ),
+                ]
+            )
+            error_cub = np.max(
+                np.abs(
+                    self.cub(self.interpolation.point(k)) - self.cub_val[k, :]
+                ),
+                initial=error_cub,
+            )
+            error_ceq = np.max(
+                np.abs(
+                    self.ceq(self.interpolation.point(k)) - self.ceq_val[k, :]
+                ),
+                initial=error_ceq,
+            )
+        tol = 10.0 * np.sqrt(EPS) * max(self.n, self.npt)
+        if error_fun > tol * np.max(np.abs(self.fun_val), initial=1.0):
+            warnings.warn(
+                "The interpolation conditions for the objective function are "
+                "not satisfied.",
+                RuntimeWarning,
+                2,
+            )
+        if error_cub > tol * np.max(np.abs(self.cub_val), initial=1.0):
+            warnings.warn(
+                "The interpolation conditions for the inequality constraint "
+                "function are not satisfied.",
+                RuntimeWarning,
+                2,
+            )
+        if error_ceq > tol * np.max(np.abs(self.ceq_val), initial=1.0):
+            warnings.warn(
+                "The interpolation conditions for the equality constraint "
+                "function are not satisfied.",
+                RuntimeWarning,
+                2,
+            )

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/problem.py

@@ -0,0 +1,1296 @@
+from contextlib import suppress
+from inspect import signature
+import copy
+
+import numpy as np
+from scipy.optimize import (
+    Bounds,
+    LinearConstraint,
+    NonlinearConstraint,
+    OptimizeResult,
+)
+from scipy.optimize._constraints import PreparedConstraint
+
+
+from .settings import PRINT_OPTIONS, BARRIER
+from .utils import CallbackSuccess, get_arrays_tol
+from .utils import exact_1d_array
+
+
+class ObjectiveFunction:
+    """
+    Real-valued objective function.
+    """
+
+    def __init__(self, fun, verbose, debug, *args):
+        """
+        Initialize the objective function.
+
+        Parameters
+        ----------
+        fun : {callable, None}
+            Function to evaluate, or None.
+
+                ``fun(x, *args) -> float``
+
+            where ``x`` is an array with shape (n,) and `args` is a tuple.
+        verbose : bool
+            Whether to print the function evaluations.
+        debug : bool
+            Whether to make debugging tests during the execution.
+        *args : tuple
+            Additional arguments to be passed to the function.
+        """
+        if debug:
+            assert fun is None or callable(fun)
+            assert isinstance(verbose, bool)
+            assert isinstance(debug, bool)
+
+        self._fun = fun
+        self._verbose = verbose
+        self._args = args
+        self._n_eval = 0
+
+    def __call__(self, x):
+        """
+        Evaluate the objective function.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the objective function is evaluated.
+
+        Returns
+        -------
+        float
+            Function value at `x`.
+        """
+        x = np.array(x, dtype=float)
+        if self._fun is None:
+            f = 0.0
+        else:
+            f = float(np.squeeze(self._fun(x, *self._args)))
+            self._n_eval += 1
+            if self._verbose:
+                with np.printoptions(**PRINT_OPTIONS):
+                    print(f"{self.name}({x}) = {f}")
+        return f
+
+    @property
+    def n_eval(self):
+        """
+        Number of function evaluations.
+
+        Returns
+        -------
+        int
+            Number of function evaluations.
+        """
+        return self._n_eval
+
+    @property
+    def name(self):
+        """
+        Name of the objective function.
+
+        Returns
+        -------
+        str
+            Name of the objective function.
+        """
+        name = ""
+        if self._fun is not None:
+            try:
+                name = self._fun.__name__
+            except AttributeError:
+                name = "fun"
+        return name
+
+
+class BoundConstraints:
+    """
+    Bound constraints ``xl <= x <= xu``.
+    """
+
+    def __init__(self, bounds):
+        """
+        Initialize the bound constraints.
+
+        Parameters
+        ----------
+        bounds : scipy.optimize.Bounds
+            Bound constraints.
+        """
+        self._xl = np.array(bounds.lb, float)
+        self._xu = np.array(bounds.ub, float)
+
+        # Remove the ill-defined bounds.
+        self.xl[np.isnan(self.xl)] = -np.inf
+        self.xu[np.isnan(self.xu)] = np.inf
+
+        self.is_feasible = (
+            np.all(self.xl <= self.xu)
+            and np.all(self.xl < np.inf)
+            and np.all(self.xu > -np.inf)
+        )
+        self.m = np.count_nonzero(self.xl > -np.inf) + np.count_nonzero(
+            self.xu < np.inf
+        )
+        self.pcs = PreparedConstraint(bounds, np.ones(bounds.lb.size))
+
+    @property
+    def xl(self):
+        """
+        Lower bound.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Lower bound.
+        """
+        return self._xl
+
+    @property
+    def xu(self):
+        """
+        Upper bound.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Upper bound.
+        """
+        return self._xu
+
+    def maxcv(self, x):
+        """
+        Evaluate the maximum constraint violation.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the maximum constraint violation is evaluated.
+
+        Returns
+        -------
+        float
+            Maximum constraint violation at `x`.
+        """
+        x = np.asarray(x, dtype=float)
+        return self.violation(x)
+
+    def violation(self, x):
+        # shortcut for no bounds
+        if self.is_feasible:
+            return np.array([0])
+        else:
+            return self.pcs.violation(x)
+
+    def project(self, x):
+        """
+        Project a point onto the feasible set.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point to be projected.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Projection of `x` onto the feasible set.
+        """
+        return np.clip(x, self.xl, self.xu) if self.is_feasible else x
+
+
+class LinearConstraints:
+    """
+    Linear constraints ``a_ub @ x <= b_ub`` and ``a_eq @ x == b_eq``.
+    """
+
+    def __init__(self, constraints, n, debug):
+        """
+        Initialize the linear constraints.
+
+        Parameters
+        ----------
+        constraints : list of LinearConstraint
+            Linear constraints.
+        n : int
+            Number of variables.
+        debug : bool
+            Whether to make debugging tests during the execution.
+        """
+        if debug:
+            assert isinstance(constraints, list)
+            for constraint in constraints:
+                assert isinstance(constraint, LinearConstraint)
+            assert isinstance(debug, bool)
+
+        self._a_ub = np.empty((0, n))
+        self._b_ub = np.empty(0)
+        self._a_eq = np.empty((0, n))
+        self._b_eq = np.empty(0)
+        for constraint in constraints:
+            is_equality = np.abs(
+                constraint.ub - constraint.lb
+            ) <= get_arrays_tol(constraint.lb, constraint.ub)
+            if np.any(is_equality):
+                self._a_eq = np.vstack((self.a_eq, constraint.A[is_equality]))
+                self._b_eq = np.concatenate(
+                    (
+                        self.b_eq,
+                        0.5
+                        * (
+                            constraint.lb[is_equality]
+                            + constraint.ub[is_equality]
+                        ),
+                    )
+                )
+            if not np.all(is_equality):
+                self._a_ub = np.vstack(
+                    (
+                        self.a_ub,
+                        constraint.A[~is_equality],
+                        -constraint.A[~is_equality],
+                    )
+                )
+                self._b_ub = np.concatenate(
+                    (
+                        self.b_ub,
+                        constraint.ub[~is_equality],
+                        -constraint.lb[~is_equality],
+                    )
+                )
+
+        # Remove the ill-defined constraints.
+        self.a_ub[np.isnan(self.a_ub)] = 0.0
+        self.a_eq[np.isnan(self.a_eq)] = 0.0
+        undef_ub = np.isnan(self.b_ub) | np.isinf(self.b_ub)
+        undef_eq = np.isnan(self.b_eq)
+        self._a_ub = self.a_ub[~undef_ub, :]
+        self._b_ub = self.b_ub[~undef_ub]
+        self._a_eq = self.a_eq[~undef_eq, :]
+        self._b_eq = self.b_eq[~undef_eq]
+        self.pcs = [
+            PreparedConstraint(c, np.ones(n)) for c in constraints if c.A.size
+        ]
+
+    @property
+    def a_ub(self):
+        """
+        Left-hand side matrix of the linear inequality constraints.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m, n)
+            Left-hand side matrix of the linear inequality constraints.
+        """
+        return self._a_ub
+
+    @property
+    def b_ub(self):
+        """
+        Right-hand side vector of the linear inequality constraints.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m, n)
+            Right-hand side vector of the linear inequality constraints.
+        """
+        return self._b_ub
+
+    @property
+    def a_eq(self):
+        """
+        Left-hand side matrix of the linear equality constraints.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m, n)
+            Left-hand side matrix of the linear equality constraints.
+        """
+        return self._a_eq
+
+    @property
+    def b_eq(self):
+        """
+        Right-hand side vector of the linear equality constraints.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m, n)
+            Right-hand side vector of the linear equality constraints.
+        """
+        return self._b_eq
+
+    @property
+    def m_ub(self):
+        """
+        Number of linear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of linear inequality constraints.
+        """
+        return self.b_ub.size
+
+    @property
+    def m_eq(self):
+        """
+        Number of linear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of linear equality constraints.
+        """
+        return self.b_eq.size
+
+    def maxcv(self, x):
+        """
+        Evaluate the maximum constraint violation.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the maximum constraint violation is evaluated.
+
+        Returns
+        -------
+        float
+            Maximum constraint violation at `x`.
+        """
+        return np.max(self.violation(x), initial=0.0)
+
+    def violation(self, x):
+        if len(self.pcs):
+            return np.concatenate([pc.violation(x) for pc in self.pcs])
+        return np.array([])
+
+
+class NonlinearConstraints:
+    """
+    Nonlinear constraints ``c_ub(x) <= 0`` and ``c_eq(x) == b_eq``.
+    """
+
+    def __init__(self, constraints, verbose, debug):
+        """
+        Initialize the nonlinear constraints.
+
+        Parameters
+        ----------
+        constraints : list
+            Nonlinear constraints.
+        verbose : bool
+            Whether to print the function evaluations.
+        debug : bool
+            Whether to make debugging tests during the execution.
+        """
+        if debug:
+            assert isinstance(constraints, list)
+            for constraint in constraints:
+                assert isinstance(constraint, NonlinearConstraint)
+            assert isinstance(verbose, bool)
+            assert isinstance(debug, bool)
+
+        self._constraints = constraints
+        self.pcs = []
+        self._verbose = verbose
+
+        # map of indexes for equality and inequality constraints
+        self._map_ub = None
+        self._map_eq = None
+        self._m_ub = self._m_eq = None
+
+    def __call__(self, x):
+        """
+        Calculates the residual (slack) for the constraints.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the constraints are evaluated.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Nonlinear inequality constraint slack values.
+        `numpy.ndarray`, shape (m_nonlinear_eq,)
+            Nonlinear equality constraint slack values.
+        """
+        if not len(self._constraints):
+            self._m_eq = self._m_ub = 0
+            return np.array([]), np.array([])
+
+        x = np.array(x, dtype=float)
+        # first time around the constraints haven't been prepared
+        if not len(self.pcs):
+            self._map_ub = []
+            self._map_eq = []
+            self._m_eq = 0
+            self._m_ub = 0
+
+            for constraint in self._constraints:
+                if not callable(constraint.jac):
+                    # having a callable constraint function prevents
+                    # constraint.fun from being evaluated when preparing
+                    # constraint
+                    c = copy.copy(constraint)
+                    c.jac = lambda x0: x0
+                    c.hess = lambda x0, v: 0.0
+                    pc = PreparedConstraint(c, x)
+                else:
+                    pc = PreparedConstraint(constraint, x)
+                # we're going to be using the same x value again immediately
+                # after this initialisation
+                pc.fun.f_updated = True
+
+                self.pcs.append(pc)
+                idx = np.arange(pc.fun.m)
+
+                # figure out equality and inequality maps
+                lb, ub = pc.bounds[0], pc.bounds[1]
+                arr_tol = get_arrays_tol(lb, ub)
+                is_equality = np.abs(ub - lb) <= arr_tol
+                self._map_eq.append(idx[is_equality])
+                self._map_ub.append(idx[~is_equality])
+
+                # these values will be corrected to their proper values later
+                self._m_eq += np.count_nonzero(is_equality)
+                self._m_ub += np.count_nonzero(~is_equality)
+
+        c_ub = []
+        c_eq = []
+        for i, pc in enumerate(self.pcs):
+            val = pc.fun.fun(x)
+            if self._verbose:
+                with np.printoptions(**PRINT_OPTIONS):
+                    with suppress(AttributeError):
+                        fun_name = self._constraints[i].fun.__name__
+                        print(f"{fun_name}({x}) = {val}")
+
+            # separate violations into c_eq and c_ub
+            eq_idx = self._map_eq[i]
+            ub_idx = self._map_ub[i]
+
+            ub_val = val[ub_idx]
+            if len(ub_idx):
+                xl = pc.bounds[0][ub_idx]
+                xu = pc.bounds[1][ub_idx]
+
+                # calculate slack within lower bound
+                finite_xl = xl > -np.inf
+                _v = xl[finite_xl] - ub_val[finite_xl]
+                c_ub.append(_v)
+
+                # calculate slack within lower bound
+                finite_xu = xu < np.inf
+                _v = ub_val[finite_xu] - xu[finite_xu]
+                c_ub.append(_v)
+
+            # equality constraints taken from midpoint between lb and ub
+            eq_val = val[eq_idx]
+            if len(eq_idx):
+                midpoint = 0.5 * (pc.bounds[1][eq_idx] + pc.bounds[0][eq_idx])
+                eq_val -= midpoint
+            c_eq.append(eq_val)
+
+        if self._m_eq:
+            c_eq = np.concatenate(c_eq)
+        else:
+            c_eq = np.array([])
+
+        if self._m_ub:
+            c_ub = np.concatenate(c_ub)
+        else:
+            c_ub = np.array([])
+
+        self._m_ub = c_ub.size
+        self._m_eq = c_eq.size
+
+        return c_ub, c_eq
+
+    @property
+    def m_ub(self):
+        """
+        Number of nonlinear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear inequality constraints.
+
+        Raises
+        ------
+        ValueError
+            If the number of nonlinear inequality constraints is unknown.
+        """
+        if self._m_ub is None:
+            raise ValueError(
+                "The number of nonlinear inequality constraints is unknown."
+            )
+        else:
+            return self._m_ub
+
+    @property
+    def m_eq(self):
+        """
+        Number of nonlinear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear equality constraints.
+
+        Raises
+        ------
+        ValueError
+            If the number of nonlinear equality constraints is unknown.
+        """
+        if self._m_eq is None:
+            raise ValueError(
+                "The number of nonlinear equality constraints is unknown."
+            )
+        else:
+            return self._m_eq
+
+    @property
+    def n_eval(self):
+        """
+        Number of function evaluations.
+
+        Returns
+        -------
+        int
+            Number of function evaluations.
+        """
+        if len(self.pcs):
+            return self.pcs[0].fun.nfev
+        else:
+            return 0
+
+    def maxcv(self, x, cub_val=None, ceq_val=None):
+        """
+        Evaluate the maximum constraint violation.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the maximum constraint violation is evaluated.
+        cub_val : array_like, shape (m_nonlinear_ub,), optional
+            Values of the nonlinear inequality constraints. If not provided,
+            the nonlinear inequality constraints are evaluated at `x`.
+        ceq_val : array_like, shape (m_nonlinear_eq,), optional
+            Values of the nonlinear equality constraints. If not provided,
+            the nonlinear equality constraints are evaluated at `x`.
+
+        Returns
+        -------
+        float
+            Maximum constraint violation at `x`.
+        """
+        return np.max(
+            self.violation(x, cub_val=cub_val, ceq_val=ceq_val), initial=0.0
+        )
+
+    def violation(self, x, cub_val=None, ceq_val=None):
+        return np.concatenate([pc.violation(x) for pc in self.pcs])
+
+
+class Problem:
+    """
+    Optimization problem.
+    """
+
+    def __init__(
+        self,
+        obj,
+        x0,
+        bounds,
+        linear,
+        nonlinear,
+        callback,
+        feasibility_tol,
+        scale,
+        store_history,
+        history_size,
+        filter_size,
+        debug,
+    ):
+        """
+        Initialize the nonlinear problem.
+
+        The problem is preprocessed to remove all the variables that are fixed
+        by the bound constraints.
+
+        Parameters
+        ----------
+        obj : ObjectiveFunction
+            Objective function.
+        x0 : array_like, shape (n,)
+            Initial guess.
+        bounds : BoundConstraints
+            Bound constraints.
+        linear : LinearConstraints
+            Linear constraints.
+        nonlinear : NonlinearConstraints
+            Nonlinear constraints.
+        callback : {callable, None}
+            Callback function.
+        feasibility_tol : float
+            Tolerance on the constraint violation.
+        scale : bool
+            Whether to scale the problem according to the bounds.
+        store_history : bool
+            Whether to store the function evaluations.
+        history_size : int
+            Maximum number of function evaluations to store.
+        filter_size : int
+            Maximum number of points in the filter.
+        debug : bool
+            Whether to make debugging tests during the execution.
+        """
+        if debug:
+            assert isinstance(obj, ObjectiveFunction)
+            assert isinstance(bounds, BoundConstraints)
+            assert isinstance(linear, LinearConstraints)
+            assert isinstance(nonlinear, NonlinearConstraints)
+            assert isinstance(feasibility_tol, float)
+            assert isinstance(scale, bool)
+            assert isinstance(store_history, bool)
+            assert isinstance(history_size, int)
+            if store_history:
+                assert history_size > 0
+            assert isinstance(filter_size, int)
+            assert filter_size > 0
+            assert isinstance(debug, bool)
+
+        self._obj = obj
+        self._linear = linear
+        self._nonlinear = nonlinear
+        if callback is not None:
+            if not callable(callback):
+                raise TypeError("The callback must be a callable function.")
+        self._callback = callback
+
+        # Check the consistency of the problem.
+        x0 = exact_1d_array(x0, "The initial guess must be a vector.")
+        n = x0.size
+        if bounds.xl.size != n:
+            raise ValueError(f"The bounds must have {n} elements.")
+        if linear.a_ub.shape[1] != n:
+            raise ValueError(
+                f"The left-hand side matrices of the linear constraints must "
+                f"have {n} columns."
+            )
+
+        # Check which variables are fixed.
+        tol = get_arrays_tol(bounds.xl, bounds.xu)
+        self._fixed_idx = (bounds.xl <= bounds.xu) & (
+            np.abs(bounds.xl - bounds.xu) < tol
+        )
+        self._fixed_val = 0.5 * (
+            bounds.xl[self._fixed_idx] + bounds.xu[self._fixed_idx]
+        )
+        self._fixed_val = np.clip(
+            self._fixed_val,
+            bounds.xl[self._fixed_idx],
+            bounds.xu[self._fixed_idx],
+        )
+
+        # Set the bound constraints.
+        self._orig_bounds = bounds
+        self._bounds = BoundConstraints(
+            Bounds(bounds.xl[~self._fixed_idx], bounds.xu[~self._fixed_idx])
+        )
+
+        # Set the initial guess.
+        self._x0 = self._bounds.project(x0[~self._fixed_idx])
+
+        # Set the linear constraints.
+        b_eq = linear.b_eq - linear.a_eq[:, self._fixed_idx] @ self._fixed_val
+        self._linear = LinearConstraints(
+            [
+                LinearConstraint(
+                    linear.a_ub[:, ~self._fixed_idx],
+                    -np.inf,
+                    linear.b_ub
+                    - linear.a_ub[:, self._fixed_idx] @ self._fixed_val,
+                ),
+                LinearConstraint(linear.a_eq[:, ~self._fixed_idx], b_eq, b_eq),
+            ],
+            self.n,
+            debug,
+        )
+
+        # Scale the problem if necessary.
+        scale = (
+            scale
+            and self._bounds.is_feasible
+            and np.all(np.isfinite(self._bounds.xl))
+            and np.all(np.isfinite(self._bounds.xu))
+        )
+        if scale:
+            self._scaling_factor = 0.5 * (self._bounds.xu - self._bounds.xl)
+            self._scaling_shift = 0.5 * (self._bounds.xu + self._bounds.xl)
+            self._bounds = BoundConstraints(
+                Bounds(-np.ones(self.n), np.ones(self.n))
+            )
+            b_eq = self._linear.b_eq - self._linear.a_eq @ self._scaling_shift
+            self._linear = LinearConstraints(
+                [
+                    LinearConstraint(
+                        self._linear.a_ub @ np.diag(self._scaling_factor),
+                        -np.inf,
+                        self._linear.b_ub
+                        - self._linear.a_ub @ self._scaling_shift,
+                    ),
+                    LinearConstraint(
+                        self._linear.a_eq @ np.diag(self._scaling_factor),
+                        b_eq,
+                        b_eq,
+                    ),
+                ],
+                self.n,
+                debug,
+            )
+            self._x0 = (self._x0 - self._scaling_shift) / self._scaling_factor
+        else:
+            self._scaling_factor = np.ones(self.n)
+            self._scaling_shift = np.zeros(self.n)
+
+        # Set the initial filter.
+        self._feasibility_tol = feasibility_tol
+        self._filter_size = filter_size
+        self._fun_filter = []
+        self._maxcv_filter = []
+        self._x_filter = []
+
+        # Set the initial history.
+        self._store_history = store_history
+        self._history_size = history_size
+        self._fun_history = []
+        self._maxcv_history = []
+        self._x_history = []
+
+    def __call__(self, x, penalty=0.0):
+        """
+        Evaluate the objective and nonlinear constraint functions.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the functions are evaluated.
+        penalty : float, optional
+            Penalty parameter used to select the point in the filter to forward
+            to the callback function.
+
+        Returns
+        -------
+        float
+            Objective function value.
+        `numpy.ndarray`, shape (m_nonlinear_ub,)
+            Nonlinear inequality constraint function values.
+        `numpy.ndarray`, shape (m_nonlinear_eq,)
+            Nonlinear equality constraint function values.
+
+        Raises
+        ------
+        `cobyqa.utils.CallbackSuccess`
+            If the callback function raises a ``StopIteration``.
+        """
+        # Evaluate the objective and nonlinear constraint functions.
+        x = np.asarray(x, dtype=float)
+        x_full = self.build_x(x)
+        fun_val = self._obj(x_full)
+        cub_val, ceq_val = self._nonlinear(x_full)
+        maxcv_val = self.maxcv(x, cub_val, ceq_val)
+        if self._store_history:
+            self._fun_history.append(fun_val)
+            self._maxcv_history.append(maxcv_val)
+            self._x_history.append(x)
+            if len(self._fun_history) > self._history_size:
+                self._fun_history.pop(0)
+                self._maxcv_history.pop(0)
+                self._x_history.pop(0)
+
+        # Add the point to the filter if it is not dominated by any point.
+        if np.isnan(fun_val) and np.isnan(maxcv_val):
+            include_point = len(self._fun_filter) == 0
+        elif np.isnan(fun_val):
+            include_point = all(
+                np.isnan(fun_filter)
+                and maxcv_val < maxcv_filter
+                or np.isnan(maxcv_filter)
+                for fun_filter, maxcv_filter in zip(
+                    self._fun_filter,
+                    self._maxcv_filter,
+                )
+            )
+        elif np.isnan(maxcv_val):
+            include_point = all(
+                np.isnan(maxcv_filter)
+                and fun_val < fun_filter
+                or np.isnan(fun_filter)
+                for fun_filter, maxcv_filter in zip(
+                    self._fun_filter,
+                    self._maxcv_filter,
+                )
+            )
+        else:
+            include_point = all(
+                fun_val < fun_filter or maxcv_val < maxcv_filter
+                for fun_filter, maxcv_filter in zip(
+                    self._fun_filter,
+                    self._maxcv_filter,
+                )
+            )
+        if include_point:
+            self._fun_filter.append(fun_val)
+            self._maxcv_filter.append(maxcv_val)
+            self._x_filter.append(x)
+
+            # Remove the points in the filter that are dominated by the new
+            # point. We must iterate in reverse order to avoid problems when
+            # removing elements from the list.
+            for k in range(len(self._fun_filter) - 2, -1, -1):
+                if np.isnan(fun_val):
+                    remove_point = np.isnan(self._fun_filter[k])
+                elif np.isnan(maxcv_val):
+                    remove_point = np.isnan(self._maxcv_filter[k])
+                else:
+                    remove_point = (
+                        np.isnan(self._fun_filter[k])
+                        or np.isnan(self._maxcv_filter[k])
+                        or fun_val <= self._fun_filter[k]
+                        and maxcv_val <= self._maxcv_filter[k]
+                    )
+                if remove_point:
+                    self._fun_filter.pop(k)
+                    self._maxcv_filter.pop(k)
+                    self._x_filter.pop(k)
+
+            # Keep only the most recent points in the filter.
+            if len(self._fun_filter) > self._filter_size:
+                self._fun_filter.pop(0)
+                self._maxcv_filter.pop(0)
+                self._x_filter.pop(0)
+
+        # Evaluate the callback function after updating the filter to ensure
+        # that the current point can be returned by the method.
+        if self._callback is not None:
+            sig = signature(self._callback)
+            try:
+                x_best, fun_best, _ = self.best_eval(penalty)
+                x_best = self.build_x(x_best)
+                if set(sig.parameters) == {"intermediate_result"}:
+                    intermediate_result = OptimizeResult(
+                        x=x_best,
+                        fun=fun_best,
+                        # maxcv=maxcv_best,
+                    )
+                    self._callback(intermediate_result=intermediate_result)
+                else:
+                    self._callback(x_best)
+            except StopIteration as exc:
+                raise CallbackSuccess from exc
+
+        # Apply the extreme barriers and return.
+        if np.isnan(fun_val):
+            fun_val = BARRIER
+        cub_val[np.isnan(cub_val)] = BARRIER
+        ceq_val[np.isnan(ceq_val)] = BARRIER
+        fun_val = max(min(fun_val, BARRIER), -BARRIER)
+        cub_val = np.maximum(np.minimum(cub_val, BARRIER), -BARRIER)
+        ceq_val = np.maximum(np.minimum(ceq_val, BARRIER), -BARRIER)
+        return fun_val, cub_val, ceq_val
+
+    @property
+    def n(self):
+        """
+        Number of variables.
+
+        Returns
+        -------
+        int
+            Number of variables.
+        """
+        return self.x0.size
+
+    @property
+    def n_orig(self):
+        """
+        Number of variables in the original problem (with fixed variables).
+
+        Returns
+        -------
+        int
+            Number of variables in the original problem (with fixed variables).
+        """
+        return self._fixed_idx.size
+
+    @property
+    def x0(self):
+        """
+        Initial guess.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Initial guess.
+        """
+        return self._x0
+
+    @property
+    def n_eval(self):
+        """
+        Number of function evaluations.
+
+        Returns
+        -------
+        int
+            Number of function evaluations.
+        """
+        return self._obj.n_eval
+
+    @property
+    def fun_name(self):
+        """
+        Name of the objective function.
+
+        Returns
+        -------
+        str
+            Name of the objective function.
+        """
+        return self._obj.name
+
+    @property
+    def bounds(self):
+        """
+        Bound constraints.
+
+        Returns
+        -------
+        BoundConstraints
+            Bound constraints.
+        """
+        return self._bounds
+
+    @property
+    def linear(self):
+        """
+        Linear constraints.
+
+        Returns
+        -------
+        LinearConstraints
+            Linear constraints.
+        """
+        return self._linear
+
+    @property
+    def m_bounds(self):
+        """
+        Number of bound constraints.
+
+        Returns
+        -------
+        int
+            Number of bound constraints.
+        """
+        return self.bounds.m
+
+    @property
+    def m_linear_ub(self):
+        """
+        Number of linear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of linear inequality constraints.
+        """
+        return self.linear.m_ub
+
+    @property
+    def m_linear_eq(self):
+        """
+        Number of linear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of linear equality constraints.
+        """
+        return self.linear.m_eq
+
+    @property
+    def m_nonlinear_ub(self):
+        """
+        Number of nonlinear inequality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear inequality constraints.
+
+        Raises
+        ------
+        ValueError
+            If the number of nonlinear inequality constraints is not known.
+        """
+        return self._nonlinear.m_ub
+
+    @property
+    def m_nonlinear_eq(self):
+        """
+        Number of nonlinear equality constraints.
+
+        Returns
+        -------
+        int
+            Number of nonlinear equality constraints.
+
+        Raises
+        ------
+        ValueError
+            If the number of nonlinear equality constraints is not known.
+        """
+        return self._nonlinear.m_eq
+
+    @property
+    def fun_history(self):
+        """
+        History of objective function evaluations.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n_eval,)
+            History of objective function evaluations.
+        """
+        return np.array(self._fun_history, dtype=float)
+
+    @property
+    def maxcv_history(self):
+        """
+        History of maximum constraint violations.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n_eval,)
+            History of maximum constraint violations.
+        """
+        return np.array(self._maxcv_history, dtype=float)
+
+    @property
+    def type(self):
+        """
+        Type of the problem.
+
+        The problem can be either 'unconstrained', 'bound-constrained',
+        'linearly constrained', or 'nonlinearly constrained'.
+
+        Returns
+        -------
+        str
+            Type of the problem.
+        """
+        try:
+            if self.m_nonlinear_ub > 0 or self.m_nonlinear_eq > 0:
+                return "nonlinearly constrained"
+            elif self.m_linear_ub > 0 or self.m_linear_eq > 0:
+                return "linearly constrained"
+            elif self.m_bounds > 0:
+                return "bound-constrained"
+            else:
+                return "unconstrained"
+        except ValueError:
+            # The number of nonlinear constraints is not known. It may be zero
+            # if the user provided a nonlinear inequality and/or equality
+            # constraint function that returns an empty array. However, as this
+            # is not known before the first call to the function, we assume
+            # that the problem is nonlinearly constrained.
+            return "nonlinearly constrained"
+
+    @property
+    def is_feasibility(self):
+        """
+        Whether the problem is a feasibility problem.
+
+        Returns
+        -------
+        bool
+            Whether the problem is a feasibility problem.
+        """
+        return self.fun_name == ""
+
+    def build_x(self, x):
+        """
+        Build the full vector of variables from the reduced vector.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Reduced vector of variables.
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n_orig,)
+            Full vector of variables.
+        """
+        x_full = np.empty(self.n_orig)
+        x_full[self._fixed_idx] = self._fixed_val
+        x_full[~self._fixed_idx] = (x * self._scaling_factor
+                                    + self._scaling_shift)
+        return self._orig_bounds.project(x_full)
+
+    def maxcv(self, x, cub_val=None, ceq_val=None):
+        """
+        Evaluate the maximum constraint violation.
+
+        Parameters
+        ----------
+        x : array_like, shape (n,)
+            Point at which the maximum constraint violation is evaluated.
+        cub_val : array_like, shape (m_nonlinear_ub,), optional
+            Values of the nonlinear inequality constraints. If not provided,
+            the nonlinear inequality constraints are evaluated at `x`.
+        ceq_val : array_like, shape (m_nonlinear_eq,), optional
+            Values of the nonlinear equality constraints. If not provided,
+            the nonlinear equality constraints are evaluated at `x`.
+
+        Returns
+        -------
+        float
+            Maximum constraint violation at `x`.
+        """
+        violation = self.violation(x, cub_val=cub_val, ceq_val=ceq_val)
+        if np.count_nonzero(violation):
+            return np.max(violation, initial=0.0)
+        else:
+            return 0.0
+
+    def violation(self, x, cub_val=None, ceq_val=None):
+        violation = []
+        if not self.bounds.is_feasible:
+            b = self.bounds.violation(x)
+            violation.append(b)
+
+        if len(self.linear.pcs):
+            lc = self.linear.violation(x)
+            violation.append(lc)
+        if len(self._nonlinear.pcs):
+            nlc = self._nonlinear.violation(x, cub_val, ceq_val)
+            violation.append(nlc)
+
+        if len(violation):
+            return np.concatenate(violation)
+
+    def best_eval(self, penalty):
+        """
+        Return the best point in the filter and the corresponding objective and
+        nonlinear constraint function evaluations.
+
+        Parameters
+        ----------
+        penalty : float
+            Penalty parameter
+
+        Returns
+        -------
+        `numpy.ndarray`, shape (n,)
+            Best point.
+        float
+            Corresponding objective function value.
+        float
+            Corresponding maximum constraint violation.
+        """
+        # If the filter is empty, i.e., if no function evaluation has been
+        # performed, we evaluate the objective and nonlinear constraint
+        # functions at the initial guess.
+        if len(self._fun_filter) == 0:
+            self(self.x0)
+
+        # Find the best point in the filter.
+        fun_filter = np.array(self._fun_filter)
+        maxcv_filter = np.array(self._maxcv_filter)
+        x_filter = np.array(self._x_filter)
+        finite_idx = np.isfinite(maxcv_filter)
+        if np.any(finite_idx):
+            # At least one point has a finite maximum constraint violation.
+            feasible_idx = maxcv_filter <= self._feasibility_tol
+            if np.any(feasible_idx) and not np.all(
+                np.isnan(fun_filter[feasible_idx])
+            ):
+                # At least one point is feasible and has a well-defined
+                # objective function value. We select the point with the least
+                # objective function value. If there is a tie, we select the
+                # point with the least maximum constraint violation. If there
+                # is still a tie, we select the most recent point.
+                fun_min_idx = feasible_idx & (
+                    fun_filter <= np.nanmin(fun_filter[feasible_idx])
+                )
+                if np.count_nonzero(fun_min_idx) > 1:
+                    fun_min_idx &= maxcv_filter <= np.min(
+                        maxcv_filter[fun_min_idx]
+                    )
+                i = np.flatnonzero(fun_min_idx)[-1]
+            elif np.any(feasible_idx):
+                # At least one point is feasible but no feasible point has a
+                # well-defined objective function value. We select the most
+                # recent feasible point.
+                i = np.flatnonzero(feasible_idx)[-1]
+            else:
+                # No point is feasible. We first compute the merit function
+                # value for each point.
+                merit_filter = np.full_like(fun_filter, np.nan)
+                merit_filter[finite_idx] = (
+                    fun_filter[finite_idx] + penalty * maxcv_filter[finite_idx]
+                )
+                if np.all(np.isnan(merit_filter)):
+                    # No point has a well-defined merit function value. In
+                    # other words, among the points with a well-defined maximum
+                    # constraint violation, none has a well-defined objective
+                    # function value. We select the point with the least
+                    # maximum constraint violation. If there is a tie, we
+                    # select the most recent point.
+                    min_maxcv_idx = maxcv_filter <= np.nanmin(maxcv_filter)
+                    i = np.flatnonzero(min_maxcv_idx)[-1]
+                else:
+                    # At least one point has a well-defined merit function
+                    # value. We select the point with the least merit function
+                    # value. If there is a tie, we select the point with the
+                    # least maximum constraint violation. If there is still a
+                    # tie, we select the point with the least objective
+                    # function value. If there is still a tie, we select the
+                    # most recent point.
+                    merit_min_idx = merit_filter <= np.nanmin(merit_filter)
+                    if np.count_nonzero(merit_min_idx) > 1:
+                        merit_min_idx &= maxcv_filter <= np.min(
+                            maxcv_filter[merit_min_idx]
+                        )
+
+                    if np.count_nonzero(merit_min_idx) > 1:
+                        merit_min_idx &= fun_filter <= np.min(
+                            fun_filter[merit_min_idx]
+                        )
+                    i = np.flatnonzero(merit_min_idx)[-1]
+        elif not np.all(np.isnan(fun_filter)):
+            # No maximum constraint violation is well-defined but at least one
+            # point has a well-defined objective function value. We select the
+            # point with the least objective function value. If there is a tie,
+            # we select the most recent point.
+            fun_min_idx = fun_filter <= np.nanmin(fun_filter)
+            i = np.flatnonzero(fun_min_idx)[-1]
+        else:
+            # No point has a well-defined maximum constraint violation or
+            # objective function value. We select the most recent point.
+            i = len(fun_filter) - 1
+        return (
+            self.bounds.project(x_filter[i, :]),
+            fun_filter[i],
+            maxcv_filter[i],
+        )

