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q9900
PENMANCodec.handle_triple
train
def handle_triple(self, lhs, relation, rhs): """ Process triples before they are added to the graph. Note that *lhs* and *rhs* are as they originally appeared, and may be inverted. Inversions are detected by is_relation_inverted() and de-inverted by invert_relation(). By default, this function: * removes initial colons on relations * de-inverts all inverted relations * sets empty relations to `None` * casts numeric string sources and targets to their numeric types (e.g. float, int) Args: lhs: the left hand side of an observed triple relation: the triple relation (possibly inverted) rhs: the right hand side of an observed triple Returns: The processed (source, relation, target) triple. By default, it is returned as a Triple object. """ relation = relation.replace(':', '', 1) # remove leading :
python
{ "resource": "" }
q9901
PENMANCodec._encode_penman
train
def _encode_penman(self, g, top=None): """ Walk graph g and find a spanning dag, then serialize the result. First, depth-first traversal of preferred orientations (whether true or inverted) to create graph p. If any triples remain, select the first remaining triple whose source in the dispreferred orientation exists in p, where 'first' is determined by the order of inserted nodes (i.e. a topological sort). Add this triple, then repeat the depth-first traversal of preferred orientations from its target. Repeat until no triples remain, or raise an error if there are no candidates in the dispreferred orientation (which likely means the graph is disconnected). """ if top is None: top = g.top remaining = set(g.triples()) variables = g.variables() store = defaultdict(lambda: ([], [])) # (preferred, dispreferred) for t in g.triples(): if t.inverted: store[t.target][0].append(t) store[t.source][1].append(Triple(*t, inverted=False)) else: store[t.source][0].append(t) store[t.target][1].append(Triple(*t, inverted=True)) p = defaultdict(list) topolist = [top] def _update(t): src, tgt = (t[2], t[0]) if t.inverted else (t[0], t[2]) p[src].append(t) remaining.remove(t) if tgt in variables and t.relation != self.TYPE_REL: topolist.append(tgt) return tgt return None def _explore_preferred(src): ts = store.get(src, ([], []))[0] for t in ts:
python
{ "resource": "" }
q9902
Graph.reentrancies
train
def reentrancies(self): """ Return a mapping of variables to their re-entrancy count. A re-entrancy is when more than one edge selects a node as its target. These graphs are rooted, so the top node always has an implicit entrancy. Only nodes with re-entrancies are reported, and the count is only for the entrant edges beyond the first. Also note that these counts are for the interpreted graph, not for the linearized form, so inverted edges are always re-entrant. """
python
{ "resource": "" }
q9903
check_1d
train
def check_1d(inp): """ Check input to be a vector. Converts lists to np.ndarray. Parameters ---------- inp : obj Input vector Returns ------- numpy.ndarray or None Input vector or None Examples -------- >>> check_1d([0, 1, 2, 3]) [0, 1, 2, 3]
python
{ "resource": "" }
q9904
check_2d
train
def check_2d(inp): """ Check input to be a matrix. Converts lists of lists to np.ndarray. Also allows the input to be a scipy sparse matrix. Parameters ---------- inp : obj Input matrix Returns ------- numpy.ndarray, scipy.sparse or None Input matrix or None
python
{ "resource": "" }
q9905
graph_to_laplacian
train
def graph_to_laplacian(G, normalized=True): """ Converts a graph from popular Python packages to Laplacian representation. Currently support NetworkX, graph_tool and igraph. Parameters ---------- G : obj Input graph normalized : bool Whether to use normalized Laplacian. Normalized and unnormalized Laplacians capture different properties of graphs, e.g. normalized Laplacian spectrum can determine whether a graph is bipartite, but not the number of its edges. We recommend using normalized Laplacian. Returns ------- scipy.sparse Laplacian matrix of the input graph Examples -------- >>> graph_to_laplacian(nx.complete_graph(3), 'unnormalized').todense() [[ 2, -1, -1], [-1, 2, -1], [-1, -1, 2]] >>> graph_to_laplacian('test') None """ try: import networkx as nx if isinstance(G, nx.Graph): if normalized: return nx.normalized_laplacian_matrix(G) else: return nx.laplacian_matrix(G) except ImportError:
python
{ "resource": "" }
q9906
netlsd
train
def netlsd(inp, timescales=np.logspace(-2, 2, 250), kernel='heat', eigenvalues='auto', normalization='empty', normalized_laplacian=True): """ Computes NetLSD signature from some given input, timescales, and normalization. Accepts matrices, common Python graph libraries' graphs, or vectors of eigenvalues. For precise definition, please refer to "NetLSD: Hearing the Shape of a Graph" by A. Tsitsulin, D. Mottin, P. Karras, A. Bronstein, E. Müller. Published at KDD'18. Parameters ---------- inp: obj 2D numpy/scipy matrix, common Python graph libraries' graph, or vector of eigenvalues timescales : numpy.ndarray Vector of discrete timesteps for the kernel computation kernel : str Either 'heat' or 'wave'. Type of a kernel to use for computation. eigenvalues : str Either string or int or tuple Number of eigenvalues to compute / use for approximation. If string, we expect either 'full' or 'auto', otherwise error will be raised. 'auto' lets the program decide based on the faithful usage. 