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/settings.py

@@ -0,0 +1,132 @@
+import sys
+from enum import Enum
+
+import numpy as np
+
+
+# Exit status.
+class ExitStatus(Enum):
+    """
+    Exit statuses.
+    """
+
+    RADIUS_SUCCESS = 0
+    TARGET_SUCCESS = 1
+    FIXED_SUCCESS = 2
+    CALLBACK_SUCCESS = 3
+    FEASIBLE_SUCCESS = 4
+    MAX_EVAL_WARNING = 5
+    MAX_ITER_WARNING = 6
+    INFEASIBLE_ERROR = -1
+    LINALG_ERROR = -2
+
+
+class Options(str, Enum):
+    """
+    Options.
+    """
+
+    DEBUG = "debug"
+    FEASIBILITY_TOL = "feasibility_tol"
+    FILTER_SIZE = "filter_size"
+    HISTORY_SIZE = "history_size"
+    MAX_EVAL = "maxfev"
+    MAX_ITER = "maxiter"
+    NPT = "nb_points"
+    RHOBEG = "radius_init"
+    RHOEND = "radius_final"
+    SCALE = "scale"
+    STORE_HISTORY = "store_history"
+    TARGET = "target"
+    VERBOSE = "disp"
+
+
+class Constants(str, Enum):
+    """
+    Constants.
+    """
+
+    DECREASE_RADIUS_FACTOR = "decrease_radius_factor"
+    INCREASE_RADIUS_FACTOR = "increase_radius_factor"
+    INCREASE_RADIUS_THRESHOLD = "increase_radius_threshold"
+    DECREASE_RADIUS_THRESHOLD = "decrease_radius_threshold"
+    DECREASE_RESOLUTION_FACTOR = "decrease_resolution_factor"
+    LARGE_RESOLUTION_THRESHOLD = "large_resolution_threshold"
+    MODERATE_RESOLUTION_THRESHOLD = "moderate_resolution_threshold"
+    LOW_RATIO = "low_ratio"
+    HIGH_RATIO = "high_ratio"
+    VERY_LOW_RATIO = "very_low_ratio"
+    PENALTY_INCREASE_THRESHOLD = "penalty_increase_threshold"
+    PENALTY_INCREASE_FACTOR = "penalty_increase_factor"
+    SHORT_STEP_THRESHOLD = "short_step_threshold"
+    LOW_RADIUS_FACTOR = "low_radius_factor"
+    BYRD_OMOJOKUN_FACTOR = "byrd_omojokun_factor"
+    THRESHOLD_RATIO_CONSTRAINTS = "threshold_ratio_constraints"
+    LARGE_SHIFT_FACTOR = "large_shift_factor"
+    LARGE_GRADIENT_FACTOR = "large_gradient_factor"
+    RESOLUTION_FACTOR = "resolution_factor"
+    IMPROVE_TCG = "improve_tcg"
+
+
+# Default options.
+DEFAULT_OPTIONS = {
+    Options.DEBUG.value: False,
+    Options.FEASIBILITY_TOL.value: np.sqrt(np.finfo(float).eps),
+    Options.FILTER_SIZE.value: sys.maxsize,
+    Options.HISTORY_SIZE.value: sys.maxsize,
+    Options.MAX_EVAL.value: lambda n: 500 * n,
+    Options.MAX_ITER.value: lambda n: 1000 * n,
+    Options.NPT.value: lambda n: 2 * n + 1,
+    Options.RHOBEG.value: 1.0,
+    Options.RHOEND.value: 1e-6,
+    Options.SCALE.value: False,
+    Options.STORE_HISTORY.value: False,
+    Options.TARGET.value: -np.inf,
+    Options.VERBOSE.value: False,
+}
+
+# Default constants.
+DEFAULT_CONSTANTS = {
+    Constants.DECREASE_RADIUS_FACTOR.value: 0.5,
+    Constants.INCREASE_RADIUS_FACTOR.value: np.sqrt(2.0),
+    Constants.INCREASE_RADIUS_THRESHOLD.value: 2.0,
+    Constants.DECREASE_RADIUS_THRESHOLD.value: 1.4,
+    Constants.DECREASE_RESOLUTION_FACTOR.value: 0.1,
+    Constants.LARGE_RESOLUTION_THRESHOLD.value: 250.0,
+    Constants.MODERATE_RESOLUTION_THRESHOLD.value: 16.0,
+    Constants.LOW_RATIO.value: 0.1,
+    Constants.HIGH_RATIO.value: 0.7,
+    Constants.VERY_LOW_RATIO.value: 0.01,
+    Constants.PENALTY_INCREASE_THRESHOLD.value: 1.5,
+    Constants.PENALTY_INCREASE_FACTOR.value: 2.0,
+    Constants.SHORT_STEP_THRESHOLD.value: 0.5,
+    Constants.LOW_RADIUS_FACTOR.value: 0.1,
+    Constants.BYRD_OMOJOKUN_FACTOR.value: 0.8,
+    Constants.THRESHOLD_RATIO_CONSTRAINTS.value: 2.0,
+    Constants.LARGE_SHIFT_FACTOR.value: 10.0,
+    Constants.LARGE_GRADIENT_FACTOR.value: 10.0,
+    Constants.RESOLUTION_FACTOR.value: 2.0,
+    Constants.IMPROVE_TCG.value: True,
+}
+
+# Printing options.
+PRINT_OPTIONS = {
+    "threshold": 6,
+    "edgeitems": 2,
+    "linewidth": sys.maxsize,
+    "formatter": {
+        "float_kind": lambda x: np.format_float_scientific(
+            x,
+            precision=3,
+            unique=False,
+            pad_left=2,
+        )
+    },
+}
+
+# Constants.
+BARRIER = 2.0 ** min(
+    100,
+    np.finfo(float).maxexp // 2,
+    -np.finfo(float).minexp // 2,
+)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/subsolvers/__init__.py

@@ -0,0 +1,14 @@
+from .geometry import cauchy_geometry, spider_geometry
+from .optim import (
+    tangential_byrd_omojokun,
+    constrained_tangential_byrd_omojokun,
+    normal_byrd_omojokun,
+)
+
+__all__ = [
+    "cauchy_geometry",
+    "spider_geometry",
+    "tangential_byrd_omojokun",
+    "constrained_tangential_byrd_omojokun",
+    "normal_byrd_omojokun",
+]

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/subsolvers/geometry.py

@@ -0,0 +1,387 @@
+import inspect
+
+import numpy as np
+
+from ..utils import get_arrays_tol
+
+
+TINY = np.finfo(float).tiny
+
+
+def cauchy_geometry(const, grad, curv, xl, xu, delta, debug):
+    r"""
+    Maximize approximately the absolute value of a quadratic function subject
+    to bound constraints in a trust region.
+
+    This function solves approximately
+
+    .. math::
+
+        \max_{s \in \mathbb{R}^n} \quad \bigg\lvert c + g^{\mathsf{T}} s +
+        \frac{1}{2} s^{\mathsf{T}} H s \bigg\rvert \quad \text{s.t.} \quad
+        \left\{ \begin{array}{l}
+            l \le s \le u,\\
+            \lVert s \rVert \le \Delta,
+        \end{array} \right.
+
+    by maximizing the objective function along the constrained Cauchy
+    direction.
+
+    Parameters
+    ----------
+    const : float
+        Constant :math:`c` as shown above.
+    grad : `numpy.ndarray`, shape (n,)
+        Gradient :math:`g` as shown above.
+    curv : callable
+        Curvature of :math:`H` along any vector.
+
+            ``curv(s) -> float``
+
+        returns :math:`s^{\mathsf{T}} H s`.
+    xl : `numpy.ndarray`, shape (n,)
+        Lower bounds :math:`l` as shown above.
+    xu : `numpy.ndarray`, shape (n,)
+        Upper bounds :math:`u` as shown above.
+    delta : float
+        Trust-region radius :math:`\Delta` as shown above.
+    debug : bool
+        Whether to make debugging tests during the execution.
+
+    Returns
+    -------
+    `numpy.ndarray`, shape (n,)
+        Approximate solution :math:`s`.
+
+    Notes
+    -----
+    This function is described as the first alternative in Section 6.5 of [1]_.
+    It is assumed that the origin is feasible with respect to the bound
+    constraints and that `delta` is finite and positive.
+
+    References
+    ----------
+    .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization Methods
+       and Software*. PhD thesis, Department of Applied Mathematics, The Hong
+       Kong Polytechnic University, Hong Kong, China, 2022. URL:
+       https://theses.lib.polyu.edu.hk/handle/200/12294.
+    """
+    if debug:
+        assert isinstance(const, float)
+        assert isinstance(grad, np.ndarray) and grad.ndim == 1
+        assert inspect.signature(curv).bind(grad)
+        assert isinstance(xl, np.ndarray) and xl.shape == grad.shape
+        assert isinstance(xu, np.ndarray) and xu.shape == grad.shape
+        assert isinstance(delta, float)
+        assert isinstance(debug, bool)
+        tol = get_arrays_tol(xl, xu)
+        assert np.all(xl <= tol)
+        assert np.all(xu >= -tol)
+        assert np.isfinite(delta) and delta > 0.0
+    xl = np.minimum(xl, 0.0)
+    xu = np.maximum(xu, 0.0)
+
+    # To maximize the absolute value of a quadratic function, we maximize the
+    # function itself or its negative, and we choose the solution that provides
+    # the largest function value.
+    step1, q_val1 = _cauchy_geom(const, grad, curv, xl, xu, delta, debug)
+    step2, q_val2 = _cauchy_geom(
+        -const,
+        -grad,
+        lambda x: -curv(x),
+        xl,
+        xu,
+        delta,
+        debug,
+    )
+    step = step1 if abs(q_val1) >= abs(q_val2) else step2
+
+    if debug:
+        assert np.all(xl <= step)
+        assert np.all(step <= xu)
+        assert np.linalg.norm(step) < 1.1 * delta
+    return step
+
+
+def spider_geometry(const, grad, curv, xpt, xl, xu, delta, debug):
+    r"""
+    Maximize approximately the absolute value of a quadratic function subject
+    to bound constraints in a trust region.
+
+    This function solves approximately
+
+    .. math::
+
+        \max_{s \in \mathbb{R}^n} \quad \bigg\lvert c + g^{\mathsf{T}} s +
+        \frac{1}{2} s^{\mathsf{T}} H s \bigg\rvert \quad \text{s.t.} \quad
+        \left\{ \begin{array}{l}
+            l \le s \le u,\\
+            \lVert s \rVert \le \Delta,
+        \end{array} \right.
+
+    by maximizing the objective function along given straight lines.
+
+    Parameters
+    ----------
+    const : float
+        Constant :math:`c` as shown above.
+    grad : `numpy.ndarray`, shape (n,)
+        Gradient :math:`g` as shown above.
+    curv : callable
+        Curvature of :math:`H` along any vector.
+
+            ``curv(s) -> float``
+
+        returns :math:`s^{\mathsf{T}} H s`.
+    xpt : `numpy.ndarray`, shape (n, npt)
+        Points defining the straight lines. The straight lines considered are
+        the ones passing through the origin and the points in `xpt`.
+    xl : `numpy.ndarray`, shape (n,)
+        Lower bounds :math:`l` as shown above.
+    xu : `numpy.ndarray`, shape (n,)
+        Upper bounds :math:`u` as shown above.
+    delta : float
+        Trust-region radius :math:`\Delta` as shown above.
+    debug : bool
+        Whether to make debugging tests during the execution.
+
+    Returns
+    -------
+    `numpy.ndarray`, shape (n,)
+        Approximate solution :math:`s`.
+
+    Notes
+    -----
+    This function is described as the second alternative in Section 6.5 of
+    [1]_. It is assumed that the origin is feasible with respect to the bound
+    constraints and that `delta` is finite and positive.
+
+    References
+    ----------
+    .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization Methods
+       and Software*. PhD thesis, Department of Applied Mathematics, The Hong
+       Kong Polytechnic University, Hong Kong, China, 2022. URL:
+       https://theses.lib.polyu.edu.hk/handle/200/12294.
+    """
+    if debug:
+        assert isinstance(const, float)
+        assert isinstance(grad, np.ndarray) and grad.ndim == 1
+        assert inspect.signature(curv).bind(grad)
+        assert (
+            isinstance(xpt, np.ndarray)
+            and xpt.ndim == 2
+            and xpt.shape[0] == grad.size
+        )
+        assert isinstance(xl, np.ndarray) and xl.shape == grad.shape
+        assert isinstance(xu, np.ndarray) and xu.shape == grad.shape
+        assert isinstance(delta, float)
+        assert isinstance(debug, bool)
+        tol = get_arrays_tol(xl, xu)
+        assert np.all(xl <= tol)
+        assert np.all(xu >= -tol)
+        assert np.isfinite(delta) and delta > 0.0
+    xl = np.minimum(xl, 0.0)
+    xu = np.maximum(xu, 0.0)
+
+    # Iterate through the straight lines.
+    step = np.zeros_like(grad)
+    q_val = const
+    s_norm = np.linalg.norm(xpt, axis=0)
+
+    # Set alpha_xl to the step size for the lower-bound constraint and
+    # alpha_xu to the step size for the upper-bound constraint.
+
+    # xl.shape = (N,)
+    # xpt.shape = (N, M)
+    # i_xl_pos.shape = (M, N)
+    i_xl_pos = (xl > -np.inf) & (xpt.T > -TINY * xl)
+    i_xl_neg = (xl > -np.inf) & (xpt.T < TINY * xl)
+    i_xu_pos = (xu < np.inf) & (xpt.T > TINY * xu)
+    i_xu_neg = (xu < np.inf) & (xpt.T < -TINY * xu)
+
+    # (M, N)
+    alpha_xl_pos = np.atleast_2d(
+        np.broadcast_to(xl, i_xl_pos.shape)[i_xl_pos] / xpt.T[i_xl_pos]
+    )
+    # (M,)
+    alpha_xl_pos = np.max(alpha_xl_pos, axis=1, initial=-np.inf)
+    # make sure it's (M,)
+    alpha_xl_pos = np.broadcast_to(np.atleast_1d(alpha_xl_pos), xpt.shape[1])
+
+    alpha_xl_neg = np.atleast_2d(
+        np.broadcast_to(xl, i_xl_neg.shape)[i_xl_neg] / xpt.T[i_xl_neg]
+    )
+    alpha_xl_neg = np.max(alpha_xl_neg, axis=1, initial=np.inf)
+    alpha_xl_neg = np.broadcast_to(np.atleast_1d(alpha_xl_neg), xpt.shape[1])
+
+    alpha_xu_neg = np.atleast_2d(
+        np.broadcast_to(xu, i_xu_neg.shape)[i_xu_neg] / xpt.T[i_xu_neg]
+    )
+    alpha_xu_neg = np.max(alpha_xu_neg, axis=1, initial=-np.inf)
+    alpha_xu_neg = np.broadcast_to(np.atleast_1d(alpha_xu_neg), xpt.shape[1])
+
+    alpha_xu_pos = np.atleast_2d(
+        np.broadcast_to(xu, i_xu_pos.shape)[i_xu_pos] / xpt.T[i_xu_pos]
+    )
+    alpha_xu_pos = np.max(alpha_xu_pos, axis=1, initial=np.inf)
+    alpha_xu_pos = np.broadcast_to(np.atleast_1d(alpha_xu_pos), xpt.shape[1])
+
+    for k in range(xpt.shape[1]):
+        # Set alpha_tr to the step size for the trust-region constraint.
+        if s_norm[k] > TINY * delta:
+            alpha_tr = max(delta / s_norm[k], 0.0)
+        else:
+            # The current straight line is basically zero.
+            continue
+
+        alpha_bd_pos = max(min(alpha_xu_pos[k], alpha_xl_neg[k]), 0.0)
+        alpha_bd_neg = min(max(alpha_xl_pos[k], alpha_xu_neg[k]), 0.0)
+
+        # Set alpha_quad_pos and alpha_quad_neg to the step size to the extrema
+        # of the quadratic function along the positive and negative directions.
+        grad_step = grad @ xpt[:, k]
+        curv_step = curv(xpt[:, k])
+        if (
+            grad_step >= 0.0
+            and curv_step < -TINY * grad_step
+            or grad_step <= 0.0
+            and curv_step > -TINY * grad_step
+        ):
+            alpha_quad_pos = max(-grad_step / curv_step, 0.0)
+        else:
+            alpha_quad_pos = np.inf
+        if (
+            grad_step >= 0.0
+            and curv_step > TINY * grad_step
+            or grad_step <= 0.0
+            and curv_step < TINY * grad_step
+        ):
+            alpha_quad_neg = min(-grad_step / curv_step, 0.0)
+        else:
+            alpha_quad_neg = -np.inf
+
+        # Select the step that provides the largest value of the objective
+        # function if it improves the current best. The best positive step is
+        # either the one that reaches the constraints or the one that reaches
+        # the extremum of the objective function along the current direction
+        # (only possible if the resulting step is feasible). We test both, and
+        # we perform similar calculations along the negative step.
+        # N.B.: we select the largest possible step among all the ones that
+        # maximize the objective function. This is to avoid returning the zero
+        # step in some extreme cases.
+        alpha_pos = min(alpha_tr, alpha_bd_pos)
+        alpha_neg = max(-alpha_tr, alpha_bd_neg)
+        q_val_pos = (
+            const + alpha_pos * grad_step + 0.5 * alpha_pos**2.0 * curv_step
+        )
+        q_val_neg = (
+            const + alpha_neg * grad_step + 0.5 * alpha_neg**2.0 * curv_step
+        )
+        if alpha_quad_pos < alpha_pos:
+            q_val_quad_pos = (
+                const
+                + alpha_quad_pos * grad_step
+                + 0.5 * alpha_quad_pos**2.0 * curv_step
+            )
+            if abs(q_val_quad_pos) > abs(q_val_pos):
+                alpha_pos = alpha_quad_pos
+                q_val_pos = q_val_quad_pos
+        if alpha_quad_neg > alpha_neg:
+            q_val_quad_neg = (
+                const
+                + alpha_quad_neg * grad_step
+                + 0.5 * alpha_quad_neg**2.0 * curv_step
+            )
+            if abs(q_val_quad_neg) > abs(q_val_neg):
+                alpha_neg = alpha_quad_neg
+                q_val_neg = q_val_quad_neg
+        if abs(q_val_pos) >= abs(q_val_neg) and abs(q_val_pos) > abs(q_val):
+            step = np.clip(alpha_pos * xpt[:, k], xl, xu)
+            q_val = q_val_pos
+        elif abs(q_val_neg) > abs(q_val_pos) and abs(q_val_neg) > abs(q_val):
+            step = np.clip(alpha_neg * xpt[:, k], xl, xu)
+            q_val = q_val_neg
+
+    if debug:
+        assert np.all(xl <= step)
+        assert np.all(step <= xu)
+        assert np.linalg.norm(step) < 1.1 * delta
+    return step
+
+
+def _cauchy_geom(const, grad, curv, xl, xu, delta, debug):
+    """
+    Same as `bound_constrained_cauchy_step` without the absolute value.
+    """
+    # Calculate the initial active set.
+    fixed_xl = (xl < 0.0) & (grad > 0.0)
+    fixed_xu = (xu > 0.0) & (grad < 0.0)
+
+    # Calculate the Cauchy step.
+    cauchy_step = np.zeros_like(grad)
+    cauchy_step[fixed_xl] = xl[fixed_xl]
+    cauchy_step[fixed_xu] = xu[fixed_xu]
+    if np.linalg.norm(cauchy_step) > delta:
+        working = fixed_xl | fixed_xu
+        while True:
+            # Calculate the Cauchy step for the directions in the working set.
+            g_norm = np.linalg.norm(grad[working])
+            delta_reduced = np.sqrt(
+                delta**2.0 - cauchy_step[~working] @ cauchy_step[~working]
+            )
+            if g_norm > TINY * abs(delta_reduced):
+                mu = max(delta_reduced / g_norm, 0.0)
+            else:
+                break
+            cauchy_step[working] = mu * grad[working]
+
+            # Update the working set.
+            fixed_xl = working & (cauchy_step < xl)
+            fixed_xu = working & (cauchy_step > xu)
+            if not np.any(fixed_xl) and not np.any(fixed_xu):
+                # Stop the calculations as the Cauchy step is now feasible.
+                break
+            cauchy_step[fixed_xl] = xl[fixed_xl]
+            cauchy_step[fixed_xu] = xu[fixed_xu]
+            working = working & ~(fixed_xl | fixed_xu)
+
+    # Calculate the step that maximizes the quadratic along the Cauchy step.
+    grad_step = grad @ cauchy_step
+    if grad_step >= 0.0:
+        # Set alpha_tr to the step size for the trust-region constraint.
+        s_norm = np.linalg.norm(cauchy_step)
+        if s_norm > TINY * delta:
+            alpha_tr = max(delta / s_norm, 0.0)
+        else:
+            # The Cauchy step is basically zero.
+            alpha_tr = 0.0
+
+        # Set alpha_quad to the step size for the maximization problem.
+        curv_step = curv(cauchy_step)
+        if curv_step < -TINY * grad_step:
+            alpha_quad = max(-grad_step / curv_step, 0.0)
+        else:
+            alpha_quad = np.inf
+
+        # Set alpha_bd to the step size for the bound constraints.
+        i_xl = (xl > -np.inf) & (cauchy_step < TINY * xl)
+        i_xu = (xu < np.inf) & (cauchy_step > TINY * xu)
+        alpha_xl = np.min(xl[i_xl] / cauchy_step[i_xl], initial=np.inf)
+        alpha_xu = np.min(xu[i_xu] / cauchy_step[i_xu], initial=np.inf)
+        alpha_bd = min(alpha_xl, alpha_xu)
+
+        # Calculate the solution and the corresponding function value.
+        alpha = min(alpha_tr, alpha_quad, alpha_bd)
+        step = np.clip(alpha * cauchy_step, xl, xu)
+        q_val = const + alpha * grad_step + 0.5 * alpha**2.0 * curv_step
+    else:
+        # This case is never reached in exact arithmetic. It prevents this
+        # function to return a step that decreases the objective function.
+        step = np.zeros_like(grad)
+        q_val = const
+
+    if debug:
+        assert np.all(xl <= step)
+        assert np.all(step <= xu)
+        assert np.linalg.norm(step) < 1.1 * delta
+    return step, q_val