'full' computes all eigenvalues. If int, compute n_eivals eigenvalues from each side and approximate using linear growth approximation. If tuple, we expect two ints, first for lower part of approximation, and second for the upper part. normalization : str or numpy.ndarray Either 'empty', 'complete' or None. If None or any ther value, return unnormalized heat kernel trace. For the details how 'empty' and 'complete' are computed, please refer to the paper. If np.ndarray, they are treated as exact normalization constants normalized_laplacian: bool Defines whether the eigenvalues came from the normalized Laplacian. It only affects 'complete' normalization. Returns ------- numpy.ndarray NetLSD signature """ if kernel not in {'heat', 'wave'}: raise AttributeError('Unirecognized kernel type: expected one of [\'heat\', \'wave\'], got {0}'.format(kernel)) if not isinstance(normalized_laplacian, bool): raise AttributeError('Unknown Laplacian type: expected bool, got {0}'.format(normalized_laplacian)) if not isinstance(eigenvalues, (int, tuple, str)): raise AttributeError('Unirecognized requested eigenvalue number: expected type of [\'str\', \'tuple\', or \'int\'], got {0}'.format(type(eigenvalues))) if not
python
{ "resource": "" }
q9907
heat
train
def heat(inp, timescales=np.logspace(-2, 2, 250), eigenvalues='auto', normalization='empty', normalized_laplacian=True): """ Computes heat kernel trace from some given input, timescales, and normalization. Accepts matrices, common Python graph libraries' graphs, or vectors of eigenvalues. For precise definition, please refer to "NetLSD: Hearing the Shape of a Graph" by A. Tsitsulin, D. Mottin, P. Karras, A. Bronstein, E. Müller. Published at KDD'18. Parameters ---------- inp: obj 2D numpy/scipy matrix, common Python graph libraries' graph, or vector of eigenvalues timescales : numpy.ndarray Vector of discrete timesteps for the kernel computation eigenvalues : str Either string or int or tuple
python
{ "resource": "" }
q9908
wave
train
def wave(inp, timescales=np.linspace(0, 2*np.pi, 250), eigenvalues='auto', normalization='empty', normalized_laplacian=True): """ Computes wave kernel trace from some given input, timescales, and normalization. Accepts matrices, common Python graph libraries' graphs, or vectors of eigenvalues. For precise definition, please refer to "NetLSD: Hearing the Shape of a Graph" by A. Tsitsulin, D. Mottin, P. Karras, A. Bronstein, E. Müller. Published at KDD'18. Parameters ---------- inp: obj 2D numpy/scipy matrix, common Python graph libraries' graph, or vector of eigenvalues timescales : numpy.ndarray Vector of discrete timesteps for the kernel computation eigenvalues : str Either string or int or tuple
python
{ "resource": "" }
q9909
_hkt
train
def _hkt(eivals, timescales, normalization, normalized_laplacian): """ Computes heat kernel trace from given eigenvalues, timescales, and normalization. For precise definition, please refer to "NetLSD: Hearing the Shape of a Graph" by A. Tsitsulin, D. Mottin, P. Karras, A. Bronstein, E. Müller. Published at KDD'18. Parameters ---------- eivals : numpy.ndarray Eigenvalue vector timescales : numpy.ndarray Vector of discrete timesteps for the kernel computation normalization : str or numpy.ndarray Either 'empty', 'complete' or None. If None or any ther value, return unnormalized heat kernel trace. For the details how 'empty' and 'complete' are computed, please refer to the paper. If np.ndarray, they are treated as exact normalization constants normalized_laplacian: bool Defines whether the eigenvalues came from the normalized Laplacian. It only affects 'complete' normalization.
python
{ "resource": "" }
q9910
_wkt
train
def _wkt(eivals, timescales, normalization, normalized_laplacian): """ Computes wave kernel trace from given eigenvalues, timescales, and normalization. For precise definition, please refer to "NetLSD: Hearing the Shape of a Graph" by A. Tsitsulin, D. Mottin, P. Karras, A. Bronstein, E. Müller. Published at KDD'18. Parameters ---------- eivals : numpy.ndarray Eigenvalue vector timescales : numpy.ndarray Vector of discrete timesteps for the kernel computation normalization : str or numpy.ndarray Either 'empty', 'complete' or None. If None or any ther value, return unnormalized wave kernel trace. For the details how 'empty' and 'complete' are computed, please refer to the paper. If np.ndarray, they are treated as exact normalization constants normalized_laplacian: bool Defines whether the eigenvalues came from the normalized Laplacian. It only affects 'complete' normalization.
python
{ "resource": "" }
q9911
SortedListWithKey.clear
train
def clear(self): """Remove all the elements from the list.""" self._len = 0 del self._maxes[:]
python
{ "resource": "" }
q9912
SortedListWithKey.islice
train
def islice(self, start=None, stop=None, reverse=False): """ Returns an iterator that slices `self` from `start` to `stop` index, inclusive and exclusive respectively. When `reverse` is `True`, values are yielded from the iterator in reverse order. Both `start` and `stop` default to `None` which is automatically inclusive of the beginning and end. """ _len = self._len if not _len: return iter(()) start, stop, step = self._slice(slice(start, stop))
python
{ "resource": "" }
q9913
SortedListWithKey.copy
train
def copy(self): """Return a shallow copy of the sorted list."""
python
{ "resource": "" }
q9914
not26
train
def not26(func): """Function decorator for methods not implemented in Python 2.6.""" @wraps(func) def errfunc(*args, **kwargs): raise NotImplementedError
python
{ "resource": "" }
q9915
SortedDict.copy
train
def copy(self): """Return a shallow copy of the sorted dictionary."""