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/subsolvers/optim.py

@@ -0,0 +1,1203 @@
+import inspect
+
+import numpy as np
+from scipy.linalg import qr
+
+from ..utils import get_arrays_tol
+
+
+TINY = np.finfo(float).tiny
+EPS = np.finfo(float).eps
+
+
+def tangential_byrd_omojokun(grad, hess_prod, xl, xu, delta, debug, **kwargs):
+    r"""
+    Minimize approximately a quadratic function subject to bound constraints in
+    a trust region.
+
+    This function solves approximately
+
+    .. math::
+
+        \min_{s \in \mathbb{R}^n} \quad g^{\mathsf{T}} s + \frac{1}{2}
+        s^{\mathsf{T}} H s \quad \text{s.t.} \quad
+        \left\{ \begin{array}{l}
+            l \le s \le u\\
+            \lVert s \rVert \le \Delta,
+        \end{array} \right.
+
+    using an active-set variation of the truncated conjugate gradient method.
+
+    Parameters
+    ----------
+    grad : `numpy.ndarray`, shape (n,)
+        Gradient :math:`g` as shown above.
+    hess_prod : callable
+        Product of the Hessian matrix :math:`H` with any vector.
+
+            ``hess_prod(s) -> `numpy.ndarray`, shape (n,)``
+
+        returns the product :math:`H s`.
+    xl : `numpy.ndarray`, shape (n,)
+        Lower bounds :math:`l` as shown above.
+    xu : `numpy.ndarray`, shape (n,)
+        Upper bounds :math:`u` as shown above.
+    delta : float
+        Trust-region radius :math:`\Delta` as shown above.
+    debug : bool
+        Whether to make debugging tests during the execution.
+
+    Returns
+    -------
+    `numpy.ndarray`, shape (n,)
+        Approximate solution :math:`s`.
+
+    Other Parameters
+    ----------------
+    improve_tcg : bool, optional
+        If True, a solution generated by the truncated conjugate gradient
+        method that is on the boundary of the trust region is improved by
+        moving around the trust-region boundary on the two-dimensional space
+        spanned by the solution and the gradient of the quadratic function at
+        the solution (default is True).
+
+    Notes
+    -----
+    This function implements Algorithm 6.2 of [1]_. It is assumed that the
+    origin is feasible with respect to the bound constraints and that `delta`
+    is finite and positive.
+
+    References
+    ----------
+    .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization Methods
+       and Software*. PhD thesis, Department of Applied Mathematics, The Hong
+       Kong Polytechnic University, Hong Kong, China, 2022. URL:
+       https://theses.lib.polyu.edu.hk/handle/200/12294.
+    """
+    if debug:
+        assert isinstance(grad, np.ndarray) and grad.ndim == 1
+        assert inspect.signature(hess_prod).bind(grad)
+        assert isinstance(xl, np.ndarray) and xl.shape == grad.shape
+        assert isinstance(xu, np.ndarray) and xu.shape == grad.shape
+        assert isinstance(delta, float)
+        assert isinstance(debug, bool)
+        tol = get_arrays_tol(xl, xu)
+        assert np.all(xl <= tol)
+        assert np.all(xu >= -tol)
+        assert np.isfinite(delta) and delta > 0.0
+    xl = np.minimum(xl, 0.0)
+    xu = np.maximum(xu, 0.0)
+
+    # Copy the arrays that may be modified by the code below.
+    n = grad.size
+    grad = np.copy(grad)
+    grad_orig = np.copy(grad)
+
+    # Calculate the initial active set.
+    free_bd = ((xl < 0.0) | (grad < 0.0)) & ((xu > 0.0) | (grad > 0.0))
+
+    # Set the initial iterate and the initial search direction.
+    step = np.zeros_like(grad)
+    sd = np.zeros_like(step)
+    sd[free_bd] = -grad[free_bd]
+
+    k = 0
+    reduct = 0.0
+    boundary_reached = False
+    while k < np.count_nonzero(free_bd):
+        # Stop the computations if sd is not a descent direction.
+        grad_sd = grad @ sd
+        if grad_sd >= -10.0 * EPS * n * max(1.0, np.linalg.norm(grad)):
+            break
+
+        # Set alpha_tr to the step size for the trust-region constraint.
+        try:
+            alpha_tr = _alpha_tr(step, sd, delta)
+        except ZeroDivisionError:
+            break
+
+        # Stop the computations if a step along sd is expected to give a
+        # relatively small reduction in the objective function.
+        if -alpha_tr * grad_sd <= 1e-8 * reduct:
+            break
+
+        # Set alpha_quad to the step size for the minimization problem.
+        hess_sd = hess_prod(sd)
+        curv_sd = sd @ hess_sd
+        if curv_sd > TINY * abs(grad_sd):
+            alpha_quad = max(-grad_sd / curv_sd, 0.0)
+        else:
+            alpha_quad = np.inf
+
+        # Stop the computations if the reduction in the objective function
+        # provided by an unconstrained step is small.
+        alpha = min(alpha_tr, alpha_quad)
+        if -alpha * (grad_sd + 0.5 * alpha * curv_sd) <= 1e-8 * reduct:
+            break
+
+        # Set alpha_bd to the step size for the bound constraints.
+        i_xl = (xl > -np.inf) & (sd < -TINY * np.abs(xl - step))
+        i_xu = (xu < np.inf) & (sd > TINY * np.abs(xu - step))
+        all_alpha_xl = np.full_like(step, np.inf)
+        all_alpha_xu = np.full_like(step, np.inf)
+        all_alpha_xl[i_xl] = np.maximum(
+            (xl[i_xl] - step[i_xl]) / sd[i_xl],
+            0.0,
+        )
+        all_alpha_xu[i_xu] = np.maximum(
+            (xu[i_xu] - step[i_xu]) / sd[i_xu],
+            0.0,
+        )
+        alpha_xl = np.min(all_alpha_xl)
+        alpha_xu = np.min(all_alpha_xu)
+        alpha_bd = min(alpha_xl, alpha_xu)
+
+        # Update the iterate.
+        alpha = min(alpha, alpha_bd)
+        if alpha > 0.0:
+            step[free_bd] = np.clip(
+                step[free_bd] + alpha * sd[free_bd],
+                xl[free_bd],
+                xu[free_bd],
+            )
+            grad += alpha * hess_sd
+            reduct -= alpha * (grad_sd + 0.5 * alpha * curv_sd)
+
+        if alpha < min(alpha_tr, alpha_bd):
+            # The current iteration is a conjugate gradient iteration. Update
+            # the search direction so that it is conjugate (with respect to H)
+            # to all the previous search directions.
+            beta = (grad[free_bd] @ hess_sd[free_bd]) / curv_sd
+            sd[free_bd] = beta * sd[free_bd] - grad[free_bd]
+            sd[~free_bd] = 0.0
+            k += 1
+        elif alpha < alpha_tr:
+            # The iterate is restricted by a bound constraint. Add this bound
+            # constraint to the active set, and restart the calculations.
+            if alpha_xl <= alpha:
+                i_new = np.argmin(all_alpha_xl)
+                step[i_new] = xl[i_new]
+            else:
+                i_new = np.argmin(all_alpha_xu)
+                step[i_new] = xu[i_new]
+            free_bd[i_new] = False
+            sd[free_bd] = -grad[free_bd]
+            sd[~free_bd] = 0.0
+            k = 0
+        else:
+            # The current iterate is on the trust-region boundary. Add all the
+            # active bounds to the working set to prepare for the improvement
+            # of the solution, and stop the iterations.
+            if alpha_xl <= alpha:
+                i_new = _argmin(all_alpha_xl)
+                step[i_new] = xl[i_new]
+                free_bd[i_new] = False
+            if alpha_xu <= alpha:
+                i_new = _argmin(all_alpha_xu)
+                step[i_new] = xu[i_new]
+                free_bd[i_new] = False
+            boundary_reached = True
+            break
+
+    # Attempt to improve the solution on the trust-region boundary.
+    if kwargs.get("improve_tcg", True) and boundary_reached:
+        step_base = np.copy(step)
+        step_comparator = grad_orig @ step_base + 0.5 * step_base @ hess_prod(
+            step_base
+        )
+
+        while np.count_nonzero(free_bd) > 0:
+            # Check whether a substantial reduction in the objective function
+            # is possible, and set the search direction.
+            step_sq = step[free_bd] @ step[free_bd]
+            grad_sq = grad[free_bd] @ grad[free_bd]
+            grad_step = grad[free_bd] @ step[free_bd]
+            grad_sd = -np.sqrt(max(step_sq * grad_sq - grad_step**2.0, 0.0))
+            sd[free_bd] = grad_step * step[free_bd] - step_sq * grad[free_bd]
+            sd[~free_bd] = 0.0
+            if grad_sd >= -1e-8 * reduct or np.any(
+                grad_sd >= -TINY * np.abs(sd[free_bd])
+            ):
+                break
+            sd[free_bd] /= -grad_sd
+
+            # Calculate an upper bound for the tangent of half the angle theta
+            # of this alternative iteration. The step will be updated as:
+            # step = cos(theta) * step + sin(theta) * sd.
+            temp_xl = np.zeros(n)
+            temp_xu = np.zeros(n)
+            temp_xl[free_bd] = (
+                step[free_bd] ** 2.0 + sd[free_bd] ** 2.0 - xl[free_bd] ** 2.0
+            )
+            temp_xu[free_bd] = (
+                step[free_bd] ** 2.0 + sd[free_bd] ** 2.0 - xu[free_bd] ** 2.0
+            )
+            temp_xl[temp_xl > 0.0] = (
+                np.sqrt(temp_xl[temp_xl > 0.0]) - sd[temp_xl > 0.0]
+            )
+            temp_xu[temp_xu > 0.0] = (
+                np.sqrt(temp_xu[temp_xu > 0.0]) + sd[temp_xu > 0.0]
+            )
+            dist_xl = np.maximum(step - xl, 0.0)
+            dist_xu = np.maximum(xu - step, 0.0)
+            i_xl = temp_xl > TINY * dist_xl
+            i_xu = temp_xu > TINY * dist_xu
+            all_t_xl = np.ones(n)
+            all_t_xu = np.ones(n)
+            all_t_xl[i_xl] = np.minimum(
+                all_t_xl[i_xl],
+                dist_xl[i_xl] / temp_xl[i_xl],
+            )
+            all_t_xu[i_xu] = np.minimum(
+                all_t_xu[i_xu],
+                dist_xu[i_xu] / temp_xu[i_xu],
+            )
+            t_xl = np.min(all_t_xl)
+            t_xu = np.min(all_t_xu)
+            t_bd = min(t_xl, t_xu)
+
+            # Calculate some curvature information.
+            hess_step = hess_prod(step)
+            hess_sd = hess_prod(sd)
+            curv_step = step @ hess_step
+            curv_sd = sd @ hess_sd
+            curv_step_sd = step @ hess_sd
+
+            # For a range of equally spaced values of tan(0.5 * theta),
+            # calculate the reduction in the objective function that would be
+            # obtained by accepting the corresponding angle.
+            n_samples = 20
+            n_samples = int((n_samples - 3) * t_bd + 3)
+            t_samples = np.linspace(t_bd / n_samples, t_bd, n_samples)
+            sin_values = 2.0 * t_samples / (1.0 + t_samples**2.0)
+            all_reduct = sin_values * (
+                grad_step * t_samples
+                - grad_sd
+                - t_samples * curv_step
+                + sin_values
+                * (t_samples * curv_step_sd - 0.5 * (curv_sd - curv_step))
+            )
+            if np.all(all_reduct <= 0.0):
+                # No reduction in the objective function is obtained.
+                break
+
+            # Accept the angle that provides the largest reduction in the
+            # objective function, and update the iterate.
+            i_max = np.argmax(all_reduct)
+            cos_value = (1.0 - t_samples[i_max] ** 2.0) / (
+                1.0 + t_samples[i_max] ** 2.0
+            )
+            step[free_bd] = (
+                cos_value * step[free_bd] + sin_values[i_max] * sd[free_bd]
+            )
+            grad += (cos_value - 1.0) * hess_step + sin_values[i_max] * hess_sd
+            reduct += all_reduct[i_max]
+
+            # If the above angle is restricted by bound constraints, add them
+            # to the working set, and restart the alternative iteration.
+            # Otherwise, the calculations are terminated.
+            if t_bd < 1.0 and i_max == n_samples - 1:
+                if t_xl <= t_bd:
+                    i_new = _argmin(all_t_xl)
+                    step[i_new] = xl[i_new]
+                    free_bd[i_new] = False
+                if t_xu <= t_bd:
+                    i_new = _argmin(all_t_xu)
+                    step[i_new] = xu[i_new]
+                    free_bd[i_new] = False
+            else:
+                break
+
+        # Ensure that the alternative iteration improves the objective
+        # function.
+        if grad_orig @ step + 0.5 * step @ hess_prod(step) > step_comparator:
+            step = step_base
+
+    if debug:
+        assert np.all(xl <= step)
+        assert np.all(step <= xu)
+        assert np.linalg.norm(step) < 1.1 * delta
+    return step
+
+
+def constrained_tangential_byrd_omojokun(
+    grad,
+    hess_prod,
+    xl,
+    xu,
+    aub,
+    bub,
+    aeq,
+    delta,
+    debug,
+    **kwargs,
+):
+    r"""
+    Minimize approximately a quadratic function subject to bound and linear
+    constraints in a trust region.
+
+    This function solves approximately
+
+    .. math::
+
+        \min_{s \in \mathbb{R}^n} \quad g^{\mathsf{T}} s + \frac{1}{2}
+        s^{\mathsf{T}} H s \quad \text{s.t.} \quad
+        \left\{ \begin{array}{l}
+            l \le s \le u,\\
+            A_{\scriptscriptstyle I} s \le b_{\scriptscriptstyle I},\\
+            A_{\scriptscriptstyle E} s = 0,\\
+            \lVert s \rVert \le \Delta,
+        \end{array} \right.
+
+    using an active-set variation of the truncated conjugate gradient method.
+
+    Parameters
+    ----------
+    grad : `numpy.ndarray`, shape (n,)
+        Gradient :math:`g` as shown above.
+    hess_prod : callable
+        Product of the Hessian matrix :math:`H` with any vector.
+
+            ``hess_prod(s) -> `numpy.ndarray`, shape (n,)``
+
+        returns the product :math:`H s`.
+    xl : `numpy.ndarray`, shape (n,)
+        Lower bounds :math:`l` as shown above.
+    xu : `numpy.ndarray`, shape (n,)
+        Upper bounds :math:`u` as shown above.
+    aub : `numpy.ndarray`, shape (m_linear_ub, n)
+        Coefficient matrix :math:`A_{\scriptscriptstyle I}` as shown above.
+    bub : `numpy.ndarray`, shape (m_linear_ub,)
+        Right-hand side :math:`b_{\scriptscriptstyle I}` as shown above.
+    aeq : `numpy.ndarray`, shape (m_linear_eq, n)
+        Coefficient matrix :math:`A_{\scriptscriptstyle E}` as shown above.
+    delta : float
+        Trust-region radius :math:`\Delta` as shown above.
+    debug : bool
+        Whether to make debugging tests during the execution.
+
+    Returns
+    -------
+    `numpy.ndarray`, shape (n,)
+        Approximate solution :math:`s`.
+
+    Other Parameters
+    ----------------
+    improve_tcg : bool, optional
+        If True, a solution generated by the truncated conjugate gradient
+        method that is on the boundary of the trust region is improved by
+        moving around the trust-region boundary on the two-dimensional space
+        spanned by the solution and the gradient of the quadratic function at
+        the solution (default is True).
+
+    Notes
+    -----
+    This function implements Algorithm 6.3 of [1]_. It is assumed that the
+    origin is feasible with respect to the bound and linear constraints, and
+    that `delta` is finite and positive.
+
+    References
+    ----------
+    .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization Methods
+       and Software*. PhD thesis, Department of Applied Mathematics, The Hong
+       Kong Polytechnic University, Hong Kong, China, 2022. URL:
+       https://theses.lib.polyu.edu.hk/handle/200/12294.
+    """
+    if debug:
+        assert isinstance(grad, np.ndarray) and grad.ndim == 1
+        assert inspect.signature(hess_prod).bind(grad)
+        assert isinstance(xl, np.ndarray) and xl.shape == grad.shape
+        assert isinstance(xu, np.ndarray) and xu.shape == grad.shape
+        assert (
+            isinstance(aub, np.ndarray)
+            and aub.ndim == 2
+            and aub.shape[1] == grad.size
+        )
+        assert (
+            isinstance(bub, np.ndarray)
+            and bub.ndim == 1
+            and bub.size == aub.shape[0]
+        )
+        assert (
+            isinstance(aeq, np.ndarray)
+            and aeq.ndim == 2
+            and aeq.shape[1] == grad.size
+        )
+        assert isinstance(delta, float)
+        assert isinstance(debug, bool)
+        tol = get_arrays_tol(xl, xu)
+        assert np.all(xl <= tol)
+        assert np.all(xu >= -tol)
+        assert np.all(bub >= -tol)
+        assert np.isfinite(delta) and delta > 0.0
+    xl = np.minimum(xl, 0.0)
+    xu = np.maximum(xu, 0.0)
+    bub = np.maximum(bub, 0.0)
+
+    # Copy the arrays that may be modified by the code below.
+    n = grad.size
+    grad = np.copy(grad)
+    grad_orig = np.copy(grad)
+
+    # Calculate the initial active set.
+    free_xl = (xl < 0.0) | (grad < 0.0)
+    free_xu = (xu > 0.0) | (grad > 0.0)
+    free_ub = (bub > 0.0) | (aub @ grad > 0.0)
+    n_act, q = qr_tangential_byrd_omojokun(aub, aeq, free_xl, free_xu, free_ub)
+
+    # Set the initial iterate and the initial search direction.
+    step = np.zeros_like(grad)
+    sd = -q[:, n_act:] @ (q[:, n_act:].T @ grad)
+    resid = np.copy(bub)
+
+    k = 0
+    reduct = 0.0
+    boundary_reached = False
+    while k < n - n_act:
+        # Stop the computations if sd is not a descent direction.
+        grad_sd = grad @ sd
+        if grad_sd >= -10.0 * EPS * n * max(1.0, np.linalg.norm(grad)):
+            break
+
+        # Set alpha_tr to the step size for the trust-region constraint.
+        try:
+            alpha_tr = _alpha_tr(step, sd, delta)
+        except ZeroDivisionError:
+            break
+
+        # Stop the computations if a step along sd is expected to give a
+        # relatively small reduction in the objective function.
+        if -alpha_tr * grad_sd <= 1e-8 * reduct:
+            break
+
+        # Set alpha_quad to the step size for the minimization problem.
+        hess_sd = hess_prod(sd)
+        curv_sd = sd @ hess_sd
+        if curv_sd > TINY * abs(grad_sd):
+            alpha_quad = max(-grad_sd / curv_sd, 0.0)
+        else:
+            alpha_quad = np.inf
+
+        # Stop the computations if the reduction in the objective function
+        # provided by an unconstrained step is small.
+        alpha = min(alpha_tr, alpha_quad)
+        if -alpha * (grad_sd + 0.5 * alpha * curv_sd) <= 1e-8 * reduct:
+            break
+
+        # Set alpha_bd to the step size for the bound constraints.
+        i_xl = free_xl & (xl > -np.inf) & (sd < -TINY * np.abs(xl - step))
+        i_xu = free_xu & (xu < np.inf) & (sd > TINY * np.abs(xu - step))
+        all_alpha_xl = np.full_like(step, np.inf)
+        all_alpha_xu = np.full_like(step, np.inf)
+        all_alpha_xl[i_xl] = np.maximum(
+            (xl[i_xl] - step[i_xl]) / sd[i_xl],
+            0.0,
+        )
+        all_alpha_xu[i_xu] = np.maximum(
+            (xu[i_xu] - step[i_xu]) / sd[i_xu],
+            0.0,
+        )
+        alpha_xl = np.min(all_alpha_xl)
+        alpha_xu = np.min(all_alpha_xu)
+        alpha_bd = min(alpha_xl, alpha_xu)
+
+        # Set alpha_ub to the step size for the linear constraints.
+        aub_sd = aub @ sd
+        i_ub = free_ub & (aub_sd > TINY * np.abs(resid))
+        all_alpha_ub = np.full_like(bub, np.inf)
+        all_alpha_ub[i_ub] = resid[i_ub] / aub_sd[i_ub]
+        alpha_ub = np.min(all_alpha_ub, initial=np.inf)
+
+        # Update the iterate.
+        alpha = min(alpha, alpha_bd, alpha_ub)
+        if alpha > 0.0:
+            step = np.clip(step + alpha * sd, xl, xu)
+            grad += alpha * hess_sd
+            resid = np.maximum(0.0, resid - alpha * aub_sd)
+            reduct -= alpha * (grad_sd + 0.5 * alpha * curv_sd)
+
+        if alpha < min(alpha_tr, alpha_bd, alpha_ub):
+            # The current iteration is a conjugate gradient iteration. Update
+            # the search direction so that it is conjugate (with respect to H)
+            # to all the previous search directions.
+            grad_proj = q[:, n_act:] @ (q[:, n_act:].T @ grad)
+            beta = (grad_proj @ hess_sd) / curv_sd
+            sd = beta * sd - grad_proj
+            k += 1
+        elif alpha < alpha_tr:
+            # The iterate is restricted by a bound/linear constraint. Add this
+            # constraint to the active set, and restart the calculations.
+            if alpha_xl <= alpha:
+                i_new = np.argmin(all_alpha_xl)
+                step[i_new] = xl[i_new]
+                free_xl[i_new] = False
+            elif alpha_xu <= alpha:
+                i_new = np.argmin(all_alpha_xu)
+                step[i_new] = xu[i_new]
+                free_xu[i_new] = False
+            else:
+                i_new = np.argmin(all_alpha_ub)
+                free_ub[i_new] = False
+            n_act, q = qr_tangential_byrd_omojokun(
+                aub,
+                aeq,
+                free_xl,
+                free_xu,
+                free_ub,
+            )
+            sd = -q[:, n_act:] @ (q[:, n_act:].T @ grad)
+            k = 0
+        else:
+            # The current iterate is on the trust-region boundary. Add all the
+            # active bound/linear constraints to the working set to prepare for
+            # the improvement of the solution, and stop the iterations.
+            if alpha_xl <= alpha:
+                i_new = _argmin(all_alpha_xl)
+                step[i_new] = xl[i_new]
+                free_xl[i_new] = False
+            if alpha_xu <= alpha:
+                i_new = _argmin(all_alpha_xu)
+                step[i_new] = xu[i_new]
+                free_xu[i_new] = False
+            if alpha_ub <= alpha:
+                i_new = _argmin(all_alpha_ub)
+                free_ub[i_new] = False
+            n_act, q = qr_tangential_byrd_omojokun(
+                aub,
+                aeq,
+                free_xl,
+                free_xu,
+                free_ub,
+            )
+            boundary_reached = True
+            break
+
+    # Attempt to improve the solution on the trust-region boundary.
+    if kwargs.get("improve_tcg", True) and boundary_reached and n_act < n:
+        step_base = np.copy(step)
+        while n_act < n:
+            # Check whether a substantial reduction in the objective function
+            # is possible, and set the search direction.
+            step_proj = q[:, n_act:] @ (q[:, n_act:].T @ step)
+            grad_proj = q[:, n_act:] @ (q[:, n_act:].T @ grad)
+            step_sq = step_proj @ step_proj
+            grad_sq = grad_proj @ grad_proj
+            grad_step = grad_proj @ step_proj
+            grad_sd = -np.sqrt(max(step_sq * grad_sq - grad_step**2.0, 0.0))
+            sd = q[:, n_act:] @ (
+                q[:, n_act:].T @ (grad_step * step - step_sq * grad)
+            )
+            if grad_sd >= -1e-8 * reduct or np.any(
+                grad_sd >= -TINY * np.abs(sd)
+            ):
+                break
+            sd /= -grad_sd
+
+            # Calculate an upper bound for the tangent of half the angle theta
+            # of this alternative iteration for the bound constraints. The step
+            # will be updated as:
+            # step += (cos(theta) - 1) * step_proj + sin(theta) * sd.
+            temp_xl = np.zeros(n)
+            temp_xu = np.zeros(n)
+            dist_xl = np.maximum(step - xl, 0.0)
+            dist_xu = np.maximum(xu - step, 0.0)
+            temp_xl[free_xl] = sd[free_xl] ** 2.0 - dist_xl[free_xl] * (