python
{ "resource": "" }
q9916
SummaryTracker.create_summary
train
def create_summary(self): """Return a summary. See also the notes on ignore_self in the class as well as the initializer documentation. """ if not self.ignore_self: res = summary.summarize(muppy.get_objects()) else: # If the user requested the data required to store summaries to be # ignored in the summaries, we need to identify all objects which # are related to each summary stored. # Thus we build a list of all objects used for summary storage as # well as a dictionary which tells us how often an object is # referenced by the summaries. # During this identification process, more objects are referenced, # namely int objects identifying referenced objects as well as the # correspondind count. # For all these objects it will be checked wether they are # referenced from outside the monitor's scope.
python
{ "resource": "" }
q9917
SummaryTracker.diff
train
def diff(self, summary1=None, summary2=None): """Compute diff between to summaries. If no summary is provided, the diff from the last to the current summary is used. If summary1 is provided the diff from summary1 to the current summary is used. If summary1 and summary2 are provided, the diff between these two is used. """ res = None if summary2 is None: self.s1 = self.create_summary() if summary1 is None:
python
{ "resource": "" }
q9918
SummaryTracker.print_diff
train
def print_diff(self, summary1=None, summary2=None): """Compute diff between to summaries and print it. If no summary is provided, the diff from the last to the current summary is used. If summary1 is provided the diff from summary1 to the current summary is used. If summary1 and summary2
python
{ "resource": "" }
q9919
ObjectTracker._get_objects
train
def _get_objects(self, ignore=[]): """Get all currently existing objects. XXX - ToDo: This method is a copy&paste from muppy.get_objects, but some modifications are applied. Specifically, it allows to ignore objects (which includes the current frame). keyword arguments ignore -- list of objects to ignore """ def remove_ignore(objects, ignore=[]): # remove all objects listed in the ignore list res = [] for o in objects: if not compat.object_in_list(o, ignore): res.append(o) return res tmp = gc.get_objects() ignore.append(inspect.currentframe()) #PYCHOK change ignore ignore.append(self) #PYCHOK change ignore if hasattr(self, 'o0'): ignore.append(self.o0) #PYCHOK change ignore if hasattr(self, 'o1'): ignore.append(self.o1) #PYCHOK change ignore ignore.append(ignore) #PYCHOK change ignore ignore.append(remove_ignore) #PYCHOK change ignore # this implies that referenced objects are also ignored tmp = remove_ignore(tmp, ignore) res = [] for o in tmp: # gc.get_objects returns only container objects, but we also want # the objects
python
{ "resource": "" }
q9920
ObjectTracker.get_diff
train
def get_diff(self, ignore=[]): """Get the diff to the last time the state of objects was measured. keyword arguments ignore -- list of objects to ignore """ # ignore this and the caller frame ignore.append(inspect.currentframe()) #PYCHOK change ignore self.o1 = self._get_objects(ignore) diff
python
{ "resource": "" }
q9921
ObjectTracker.print_diff
train
def print_diff(self, ignore=[]): """Print the diff to the last time the state of objects was measured. keyword arguments ignore -- list of objects to ignore """ # ignore this and the caller frame ignore.append(inspect.currentframe()) #PYCHOK change ignore diff = self.get_diff(ignore) print("Added objects:")
python
{ "resource": "" }
q9922
jaccard
train
def jaccard(seq1, seq2): """Compute the Jaccard distance between the two sequences `seq1` and `seq2`. They should contain hashable items. The return value is a float between 0 and 1, where 0 means equal,
python
{ "resource": "" }
q9923
sorensen
train
def sorensen(seq1, seq2): """Compute the Sorensen distance between the two sequences `seq1` and `seq2`. They should contain hashable items. The return value is a float between 0 and 1, where 0 means equal, and
python
{ "resource": "" }
q9924
_long2bytes
train
def _long2bytes(n, blocksize=0): """Convert a long integer to a byte string. If optional blocksize is given and greater than zero, pad the front of the byte string with binary zeros so that the length is a multiple of blocksize. """ # After much testing, this algorithm was deemed to be the fastest. s = '' pack = struct.pack while n > 0: ### CHANGED FROM '>I' TO '<I'. (DCG) s = pack('<I', n & 0xffffffffL) + s ### -------------------------- n = n >> 32 # Strip off leading zeros. for i in range(len(s)): if s[i]
python
{ "resource": "" }
q9925
MD5.init
train
def init(self): "Initialize the message-digest and set all fields to zero." self.length = 0L self.input = [] # Load magic initialization constants.
python
{ "resource": "" }
q9926
MeliaeAdapter.value
train
def value( self, node, parent=None ): """Return value used to compare size of this node""" # this is the *weighted* size/contribution of the node try: return node['contribution'] except KeyError, err:
python
{ "resource": "" }
q9927
MeliaeAdapter.label
train
def label( self, node ): """Return textual description of this node""" result = [] if node.get('type'): result.append( node['type'] ) if node.get('name' ): result.append( node['name'] ) elif node.get('value') is not None: result.append( unicode(node['value'])[:32]) if 'module' in node and not node['module'] in result: result.append( ' in %s'%( node['module'] )) if node.get( 'size' ): result.append( '%s'%( mb( node['size'] ))) if
python
{ "resource": "" }
q9928
MeliaeAdapter.best_parent
train
def best_parent( self, node, tree_type=None ): """Choose the best parent for a given node""" parents = self.parents(node) selected_parent = None if node['type'] == 'type': module = ".".join( node['name'].split( '.' )[:-1] ) if module: for mod in parents: if mod['type'] == 'module' and mod['name'] == module:
python
{ "resource": "" }
q9929
Stats.load_stats
train
def load_stats(self, fdump): """ Load the data from a dump file. The argument `fdump` can be either a filename or an open file object that requires read access. """ if isinstance(fdump, type('')):
python
{ "resource": "" }
q9930
Stats.annotate_snapshot
train
def annotate_snapshot(self, snapshot): """ Store additional statistical data in snapshot. """ if hasattr(snapshot, 'classes'): return snapshot.classes = {} for classname in list(self.index.keys()): total = 0 active = 0 merged = Asized(0, 0) for tobj in self.index[classname]: _merge_objects(snapshot.timestamp, merged, tobj) total += tobj.get_size_at_time(snapshot.timestamp) if tobj.birth < snapshot.timestamp and \ (tobj.death is None or tobj.death > snapshot.timestamp): active += 1 try: pct = total * 100.0 / snapshot.total except ZeroDivisionError: # pragma: no cover pct = 0
python
{ "resource": "" }
q9931
ConsoleStats.print_object
train
def print_object(self, tobj): """ Print the gathered information of object `tobj` in human-readable format. """ if tobj.death: self.stream.write('%-32s ( free ) %-35s\n' % ( trunc(tobj.name, 32, left=1), trunc(tobj.repr, 35))) else: self.stream.write('%-32s 0x%08x %-35s\n' % ( trunc(tobj.name, 32, left=1), tobj.id, trunc(tobj.repr, 35) )) if tobj.trace:
python
{ "resource": "" }
q9932
ConsoleStats.print_stats
train
def print_stats(self, clsname=None, limit=1.0): """ Write tracked objects to stdout. The output can be filtered and pruned. Only objects are printed whose classname contain the substring supplied by the `clsname` argument. The output can be pruned by passing a `limit` value. :param clsname: Only print objects whose classname contain the given substring. :param limit: If `limit` is a float smaller than one, only the supplied percentage of the total tracked data is printed. If `limit` is bigger than one, this number of tracked objects are printed. Tracked objects are first filtered, and then pruned (if specified).
python
{ "resource": "" }
q9933
ConsoleStats.print_summary
train
def print_summary(self): """ Print per-class summary for each snapshot. """ # Emit class summaries for each snapshot classlist = self.tracked_classes fobj = self.stream fobj.write('---- SUMMARY '+'-'*66+'\n') for snapshot in self.snapshots: self.annotate_snapshot(snapshot) fobj.write('%-35s %11s %12s %12s %5s\n' % (
python
{ "resource": "" }
q9934
HtmlStats.print_class_details
train
def print_class_details(self, fname, classname): """ Print detailed statistics and instances for the class `classname`. All data will be written to the file `fname`. """ fobj = open(fname, "w") fobj.write(self.header % (classname, self.style)) fobj.write("<h1>%s</h1>\n" % (classname)) sizes = [tobj.get_max_size() for tobj in self.index[classname]] total = 0 for s in sizes: total += s data = {'cnt': len(self.index[classname]), 'cls': classname} data['avg'] = pp(total / len(sizes)) data['max'] = pp(max(sizes)) data['min'] = pp(min(sizes)) fobj.write(self.class_summary % data) fobj.write(self.charts[classname]) fobj.write("<h2>Coalesced Referents per Snapshot</h2>\n") for snapshot in self.snapshots: if classname in snapshot.classes: merged = snapshot.classes[classname]['merged'] fobj.write(self.class_snapshot % { 'name': snapshot.desc, 'cls':classname, 'total': pp(merged.size) }) if merged.refs: self._print_refs(fobj, merged.refs, merged.size) else: fobj.write('<p>No per-referent sizes recorded.</p>\n') fobj.write("<h2>Instances</h2>\n") for tobj
python
{ "resource": "" }
q9935
HtmlStats.relative_path
train
def relative_path(self, filepath, basepath=None): """ Convert the filepath path to a relative path against basepath. By default basepath is self.basedir. """ if basepath is None: basepath = self.basedir if
python
{ "resource": "" }
q9936
HtmlStats.create_title_page
train