+                dist_xl[free_xl] - 2.0 * step_proj[free_xl]
+            )
+            temp_xu[free_xu] = sd[free_xu] ** 2.0 - dist_xu[free_xu] * (
+                dist_xu[free_xu] + 2.0 * step_proj[free_xu]
+            )
+            temp_xl[temp_xl > 0.0] = (
+                np.sqrt(temp_xl[temp_xl > 0.0]) - sd[temp_xl > 0.0]
+            )
+            temp_xu[temp_xu > 0.0] = (
+                np.sqrt(temp_xu[temp_xu > 0.0]) + sd[temp_xu > 0.0]
+            )
+            i_xl = temp_xl > TINY * dist_xl
+            i_xu = temp_xu > TINY * dist_xu
+            all_t_xl = np.ones(n)
+            all_t_xu = np.ones(n)
+            all_t_xl[i_xl] = np.minimum(
+                all_t_xl[i_xl],
+                dist_xl[i_xl] / temp_xl[i_xl],
+            )
+            all_t_xu[i_xu] = np.minimum(
+                all_t_xu[i_xu],
+                dist_xu[i_xu] / temp_xu[i_xu],
+            )
+            t_xl = np.min(all_t_xl)
+            t_xu = np.min(all_t_xu)
+            t_bd = min(t_xl, t_xu)
+
+            # Calculate an upper bound for the tangent of half the angle theta
+            # of this alternative iteration for the linear constraints.
+            temp_ub = np.zeros_like(resid)
+            aub_step = aub @ step_proj
+            aub_sd = aub @ sd
+            temp_ub[free_ub] = aub_sd[free_ub] ** 2.0 - resid[free_ub] * (
+                resid[free_ub] + 2.0 * aub_step[free_ub]
+            )
+            temp_ub[temp_ub > 0.0] = (
+                np.sqrt(temp_ub[temp_ub > 0.0]) + aub_sd[temp_ub > 0.0]
+            )
+            i_ub = temp_ub > TINY * resid
+            all_t_ub = np.ones_like(resid)
+            all_t_ub[i_ub] = np.minimum(
+                all_t_ub[i_ub],
+                resid[i_ub] / temp_ub[i_ub],
+            )
+            t_ub = np.min(all_t_ub, initial=1.0)
+            t_min = min(t_bd, t_ub)
+
+            # Calculate some curvature information.
+            hess_step = hess_prod(step_proj)
+            hess_sd = hess_prod(sd)
+            curv_step = step_proj @ hess_step
+            curv_sd = sd @ hess_sd
+            curv_step_sd = step_proj @ hess_sd
+
+            # For a range of equally spaced values of tan(0.5 * theta),
+            # calculate the reduction in the objective function that would be
+            # obtained by accepting the corresponding angle.
+            n_samples = 20
+            n_samples = int((n_samples - 3) * t_min + 3)
+            t_samples = np.linspace(t_min / n_samples, t_min, n_samples)
+            sin_values = 2.0 * t_samples / (1.0 + t_samples**2.0)
+            all_reduct = sin_values * (
+                grad_step * t_samples
+                - grad_sd
+                - sin_values
+                * (
+                    0.5 * t_samples**2.0 * curv_step
+                    - 2.0 * t_samples * curv_step_sd
+                    + 0.5 * curv_sd
+                )
+            )
+            if np.all(all_reduct <= 0.0):
+                # No reduction in the objective function is obtained.
+                break
+
+            # Accept the angle that provides the largest reduction in the
+            # objective function, and update the iterate.
+            i_max = np.argmax(all_reduct)
+            cos_value = (1.0 - t_samples[i_max] ** 2.0) / (
+                1.0 + t_samples[i_max] ** 2.0
+            )
+            step = np.clip(
+                step + (cos_value - 1.0) * step_proj + sin_values[i_max] * sd,
+                xl,
+                xu,
+            )
+            grad += (cos_value - 1.0) * hess_step + sin_values[i_max] * hess_sd
+            resid = np.maximum(
+                0.0,
+                resid
+                - (cos_value - 1.0) * aub_step
+                - sin_values[i_max] * aub_sd,
+            )
+            reduct += all_reduct[i_max]
+
+            # If the above angle is restricted by bound constraints, add them
+            # to the working set, and restart the alternative iteration.
+            # Otherwise, the calculations are terminated.
+            if t_min < 1.0 and i_max == n_samples - 1:
+                if t_xl <= t_min:
+                    i_new = _argmin(all_t_xl)
+                    step[i_new] = xl[i_new]
+                    free_xl[i_new] = False
+                if t_xu <= t_min:
+                    i_new = _argmin(all_t_xu)
+                    step[i_new] = xu[i_new]
+                    free_xl[i_new] = False
+                if t_ub <= t_min:
+                    i_new = _argmin(all_t_ub)
+                    free_ub[i_new] = False
+                n_act, q = qr_tangential_byrd_omojokun(
+                    aub,
+                    aeq,
+                    free_xl,
+                    free_xu,
+                    free_ub,
+                )
+            else:
+                break
+
+        # Ensure that the alternative iteration improves the objective
+        # function.
+        if grad_orig @ step + 0.5 * step @ hess_prod(
+            step
+        ) > grad_orig @ step_base + 0.5 * step_base @ hess_prod(step_base):
+            step = step_base
+
+    if debug:
+        tol = get_arrays_tol(xl, xu)
+        assert np.all(xl <= step)
+        assert np.all(step <= xu)
+        assert np.all(aub @ step <= bub + tol)
+        assert np.all(np.abs(aeq @ step) <= tol)
+        assert np.linalg.norm(step) < 1.1 * delta
+    return step
+
+
+def normal_byrd_omojokun(aub, bub, aeq, beq, xl, xu, delta, debug, **kwargs):
+    r"""
+    Minimize approximately a linear constraint violation subject to bound
+    constraints in a trust region.
+
+    This function solves approximately
+
+    .. math::
+
+        \min_{s \in \mathbb{R}^n} \quad \frac{1}{2} \big( \lVert \max \{
+        A_{\scriptscriptstyle I} s - b_{\scriptscriptstyle I}, 0 \} \rVert^2 +
+        \lVert A_{\scriptscriptstyle E} s - b_{\scriptscriptstyle E} \rVert^2
+        \big) \quad \text{s.t.}
+        \quad
+        \left\{ \begin{array}{l}
+            l \le s \le u,\\
+            \lVert s \rVert \le \Delta,
+        \end{array} \right.
+
+    using a variation of the truncated conjugate gradient method.
+
+    Parameters
+    ----------
+    aub : `numpy.ndarray`, shape (m_linear_ub, n)
+        Matrix :math:`A_{\scriptscriptstyle I}` as shown above.
+    bub : `numpy.ndarray`, shape (m_linear_ub,)
+        Vector :math:`b_{\scriptscriptstyle I}` as shown above.
+    aeq : `numpy.ndarray`, shape (m_linear_eq, n)
+        Matrix :math:`A_{\scriptscriptstyle E}` as shown above.
+    beq : `numpy.ndarray`, shape (m_linear_eq,)
+        Vector :math:`b_{\scriptscriptstyle E}` as shown above.
+    xl : `numpy.ndarray`, shape (n,)
+        Lower bounds :math:`l` as shown above.
+    xu : `numpy.ndarray`, shape (n,)
+        Upper bounds :math:`u` as shown above.
+    delta : float
+        Trust-region radius :math:`\Delta` as shown above.
+    debug : bool
+        Whether to make debugging tests during the execution.
+
+    Returns
+    -------
+    `numpy.ndarray`, shape (n,)
+        Approximate solution :math:`s`.
+
+    Other Parameters
+    ----------------
+    improve_tcg : bool, optional
+        If True, a solution generated by the truncated conjugate gradient
+        method that is on the boundary of the trust region is improved by
+        moving around the trust-region boundary on the two-dimensional space
+        spanned by the solution and the gradient of the quadratic function at
+        the solution (default is True).
+
+    Notes
+    -----
+    This function implements Algorithm 6.4 of [1]_. It is assumed that the
+    origin is feasible with respect to the bound constraints and that `delta`
+    is finite and positive.
+
+    References
+    ----------
+    .. [1] T. M. Ragonneau. *Model-Based Derivative-Free Optimization Methods
+       and Software*. PhD thesis, Department of Applied Mathematics, The Hong
+       Kong Polytechnic University, Hong Kong, China, 2022. URL:
+       https://theses.lib.polyu.edu.hk/handle/200/12294.
+    """
+    if debug:
+        assert isinstance(aub, np.ndarray) and aub.ndim == 2
+        assert (
+            isinstance(bub, np.ndarray)
+            and bub.ndim == 1
+            and bub.size == aub.shape[0]
+        )
+        assert (
+            isinstance(aeq, np.ndarray)
+            and aeq.ndim == 2
+            and aeq.shape[1] == aub.shape[1]
+        )
+        assert (
+            isinstance(beq, np.ndarray)
+            and beq.ndim == 1
+            and beq.size == aeq.shape[0]
+        )
+        assert isinstance(xl, np.ndarray) and xl.shape == (aub.shape[1],)
+        assert isinstance(xu, np.ndarray) and xu.shape == (aub.shape[1],)
+        assert isinstance(delta, float)
+        assert isinstance(debug, bool)
+        tol = get_arrays_tol(xl, xu)
+        assert np.all(xl <= tol)
+        assert np.all(xu >= -tol)
+        assert np.isfinite(delta) and delta > 0.0
+    xl = np.minimum(xl, 0.0)
+    xu = np.maximum(xu, 0.0)
+
+    # Calculate the initial active set.
+    m_linear_ub, n = aub.shape
+    grad = np.r_[aeq.T @ -beq, np.maximum(0.0, -bub)]
+    free_xl = (xl < 0.0) | (grad[:n] < 0.0)
+    free_xu = (xu > 0.0) | (grad[:n] > 0.0)
+    free_slack = bub < 0.0
+    free_ub = (bub > 0.0) | (aub @ grad[:n] - grad[n:] > 0.0)
+    n_act, q = qr_normal_byrd_omojokun(
+        aub,
+        free_xl,
+        free_xu,
+        free_slack,
+        free_ub,
+    )
+
+    # Calculate an upper bound on the norm of the slack variables. It is not
+    # used in the original algorithm, but it may prevent undesired behaviors
+    # engendered by computer rounding errors.
+    delta_slack = np.sqrt(beq @ beq + grad[n:] @ grad[n:])
+
+    # Set the initial iterate and the initial search direction.
+    step = np.zeros(n)
+    sd = -q[:, n_act:] @ (q[:, n_act:].T @ grad)
+    resid = bub + grad[n:]
+
+    k = 0
+    reduct = 0.0
+    boundary_reached = False
+    while k < n + m_linear_ub - n_act:
+        # Stop the computations if sd is not a descent direction.
+        grad_sd = grad @ sd
+        if grad_sd >= -10.0 * EPS * n * max(1.0, np.linalg.norm(grad)):
+            break
+
+        # Set alpha_tr to the step size for the trust-region constraint.
+        try:
+            alpha_tr = _alpha_tr(step, sd[:n], delta)
+        except ZeroDivisionError:
+            alpha_tr = np.inf
+
+        # Prevent undesired behaviors engendered by computer rounding errors by
+        # considering the trust-region constraint on the slack variables.
+        try:
+            alpha_tr = min(alpha_tr, _alpha_tr(grad[n:], sd[n:], delta_slack))
+        except ZeroDivisionError:
+            pass
+
+        # Stop the computations if a step along sd is expected to give a
+        # relatively small reduction in the objective function.
+        if -alpha_tr * grad_sd <= 1e-8 * reduct:
+            break
+
+        # Set alpha_quad to the step size for the minimization problem.
+        hess_sd = np.r_[aeq.T @ (aeq @ sd[:n]), sd[n:]]
+        curv_sd = sd @ hess_sd
+        if curv_sd > TINY * abs(grad_sd):
+            alpha_quad = max(-grad_sd / curv_sd, 0.0)
+        else:
+            alpha_quad = np.inf
+
+        # Stop the computations if the reduction in the objective function
+        # provided by an unconstrained step is small.
+        alpha = min(alpha_tr, alpha_quad)
+        if -alpha * (grad_sd + 0.5 * alpha * curv_sd) <= 1e-8 * reduct:
+            break
+
+        # Set alpha_bd to the step size for the bound constraints.
+        i_xl = free_xl & (xl > -np.inf) & (sd[:n] < -TINY * np.abs(xl - step))
+        i_xu = free_xu & (xu < np.inf) & (sd[:n] > TINY * np.abs(xu - step))
+        i_slack = free_slack & (sd[n:] < -TINY * np.abs(grad[n:]))
+        all_alpha_xl = np.full_like(step, np.inf)
+        all_alpha_xu = np.full_like(step, np.inf)
+        all_alpha_slack = np.full_like(bub, np.inf)
+        all_alpha_xl[i_xl] = np.maximum(
+            (xl[i_xl] - step[i_xl]) / sd[:n][i_xl],
+            0.0,
+        )
+        all_alpha_xu[i_xu] = np.maximum(
+            (xu[i_xu] - step[i_xu]) / sd[:n][i_xu],
+            0.0,
+        )
+        all_alpha_slack[i_slack] = np.maximum(
+            -grad[n:][i_slack] / sd[n:][i_slack],
+            0.0,
+        )
+        alpha_xl = np.min(all_alpha_xl)
+        alpha_xu = np.min(all_alpha_xu)
+        alpha_slack = np.min(all_alpha_slack, initial=np.inf)
+        alpha_bd = min(alpha_xl, alpha_xu, alpha_slack)
+
+        # Set alpha_ub to the step size for the linear constraints.
+        aub_sd = aub @ sd[:n] - sd[n:]
+        i_ub = free_ub & (aub_sd > TINY * np.abs(resid))
+        all_alpha_ub = np.full_like(bub, np.inf)
+        all_alpha_ub[i_ub] = resid[i_ub] / aub_sd[i_ub]
+        alpha_ub = np.min(all_alpha_ub, initial=np.inf)
+
+        # Update the iterate.
+        alpha = min(alpha, alpha_bd, alpha_ub)
+        if alpha > 0.0:
+            step = np.clip(step + alpha * sd[:n], xl, xu)
+            grad += alpha * hess_sd
+            resid = np.maximum(0.0, resid - alpha * aub_sd)
+            reduct -= alpha * (grad_sd + 0.5 * alpha * curv_sd)
+
+        if alpha < min(alpha_tr, alpha_bd, alpha_ub):
+            # The current iteration is a conjugate gradient iteration. Update
+            # the search direction so that it is conjugate (with respect to H)
+            # to all the previous search directions.
+            grad_proj = q[:, n_act:] @ (q[:, n_act:].T @ grad)
+            beta = (grad_proj @ hess_sd) / curv_sd
+            sd = beta * sd - grad_proj
+            k += 1
+        elif alpha < alpha_tr:
+            # The iterate is restricted by a bound/linear constraint. Add this
+            # constraint to the active set, and restart the calculations.
+            if alpha_xl <= alpha:
+                i_new = np.argmin(all_alpha_xl)
+                step[i_new] = xl[i_new]
+                free_xl[i_new] = False
+            elif alpha_xu <= alpha:
+                i_new = np.argmin(all_alpha_xu)
+                step[i_new] = xu[i_new]
+                free_xu[i_new] = False
+            elif alpha_slack <= alpha:
+                i_new = np.argmin(all_alpha_slack)
+                free_slack[i_new] = False
+            else:
+                i_new = np.argmin(all_alpha_ub)
+                free_ub[i_new] = False
+            n_act, q = qr_normal_byrd_omojokun(
+                aub, free_xl, free_xu, free_slack, free_ub
+            )
+            sd = -q[:, n_act:] @ (q[:, n_act:].T @ grad)
+            k = 0
+        else:
+            # The current iterate is on the trust-region boundary. Add all the
+            # active bound constraints to the working set to prepare for the
+            # improvement of the solution, and stop the iterations.
+            if alpha_xl <= alpha:
+                i_new = _argmin(all_alpha_xl)
+                step[i_new] = xl[i_new]
+                free_xl[i_new] = False
+            if alpha_xu <= alpha:
+                i_new = _argmin(all_alpha_xu)
+                step[i_new] = xu[i_new]
+                free_xu[i_new] = False
+            boundary_reached = True
+            break
+
+    # Attempt to improve the solution on the trust-region boundary.
+    if kwargs.get("improve_tcg", True) and boundary_reached:
+        step_base = np.copy(step)
+        free_bd = free_xl & free_xu
+        grad = aub.T @ np.maximum(aub @ step - bub, 0.0) + aeq.T @ (
+            aeq @ step - beq
+        )
+        sd = np.zeros(n)
+        while np.count_nonzero(free_bd) > 0:
+            # Check whether a substantial reduction in the objective function
+            # is possible, and set the search direction.
+            step_sq = step[free_bd] @ step[free_bd]
+            grad_sq = grad[free_bd] @ grad[free_bd]
+            grad_step = grad[free_bd] @ step[free_bd]
+            grad_sd = -np.sqrt(max(step_sq * grad_sq - grad_step**2.0, 0.0))
+            sd[free_bd] = grad_step * step[free_bd] - step_sq * grad[free_bd]
+            sd[~free_bd] = 0.0
+            if grad_sd >= -1e-8 * reduct or np.any(
+                grad_sd >= -TINY * np.abs(sd[free_bd])
+            ):
+                break
+            sd[free_bd] /= -grad_sd
+
+            # Calculate an upper bound for the tangent of half the angle theta
+            # of this alternative iteration. The step will be updated as:
+            # step = cos(theta) * step + sin(theta) * sd.
+            temp_xl = np.zeros(n)
+            temp_xu = np.zeros(n)
+            temp_xl[free_bd] = (
+                step[free_bd] ** 2.0 + sd[free_bd] ** 2.0 - xl[free_bd] ** 2.0
+            )
+            temp_xu[free_bd] = (
+                step[free_bd] ** 2.0 + sd[free_bd] ** 2.0 - xu[free_bd] ** 2.0
+            )
+            temp_xl[temp_xl > 0.0] = (
+                np.sqrt(temp_xl[temp_xl > 0.0]) - sd[temp_xl > 0.0]
+            )
+            temp_xu[temp_xu > 0.0] = (
+                np.sqrt(temp_xu[temp_xu > 0.0]) + sd[temp_xu > 0.0]
+            )
+            dist_xl = np.maximum(step - xl, 0.0)
+            dist_xu = np.maximum(xu - step, 0.0)
+            i_xl = temp_xl > TINY * dist_xl
+            i_xu = temp_xu > TINY * dist_xu
+            all_t_xl = np.ones(n)
+            all_t_xu = np.ones(n)
+            all_t_xl[i_xl] = np.minimum(
+                all_t_xl[i_xl],
+                dist_xl[i_xl] / temp_xl[i_xl],
+            )
+            all_t_xu[i_xu] = np.minimum(
+                all_t_xu[i_xu],
+                dist_xu[i_xu] / temp_xu[i_xu],
+            )
+            t_xl = np.min(all_t_xl)
+            t_xu = np.min(all_t_xu)
+            t_bd = min(t_xl, t_xu)
+
+            # For a range of equally spaced values of tan(0.5 * theta),
+            # calculate the reduction in the objective function that would be
+            # obtained by accepting the corresponding angle.
+            n_samples = 20
+            n_samples = int((n_samples - 3) * t_bd + 3)
+            t_samples = np.linspace(t_bd / n_samples, t_bd, n_samples)
+            resid_ub = np.maximum(aub @ step - bub, 0.0)
+            resid_eq = aeq @ step - beq
+            step_proj = np.copy(step)
+            step_proj[~free_bd] = 0.0
+            all_reduct = np.empty(n_samples)
+            for i in range(n_samples):
+                sin_value = 2.0 * t_samples[i] / (1.0 + t_samples[i] ** 2.0)
+                step_alt = np.clip(
+                    step + sin_value * (sd - t_samples[i] * step_proj),
+                    xl,
+                    xu,
+                )
+                resid_ub_alt = np.maximum(aub @ step_alt - bub, 0.0)
+                resid_eq_alt = aeq @ step_alt - beq
+                all_reduct[i] = 0.5 * (
+                    resid_ub @ resid_ub
+                    + resid_eq @ resid_eq
+                    - resid_ub_alt @ resid_ub_alt
+                    - resid_eq_alt @ resid_eq_alt
+                )
+            if np.all(all_reduct <= 0.0):
+                # No reduction in the objective function is obtained.
+                break
+
+            # Accept the angle that provides the largest reduction in the
+            # objective function, and update the iterate.
+            i_max = np.argmax(all_reduct)
+            cos_value = (1.0 - t_samples[i_max] ** 2.0) / (
+                1.0 + t_samples[i_max] ** 2.0
+            )
+            sin_value = (2.0 * t_samples[i_max]
+                         / (1.0 + t_samples[i_max] ** 2.0))
+            step[free_bd] = cos_value * step[free_bd] + sin_value * sd[free_bd]
+            grad = aub.T @ np.maximum(aub @ step - bub, 0.0) + aeq.T @ (
+                aeq @ step - beq
+            )
+            reduct += all_reduct[i_max]
+
+            # If the above angle is restricted by bound constraints, add them
+            # to the working set, and restart the alternative iteration.
+            # Otherwise, the calculations are terminated.
+            if t_bd < 1.0 and i_max == n_samples - 1:
+                if t_xl <= t_bd:
+                    i_new = _argmin(all_t_xl)
+                    step[i_new] = xl[i_new]
+                    free_bd[i_new] = False
+                if t_xu <= t_bd:
+                    i_new = _argmin(all_t_xu)
+                    step[i_new] = xu[i_new]
+                    free_bd[i_new] = False
+            else:
+                break
+
+        # Ensure that the alternative iteration improves the objective
+        # function.
+        resid_ub = np.maximum(aub @ step - bub, 0.0)
+        resid_ub_base = np.maximum(aub @ step_base - bub, 0.0)
+        resid_eq = aeq @ step - beq
+        resid_eq_base = aeq @ step_base - beq
+        if (
+            resid_ub @ resid_ub + resid_eq @ resid_eq
+            > resid_ub_base @ resid_ub_base + resid_eq_base @ resid_eq_base
+        ):
+            step = step_base
+
+    if debug:
+        assert np.all(xl <= step)
+        assert np.all(step <= xu)
+        assert np.linalg.norm(step) < 1.1 * delta
+    return step
+
+
+def qr_tangential_byrd_omojokun(aub, aeq, free_xl, free_xu, free_ub):
+    n = free_xl.size
+    identity = np.eye(n)
+    q, r, _ = qr(
+        np.block(
+            [
+                [aeq],
+                [aub[~free_ub, :]],
+                [-identity[~free_xl, :]],
+                [identity[~free_xu, :]],
+            ]
+        ).T,
+        pivoting=True,
+    )
+    n_act = np.count_nonzero(
+        np.abs(np.diag(r))
+        >= 10.0
+        * EPS
+        * n
+        * np.linalg.norm(r[: np.min(r.shape), : np.min(r.shape)], axis=0)
+    )
+    return n_act, q
+
+
+def qr_normal_byrd_omojokun(aub, free_xl, free_xu, free_slack, free_ub):
+    m_linear_ub, n = aub.shape
+    identity_n = np.eye(n)
+    identity_m = np.eye(m_linear_ub)
+    q, r, _ = qr(
+        np.block(
+            [
+                [
+                    aub[~free_ub, :],
+                    -identity_m[~free_ub, :],
+                ],
+                [
+                    np.zeros((m_linear_ub - np.count_nonzero(free_slack), n)),
+                    -identity_m[~free_slack, :],
+                ],
+                [
+                    -identity_n[~free_xl, :],
+                    np.zeros((n - np.count_nonzero(free_xl), m_linear_ub)),
+                ],
+                [
+                    identity_n[~free_xu, :],
+                    np.zeros((n - np.count_nonzero(free_xu), m_linear_ub)),
+                ],
+            ]
+        ).T,
+        pivoting=True,
+    )
+    n_act = np.count_nonzero(
+        np.abs(np.diag(r))
+        >= 10.0
+        * EPS
+        * (n + m_linear_ub)
+        * np.linalg.norm(r[: np.min(r.shape), : np.min(r.shape)], axis=0)
+    )
+    return n_act, q
+
+
+def _alpha_tr(step, sd, delta):
+    step_sd = step @ sd
+    sd_sq = sd @ sd
+    dist_tr_sq = delta**2.0 - step @ step
+    temp = np.sqrt(max(step_sd**2.0 + sd_sq * dist_tr_sq, 0.0))
+    if step_sd <= 0.0 and sd_sq > TINY * abs(temp - step_sd):
+        alpha_tr = max((temp - step_sd) / sd_sq, 0.0)
+    elif abs(temp + step_sd) > TINY * dist_tr_sq:
+        alpha_tr = max(dist_tr_sq / (temp + step_sd), 0.0)
+    else:
+        raise ZeroDivisionError
+    return alpha_tr
+
+
+def _argmax(x):
+    return np.flatnonzero(x >= np.max(x))
+
+
+def _argmin(x):
+    return np.flatnonzero(x <= np.min(x))