def create_title_page(self, filename, title=''): """ Output the title page. """ fobj = open(filename, "w") fobj.write(self.header % (title, self.style)) fobj.write("<h1>%s</h1>\n" % title) fobj.write("<h2>Memory distribution over time</h2>\n") fobj.write(self.charts['snapshots']) fobj.write("<h2>Snapshots statistics</h2>\n") fobj.write('<table id="nb">\n') classlist = list(self.index.keys()) classlist.sort() for snapshot in self.snapshots: fobj.write('<tr><td>\n') fobj.write('<table id="tl" rules="rows">\n') fobj.write("<h3>%s snapshot at %s</h3>\n" % ( snapshot.desc or 'Untitled', pp_timestamp(snapshot.timestamp) )) data = {} data['sys'] = pp(snapshot.system_total.vsz) data['tracked'] = pp(snapshot.tracked_total) data['asizeof'] = pp(snapshot.asizeof_total) data['overhead'] = pp(getattr(snapshot, 'overhead', 0)) fobj.write(self.snapshot_summary % data) if snapshot.tracked_total:
python
{ "resource": "" }
q9937
HtmlStats.create_lifetime_chart
train
def create_lifetime_chart(self, classname, filename=''): """ Create chart that depicts the lifetime of the instance registered with `classname`. The output is written to `filename`. """ try: from pylab import figure, title, xlabel, ylabel, plot, savefig except ImportError: return HtmlStats.nopylab_msg % (classname+" lifetime") cnt = []
python
{ "resource": "" }
q9938
HtmlStats.create_snapshot_chart
train
def create_snapshot_chart(self, filename=''): """ Create chart that depicts the memory allocation over time apportioned to the tracked classes. """ try: from pylab import figure, title, xlabel, ylabel, plot, fill, legend, savefig import matplotlib.mlab as mlab except ImportError: return self.nopylab_msg % ("memory allocation") classlist = self.tracked_classes times = [snapshot.timestamp for snapshot in self.snapshots] base = [0] * len(self.snapshots) poly_labels = [] polys = [] for cn in classlist: pct = [snapshot.classes[cn]['pct'] for snapshot in self.snapshots] if max(pct) > 3.0: sz = [float(fp.classes[cn]['sum'])/(1024*1024) for fp in self.snapshots] sz = [sx+sy for sx, sy in zip(base, sz)] xp, yp = mlab.poly_between(times, base, sz) polys.append( ((xp, yp), {'label': cn}) ) poly_labels.append(cn) base
python
{ "resource": "" }
q9939
HtmlStats.create_pie_chart
train
def create_pie_chart(self, snapshot, filename=''): """ Create a pie chart that depicts the distribution of the allocated memory for a given `snapshot`. The chart is saved to `filename`. """ try: from pylab import figure, title, pie, axes, savefig from pylab import sum as pylab_sum except ImportError: return self.nopylab_msg % ("pie_chart") # Don't bother illustrating a pie without pieces. if not snapshot.tracked_total: return '' classlist = [] sizelist = [] for k, v in list(snapshot.classes.items()):
python
{ "resource": "" }
q9940
HtmlStats.create_html
train
def create_html(self, fname, title="ClassTracker Statistics"): """ Create HTML page `fname` and additional files in a directory derived from `fname`. """ # Create a folder to store the charts and additional HTML files. self.basedir = os.path.dirname(os.path.abspath(fname)) self.filesdir = os.path.splitext(fname)[0] + '_files' if not os.path.isdir(self.filesdir): os.mkdir(self.filesdir) self.filesdir = os.path.abspath(self.filesdir) self.links = {} # Annotate all snapshots in advance self.annotate() # Create charts. The tags to show the images are returned and stored in # the self.charts dictionary. This allows to return alternative text if # the chart creation framework is not available. self.charts = {} fn = os.path.join(self.filesdir, 'timespace.png') self.charts['snapshots'] = self.create_snapshot_chart(fn)
python
{ "resource": "" }
q9941
Path.write_bytes
train
def write_bytes(self, data): """ Open the file in bytes mode, write to it, and close the file. """ if not isinstance(data, six.binary_type): raise TypeError( 'data must be %s, not %s'
python
{ "resource": "" }
q9942
Path.write_text
train
def write_text(self, data, encoding=None, errors=None): """ Open the file in text mode, write to it, and close the file. """ if not isinstance(data, six.text_type): raise TypeError( 'data must be %s, not
python
{ "resource": "" }
q9943
sort_group
train
def sort_group(d, return_only_first=False): ''' Sort a dictionary of relative paths and cluster equal paths together at the same time ''' # First, sort the paths in order (this must be a couple: (parent_dir, filename), so that there's no ambiguity because else a file at root will be considered as being after a folder/file since the ordering is done alphabetically without any notion of tree structure). d_sort = sort_dict_of_paths(d) # Pop the first item in the ordered list base_elt = (-1, None) while (base_elt[1] is None and d_sort): base_elt = d_sort.pop(0) # No element, then we just return if base_elt[1] is None: return None # Else, we will now group equivalent files together (remember we are working on multiple directories, so we can have multiple equivalent relative filepaths, but of course the absolute filepaths are different). else: # Init by creating the first group and pushing the first ordered filepath into the first group lst = [] lst.append([base_elt]) if d_sort: # For each subsequent filepath for elt in d_sort: # If the filepath is not empty (generator died)
python
{ "resource": "" }
q9944
RefBrowser.get_tree
train
def get_tree(self): """Get a tree of referrers of the root object.""" self.ignore.append(inspect.currentframe())
python
{ "resource": "" }
q9945
RefBrowser._get_tree
train