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/utils/__init__.py

@@ -0,0 +1,18 @@
+from .exceptions import (
+    MaxEvalError,
+    TargetSuccess,
+    CallbackSuccess,
+    FeasibleSuccess,
+)
+from .math import get_arrays_tol, exact_1d_array
+from .versions import show_versions
+
+__all__ = [
+    "MaxEvalError",
+    "TargetSuccess",
+    "CallbackSuccess",
+    "FeasibleSuccess",
+    "get_arrays_tol",
+    "exact_1d_array",
+    "show_versions",
+]

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/utils/exceptions.py

@@ -0,0 +1,22 @@
+class MaxEvalError(Exception):
+    """
+    Exception raised when the maximum number of evaluations is reached.
+    """
+
+
+class TargetSuccess(Exception):
+    """
+    Exception raised when the target value is reached.
+    """
+
+
+class CallbackSuccess(StopIteration):
+    """
+    Exception raised when the callback function raises a ``StopIteration``.
+    """
+
+
+class FeasibleSuccess(Exception):
+    """
+    Exception raised when a feasible point of a feasible problem is found.
+    """

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/utils/math.py

@@ -0,0 +1,77 @@
+import numpy as np
+
+
+EPS = np.finfo(float).eps
+
+
+def get_arrays_tol(*arrays):
+    """
+    Get a relative tolerance for a set of arrays.
+
+    Parameters
+    ----------
+    *arrays: tuple
+        Set of `numpy.ndarray` to get the tolerance for.
+
+    Returns
+    -------
+    float
+        Relative tolerance for the set of arrays.
+
+    Raises
+    ------
+    ValueError
+        If no array is provided.
+    """
+    if len(arrays) == 0:
+        raise ValueError("At least one array must be provided.")
+    size = max(array.size for array in arrays)
+    weight = max(
+        np.max(np.abs(array[np.isfinite(array)]), initial=1.0)
+        for array in arrays
+    )
+    return 10.0 * EPS * max(size, 1.0) * weight
+
+
+def exact_1d_array(x, message):
+    """
+    Preprocess a 1-dimensional array.
+
+    Parameters
+    ----------
+    x : array_like
+        Array to be preprocessed.
+    message : str
+        Error message if `x` cannot be interpreter as a 1-dimensional array.
+
+    Returns
+    -------
+    `numpy.ndarray`
+        Preprocessed array.
+    """
+    x = np.atleast_1d(np.squeeze(x)).astype(float)
+    if x.ndim != 1:
+        raise ValueError(message)
+    return x
+
+
+def exact_2d_array(x, message):
+    """
+    Preprocess a 2-dimensional array.
+
+    Parameters
+    ----------
+    x : array_like
+        Array to be preprocessed.
+    message : str
+        Error message if `x` cannot be interpreter as a 2-dimensional array.
+
+    Returns
+    -------
+    `numpy.ndarray`
+        Preprocessed array.
+    """
+    x = np.atleast_2d(x).astype(float)
+    if x.ndim != 2:
+        raise ValueError(message)
+    return x

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/cobyqa/utils/versions.py

@@ -0,0 +1,67 @@
+import os
+import platform
+import sys
+from importlib.metadata import PackageNotFoundError, version
+
+
+def _get_sys_info():
+    """
+    Get useful system information.
+
+    Returns
+    -------
+    dict
+        Useful system information.
+    """
+    return {
+        "python": sys.version.replace(os.linesep, " "),
+        "executable": sys.executable,
+        "machine": platform.platform(),
+    }
+
+
+def _get_deps_info():
+    """
+    Get the versions of the dependencies.
+
+    Returns
+    -------
+    dict
+        Versions of the dependencies.
+    """
+    deps = ["cobyqa", "numpy", "scipy", "setuptools", "pip"]
+    deps_info = {}
+    for module in deps:
+        try:
+            deps_info[module] = version(module)
+        except PackageNotFoundError:
+            deps_info[module] = None
+    return deps_info
+
+
+def show_versions():
+    """
+    Display useful system and dependencies information.
+
+    When reporting issues, please include this information.
+    """
+    print("System settings")
+    print("---------------")
+    sys_info = _get_sys_info()
+    print(
+        "\n".join(
+            f"{k:>{max(map(len, sys_info.keys())) + 1}}: {v}"
+            for k, v in sys_info.items()
+        )
+    )
+
+    print()
+    print("Python dependencies")
+    print("-------------------")
+    deps_info = _get_deps_info()
+    print(
+        "\n".join(
+            f"{k:>{max(map(len, deps_info.keys())) + 1}}: {v}"
+            for k, v in deps_info.items()
+        )
+    )

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test__gcutils.py

@@ -0,0 +1,110 @@
+""" Test for assert_deallocated context manager and gc utilities
+"""
+import gc
+from threading import Lock
+
+from scipy._lib._gcutils import (set_gc_state, gc_state, assert_deallocated,
+                                 ReferenceError, IS_PYPY)
+
+from numpy.testing import assert_equal
+
+import pytest
+
+
+@pytest.fixture
+def gc_lock():
+    return Lock()
+
+
+def test_set_gc_state(gc_lock):
+    with gc_lock:
+        gc_status = gc.isenabled()
+        try:
+            for state in (True, False):
+                gc.enable()
+                set_gc_state(state)
+                assert_equal(gc.isenabled(), state)
+                gc.disable()
+                set_gc_state(state)
+                assert_equal(gc.isenabled(), state)
+        finally:
+            if gc_status:
+                gc.enable()
+
+
+def test_gc_state(gc_lock):
+    # Test gc_state context manager
+    with gc_lock:
+        gc_status = gc.isenabled()
+        try:
+            for pre_state in (True, False):
+                set_gc_state(pre_state)
+                for with_state in (True, False):
+                    # Check the gc state is with_state in with block
+                    with gc_state(with_state):
+                        assert_equal(gc.isenabled(), with_state)
+                    # And returns to previous state outside block
+                    assert_equal(gc.isenabled(), pre_state)
+                    # Even if the gc state is set explicitly within the block
+                    with gc_state(with_state):
+                        assert_equal(gc.isenabled(), with_state)
+                        set_gc_state(not with_state)
+                    assert_equal(gc.isenabled(), pre_state)
+        finally:
+            if gc_status:
+                gc.enable()
+
+
+@pytest.mark.skipif(IS_PYPY, reason="Test not meaningful on PyPy")
+def test_assert_deallocated(gc_lock):
+    # Ordinary use
+    class C:
+        def __init__(self, arg0, arg1, name='myname'):
+            self.name = name
+    with gc_lock:
+        for gc_current in (True, False):
+            with gc_state(gc_current):
+                # We are deleting from with-block context, so that's OK
+                with assert_deallocated(C, 0, 2, 'another name') as c:
+                    assert_equal(c.name, 'another name')
+                    del c
+                # Or not using the thing in with-block context, also OK
+                with assert_deallocated(C, 0, 2, name='third name'):
+                    pass
+                assert_equal(gc.isenabled(), gc_current)
+
+
+@pytest.mark.skipif(IS_PYPY, reason="Test not meaningful on PyPy")
+def test_assert_deallocated_nodel():
+    class C:
+        pass
+    with pytest.raises(ReferenceError):
+        # Need to delete after using if in with-block context
+        # Note: assert_deallocated(C) needs to be assigned for the test
+        # to function correctly.  It is assigned to _, but _ itself is
+        # not referenced in the body of the with, it is only there for
+        # the refcount.
+        with assert_deallocated(C) as _:
+            pass
+
+
+@pytest.mark.skipif(IS_PYPY, reason="Test not meaningful on PyPy")
+def test_assert_deallocated_circular():
+    class C:
+        def __init__(self):
+            self._circular = self
+    with pytest.raises(ReferenceError):
+        # Circular reference, no automatic garbage collection
+        with assert_deallocated(C) as c:
+            del c
+
+
+@pytest.mark.skipif(IS_PYPY, reason="Test not meaningful on PyPy")
+def test_assert_deallocated_circular2():
+    class C:
+        def __init__(self):
+            self._circular = self
+    with pytest.raises(ReferenceError):
+        # Still circular reference, no automatic garbage collection
+        with assert_deallocated(C):
+            pass

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test__pep440.py

@@ -0,0 +1,67 @@
+from pytest import raises as assert_raises
+from scipy._lib._pep440 import Version, parse
+
+
+def test_main_versions():
+    assert Version('1.8.0') == Version('1.8.0')
+    for ver in ['1.9.0', '2.0.0', '1.8.1']:
+        assert Version('1.8.0') < Version(ver)
+
+    for ver in ['1.7.0', '1.7.1', '0.9.9']:
+        assert Version('1.8.0') > Version(ver)
+
+
+def test_version_1_point_10():
+    # regression test for gh-2998.
+    assert Version('1.9.0') < Version('1.10.0')
+    assert Version('1.11.0') < Version('1.11.1')
+    assert Version('1.11.0') == Version('1.11.0')
+    assert Version('1.99.11') < Version('1.99.12')
+
+
+def test_alpha_beta_rc():
+    assert Version('1.8.0rc1') == Version('1.8.0rc1')
+    for ver in ['1.8.0', '1.8.0rc2']:
+        assert Version('1.8.0rc1') < Version(ver)
+
+    for ver in ['1.8.0a2', '1.8.0b3', '1.7.2rc4']:
+        assert Version('1.8.0rc1') > Version(ver)
+
+    assert Version('1.8.0b1') > Version('1.8.0a2')
+
+
+def test_dev_version():
+    assert Version('1.9.0.dev+Unknown') < Version('1.9.0')
+    for ver in ['1.9.0', '1.9.0a1', '1.9.0b2', '1.9.0b2.dev+ffffffff', '1.9.0.dev1']:
+        assert Version('1.9.0.dev+f16acvda') < Version(ver)
+
+    assert Version('1.9.0.dev+f16acvda') == Version('1.9.0.dev+f16acvda')
+
+
+def test_dev_a_b_rc_mixed():
+    assert Version('1.9.0a2.dev+f16acvda') == Version('1.9.0a2.dev+f16acvda')
+    assert Version('1.9.0a2.dev+6acvda54') < Version('1.9.0a2')
+
+
+def test_dev0_version():
+    assert Version('1.9.0.dev0+Unknown') < Version('1.9.0')
+    for ver in ['1.9.0', '1.9.0a1', '1.9.0b2', '1.9.0b2.dev0+ffffffff']:
+        assert Version('1.9.0.dev0+f16acvda') < Version(ver)
+
+    assert Version('1.9.0.dev0+f16acvda') == Version('1.9.0.dev0+f16acvda')
+
+
+def test_dev0_a_b_rc_mixed():
+    assert Version('1.9.0a2.dev0+f16acvda') == Version('1.9.0a2.dev0+f16acvda')
+    assert Version('1.9.0a2.dev0+6acvda54') < Version('1.9.0a2')
+
+
+def test_raises():
+    for ver in ['1,9.0', '1.7.x']:
+        assert_raises(ValueError, Version, ver)
+
+def test_legacy_version():
+    # Non-PEP-440 version identifiers always compare less. For NumPy this only
+    # occurs on dev builds prior to 1.10.0 which are unsupported anyway.
+    assert parse('invalid') < Version('0.0.0')
+    assert parse('1.9.0-f16acvda') < Version('1.0.0')

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test__testutils.py

@@ -0,0 +1,32 @@
+import sys
+from scipy._lib._testutils import _parse_size, _get_mem_available
+import pytest
+
+
+def test__parse_size():
+    expected = {
+        '12': 12e6,
+        '12 b': 12,
+        '12k': 12e3,
+        '  12  M  ': 12e6,
+        '  12  G  ': 12e9,
+        ' 12Tb ': 12e12,
+        '12  Mib ': 12 * 1024.0**2,
+        '12Tib': 12 * 1024.0**4,
+    }
+
+    for inp, outp in sorted(expected.items()):
+        if outp is None:
+            with pytest.raises(ValueError):
+                _parse_size(inp)
+        else:
+            assert _parse_size(inp) == outp
+
+
+def test__mem_available():
+    # May return None on non-Linux platforms
+    available = _get_mem_available()
+    if sys.platform.startswith('linux'):
+        assert available >= 0
+    else:
+        assert available is None or available >= 0

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test__threadsafety.py

@@ -0,0 +1,51 @@
+import threading
+import time
+import traceback
+
+from numpy.testing import assert_
+from pytest import raises as assert_raises
+
+from scipy._lib._threadsafety import ReentrancyLock, non_reentrant, ReentrancyError
+
+
+def test_parallel_threads():
+    # Check that ReentrancyLock serializes work in parallel threads.
+    #
+    # The test is not fully deterministic, and may succeed falsely if
+    # the timings go wrong.
+
+    lock = ReentrancyLock("failure")
+
+    failflag = [False]
+    exceptions_raised = []
+
+    def worker(k):
+        try:
+            with lock:
+                assert_(not failflag[0])
+                failflag[0] = True
+                time.sleep(0.1 * k)
+                assert_(failflag[0])
+                failflag[0] = False
+        except Exception:
+            exceptions_raised.append(traceback.format_exc(2))
+
+    threads = [threading.Thread(target=lambda k=k: worker(k))
+               for k in range(3)]
+    for t in threads:
+        t.start()
+    for t in threads:
+        t.join()
+
+    exceptions_raised = "\n".join(exceptions_raised)
+    assert_(not exceptions_raised, exceptions_raised)
+
+
+def test_reentering():
+    # Check that ReentrancyLock prevents re-entering from the same thread.
+
+    @non_reentrant()
+    def func(x):
+        return func(x)
+
+    assert_raises(ReentrancyError, func, 0)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test__util.py