def _get_tree(self, root, maxdepth): """Workhorse of the get_tree implementation. This is an recursive method which is why we have a wrapper method. root is the current root object of the tree which should be returned. Note that root is not of the type _Node. maxdepth defines how much further down the from the root the tree should be build. """ self.ignore.append(inspect.currentframe()) res = _Node(root, self.str_func) #PYCHOK use root parameter self.already_included.add(id(root)) #PYCHOK use root parameter if maxdepth == 0: return res objects = gc.get_referrers(root) #PYCHOK use root parameter self.ignore.append(objects) for o in objects: # XXX: find a better way to ignore dict of _Node objects if isinstance(o, dict): sampleNode = _Node(1) if list(sampleNode.__dict__.keys()) == list(o.keys()):
python
{ "resource": "" }
q9946
StreamBrowser.print_tree
train
def print_tree(self, tree=None): """ Print referrers tree to console. keyword arguments tree -- if not None, the passed tree will be printed. Otherwise it is based on the rootobject. """
python
{ "resource": "" }
q9947
StreamBrowser._print
train
def _print(self, tree, prefix, carryon): """Compute and print a new line of the tree. This is a recursive function. arguments tree -- tree to print prefix -- prefix to the current line to print carryon -- prefix which is used to carry on the vertical lines """ level = prefix.count(self.cross) + prefix.count(self.vline) len_children = 0 if isinstance(tree , _Node): len_children = len(tree.children) # add vertex prefix += str(tree) # and as many spaces as the vertex is long carryon += self.space * len(str(tree)) if (level == self.maxdepth) or (not isinstance(tree, _Node)) or\ (len_children == 0): self.stream.write(prefix+'\n') return else: # add
python
{ "resource": "" }
q9948
InteractiveBrowser.main
train
def main(self, standalone=False): """Create interactive browser window. keyword arguments standalone -- Set to true, if the browser is not attached to other windows """ window = _Tkinter.Tk()
python
{ "resource": "" }
q9949
format_meter
train
def format_meter(n, total, elapsed, ncols=None, prefix='', unit=None, unit_scale=False, ascii=False): """ Return a string-based progress bar given some parameters Parameters ---------- n : int Number of finished iterations. total : int The expected total number of iterations. If None, only basic progress statistics are displayed (no ETA). elapsed : float Number of seconds passed since start. ncols : int, optional The width of the entire output message. If sepcified, dynamically resizes the progress meter [default: None]. The fallback meter width is 10. prefix : str, optional Prefix message (included in total width). unit : str, optional String that will be used to define the unit of each iteration. [default: "it"] unit_scale : bool, optional If set, the number of iterations will be reduced/scaled automatically and a metric prefix following the International System of Units standard will be added (kilo, mega, etc.). [default: False] ascii : bool, optional If not set, use unicode (smooth blocks) to fill the meter [default: False]. The fallback is to use ASCII characters (1-9 #). Returns ------- out : Formatted meter and stats, ready to display. """ # in case the total is wrong (n is above the total), then # we switch to the mode without showing the total prediction # (since ETA would be wrong anyway) if total and n > total: total = None elapsed_str = format_interval(elapsed) if elapsed: if unit_scale: rate = format_sizeof(n / elapsed, suffix='') else: rate = '{0:5.2f}'.format(n / elapsed) else: rate = '?' rate_unit = unit if unit else 'it' if not unit: unit = '' n_fmt = str(n) total_fmt = str(total) if unit_scale: n_fmt = format_sizeof(n, suffix='') if total: total_fmt = format_sizeof(total, suffix='') if total: frac = n / total percentage = frac * 100 remaining_str = format_interval(elapsed * (total-n) / n) if n else '?' l_bar = '{1}{0:.0f}%|'.format(percentage, prefix) if prefix else \
python
{ "resource": "" }
q9950
getIcon
train
def getIcon( data ): """Return the data from the resource as a wxIcon""" import cStringIO stream =
python
{ "resource": "" }
q9951
main
train
def main(): """Mainloop for the application""" logging.basicConfig(level=logging.INFO)
python
{ "resource": "" }
q9952
MainFrame.CreateMenuBar
train
def CreateMenuBar(self): """Create our menu-bar for triggering operations""" menubar = wx.MenuBar() menu = wx.Menu() menu.Append(ID_OPEN, _('&Open Profile'), _('Open a cProfile file')) menu.Append(ID_OPEN_MEMORY, _('Open &Memory'), _('Open a Meliae memory-dump file')) menu.AppendSeparator() menu.Append(ID_EXIT, _('&Close'), _('Close this RunSnakeRun window')) menubar.Append(menu, _('&File')) menu = wx.Menu() # self.packageMenuItem = menu.AppendCheckItem( # ID_PACKAGE_VIEW, _('&File View'), # _('View time spent by package/module') # ) self.percentageMenuItem = menu.AppendCheckItem( ID_PERCENTAGE_VIEW, _('&Percentage View'), _('View time spent as percent of overall time') ) self.rootViewItem = menu.Append( ID_ROOT_VIEW, _('&Root View (Home)'), _('View the root of the tree') ) self.backViewItem = menu.Append( ID_BACK_VIEW, _('&Back'), _('Go back in your viewing history') ) self.upViewItem = menu.Append( ID_UP_VIEW, _('&Up'), _('Go "up" to the parent of this node with the largest cumulative total') ) self.moreSquareViewItem = menu.AppendCheckItem( ID_MORE_SQUARE, _('&Hierarchic Squares'), _('Toggle hierarchic squares in the square-map view') ) # This stuff isn't really all that useful for profiling,
python
{ "resource": "" }
q9953
MainFrame.CreateSourceWindow
train