@@ -0,0 +1,657 @@
+from multiprocessing import Pool
+from multiprocessing.pool import Pool as PWL
+import re
+import math
+from fractions import Fraction
+
+import numpy as np
+from numpy.testing import assert_equal, assert_
+import pytest
+from pytest import raises as assert_raises
+import hypothesis.extra.numpy as npst
+from hypothesis import given, strategies, reproduce_failure  # noqa: F401
+from scipy.conftest import array_api_compatible, skip_xp_invalid_arg
+
+from scipy._lib._array_api import (xp_assert_equal, xp_assert_close, is_numpy,
+                                   xp_copy, is_array_api_strict)
+from scipy._lib._util import (_aligned_zeros, check_random_state, MapWrapper,
+                              getfullargspec_no_self, FullArgSpec,
+                              rng_integers, _validate_int, _rename_parameter,
+                              _contains_nan, _rng_html_rewrite, _lazywhere)
+from scipy import cluster, interpolate, linalg, optimize, sparse, spatial, stats
+
+skip_xp_backends = pytest.mark.skip_xp_backends
+
+
+@pytest.mark.slow
+def test__aligned_zeros():
+    niter = 10
+
+    def check(shape, dtype, order, align):
+        err_msg = repr((shape, dtype, order, align))
+        x = _aligned_zeros(shape, dtype, order, align=align)
+        if align is None:
+            align = np.dtype(dtype).alignment
+        assert_equal(x.__array_interface__['data'][0] % align, 0)
+        if hasattr(shape, '__len__'):
+            assert_equal(x.shape, shape, err_msg)
+        else:
+            assert_equal(x.shape, (shape,), err_msg)
+        assert_equal(x.dtype, dtype)
+        if order == "C":
+            assert_(x.flags.c_contiguous, err_msg)
+        elif order == "F":
+            if x.size > 0:
+                # Size-0 arrays get invalid flags on NumPy 1.5
+                assert_(x.flags.f_contiguous, err_msg)
+        elif order is None:
+            assert_(x.flags.c_contiguous, err_msg)
+        else:
+            raise ValueError()
+
+    # try various alignments
+    for align in [1, 2, 3, 4, 8, 16, 32, 64, None]:
+        for n in [0, 1, 3, 11]:
+            for order in ["C", "F", None]:
+                for dtype in [np.uint8, np.float64]:
+                    for shape in [n, (1, 2, 3, n)]:
+                        for j in range(niter):
+                            check(shape, dtype, order, align)
+
+
+def test_check_random_state():
+    # If seed is None, return the RandomState singleton used by np.random.
+    # If seed is an int, return a new RandomState instance seeded with seed.
+    # If seed is already a RandomState instance, return it.
+    # Otherwise raise ValueError.
+    rsi = check_random_state(1)
+    assert_equal(type(rsi), np.random.RandomState)
+    rsi = check_random_state(rsi)
+    assert_equal(type(rsi), np.random.RandomState)
+    rsi = check_random_state(None)
+    assert_equal(type(rsi), np.random.RandomState)
+    assert_raises(ValueError, check_random_state, 'a')
+    rg = np.random.Generator(np.random.PCG64())
+    rsi = check_random_state(rg)
+    assert_equal(type(rsi), np.random.Generator)
+
+
+def test_getfullargspec_no_self():
+    p = MapWrapper(1)
+    argspec = getfullargspec_no_self(p.__init__)
+    assert_equal(argspec, FullArgSpec(['pool'], None, None, (1,), [],
+                                      None, {}))
+    argspec = getfullargspec_no_self(p.__call__)
+    assert_equal(argspec, FullArgSpec(['func', 'iterable'], None, None, None,
+                                      [], None, {}))
+
+    class _rv_generic:
+        def _rvs(self, a, b=2, c=3, *args, size=None, **kwargs):
+            return None
+
+    rv_obj = _rv_generic()
+    argspec = getfullargspec_no_self(rv_obj._rvs)
+    assert_equal(argspec, FullArgSpec(['a', 'b', 'c'], 'args', 'kwargs',
+                                      (2, 3), ['size'], {'size': None}, {}))
+
+
+def test_mapwrapper_serial():
+    in_arg = np.arange(10.)
+    out_arg = np.sin(in_arg)
+
+    p = MapWrapper(1)
+    assert_(p._mapfunc is map)
+    assert_(p.pool is None)
+    assert_(p._own_pool is False)
+    out = list(p(np.sin, in_arg))
+    assert_equal(out, out_arg)
+
+    with assert_raises(RuntimeError):
+        p = MapWrapper(0)
+
+
+def test_pool():
+    with Pool(2) as p:
+        p.map(math.sin, [1, 2, 3, 4])
+
+
+def test_mapwrapper_parallel():
+    in_arg = np.arange(10.)
+    out_arg = np.sin(in_arg)
+
+    with MapWrapper(2) as p:
+        out = p(np.sin, in_arg)
+        assert_equal(list(out), out_arg)
+
+        assert_(p._own_pool is True)
+        assert_(isinstance(p.pool, PWL))
+        assert_(p._mapfunc is not None)
+
+    # the context manager should've closed the internal pool
+    # check that it has by asking it to calculate again.
+    with assert_raises(Exception) as excinfo:
+        p(np.sin, in_arg)
+
+    assert_(excinfo.type is ValueError)
+
+    # can also set a PoolWrapper up with a map-like callable instance
+    with Pool(2) as p:
+        q = MapWrapper(p.map)
+
+        assert_(q._own_pool is False)
+        q.close()
+
+        # closing the PoolWrapper shouldn't close the internal pool
+        # because it didn't create it
+        out = p.map(np.sin, in_arg)
+        assert_equal(list(out), out_arg)
+
+
+def test_rng_integers():
+    rng = np.random.RandomState()
+
+    # test that numbers are inclusive of high point
+    arr = rng_integers(rng, low=2, high=5, size=100, endpoint=True)
+    assert np.max(arr) == 5
+    assert np.min(arr) == 2
+    assert arr.shape == (100, )
+
+    # test that numbers are inclusive of high point
+    arr = rng_integers(rng, low=5, size=100, endpoint=True)
+    assert np.max(arr) == 5
+    assert np.min(arr) == 0
+    assert arr.shape == (100, )
+
+    # test that numbers are exclusive of high point
+    arr = rng_integers(rng, low=2, high=5, size=100, endpoint=False)
+    assert np.max(arr) == 4
+    assert np.min(arr) == 2
+    assert arr.shape == (100, )
+
+    # test that numbers are exclusive of high point
+    arr = rng_integers(rng, low=5, size=100, endpoint=False)
+    assert np.max(arr) == 4
+    assert np.min(arr) == 0
+    assert arr.shape == (100, )
+
+    # now try with np.random.Generator
+    try:
+        rng = np.random.default_rng()
+    except AttributeError:
+        return
+
+    # test that numbers are inclusive of high point
+    arr = rng_integers(rng, low=2, high=5, size=100, endpoint=True)
+    assert np.max(arr) == 5
+    assert np.min(arr) == 2
+    assert arr.shape == (100, )
+
+    # test that numbers are inclusive of high point
+    arr = rng_integers(rng, low=5, size=100, endpoint=True)
+    assert np.max(arr) == 5
+    assert np.min(arr) == 0
+    assert arr.shape == (100, )
+
+    # test that numbers are exclusive of high point
+    arr = rng_integers(rng, low=2, high=5, size=100, endpoint=False)
+    assert np.max(arr) == 4
+    assert np.min(arr) == 2
+    assert arr.shape == (100, )
+
+    # test that numbers are exclusive of high point
+    arr = rng_integers(rng, low=5, size=100, endpoint=False)
+    assert np.max(arr) == 4
+    assert np.min(arr) == 0
+    assert arr.shape == (100, )
+
+
+class TestValidateInt:
+
+    @pytest.mark.parametrize('n', [4, np.uint8(4), np.int16(4), np.array(4)])
+    def test_validate_int(self, n):
+        n = _validate_int(n, 'n')
+        assert n == 4
+
+    @pytest.mark.parametrize('n', [4.0, np.array([4]), Fraction(4, 1)])
+    def test_validate_int_bad(self, n):
+        with pytest.raises(TypeError, match='n must be an integer'):
+            _validate_int(n, 'n')
+
+    def test_validate_int_below_min(self):
+        with pytest.raises(ValueError, match='n must be an integer not '
+                                             'less than 0'):
+            _validate_int(-1, 'n', 0)
+
+
+class TestRenameParameter:
+    # check that wrapper `_rename_parameter` for backward-compatible
+    # keyword renaming works correctly
+
+    # Example method/function that still accepts keyword `old`
+    @_rename_parameter("old", "new")
+    def old_keyword_still_accepted(self, new):
+        return new
+
+    # Example method/function for which keyword `old` is deprecated
+    @_rename_parameter("old", "new", dep_version="1.9.0")
+    def old_keyword_deprecated(self, new):
+        return new
+
+    def test_old_keyword_still_accepted(self):
+        # positional argument and both keyword work identically
+        res1 = self.old_keyword_still_accepted(10)
+        res2 = self.old_keyword_still_accepted(new=10)
+        res3 = self.old_keyword_still_accepted(old=10)
+        assert res1 == res2 == res3 == 10
+
+        # unexpected keyword raises an error
+        message = re.escape("old_keyword_still_accepted() got an unexpected")
+        with pytest.raises(TypeError, match=message):
+            self.old_keyword_still_accepted(unexpected=10)
+
+        # multiple values for the same parameter raises an error
+        message = re.escape("old_keyword_still_accepted() got multiple")
+        with pytest.raises(TypeError, match=message):
+            self.old_keyword_still_accepted(10, new=10)
+        with pytest.raises(TypeError, match=message):
+            self.old_keyword_still_accepted(10, old=10)
+        with pytest.raises(TypeError, match=message):
+            self.old_keyword_still_accepted(new=10, old=10)
+
+    @pytest.fixture
+    def kwarg_lock(self):
+        from threading import Lock
+        return Lock()
+
+    def test_old_keyword_deprecated(self, kwarg_lock):
+        # positional argument and both keyword work identically,
+        # but use of old keyword results in DeprecationWarning
+        dep_msg = "Use of keyword argument `old` is deprecated"
+        res1 = self.old_keyword_deprecated(10)
+        res2 = self.old_keyword_deprecated(new=10)
+        # pytest warning filter is not thread-safe, enforce serialization
+        with kwarg_lock:
+            with pytest.warns(DeprecationWarning, match=dep_msg):
+                    res3 = self.old_keyword_deprecated(old=10)
+        assert res1 == res2 == res3 == 10
+
+        # unexpected keyword raises an error
+        message = re.escape("old_keyword_deprecated() got an unexpected")
+        with pytest.raises(TypeError, match=message):
+            self.old_keyword_deprecated(unexpected=10)
+
+        # multiple values for the same parameter raises an error and,
+        # if old keyword is used, results in DeprecationWarning
+        message = re.escape("old_keyword_deprecated() got multiple")
+        with pytest.raises(TypeError, match=message):
+            self.old_keyword_deprecated(10, new=10)
+        with kwarg_lock:
+            with pytest.raises(TypeError, match=message), \
+                    pytest.warns(DeprecationWarning, match=dep_msg):
+                    # breakpoint()
+                    self.old_keyword_deprecated(10, old=10)
+        with kwarg_lock:
+            with pytest.raises(TypeError, match=message), \
+                    pytest.warns(DeprecationWarning, match=dep_msg):
+                    self.old_keyword_deprecated(new=10, old=10)
+
+
+class TestContainsNaNTest:
+
+    def test_policy(self):
+        data = np.array([1, 2, 3, np.nan])
+
+        contains_nan, nan_policy = _contains_nan(data, nan_policy="propagate")
+        assert contains_nan
+        assert nan_policy == "propagate"
+
+        contains_nan, nan_policy = _contains_nan(data, nan_policy="omit")
+        assert contains_nan
+        assert nan_policy == "omit"
+
+        msg = "The input contains nan values"
+        with pytest.raises(ValueError, match=msg):
+            _contains_nan(data, nan_policy="raise")
+
+        msg = "nan_policy must be one of"
+        with pytest.raises(ValueError, match=msg):
+            _contains_nan(data, nan_policy="nan")
+
+    def test_contains_nan(self):
+        data1 = np.array([1, 2, 3])
+        assert not _contains_nan(data1)[0]
+
+        data2 = np.array([1, 2, 3, np.nan])
+        assert _contains_nan(data2)[0]
+
+        data3 = np.array([np.nan, 2, 3, np.nan])
+        assert _contains_nan(data3)[0]
+
+        data4 = np.array([[1, 2], [3, 4]])
+        assert not _contains_nan(data4)[0]
+
+        data5 = np.array([[1, 2], [3, np.nan]])
+        assert _contains_nan(data5)[0]
+
+    @skip_xp_invalid_arg
+    def test_contains_nan_with_strings(self):
+        data1 = np.array([1, 2, "3", np.nan])  # converted to string "nan"
+        assert not _contains_nan(data1)[0]
+
+        data2 = np.array([1, 2, "3", np.nan], dtype='object')
+        assert _contains_nan(data2)[0]
+
+        data3 = np.array([["1", 2], [3, np.nan]])  # converted to string "nan"
+        assert not _contains_nan(data3)[0]
+
+        data4 = np.array([["1", 2], [3, np.nan]], dtype='object')
+        assert _contains_nan(data4)[0]
+
+    @skip_xp_backends('jax.numpy',
+                      reason="JAX arrays do not support item assignment")
+    @pytest.mark.usefixtures("skip_xp_backends")
+    @array_api_compatible
+    @pytest.mark.parametrize("nan_policy", ['propagate', 'omit', 'raise'])
+    def test_array_api(self, xp, nan_policy):
+        rng = np.random.default_rng(932347235892482)
+        x0 = rng.random(size=(2, 3, 4))
+        x = xp.asarray(x0)
+        x_nan = xp_copy(x, xp=xp)
+        x_nan[1, 2, 1] = np.nan
+
+        contains_nan, nan_policy_out = _contains_nan(x, nan_policy=nan_policy)
+        assert not contains_nan
+        assert nan_policy_out == nan_policy
+
+        if nan_policy == 'raise':
+            message = 'The input contains...'
+            with pytest.raises(ValueError, match=message):
+                _contains_nan(x_nan, nan_policy=nan_policy)
+        elif nan_policy == 'omit' and not is_numpy(xp):
+            message = "`nan_policy='omit' is incompatible..."
+            with pytest.raises(ValueError, match=message):
+                _contains_nan(x_nan, nan_policy=nan_policy)
+        elif nan_policy == 'propagate':
+            contains_nan, nan_policy_out = _contains_nan(
+                x_nan, nan_policy=nan_policy)
+            assert contains_nan
+            assert nan_policy_out == nan_policy
+
+
+def test__rng_html_rewrite():
+    def mock_str():
+        lines = [
+            'np.random.default_rng(8989843)',
+            'np.random.default_rng(seed)',
+            'np.random.default_rng(0x9a71b21474694f919882289dc1559ca)',
+            ' bob ',
+        ]
+        return lines
+
+    res = _rng_html_rewrite(mock_str)()
+    ref = [
+        'np.random.default_rng()',
+        'np.random.default_rng(seed)',
+        'np.random.default_rng()',
+        ' bob ',
+    ]
+
+    assert res == ref
+
+
+class TestTransitionToRNG:
+    def kmeans(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        return cluster.vq.kmeans2(rng.random(size=(20, 3)), 3, **kwargs)
+
+    def kmeans2(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        return cluster.vq.kmeans2(rng.random(size=(20, 3)), 3, **kwargs)
+
+    def barycentric(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        x1, x2, y1 = rng.random((3, 10))
+        f = interpolate.BarycentricInterpolator(x1, y1, **kwargs)
+        return f(x2)
+
+    def clarkson_woodruff_transform(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        return linalg.clarkson_woodruff_transform(rng.random((10, 10)), 3, **kwargs)
+
+    def basinhopping(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        return optimize.basinhopping(optimize.rosen, rng.random(3), **kwargs).x
+
+    def opt(self, fun, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        bounds = optimize.Bounds(-rng.random(3) * 10, rng.random(3) * 10)
+        return fun(optimize.rosen, bounds, **kwargs).x
+
+    def differential_evolution(self, **kwargs):
+        return self.opt(optimize.differential_evolution, **kwargs)
+
+    def dual_annealing(self, **kwargs):
+        return self.opt(optimize.dual_annealing, **kwargs)
+
+    def check_grad(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        x = rng.random(3)
+        return optimize.check_grad(optimize.rosen, optimize.rosen_der, x,
+                                   direction='random', **kwargs)
+
+    def random_array(self, **kwargs):
+        return sparse.random_array((10, 10), density=1.0, **kwargs).toarray()
+
+    def random(self, **kwargs):
+        return sparse.random(10, 10, density=1.0, **kwargs).toarray()
+
+    def rand(self, **kwargs):
+        return sparse.rand(10, 10, density=1.0, **kwargs).toarray()
+
+    def svds(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        A = rng.random((10, 10))
+        return sparse.linalg.svds(A, **kwargs)
+
+    def random_rotation(self, **kwargs):
+        return spatial.transform.Rotation.random(3, **kwargs).as_matrix()
+
+    def goodness_of_fit(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        data = rng.random(100)
+        return stats.goodness_of_fit(stats.laplace, data, **kwargs).pvalue
+
+    def permutation_test(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        data = tuple(rng.random((2, 100)))
+        def statistic(x, y, axis): return np.mean(x, axis=axis) - np.mean(y, axis=axis)
+        return stats.permutation_test(data, statistic, **kwargs).pvalue
+
+    def bootstrap(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        data = (rng.random(100),)
+        return stats.bootstrap(data, np.mean, **kwargs).confidence_interval
+
+    def dunnett(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        x, y, control = rng.random((3, 100))
+        return stats.dunnett(x, y, control=control, **kwargs).pvalue
+
+    def sobol_indices(self, **kwargs):
+        def f_ishigami(x): return (np.sin(x[0]) + 7 * np.sin(x[1]) ** 2
+                                   + 0.1 * (x[2] ** 4) * np.sin(x[0]))
+        dists = [stats.uniform(loc=-np.pi, scale=2 * np.pi),
+                 stats.uniform(loc=-np.pi, scale=2 * np.pi),
+                 stats.uniform(loc=-np.pi, scale=2 * np.pi)]
+        res = stats.sobol_indices(func=f_ishigami, n=1024, dists=dists, **kwargs)
+        return res.first_order
+
+    def qmc_engine(self, engine, **kwargs):
+        qrng = engine(d=1, **kwargs)
+        return qrng.random(4)
+
+    def halton(self, **kwargs):
+        return self.qmc_engine(stats.qmc.Halton, **kwargs)
+
+    def sobol(self, **kwargs):
+        return self.qmc_engine(stats.qmc.Sobol, **kwargs)
+
+    def latin_hypercube(self, **kwargs):
+        return self.qmc_engine(stats.qmc.LatinHypercube, **kwargs)
+
+    def poisson_disk(self, **kwargs):
+        return self.qmc_engine(stats.qmc.PoissonDisk, **kwargs)
+
+    def multivariate_normal_qmc(self, **kwargs):
+        X = stats.qmc.MultivariateNormalQMC([0], **kwargs)
+        return X.random(4)
+
+    def multinomial_qmc(self, **kwargs):
+        X = stats.qmc.MultinomialQMC([0.5, 0.5], 4, **kwargs)
+        return X.random(4)
+
+    def permutation_method(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        data = tuple(rng.random((2, 100)))
+        method = stats.PermutationMethod(**kwargs)
+        return stats.pearsonr(*data, method=method).pvalue
+
+    def bootstrap_method(self, **kwargs):
+        rng = np.random.default_rng(3458934594269824562)
+        data = tuple(rng.random((2, 100)))
+        res = stats.pearsonr(*data)
+        method = stats.BootstrapMethod(**kwargs)
+        return res.confidence_interval(method=method)
+
+    @pytest.mark.fail_slow(10)
+    @pytest.mark.slow
+    @pytest.mark.parametrize("method, arg_name", [
+        (kmeans, "seed"),
+        (kmeans2, "seed"),
+        (barycentric, "random_state"),
+        (clarkson_woodruff_transform, "seed"),
+        (basinhopping, "seed"),
+        (differential_evolution, "seed"),
+        (dual_annealing, "seed"),
+        (check_grad, "seed"),
+        (random_array, 'random_state'),
+        (random, 'random_state'),
+        (rand, 'random_state'),
+        (svds, "random_state"),
+        (random_rotation, "random_state"),
+        (goodness_of_fit, "random_state"),
+        (permutation_test, "random_state"),
+        (bootstrap, "random_state"),
+        (permutation_method, "random_state"),
+        (bootstrap_method, "random_state"),
+        (dunnett, "random_state"),
+        (sobol_indices, "random_state"),
+        (halton, "seed"),
+        (sobol, "seed"),
+        (latin_hypercube, "seed"),
+        (poisson_disk, "seed"),
+        (multivariate_normal_qmc, "seed"),
+        (multinomial_qmc, "seed"),
+    ])
+    def test_rng_deterministic(self, method, arg_name):
+        np.random.seed(None)
+        seed = 2949672964
+
+        rng = np.random.default_rng(seed)
+        message = "got multiple values for argument now known as `rng`"
+        with pytest.raises(TypeError, match=message):
+            method(self, **{'rng': rng, arg_name: seed})
+
+        rng = np.random.default_rng(seed)
+        res1 = method(self, rng=rng)
+        res2 = method(self, rng=seed)
+        assert_equal(res2, res1)
+
+        if method.__name__ in {"dunnett", "sobol_indices"}:
+            # the two kwargs have essentially the same behavior for these functions
+            res3 = method(self, **{arg_name: seed})
+            assert_equal(res3, res1)
+            return
+
+        rng = np.random.RandomState(seed)
+        res1 = method(self, **{arg_name: rng})
+        res2 = method(self, **{arg_name: seed})
+
+        if method.__name__ in {"halton", "sobol", "latin_hypercube", "poisson_disk",
+                               "multivariate_normal_qmc", "multinomial_qmc"}:
+            # For these, passing `random_state=RandomState(seed)` is not the same as
+            # passing integer `seed`.
+            res1b = method(self, **{arg_name: np.random.RandomState(seed)})
+            assert_equal(res1b, res1)
+            res2b = method(self, **{arg_name: seed})
+            assert_equal(res2b, res2)
+            return
+
+        np.random.seed(seed)
+        res3 = method(self, **{arg_name: None})
+        assert_equal(res2, res1)
+        assert_equal(res3, res1)
+
+
+class TestLazywhere:
+    n_arrays = strategies.integers(min_value=1, max_value=3)
+    rng_seed = strategies.integers(min_value=1000000000, max_value=9999999999)
+    dtype = strategies.sampled_from((np.float32, np.float64))
+    p = strategies.floats(min_value=0, max_value=1)
+    data = strategies.data()
+
+    @pytest.mark.fail_slow(10)
+    @pytest.mark.filterwarnings('ignore::RuntimeWarning')  # overflows, etc.
+    @skip_xp_backends('jax.numpy',
+                      reason="JAX arrays do not support item assignment")
+    @pytest.mark.usefixtures("skip_xp_backends")
+    @array_api_compatible
+    @given(n_arrays=n_arrays, rng_seed=rng_seed, dtype=dtype, p=p, data=data)
+    @pytest.mark.thread_unsafe
+    def test_basic(self, n_arrays, rng_seed, dtype, p, data, xp):
+        mbs = npst.mutually_broadcastable_shapes(num_shapes=n_arrays+1,
+                                                 min_side=0)
+        input_shapes, result_shape = data.draw(mbs)
+        cond_shape, *shapes = input_shapes
+        elements = {'allow_subnormal': False}  # cupy/cupy#8382
+        fillvalue = xp.asarray(data.draw(npst.arrays(dtype=dtype, shape=tuple(),
+                                                     elements=elements)))
+        float_fillvalue = float(fillvalue)
+        arrays = [xp.asarray(data.draw(npst.arrays(dtype=dtype, shape=shape)))
+                  for shape in shapes]
+
+        def f(*args):
+            return sum(arg for arg in args)
+
+        def f2(*args):
+            return sum(arg for arg in args) / 2
+
+        rng = np.random.default_rng(rng_seed)
+        cond = xp.asarray(rng.random(size=cond_shape) > p)
+
+        res1 = _lazywhere(cond, arrays, f, fillvalue)
+        res2 = _lazywhere(cond, arrays, f, f2=f2)
+        if not is_array_api_strict(xp):
+            res3 = _lazywhere(cond, arrays, f, float_fillvalue)
+
+        # Ensure arrays are at least 1d to follow sane type promotion rules.
+        # This can be removed when minimum supported NumPy is 2.0
+        if xp == np:
+            cond, fillvalue, *arrays = np.atleast_1d(cond, fillvalue, *arrays)
+
+        ref1 = xp.where(cond, f(*arrays), fillvalue)
+        ref2 = xp.where(cond, f(*arrays), f2(*arrays))
+        if not is_array_api_strict(xp):
+            # Array API standard doesn't currently define behavior when fillvalue is a
+            # Python scalar. When it does, test can be run with array_api_strict, too.
+            ref3 = xp.where(cond, f(*arrays), float_fillvalue)
+
+        if xp == np:  # because we ensured arrays are at least 1d
+            ref1 = ref1.reshape(result_shape)
+            ref2 = ref2.reshape(result_shape)
+            ref3 = ref3.reshape(result_shape)
+
+        xp_assert_close(res1, ref1, rtol=2e-16)
+        xp_assert_equal(res2, ref2)
+        if not is_array_api_strict(xp):
+            xp_assert_equal(res3, ref3)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_array_api.py

@@ -0,0 +1,187 @@
+import numpy as np
+import pytest
+
+from scipy.conftest import array_api_compatible
+from scipy._lib._array_api import (
+    _GLOBAL_CONFIG, array_namespace, _asarray, xp_copy, xp_assert_equal, is_numpy,
+    np_compat,
+)
+from scipy._lib._array_api_no_0d import xp_assert_equal as xp_assert_equal_no_0d
+
+skip_xp_backends = pytest.mark.skip_xp_backends
+
+
+@pytest.mark.skipif(not _GLOBAL_CONFIG["SCIPY_ARRAY_API"],
+        reason="Array API test; set environment variable SCIPY_ARRAY_API=1 to run it")
+class TestArrayAPI:
+
+    def test_array_namespace(self):
+        x, y = np.array([0, 1, 2]), np.array([0, 1, 2])
+        xp = array_namespace(x, y)
+        assert 'array_api_compat.numpy' in xp.__name__
+
+        _GLOBAL_CONFIG["SCIPY_ARRAY_API"] = False
+        xp = array_namespace(x, y)
+        assert 'array_api_compat.numpy' in xp.__name__
+        _GLOBAL_CONFIG["SCIPY_ARRAY_API"] = True
+
+    @array_api_compatible
+    def test_asarray(self, xp):
+        x, y = _asarray([0, 1, 2], xp=xp), _asarray(np.arange(3), xp=xp)
+        ref = xp.asarray([0, 1, 2])
+        xp_assert_equal(x, ref)
+        xp_assert_equal(y, ref)
+
+    @pytest.mark.filterwarnings("ignore: the matrix subclass")
+    def test_raises(self):
+        msg = "of type `numpy.ma.MaskedArray` are not supported"
+        with pytest.raises(TypeError, match=msg):
+            array_namespace(np.ma.array(1), np.array(1))
+
+        msg = "of type `numpy.matrix` are not supported"
+        with pytest.raises(TypeError, match=msg):
+            array_namespace(np.array(1), np.matrix(1))
+
+        msg = "only boolean and numerical dtypes are supported"
+        with pytest.raises(TypeError, match=msg):
+            array_namespace([object()])
+        with pytest.raises(TypeError, match=msg):
+            array_namespace('abc')
+
+    def test_array_likes(self):
+        # should be no exceptions
+        array_namespace([0, 1, 2])
+        array_namespace(1, 2, 3)
+        array_namespace(1)
+
+    @skip_xp_backends('jax.numpy',
+                      reason="JAX arrays do not support item assignment")
+    @pytest.mark.usefixtures("skip_xp_backends")
+    @array_api_compatible
+    def test_copy(self, xp):
+        for _xp in [xp, None]:
+            x = xp.asarray([1, 2, 3])
+            y = xp_copy(x, xp=_xp)
+            # with numpy we'd want to use np.shared_memory, but that's not specified
+            # in the array-api
+            x[0] = 10
+            x[1] = 11
+            x[2] = 12
+
+            assert x[0] != y[0]
+            assert x[1] != y[1]
+            assert x[2] != y[2]
+            assert id(x) != id(y)
+
+    @array_api_compatible
+    @pytest.mark.parametrize('dtype', ['int32', 'int64', 'float32', 'float64'])
+    @pytest.mark.parametrize('shape', [(), (3,)])
+    def test_strict_checks(self, xp, dtype, shape):
+        # Check that `_strict_check` behaves as expected
+        dtype = getattr(xp, dtype)
+        x = xp.broadcast_to(xp.asarray(1, dtype=dtype), shape)
+        x = x if shape else x[()]
+        y = np_compat.asarray(1)[()]
+
+        kwarg_names = ["check_namespace", "check_dtype", "check_shape", "check_0d"]
+        options = dict(zip(kwarg_names, [True, False, False, False]))
+        if xp == np:
+            xp_assert_equal(x, y, **options)
+        else:
+            with pytest.raises(AssertionError, match="Namespaces do not match."):
+                xp_assert_equal(x, y, **options)
+
+        options = dict(zip(kwarg_names, [False, True, False, False]))
+        if y.dtype.name in str(x.dtype):
+            xp_assert_equal(x, y, **options)
+        else:
+            with pytest.raises(AssertionError, match="dtypes do not match."):
+                xp_assert_equal(x, y, **options)
+
+        options = dict(zip(kwarg_names, [False, False, True, False]))
+        if x.shape == y.shape:
+            xp_assert_equal(x, y, **options)
+        else:
+            with pytest.raises(AssertionError, match="Shapes do not match."):
+                xp_assert_equal(x, xp.asarray(y), **options)
+
+        options = dict(zip(kwarg_names, [False, False, False, True]))
+        if is_numpy(xp) and x.shape == y.shape:
+            xp_assert_equal(x, y, **options)
+        elif is_numpy(xp):
+            with pytest.raises(AssertionError, match="Array-ness does not match."):
+                xp_assert_equal(x, y, **options)
+
+
+    @array_api_compatible
+    def test_check_scalar(self, xp):
+        if not is_numpy(xp):
+            pytest.skip("Scalars only exist in NumPy")
+
+        # identity always passes
+        xp_assert_equal(xp.float64(0), xp.float64(0))
+        xp_assert_equal(xp.asarray(0.), xp.asarray(0.))
+        xp_assert_equal(xp.float64(0), xp.float64(0), check_0d=False)
+        xp_assert_equal(xp.asarray(0.), xp.asarray(0.), check_0d=False)
+
+        # Check default convention: 0d-arrays are distinguished from scalars
+        message = "Array-ness does not match:.*"
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal(xp.asarray(0.), xp.float64(0))
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal(xp.float64(0), xp.asarray(0.))
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal(xp.asarray(42), xp.int64(42))
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal(xp.int64(42), xp.asarray(42))
+
+        # with `check_0d=False`, scalars-vs-0d passes (if values match)
+        xp_assert_equal(xp.asarray(0.), xp.float64(0), check_0d=False)
+        xp_assert_equal(xp.float64(0), xp.asarray(0.), check_0d=False)
+        # also with regular python objects
+        xp_assert_equal(xp.asarray(0.), 0., check_0d=False)
+        xp_assert_equal(0., xp.asarray(0.), check_0d=False)
+        xp_assert_equal(xp.asarray(42), 42, check_0d=False)
+        xp_assert_equal(42, xp.asarray(42), check_0d=False)
+
+        # as an alternative to `check_0d=False`, explicitly expect scalar
+        xp_assert_equal(xp.float64(0), xp.asarray(0.)[()])
+
+
+    @array_api_compatible
+    def test_check_scalar_no_0d(self, xp):
+        if not is_numpy(xp):
+            pytest.skip("Scalars only exist in NumPy")
+
+        # identity passes, if first argument is not 0d (or check_0d=True)
+        xp_assert_equal_no_0d(xp.float64(0), xp.float64(0))
+        xp_assert_equal_no_0d(xp.float64(0), xp.float64(0), check_0d=True)
+        xp_assert_equal_no_0d(xp.asarray(0.), xp.asarray(0.), check_0d=True)
+
+        # by default, 0d values are forbidden as the first argument
+        message = "Result is a NumPy 0d-array.*"
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.asarray(0.), xp.asarray(0.))
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.asarray(0.), xp.float64(0))
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.asarray(42), xp.int64(42))
+
+        # Check default convention: 0d-arrays are NOT distinguished from scalars
+        xp_assert_equal_no_0d(xp.float64(0), xp.asarray(0.))
+        xp_assert_equal_no_0d(xp.int64(42), xp.asarray(42))
+
+        # opt in to 0d-check remains possible
+        message = "Array-ness does not match:.*"
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.asarray(0.), xp.float64(0), check_0d=True)
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.float64(0), xp.asarray(0.), check_0d=True)
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.asarray(42), xp.int64(0), check_0d=True)
+        with pytest.raises(AssertionError, match=message):
+            xp_assert_equal_no_0d(xp.int64(0), xp.asarray(42), check_0d=True)
+
+        # scalars-vs-0d passes (if values match) also with regular python objects
+        xp_assert_equal_no_0d(0., xp.asarray(0.))
+        xp_assert_equal_no_0d(42, xp.asarray(42))

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_bunch.py

@@ -0,0 +1,162 @@
+import pytest
+import pickle
+from numpy.testing import assert_equal
+from scipy._lib._bunch import _make_tuple_bunch
+
+
+# `Result` is defined at the top level of the module so it can be
+# used to test pickling.
+Result = _make_tuple_bunch('Result', ['x', 'y', 'z'], ['w', 'beta'])
+
+
+class TestMakeTupleBunch:
+
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+    # Tests with Result
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+    def setup_method(self):
+        # Set up an instance of Result.
+        self.result = Result(x=1, y=2, z=3, w=99, beta=0.5)
+
+    def test_attribute_access(self):
+        assert_equal(self.result.x, 1)
+        assert_equal(self.result.y, 2)
+        assert_equal(self.result.z, 3)
+        assert_equal(self.result.w, 99)
+        assert_equal(self.result.beta, 0.5)
+
+    def test_indexing(self):
+        assert_equal(self.result[0], 1)
+        assert_equal(self.result[1], 2)
+        assert_equal(self.result[2], 3)
+        assert_equal(self.result[-1], 3)
+        with pytest.raises(IndexError, match='index out of range'):
+            self.result[3]
+
+    def test_unpacking(self):
+        x0, y0, z0 = self.result
+        assert_equal((x0, y0, z0), (1, 2, 3))
+        assert_equal(self.result, (1, 2, 3))
+
+    def test_slice(self):
+        assert_equal(self.result[1:], (2, 3))
+        assert_equal(self.result[::2], (1, 3))
+        assert_equal(self.result[::-1], (3, 2, 1))
+
+    def test_len(self):
+        assert_equal(len(self.result), 3)
+
+    def test_repr(self):
+        s = repr(self.result)
+        assert_equal(s, 'Result(x=1, y=2, z=3, w=99, beta=0.5)')
+
+    def test_hash(self):
+        assert_equal(hash(self.result), hash((1, 2, 3)))
+
+    def test_pickle(self):
+        s = pickle.dumps(self.result)
+        obj = pickle.loads(s)
+        assert isinstance(obj, Result)
+        assert_equal(obj.x, self.result.x)
+        assert_equal(obj.y, self.result.y)
+        assert_equal(obj.z, self.result.z)
+        assert_equal(obj.w, self.result.w)
+        assert_equal(obj.beta, self.result.beta)
+
+    def test_read_only_existing(self):
+        with pytest.raises(AttributeError, match="can't set attribute"):
+            self.result.x = -1
+
+    def test_read_only_new(self):
+        self.result.plate_of_shrimp = "lattice of coincidence"
+        assert self.result.plate_of_shrimp == "lattice of coincidence"
+
+    def test_constructor_missing_parameter(self):
+        with pytest.raises(TypeError, match='missing'):
+            # `w` is missing.
+            Result(x=1, y=2, z=3, beta=0.75)
+
+    def test_constructor_incorrect_parameter(self):
+        with pytest.raises(TypeError, match='unexpected'):
+            # `foo` is not an existing field.
+            Result(x=1, y=2, z=3, w=123, beta=0.75, foo=999)
+
+    def test_module(self):
+        m = 'scipy._lib.tests.test_bunch'
+        assert_equal(Result.__module__, m)
+        assert_equal(self.result.__module__, m)
+
+    def test_extra_fields_per_instance(self):
+        # This test exists to ensure that instances of the same class
+        # store their own values for the extra fields. That is, the values
+        # are stored per instance and not in the class.
+        result1 = Result(x=1, y=2, z=3, w=-1, beta=0.0)
+        result2 = Result(x=4, y=5, z=6, w=99, beta=1.0)
+        assert_equal(result1.w, -1)
+        assert_equal(result1.beta, 0.0)
+        # The rest of these checks aren't essential, but let's check
+        # them anyway.
+        assert_equal(result1[:], (1, 2, 3))
+        assert_equal(result2.w, 99)
+        assert_equal(result2.beta, 1.0)
+        assert_equal(result2[:], (4, 5, 6))
+
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+    # Other tests
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+    def test_extra_field_names_is_optional(self):
+        Square = _make_tuple_bunch('Square', ['width', 'height'])
+        sq = Square(width=1, height=2)
+        assert_equal(sq.width, 1)
+        assert_equal(sq.height, 2)
+        s = repr(sq)
+        assert_equal(s, 'Square(width=1, height=2)')
+
+    def test_tuple_like(self):
+        Tup = _make_tuple_bunch('Tup', ['a', 'b'])
+        tu = Tup(a=1, b=2)
+        assert isinstance(tu, tuple)
+        assert isinstance(tu + (1,), tuple)
+
+    def test_explicit_module(self):
+        m = 'some.module.name'
+        Foo = _make_tuple_bunch('Foo', ['x'], ['a', 'b'], module=m)
+        foo = Foo(x=1, a=355, b=113)
+        assert_equal(Foo.__module__, m)
+        assert_equal(foo.__module__, m)
+
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+    # Argument validation
+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+    @pytest.mark.parametrize('args', [('123', ['a'], ['b']),
+                                      ('Foo', ['-3'], ['x']),
+                                      ('Foo', ['a'], ['+-*/'])])
+    def test_identifiers_not_allowed(self, args):
+        with pytest.raises(ValueError, match='identifiers'):
+            _make_tuple_bunch(*args)
+
+    @pytest.mark.parametrize('args', [('Foo', ['a', 'b', 'a'], ['x']),
+                                      ('Foo', ['a', 'b'], ['b', 'x'])])
+    def test_repeated_field_names(self, args):
+        with pytest.raises(ValueError, match='Duplicate'):
+            _make_tuple_bunch(*args)
+
+    @pytest.mark.parametrize('args', [('Foo', ['_a'], ['x']),
+                                      ('Foo', ['a'], ['_x'])])
+    def test_leading_underscore_not_allowed(self, args):
+        with pytest.raises(ValueError, match='underscore'):
+            _make_tuple_bunch(*args)
+
+    @pytest.mark.parametrize('args', [('Foo', ['def'], ['x']),
+                                      ('Foo', ['a'], ['or']),
+                                      ('and', ['a'], ['x'])])
+    def test_keyword_not_allowed_in_fields(self, args):
+        with pytest.raises(ValueError, match='keyword'):
+            _make_tuple_bunch(*args)
+
+    def test_at_least_one_field_name_required(self):
+        with pytest.raises(ValueError, match='at least one name'):
+            _make_tuple_bunch('Qwerty', [], ['a', 'b'])

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_ccallback.py

@@ -0,0 +1,204 @@
+from numpy.testing import assert_equal, assert_
+from pytest import raises as assert_raises
+
+import time
+import pytest
+import ctypes
+import threading
+from scipy._lib import _ccallback_c as _test_ccallback_cython
+from scipy._lib import _test_ccallback
+from scipy._lib._ccallback import LowLevelCallable
+
+try:
+    import cffi
+    HAVE_CFFI = True
+except ImportError:
+    HAVE_CFFI = False
+
+
+ERROR_VALUE = 2.0
+
+
+def callback_python(a, user_data=None):
+    if a == ERROR_VALUE:
+        raise ValueError("bad value")
+
+    if user_data is None:
+        return a + 1
+    else:
+        return a + user_data
+
+def _get_cffi_func(base, signature):
+    if not HAVE_CFFI:
+        pytest.skip("cffi not installed")
+
+    # Get function address
+    voidp = ctypes.cast(base, ctypes.c_void_p)
+    address = voidp.value
+
+    # Create corresponding cffi handle
+    ffi = cffi.FFI()
+    func = ffi.cast(signature, address)
+    return func
+
+
+def _get_ctypes_data():
+    value = ctypes.c_double(2.0)
+    return ctypes.cast(ctypes.pointer(value), ctypes.c_voidp)
+
+
+def _get_cffi_data():
+    if not HAVE_CFFI:
+        pytest.skip("cffi not installed")
+    ffi = cffi.FFI()
+    return ffi.new('double *', 2.0)
+
+
+CALLERS = {
+    'simple': _test_ccallback.test_call_simple,
+    'nodata': _test_ccallback.test_call_nodata,
+    'nonlocal': _test_ccallback.test_call_nonlocal,
+    'cython': _test_ccallback_cython.test_call_cython,
+}
+
+# These functions have signatures known to the callers
+FUNCS = {
+    'python': lambda: callback_python,
+    'capsule': lambda: _test_ccallback.test_get_plus1_capsule(),
+    'cython': lambda: LowLevelCallable.from_cython(_test_ccallback_cython,
+                                                   "plus1_cython"),
+    'ctypes': lambda: _test_ccallback_cython.plus1_ctypes,
+    'cffi': lambda: _get_cffi_func(_test_ccallback_cython.plus1_ctypes,
+                                   'double (*)(double, int *, void *)'),
+    'capsule_b': lambda: _test_ccallback.test_get_plus1b_capsule(),
+    'cython_b': lambda: LowLevelCallable.from_cython(_test_ccallback_cython,
+                                                     "plus1b_cython"),
+    'ctypes_b': lambda: _test_ccallback_cython.plus1b_ctypes,
+    'cffi_b': lambda: _get_cffi_func(_test_ccallback_cython.plus1b_ctypes,
+                                     'double (*)(double, double, int *, void *)'),
+}
+
+# These functions have signatures the callers don't know
+BAD_FUNCS = {
+    'capsule_bc': lambda: _test_ccallback.test_get_plus1bc_capsule(),
+    'cython_bc': lambda: LowLevelCallable.from_cython(_test_ccallback_cython,
+                                                      "plus1bc_cython"),
+    'ctypes_bc': lambda: _test_ccallback_cython.plus1bc_ctypes,
+    'cffi_bc': lambda: _get_cffi_func(
+        _test_ccallback_cython.plus1bc_ctypes,
+        'double (*)(double, double, double, int *, void *)'
+    ),
+}
+
+USER_DATAS = {
+    'ctypes': _get_ctypes_data,
+    'cffi': _get_cffi_data,
+    'capsule': _test_ccallback.test_get_data_capsule,
+}
+
+
+def test_callbacks():
+    def check(caller, func, user_data):
+        caller = CALLERS[caller]
+        func = FUNCS[func]()
+        user_data = USER_DATAS[user_data]()
+
+        if func is callback_python:
+            def func2(x):
+                return func(x, 2.0)
+        else:
+            func2 = LowLevelCallable(func, user_data)
+            func = LowLevelCallable(func)
+
+        # Test basic call
+        assert_equal(caller(func, 1.0), 2.0)
+
+        # Test 'bad' value resulting to an error
+        assert_raises(ValueError, caller, func, ERROR_VALUE)
+
+        # Test passing in user_data
+        assert_equal(caller(func2, 1.0), 3.0)
+
+    for caller in sorted(CALLERS.keys()):
+        for func in sorted(FUNCS.keys()):
+            for user_data in sorted(USER_DATAS.keys()):
+                check(caller, func, user_data)
+
+
+def test_bad_callbacks():
+    def check(caller, func, user_data):
+        caller = CALLERS[caller]
+        user_data = USER_DATAS[user_data]()
+        func = BAD_FUNCS[func]()
+
+        if func is callback_python:
+            def func2(x):
+                return func(x, 2.0)
+        else:
+            func2 = LowLevelCallable(func, user_data)
+            func = LowLevelCallable(func)
+
+        # Test that basic call fails
+        assert_raises(ValueError, caller, LowLevelCallable(func), 1.0)
+
+        # Test that passing in user_data also fails
+        assert_raises(ValueError, caller, func2, 1.0)
+
+        # Test error message
+        llfunc = LowLevelCallable(func)
+        try:
+            caller(llfunc, 1.0)
+        except ValueError as err:
+            msg = str(err)
+            assert_(llfunc.signature in msg, msg)
+            assert_('double (double, double, int *, void *)' in msg, msg)
+
+    for caller in sorted(CALLERS.keys()):
+        for func in sorted(BAD_FUNCS.keys()):
+            for user_data in sorted(USER_DATAS.keys()):
+                check(caller, func, user_data)
+
+
+def test_signature_override():
+    caller = _test_ccallback.test_call_simple
+    func = _test_ccallback.test_get_plus1_capsule()
+
+    llcallable = LowLevelCallable(func, signature="bad signature")
+    assert_equal(llcallable.signature, "bad signature")
+    assert_raises(ValueError, caller, llcallable, 3)
+
+    llcallable = LowLevelCallable(func, signature="double (double, int *, void *)")
+    assert_equal(llcallable.signature, "double (double, int *, void *)")
+    assert_equal(caller(llcallable, 3), 4)
+
+
+def test_threadsafety():
+    def callback(a, caller):
+        if a <= 0:
+            return 1
+        else:
+            res = caller(lambda x: callback(x, caller), a - 1)
+            return 2*res
+
+    def check(caller):
+        caller = CALLERS[caller]
+
+        results = []
+
+        count = 10
+
+        def run():
+            time.sleep(0.01)
+            r = caller(lambda x: callback(x, caller), count)
+            results.append(r)
+
+        threads = [threading.Thread(target=run) for j in range(20)]
+        for thread in threads:
+            thread.start()
+        for thread in threads:
+            thread.join()
+
+        assert_equal(results, [2.0**count]*len(threads))
+
+    for caller in CALLERS.keys():
+        check(caller)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_config.py

@@ -0,0 +1,45 @@
+"""
+Check the SciPy config is valid.
+"""
+import scipy
+import pytest
+from unittest.mock import patch
+
+pytestmark = pytest.mark.skipif(
+    not hasattr(scipy.__config__, "_built_with_meson"),
+    reason="Requires Meson builds",
+)
+
+
+class TestSciPyConfigs:
+    REQUIRED_CONFIG_KEYS = [
+        "Compilers",
+        "Machine Information",
+        "Python Information",
+    ]
+
+    @pytest.mark.thread_unsafe
+    @patch("scipy.__config__._check_pyyaml")
+    def test_pyyaml_not_found(self, mock_yaml_importer):
+        mock_yaml_importer.side_effect = ModuleNotFoundError()
+        with pytest.warns(UserWarning):
+            scipy.show_config()
+
+    def test_dict_mode(self):
+        config = scipy.show_config(mode="dicts")
+
+        assert isinstance(config, dict)
+        assert all([key in config for key in self.REQUIRED_CONFIG_KEYS]), (
+            "Required key missing,"
+            " see index of `False` with `REQUIRED_CONFIG_KEYS`"
+        )
+
+    def test_invalid_mode(self):
+        with pytest.raises(AttributeError):
+            scipy.show_config(mode="foo")
+
+    def test_warn_to_add_tests(self):
+        assert len(scipy.__config__.DisplayModes) == 2, (
+            "New mode detected,"
+            " please add UT if applicable and increment this count"
+        )

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_deprecation.py

@@ -0,0 +1,10 @@
+import pytest
+
+@pytest.mark.thread_unsafe
+def test_cython_api_deprecation():
+    match = ("`scipy._lib._test_deprecation_def.foo_deprecated` "
+             "is deprecated, use `foo` instead!\n"
+             "Deprecated in Scipy 42.0.0")
+    with pytest.warns(DeprecationWarning, match=match):
+        from .. import _test_deprecation_call
+    assert _test_deprecation_call.call() == (1, 1)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_doccer.py

@@ -0,0 +1,143 @@
+''' Some tests for the documenting decorator and support functions '''
+
+import sys
+import pytest
+from numpy.testing import assert_equal, suppress_warnings
+
+from scipy._lib import doccer
+
+# python -OO strips docstrings
+DOCSTRINGS_STRIPPED = sys.flags.optimize > 1
+
+docstring = \
+"""Docstring
+    %(strtest1)s
+        %(strtest2)s
+     %(strtest3)s
+"""
+param_doc1 = \
+"""Another test
+   with some indent"""
+
+param_doc2 = \
+"""Another test, one line"""
+
+param_doc3 = \
+"""    Another test
+       with some indent"""
+
+doc_dict = {'strtest1':param_doc1,
+            'strtest2':param_doc2,
+            'strtest3':param_doc3}
+
+filled_docstring = \
+"""Docstring
+    Another test
+       with some indent
+        Another test, one line
+     Another test
+       with some indent
+"""
+
+
+def test_unindent():
+    with suppress_warnings() as sup:
+        sup.filter(category=DeprecationWarning)
+        assert_equal(doccer.unindent_string(param_doc1), param_doc1)
+        assert_equal(doccer.unindent_string(param_doc2), param_doc2)
+        assert_equal(doccer.unindent_string(param_doc3), param_doc1)
+
+
+def test_unindent_dict():
+    with suppress_warnings() as sup:
+        sup.filter(category=DeprecationWarning)
+        d2 = doccer.unindent_dict(doc_dict)
+    assert_equal(d2['strtest1'], doc_dict['strtest1'])
+    assert_equal(d2['strtest2'], doc_dict['strtest2'])
+    assert_equal(d2['strtest3'], doc_dict['strtest1'])
+
+
+def test_docformat():
+    with suppress_warnings() as sup:
+        sup.filter(category=DeprecationWarning)
+        udd = doccer.unindent_dict(doc_dict)
+        formatted = doccer.docformat(docstring, udd)
+        assert_equal(formatted, filled_docstring)
+        single_doc = 'Single line doc %(strtest1)s'
+        formatted = doccer.docformat(single_doc, doc_dict)
+        # Note - initial indent of format string does not
+        # affect subsequent indent of inserted parameter
+        assert_equal(formatted, """Single line doc Another test
+   with some indent""")
+
+
+@pytest.mark.skipif(DOCSTRINGS_STRIPPED, reason="docstrings stripped")
+def test_decorator():
+    with suppress_warnings() as sup:
+        sup.filter(category=DeprecationWarning)
+        # with unindentation of parameters
+        decorator = doccer.filldoc(doc_dict, True)
+
+        @decorator
+        def func():
+            """ Docstring
+            %(strtest3)s
+            """
+
+        def expected():
+            """ Docstring
+            Another test
+               with some indent
+            """
+        assert_equal(func.__doc__, expected.__doc__)
+
+        # without unindentation of parameters
+
+        # The docstring should be unindented for Python 3.13+
+        # because of https://github.com/python/cpython/issues/81283
+        decorator = doccer.filldoc(doc_dict, False if \
+                                   sys.version_info < (3, 13) else True)
+
+        @decorator
+        def func():
+            """ Docstring
+            %(strtest3)s
+            """
+        def expected():
+            """ Docstring
+                Another test
+                   with some indent
+            """
+        assert_equal(func.__doc__, expected.__doc__)
+
+
+@pytest.mark.skipif(DOCSTRINGS_STRIPPED, reason="docstrings stripped")
+def test_inherit_docstring_from():
+
+    with suppress_warnings() as sup:
+        sup.filter(category=DeprecationWarning)
+
+        class Foo:
+            def func(self):
+                '''Do something useful.'''
+                return
+
+            def func2(self):
+                '''Something else.'''
+
+        class Bar(Foo):
+            @doccer.inherit_docstring_from(Foo)
+            def func(self):
+                '''%(super)sABC'''
+                return
+
+            @doccer.inherit_docstring_from(Foo)
+            def func2(self):
+                # No docstring.
+                return
+
+    assert_equal(Bar.func.__doc__, Foo.func.__doc__ + 'ABC')
+    assert_equal(Bar.func2.__doc__, Foo.func2.__doc__)
+    bar = Bar()
+    assert_equal(bar.func.__doc__, Foo.func.__doc__ + 'ABC')
+    assert_equal(bar.func2.__doc__, Foo.func2.__doc__)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_import_cycles.py

@@ -0,0 +1,18 @@
+import pytest
+import sys
+import subprocess
+
+from .test_public_api import PUBLIC_MODULES
+
+# Regression tests for gh-6793.
+# Check that all modules are importable in a new Python process.
+# This is not necessarily true if there are import cycles present.
+
+@pytest.mark.fail_slow(40)
+@pytest.mark.slow
+@pytest.mark.thread_unsafe
+def test_public_modules_importable():
+    pids = [subprocess.Popen([sys.executable, '-c', f'import {module}'])
+            for module in PUBLIC_MODULES]
+    for i, pid in enumerate(pids):
+        assert pid.wait() == 0, f'Failed to import {PUBLIC_MODULES[i]}'