def CreateSourceWindow(self, tabs): """Create our source-view window for tabs""" if editor and self.sourceCodeControl is None: self.sourceCodeControl = wx.py.editwindow.EditWindow( self.tabs, -1 )
python
{ "resource": "" }
q9954
MainFrame.SetupToolBar
train
def SetupToolBar(self): """Create the toolbar for common actions""" tb = self.CreateToolBar(self.TBFLAGS) tsize = (24, 24) tb.ToolBitmapSize = tsize open_bmp = wx.ArtProvider.GetBitmap(wx.ART_FILE_OPEN, wx.ART_TOOLBAR, tsize) tb.AddLabelTool(ID_OPEN, "Open", open_bmp, shortHelp="Open", longHelp="Open a (c)Profile trace file") if not osx: tb.AddSeparator() # self.Bind(wx.EVT_TOOL, self.OnOpenFile, id=ID_OPEN) self.rootViewTool = tb.AddLabelTool( ID_ROOT_VIEW, _("Root View"), wx.ArtProvider.GetBitmap(wx.ART_GO_HOME, wx.ART_TOOLBAR, tsize), shortHelp=_("Display the root of the current view tree (home view)") ) self.rootViewTool = tb.AddLabelTool( ID_BACK_VIEW, _("Back"), wx.ArtProvider.GetBitmap(wx.ART_GO_BACK, wx.ART_TOOLBAR, tsize), shortHelp=_("Back to the previously activated node in the call tree") ) self.upViewTool = tb.AddLabelTool( ID_UP_VIEW, _("Up"), wx.ArtProvider.GetBitmap(wx.ART_GO_UP, wx.ART_TOOLBAR, tsize), shortHelp=_("Go one level up the call tree (highest-percentage parent)") ) if not osx: tb.AddSeparator()
python
{ "resource": "" }
q9955
MainFrame.OnViewTypeTool
train
def OnViewTypeTool( self, event ): """When the user changes the selection, make that our selection""" new = self.viewTypeTool.GetStringSelection()
python
{ "resource": "" }
q9956
MainFrame.SetPercentageView
train
def SetPercentageView(self, percentageView): """Set whether to display percentage or absolute values""" self.percentageView = percentageView self.percentageMenuItem.Check(self.percentageView)
python
{ "resource": "" }
q9957
MainFrame.OnUpView
train
def OnUpView(self, event): """Request to move up the hierarchy to highest-weight parent""" node = self.activated_node parents = [] selected_parent = None if node: if hasattr( self.adapter, 'best_parent' ): selected_parent = self.adapter.best_parent( node ) else: parents = self.adapter.parents( node )
python
{ "resource": "" }
q9958
MainFrame.OnBackView
train
def OnBackView(self, event): """Request to move backward in the history""" self.historyIndex -= 1 try:
python
{ "resource": "" }
q9959
MainFrame.OnRootView
train
def OnRootView(self, event): """Reset view to the root of the tree""" self.adapter, tree, rows = self.RootNode()
python
{ "resource": "" }
q9960
MainFrame.OnNodeActivated
train
def OnNodeActivated(self, event): """Double-click or enter on a node in some control...""" self.activated_node = self.selected_node = event.node self.squareMap.SetModel(event.node, self.adapter) self.squareMap.SetSelected( event.node ) if editor: if self.SourceShowFile(event.node):
python
{ "resource": "" }
q9961
MainFrame.RecordHistory
train
def RecordHistory(self): """Add the given node to the history-set""" if not self.restoringHistory: record = self.activated_node if self.historyIndex < -1: try: del self.history[self.historyIndex+1:] except AttributeError, err: pass
python
{ "resource": "" }
q9962
MainFrame.RootNode
train
def RootNode(self): """Return our current root node and appropriate adapter for it""" tree = self.loader.get_root( self.viewType ) adapter = self.loader.get_adapter( self.viewType ) rows = self.loader.get_rows( self.viewType )
python
{ "resource": "" }
q9963
MainFrame.SaveState
train
def SaveState( self, config_parser ): """Retrieve window state to be restored on the next run...""" if not config_parser.has_section( 'window' ): config_parser.add_section( 'window' ) if self.IsMaximized(): config_parser.set( 'window', 'maximized', str(True)) else: config_parser.set( 'window', 'maximized', str(False)) size = self.GetSizeTuple() position = self.GetPositionTuple() config_parser.set( 'window', 'width',
python
{ "resource": "" }
q9964
MainFrame.LoadState
train
def LoadState( self, config_parser ): """Set our window state from the given config_parser instance""" if not config_parser: return if ( not config_parser.has_section( 'window' ) or ( config_parser.has_option( 'window','maximized' ) and config_parser.getboolean( 'window', 'maximized' ) ) ): self.Maximize(True) try: width,height,x,y = [ config_parser.getint( 'window',key ) for key in ['width','height','x','y'] ] self.SetPosition( (x,y)) self.SetSize( (width,height)) except ConfigParser.NoSectionError, err: # the file isn't written yet, so don't even warn... pass except Exception, err: # this is just convenience, if it breaks in *any* way, ignore it... log.error( "Unable to load window preferences, ignoring: %s", traceback.format_exc() ) try:
python
{ "resource": "" }
q9965
is_file
train
def is_file(dirname): '''Checks if a path is an actual file that exists''' if not os.path.isfile(dirname): msg = "{0} is not an existing file".format(dirname)
python
{ "resource": "" }
q9966
is_dir
train
def is_dir(dirname): '''Checks if a path is an actual directory that exists''' if not os.path.isdir(dirname): msg = "{0} is not a directory".format(dirname)
python
{ "resource": "" }
q9967
is_dir_or_file
train
def is_dir_or_file(dirname): '''Checks if a path is an actual directory that exists or a file''' if not os.path.isdir(dirname) and not os.path.isfile(dirname): msg = "{0} is not a directory
python
{ "resource": "" }
q9968
fullpath