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_public_api.py

@@ -0,0 +1,469 @@
+"""
+This test script is adopted from:
+    https://github.com/numpy/numpy/blob/main/numpy/tests/test_public_api.py
+"""
+
+import pkgutil
+import types
+import importlib
+import warnings
+from importlib import import_module
+
+import pytest
+
+import numpy as np
+import scipy
+
+from scipy.conftest import xp_available_backends
+
+
+def test_dir_testing():
+    """Assert that output of dir has only one "testing/tester"
+    attribute without duplicate"""
+    assert len(dir(scipy)) == len(set(dir(scipy)))
+
+
+# Historically SciPy has not used leading underscores for private submodules
+# much.  This has resulted in lots of things that look like public modules
+# (i.e. things that can be imported as `import scipy.somesubmodule.somefile`),
+# but were never intended to be public.  The PUBLIC_MODULES list contains
+# modules that are either public because they were meant to be, or because they
+# contain public functions/objects that aren't present in any other namespace
+# for whatever reason and therefore should be treated as public.
+PUBLIC_MODULES = ["scipy." + s for s in [
+    "cluster",
+    "cluster.vq",
+    "cluster.hierarchy",
+    "constants",
+    "datasets",
+    "differentiate",
+    "fft",
+    "fftpack",
+    "integrate",
+    "interpolate",
+    "io",
+    "io.arff",
+    "io.matlab",
+    "io.wavfile",
+    "linalg",
+    "linalg.blas",
+    "linalg.cython_blas",
+    "linalg.lapack",
+    "linalg.cython_lapack",
+    "linalg.interpolative",
+    "ndimage",
+    "odr",
+    "optimize",
+    "optimize.elementwise",
+    "signal",
+    "signal.windows",
+    "sparse",
+    "sparse.linalg",
+    "sparse.csgraph",
+    "spatial",
+    "spatial.distance",
+    "spatial.transform",
+    "special",
+    "stats",
+    "stats.contingency",
+    "stats.distributions",
+    "stats.mstats",
+    "stats.qmc",
+    "stats.sampling"
+]]
+
+# The PRIVATE_BUT_PRESENT_MODULES list contains modules that lacked underscores
+# in their name and hence looked public, but weren't meant to be. All these
+# namespace were deprecated in the 1.8.0 release - see "clear split between
+# public and private API" in the 1.8.0 release notes.
+# These private modules support will be removed in SciPy v2.0.0, as the
+# deprecation messages emitted by each of these modules say.
+PRIVATE_BUT_PRESENT_MODULES = [
+    'scipy.constants.codata',
+    'scipy.constants.constants',
+    'scipy.fftpack.basic',
+    'scipy.fftpack.convolve',
+    'scipy.fftpack.helper',
+    'scipy.fftpack.pseudo_diffs',
+    'scipy.fftpack.realtransforms',
+    'scipy.integrate.dop',
+    'scipy.integrate.lsoda',
+    'scipy.integrate.odepack',
+    'scipy.integrate.quadpack',
+    'scipy.integrate.vode',
+    'scipy.interpolate.dfitpack',
+    'scipy.interpolate.fitpack',
+    'scipy.interpolate.fitpack2',
+    'scipy.interpolate.interpnd',
+    'scipy.interpolate.interpolate',
+    'scipy.interpolate.ndgriddata',
+    'scipy.interpolate.polyint',
+    'scipy.interpolate.rbf',
+    'scipy.io.arff.arffread',
+    'scipy.io.harwell_boeing',
+    'scipy.io.idl',
+    'scipy.io.matlab.byteordercodes',
+    'scipy.io.matlab.mio',
+    'scipy.io.matlab.mio4',
+    'scipy.io.matlab.mio5',
+    'scipy.io.matlab.mio5_params',
+    'scipy.io.matlab.mio5_utils',
+    'scipy.io.matlab.mio_utils',
+    'scipy.io.matlab.miobase',
+    'scipy.io.matlab.streams',
+    'scipy.io.mmio',
+    'scipy.io.netcdf',
+    'scipy.linalg.basic',
+    'scipy.linalg.decomp',
+    'scipy.linalg.decomp_cholesky',
+    'scipy.linalg.decomp_lu',
+    'scipy.linalg.decomp_qr',
+    'scipy.linalg.decomp_schur',
+    'scipy.linalg.decomp_svd',
+    'scipy.linalg.matfuncs',
+    'scipy.linalg.misc',
+    'scipy.linalg.special_matrices',
+    'scipy.misc',
+    'scipy.misc.common',
+    'scipy.misc.doccer',
+    'scipy.ndimage.filters',
+    'scipy.ndimage.fourier',
+    'scipy.ndimage.interpolation',
+    'scipy.ndimage.measurements',
+    'scipy.ndimage.morphology',
+    'scipy.odr.models',
+    'scipy.odr.odrpack',
+    'scipy.optimize.cobyla',
+    'scipy.optimize.cython_optimize',
+    'scipy.optimize.lbfgsb',
+    'scipy.optimize.linesearch',
+    'scipy.optimize.minpack',
+    'scipy.optimize.minpack2',
+    'scipy.optimize.moduleTNC',
+    'scipy.optimize.nonlin',
+    'scipy.optimize.optimize',
+    'scipy.optimize.slsqp',
+    'scipy.optimize.tnc',
+    'scipy.optimize.zeros',
+    'scipy.signal.bsplines',
+    'scipy.signal.filter_design',
+    'scipy.signal.fir_filter_design',
+    'scipy.signal.lti_conversion',
+    'scipy.signal.ltisys',
+    'scipy.signal.signaltools',
+    'scipy.signal.spectral',
+    'scipy.signal.spline',
+    'scipy.signal.waveforms',
+    'scipy.signal.wavelets',
+    'scipy.signal.windows.windows',
+    'scipy.sparse.base',
+    'scipy.sparse.bsr',
+    'scipy.sparse.compressed',
+    'scipy.sparse.construct',
+    'scipy.sparse.coo',
+    'scipy.sparse.csc',
+    'scipy.sparse.csr',
+    'scipy.sparse.data',
+    'scipy.sparse.dia',
+    'scipy.sparse.dok',
+    'scipy.sparse.extract',
+    'scipy.sparse.lil',
+    'scipy.sparse.linalg.dsolve',
+    'scipy.sparse.linalg.eigen',
+    'scipy.sparse.linalg.interface',
+    'scipy.sparse.linalg.isolve',
+    'scipy.sparse.linalg.matfuncs',
+    'scipy.sparse.sparsetools',
+    'scipy.sparse.spfuncs',
+    'scipy.sparse.sputils',
+    'scipy.spatial.ckdtree',
+    'scipy.spatial.kdtree',
+    'scipy.spatial.qhull',
+    'scipy.spatial.transform.rotation',
+    'scipy.special.add_newdocs',
+    'scipy.special.basic',
+    'scipy.special.cython_special',
+    'scipy.special.orthogonal',
+    'scipy.special.sf_error',
+    'scipy.special.specfun',
+    'scipy.special.spfun_stats',
+    'scipy.stats.biasedurn',
+    'scipy.stats.kde',
+    'scipy.stats.morestats',
+    'scipy.stats.mstats_basic',
+    'scipy.stats.mstats_extras',
+    'scipy.stats.mvn',
+    'scipy.stats.stats',
+]
+
+
+def is_unexpected(name):
+    """Check if this needs to be considered."""
+    if '._' in name or '.tests' in name or '.setup' in name:
+        return False
+
+    if name in PUBLIC_MODULES:
+        return False
+
+    if name in PRIVATE_BUT_PRESENT_MODULES:
+        return False
+
+    return True
+
+
+SKIP_LIST = [
+    'scipy.conftest',
+    'scipy.version',
+    'scipy.special.libsf_error_state'
+]
+
+
+# XXX: this test does more than it says on the tin - in using `pkgutil.walk_packages`,
+# it will raise if it encounters any exceptions which are not handled by `ignore_errors`
+# while attempting to import each discovered package.
+# For now, `ignore_errors` only ignores what is necessary, but this could be expanded -
+# for example, to all errors from private modules or git subpackages - if desired.
+@pytest.mark.thread_unsafe
+def test_all_modules_are_expected():
+    """
+    Test that we don't add anything that looks like a new public module by
+    accident.  Check is based on filenames.
+    """
+
+    def ignore_errors(name):
+        # if versions of other array libraries are installed which are incompatible
+        # with the installed NumPy version, there can be errors on importing
+        # `array_api_compat`. This should only raise if SciPy is configured with
+        # that library as an available backend.
+        backends = {'cupy', 'torch', 'dask.array'}
+        for backend in backends:
+            path = f'array_api_compat.{backend}'
+            if path in name and backend not in xp_available_backends:
+                return
+        raise
+
+    modnames = []
+
+    with np.testing.suppress_warnings() as sup:
+        sup.filter(DeprecationWarning,"scipy.misc")
+        for _, modname, _ in pkgutil.walk_packages(path=scipy.__path__,
+                                                   prefix=scipy.__name__ + '.',
+                                                   onerror=ignore_errors):
+            if is_unexpected(modname) and modname not in SKIP_LIST:
+                # We have a name that is new.  If that's on purpose, add it to
+                # PUBLIC_MODULES.  We don't expect to have to add anything to
+                # PRIVATE_BUT_PRESENT_MODULES.  Use an underscore in the name!
+                modnames.append(modname)
+
+    if modnames:
+        raise AssertionError(f'Found unexpected modules: {modnames}')
+
+
+# Stuff that clearly shouldn't be in the API and is detected by the next test
+# below
+SKIP_LIST_2 = [
+    'scipy.char',
+    'scipy.rec',
+    'scipy.emath',
+    'scipy.math',
+    'scipy.random',
+    'scipy.ctypeslib',
+    'scipy.ma'
+]
+
+
+def test_all_modules_are_expected_2():
+    """
+    Method checking all objects. The pkgutil-based method in
+    `test_all_modules_are_expected` does not catch imports into a namespace,
+    only filenames.
+    """
+
+    def find_unexpected_members(mod_name):
+        members = []
+        module = importlib.import_module(mod_name)
+        if hasattr(module, '__all__'):
+            objnames = module.__all__
+        else:
+            objnames = dir(module)
+
+        for objname in objnames:
+            if not objname.startswith('_'):
+                fullobjname = mod_name + '.' + objname
+                if isinstance(getattr(module, objname), types.ModuleType):
+                    if is_unexpected(fullobjname) and fullobjname not in SKIP_LIST_2:
+                        members.append(fullobjname)
+
+        return members
+    with np.testing.suppress_warnings() as sup:
+        sup.filter(DeprecationWarning, "scipy.misc")
+        unexpected_members = find_unexpected_members("scipy")
+
+    for modname in PUBLIC_MODULES:
+        unexpected_members.extend(find_unexpected_members(modname))
+
+    if unexpected_members:
+        raise AssertionError("Found unexpected object(s) that look like "
+                             f"modules: {unexpected_members}")
+
+
+def test_api_importable():
+    """
+    Check that all submodules listed higher up in this file can be imported
+    Note that if a PRIVATE_BUT_PRESENT_MODULES entry goes missing, it may
+    simply need to be removed from the list (deprecation may or may not be
+    needed - apply common sense).
+    """
+    def check_importable(module_name):
+        try:
+            importlib.import_module(module_name)
+        except (ImportError, AttributeError):
+            return False
+
+        return True
+
+    module_names = []
+    for module_name in PUBLIC_MODULES:
+        if not check_importable(module_name):
+            module_names.append(module_name)
+
+    if module_names:
+        raise AssertionError("Modules in the public API that cannot be "
+                             f"imported: {module_names}")
+
+    with warnings.catch_warnings(record=True):
+        warnings.filterwarnings('always', category=DeprecationWarning)
+        warnings.filterwarnings('always', category=ImportWarning)
+        for module_name in PRIVATE_BUT_PRESENT_MODULES:
+            if not check_importable(module_name):
+                module_names.append(module_name)
+
+    if module_names:
+        raise AssertionError("Modules that are not really public but looked "
+                             "public and can not be imported: "
+                             f"{module_names}")
+
+
+@pytest.mark.thread_unsafe
+@pytest.mark.parametrize(("module_name", "correct_module"),
+                         [('scipy.constants.codata', None),
+                          ('scipy.constants.constants', None),
+                          ('scipy.fftpack.basic', None),
+                          ('scipy.fftpack.helper', None),
+                          ('scipy.fftpack.pseudo_diffs', None),
+                          ('scipy.fftpack.realtransforms', None),
+                          ('scipy.integrate.dop', None),
+                          ('scipy.integrate.lsoda', None),
+                          ('scipy.integrate.odepack', None),
+                          ('scipy.integrate.quadpack', None),
+                          ('scipy.integrate.vode', None),
+                          ('scipy.interpolate.fitpack', None),
+                          ('scipy.interpolate.fitpack2', None),
+                          ('scipy.interpolate.interpolate', None),
+                          ('scipy.interpolate.ndgriddata', None),
+                          ('scipy.interpolate.polyint', None),
+                          ('scipy.interpolate.rbf', None),
+                          ('scipy.io.harwell_boeing', None),
+                          ('scipy.io.idl', None),
+                          ('scipy.io.mmio', None),
+                          ('scipy.io.netcdf', None),
+                          ('scipy.io.arff.arffread', 'arff'),
+                          ('scipy.io.matlab.byteordercodes', 'matlab'),
+                          ('scipy.io.matlab.mio_utils', 'matlab'),
+                          ('scipy.io.matlab.mio', 'matlab'),
+                          ('scipy.io.matlab.mio4', 'matlab'),
+                          ('scipy.io.matlab.mio5_params', 'matlab'),
+                          ('scipy.io.matlab.mio5_utils', 'matlab'),
+                          ('scipy.io.matlab.mio5', 'matlab'),
+                          ('scipy.io.matlab.miobase', 'matlab'),
+                          ('scipy.io.matlab.streams', 'matlab'),
+                          ('scipy.linalg.basic', None),
+                          ('scipy.linalg.decomp', None),
+                          ('scipy.linalg.decomp_cholesky', None),
+                          ('scipy.linalg.decomp_lu', None),
+                          ('scipy.linalg.decomp_qr', None),
+                          ('scipy.linalg.decomp_schur', None),
+                          ('scipy.linalg.decomp_svd', None),
+                          ('scipy.linalg.matfuncs', None),
+                          ('scipy.linalg.misc', None),
+                          ('scipy.linalg.special_matrices', None),
+                          ('scipy.ndimage.filters', None),
+                          ('scipy.ndimage.fourier', None),
+                          ('scipy.ndimage.interpolation', None),
+                          ('scipy.ndimage.measurements', None),
+                          ('scipy.ndimage.morphology', None),
+                          ('scipy.odr.models', None),
+                          ('scipy.odr.odrpack', None),
+                          ('scipy.optimize.cobyla', None),
+                          ('scipy.optimize.lbfgsb', None),
+                          ('scipy.optimize.linesearch', None),
+                          ('scipy.optimize.minpack', None),
+                          ('scipy.optimize.minpack2', None),
+                          ('scipy.optimize.moduleTNC', None),
+                          ('scipy.optimize.nonlin', None),
+                          ('scipy.optimize.optimize', None),
+                          ('scipy.optimize.slsqp', None),
+                          ('scipy.optimize.tnc', None),
+                          ('scipy.optimize.zeros', None),
+                          ('scipy.signal.bsplines', None),
+                          ('scipy.signal.filter_design', None),
+                          ('scipy.signal.fir_filter_design', None),
+                          ('scipy.signal.lti_conversion', None),
+                          ('scipy.signal.ltisys', None),
+                          ('scipy.signal.signaltools', None),
+                          ('scipy.signal.spectral', None),
+                          ('scipy.signal.waveforms', None),
+                          ('scipy.signal.wavelets', None),
+                          ('scipy.signal.windows.windows', 'windows'),
+                          ('scipy.sparse.lil', None),
+                          ('scipy.sparse.linalg.dsolve', 'linalg'),
+                          ('scipy.sparse.linalg.eigen', 'linalg'),
+                          ('scipy.sparse.linalg.interface', 'linalg'),
+                          ('scipy.sparse.linalg.isolve', 'linalg'),
+                          ('scipy.sparse.linalg.matfuncs', 'linalg'),
+                          ('scipy.sparse.sparsetools', None),
+                          ('scipy.sparse.spfuncs', None),
+                          ('scipy.sparse.sputils', None),
+                          ('scipy.spatial.ckdtree', None),
+                          ('scipy.spatial.kdtree', None),
+                          ('scipy.spatial.qhull', None),
+                          ('scipy.spatial.transform.rotation', 'transform'),
+                          ('scipy.special.add_newdocs', None),
+                          ('scipy.special.basic', None),
+                          ('scipy.special.orthogonal', None),
+                          ('scipy.special.sf_error', None),
+                          ('scipy.special.specfun', None),
+                          ('scipy.special.spfun_stats', None),
+                          ('scipy.stats.biasedurn', None),
+                          ('scipy.stats.kde', None),
+                          ('scipy.stats.morestats', None),
+                          ('scipy.stats.mstats_basic', 'mstats'),
+                          ('scipy.stats.mstats_extras', 'mstats'),
+                          ('scipy.stats.mvn', None),
+                          ('scipy.stats.stats', None)])
+def test_private_but_present_deprecation(module_name, correct_module):
+    # gh-18279, gh-17572, gh-17771 noted that deprecation warnings
+    # for imports from private modules
+    # were misleading. Check that this is resolved.
+    module = import_module(module_name)
+    if correct_module is None:
+        import_name = f'scipy.{module_name.split(".")[1]}'
+    else:
+        import_name = f'scipy.{module_name.split(".")[1]}.{correct_module}'
+
+    correct_import = import_module(import_name)
+
+    # Attributes that were formerly in `module_name` can still be imported from
+    # `module_name`, albeit with a deprecation warning.
+    for attr_name in module.__all__:
+        # ensure attribute is present where the warning is pointing
+        assert getattr(correct_import, attr_name, None) is not None
+        message = f"Please import `{attr_name}` from the `{import_name}`..."
+        with pytest.deprecated_call(match=message):
+            getattr(module, attr_name)
+
+    # Attributes that were not in `module_name` get an error notifying the user
+    # that the attribute is not in `module_name` and that `module_name` is deprecated.
+    message = f"`{module_name}` is deprecated..."
+    with pytest.raises(AttributeError, match=message):
+        getattr(module, "ekki")

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_scipy_version.py

@@ -0,0 +1,28 @@
+import re
+
+import scipy
+import scipy.version
+
+
+def test_valid_scipy_version():
+    # Verify that the SciPy version is a valid one (no .post suffix or other
+    # nonsense). See NumPy issue gh-6431 for an issue caused by an invalid
+    # version.
+    version_pattern = r"^[0-9]+\.[0-9]+\.[0-9]+(|a[0-9]|b[0-9]|rc[0-9])"
+    dev_suffix = r"((.dev0)|(\.dev0+\+git[0-9]{8}.[0-9a-f]{7}))"
+    if scipy.version.release:
+        res = re.match(version_pattern, scipy.__version__)
+    else:
+        res = re.match(version_pattern + dev_suffix, scipy.__version__)
+
+    assert res is not None
+    assert scipy.__version__
+
+
+def test_version_submodule_members():
+    """`scipy.version` may not be quite public, but we install it.
+
+    So check that we don't silently change its contents.
+    """
+    for attr in ('version', 'full_version', 'short_version', 'git_revision', 'release'):
+        assert hasattr(scipy.version, attr)

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_tmpdirs.py

@@ -0,0 +1,48 @@
+""" Test tmpdirs module """
+from os import getcwd
+from os.path import realpath, abspath, dirname, isfile, join as pjoin, exists
+
+from scipy._lib._tmpdirs import tempdir, in_tempdir, in_dir
+
+from numpy.testing import assert_, assert_equal
+
+import pytest
+
+
+MY_PATH = abspath(__file__)
+MY_DIR = dirname(MY_PATH)
+
+
+@pytest.mark.thread_unsafe
+def test_tempdir():
+    with tempdir() as tmpdir:
+        fname = pjoin(tmpdir, 'example_file.txt')
+        with open(fname, "w") as fobj:
+            fobj.write('a string\\n')
+    assert_(not exists(tmpdir))
+
+
+@pytest.mark.thread_unsafe
+def test_in_tempdir():
+    my_cwd = getcwd()
+    with in_tempdir() as tmpdir:
+        with open('test.txt', "w") as f:
+            f.write('some text')
+        assert_(isfile('test.txt'))
+        assert_(isfile(pjoin(tmpdir, 'test.txt')))
+    assert_(not exists(tmpdir))
+    assert_equal(getcwd(), my_cwd)
+
+
+@pytest.mark.thread_unsafe
+def test_given_directory():
+    # Test InGivenDirectory
+    cwd = getcwd()
+    with in_dir() as tmpdir:
+        assert_equal(tmpdir, abspath(cwd))
+        assert_equal(tmpdir, abspath(getcwd()))
+    with in_dir(MY_DIR) as tmpdir:
+        assert_equal(tmpdir, MY_DIR)
+        assert_equal(realpath(MY_DIR), realpath(abspath(getcwd())))
+    # We were deleting the given directory! Check not so now.
+    assert_(isfile(MY_PATH))

mantis_evalkit/lib/python3.10/site-packages/scipy/_lib/tests/test_warnings.py

@@ -0,0 +1,137 @@
+"""
+Tests which scan for certain occurrences in the code, they may not find
+all of these occurrences but should catch almost all. This file was adapted
+from NumPy.
+"""
+
+
+import os
+from pathlib import Path
+import ast
+import tokenize
+
+import scipy
+
+import pytest
+
+
+class ParseCall(ast.NodeVisitor):
+    def __init__(self):
+        self.ls = []
+
+    def visit_Attribute(self, node):
+        ast.NodeVisitor.generic_visit(self, node)
+        self.ls.append(node.attr)
+
+    def visit_Name(self, node):
+        self.ls.append(node.id)
+
+
+class FindFuncs(ast.NodeVisitor):
+    def __init__(self, filename):
+        super().__init__()
+        self.__filename = filename
+        self.bad_filters = []
+        self.bad_stacklevels = []
+
+    def visit_Call(self, node):
+        p = ParseCall()
+        p.visit(node.func)
+        ast.NodeVisitor.generic_visit(self, node)
+
+        if p.ls[-1] == 'simplefilter' or p.ls[-1] == 'filterwarnings':
+            # get first argument of the `args` node of the filter call
+            match node.args[0]:
+                case ast.Constant() as c:
+                    argtext = c.value
+                case ast.JoinedStr() as js:
+                    # if we get an f-string, discard the templated pieces, which
+                    # are likely the type or specific message; we're interested
+                    # in the action, which is less likely to use a template
+                    argtext = "".join(
+                        x.value for x in js.values if isinstance(x, ast.Constant)
+                    )
+                case _:
+                    raise ValueError("unknown ast node type")
+            # check if filter is set to ignore
+            if argtext == "ignore":
+                self.bad_filters.append(
+                    f"{self.__filename}:{node.lineno}")
+
+        if p.ls[-1] == 'warn' and (
+                len(p.ls) == 1 or p.ls[-2] == 'warnings'):
+
+            if self.__filename == "_lib/tests/test_warnings.py":
+                # This file
+                return
+
+            # See if stacklevel exists:
+            if len(node.args) == 3:
+                return
+            args = {kw.arg for kw in node.keywords}
+            if "stacklevel" not in args:
+                self.bad_stacklevels.append(
+                    f"{self.__filename}:{node.lineno}")
+
+
+@pytest.fixture(scope="session")
+def warning_calls():
+    # combined "ignore" and stacklevel error
+    base = Path(scipy.__file__).parent
+
+    bad_filters = []
+    bad_stacklevels = []
+
+    for path in base.rglob("*.py"):
+        # use tokenize to auto-detect encoding on systems where no
+        # default encoding is defined (e.g., LANG='C')
+        with tokenize.open(str(path)) as file:
+            tree = ast.parse(file.read(), filename=str(path))
+            finder = FindFuncs(path.relative_to(base))
+            finder.visit(tree)
+            bad_filters.extend(finder.bad_filters)
+            bad_stacklevels.extend(finder.bad_stacklevels)
+
+    return bad_filters, bad_stacklevels
+
+
+@pytest.mark.fail_slow(40)
+@pytest.mark.slow
+def test_warning_calls_filters(warning_calls):
+    bad_filters, bad_stacklevels = warning_calls
+
+    # We try not to add filters in the code base, because those filters aren't
+    # thread-safe. We aim to only filter in tests with
+    # np.testing.suppress_warnings. However, in some cases it may prove
+    # necessary to filter out warnings, because we can't (easily) fix the root
+    # cause for them and we don't want users to see some warnings when they use
+    # SciPy correctly. So we list exceptions here.  Add new entries only if
+    # there's a good reason.
+    allowed_filters = (
+        os.path.join('datasets', '_fetchers.py'),
+        os.path.join('datasets', '__init__.py'),
+        os.path.join('optimize', '_optimize.py'),
+        os.path.join('optimize', '_constraints.py'),
+        os.path.join('optimize', '_nnls.py'),
+        os.path.join('signal', '_ltisys.py'),
+        os.path.join('sparse', '__init__.py'),  # np.matrix pending-deprecation
+        os.path.join('special', '_basic.py'),  # gh-21801
+        os.path.join('stats', '_discrete_distns.py'),  # gh-14901
+        os.path.join('stats', '_continuous_distns.py'),
+        os.path.join('stats', '_binned_statistic.py'),  # gh-19345
+        os.path.join('stats', '_stats_py.py'),  # gh-20743
+        os.path.join('stats', 'tests', 'test_axis_nan_policy.py'),  # gh-20694
+        os.path.join('_lib', '_util.py'),  # gh-19341
+        os.path.join('sparse', 'linalg', '_dsolve', 'linsolve.py'),  # gh-17924
+        "conftest.py",
+    )
+    bad_filters = [item for item in bad_filters if item.split(':')[0] not in
+                   allowed_filters]
+
+    if bad_filters:
+        raise AssertionError(
+            "warning ignore filter should not be used, instead, use\n"
+            "numpy.testing.suppress_warnings (in tests only);\n"
+            "found in:\n    {}".format(
+                "\n    ".join(bad_filters)))
+