train
def fullpath(relpath): '''Relative path to absolute''' if (type(relpath) is object
python
{ "resource": "" }
q9969
remove_if_exist
train
def remove_if_exist(path): # pragma: no cover """Delete a file or a directory recursively if it exists, else no exception is raised""" if os.path.exists(path): if os.path.isdir(path): shutil.rmtree(path)
python
{ "resource": "" }
q9970
copy_any
train
def copy_any(src, dst, only_missing=False): # pragma: no cover """Copy a file or a directory tree, deleting the destination before processing""" if not only_missing: remove_if_exist(dst) if os.path.exists(src): if os.path.isdir(src): if not only_missing: shutil.copytree(src, dst, symlinks=False, ignore=None) else: for dirpath, filepath in recwalk(src):
python
{ "resource": "" }
q9971
group_files_by_size
train
def group_files_by_size(fileslist, multi): # pragma: no cover ''' Cluster files into the specified number of groups, where each groups total size is as close as possible to each other. Pseudo-code (O(n^g) time complexity): Input: number of groups G per cluster, list of files F with respective sizes - Order F by descending size - Until F is empty: - Create a cluster X - A = Pop first item in F - Put A in X[0] (X[0] is thus the first group in cluster X) For g in 1..len(G)-1 : - B = Pop first item in F - Put B in X[g] - group_size := size(B) If group_size != size(A): While group_size < size(A): - Find next item C in F which size(C) <= size(A) - group_size - Put C in X[g] - group_size := group_size + size(C) ''' flord = OrderedDict(sorted(fileslist.items(), key=lambda x: x[1], reverse=True)) if multi <= 1: fgrouped = {} i = 0 for x in flord.keys(): i += 1 fgrouped[i] = [[x]] return fgrouped fgrouped = {} i = 0 while flord: i += 1
python
{ "resource": "" }
q9972
group_files_by_size_fast
train
def group_files_by_size_fast(fileslist, nbgroups, mode=1): # pragma: no cover '''Given a files list with sizes, output a list where the files are grouped in nbgroups per cluster. Pseudo-code for algorithm in O(n log(g)) (thank's to insertion sort or binary search trees) See for more infos: http://cs.stackexchange.com/questions/44406/fast-algorithm-for-clustering-groups-of-elements-given-their-size-time/44614#44614 For each file: - If to-fill list is empty or file.size > first-key(to-fill): * Create cluster c with file in first group g1 * Add to-fill[file.size].append([c, g2], [c, g3], ..., [c, gn]) - Else: * ksize = first-key(to-fill) * c, g = to-fill[ksize].popitem(0) * Add file to cluster c in group g * nsize = ksize - file.size * if nsize > 0: . to-fill[nsize].append([c, g]) . sort to-fill if not an automatic ordering structure ''' ftofill = SortedList() ftofill_pointer = {} fgrouped = [] # [] or {} ford = sorted(fileslist.iteritems(), key=lambda x: x[1]) last_cid = -1 while ford: fname, fsize = ford.pop() #print "----\n"+fname, fsize #if ftofill: print "beforebranch", fsize, ftofill[-1] #print ftofill if not ftofill or fsize > ftofill[-1]: last_cid += 1 #print "Branch A: create cluster %i" % last_cid fgrouped.append([]) #fgrouped[last_cid] = [] fgrouped[last_cid].append([fname]) if mode==0: for g in xrange(nbgroups-1, 0, -1): fgrouped[last_cid].append([]) if not fsize in ftofill_pointer: ftofill_pointer[fsize] = [] ftofill_pointer[fsize].append((last_cid, g)) ftofill.add(fsize) else:
python
{ "resource": "" }
q9973
grouped_count_sizes
train
def grouped_count_sizes(fileslist, fgrouped): # pragma: no cover '''Compute the total size per group and total number of files. Useful to check that everything is OK.''' fsizes = {} total_files = 0 allitems = None if isinstance(fgrouped, dict): allitems = fgrouped.iteritems() elif isinstance(fgrouped, list): allitems = enumerate(fgrouped) for fkey, cluster in allitems: fsizes[fkey] = [] for subcluster in cluster: tot = 0
python
{ "resource": "" }
q9974
ConfigPanel.GetOptions
train
def GetOptions(self): """ returns the collective values from all of the widgets contained in the panel""" values = [c.GetValue()
python
{ "resource": "" }
q9975
Positional.GetValue
train
def GetValue(self): ''' Positionals have no associated options_string, so only the supplied arguments are returned. The order is assumed to be the same as the order of declaration in the client code Returns "argument_value" '''
python
{ "resource": "" }
q9976
Flag.Update
train
def Update(self, size): ''' Custom wrapper calculator to account for the increased size of the _msg widget after being inlined with the wx.CheckBox ''' if self._msg is None: return help_msg = self._msg
python
{ "resource": "" }
q9977
get_path
train
def get_path(language): ''' Returns the full path to the language file ''' filename = language.lower() + '.json' lang_file_path = os.path.join(_DEFAULT_DIR, filename) if not os.path.exists(lang_file_path):
python
{ "resource": "" }
q9978
trunc
train
def trunc(obj, max, left=0): """ Convert `obj` to string, eliminate newlines and truncate the string to `max` characters. If there are more characters in the string add ``...`` to the string. With `left=True`, the string can be truncated at the beginning. @note: Does not catch exceptions when converting `obj` to string with `str`. >>> trunc('This is a long text.', 8) This ...
python
{ "resource": "" }
q9979
pp
train
def pp(i, base=1024): """ Pretty-print the integer `i` as a human-readable size representation. """ degree = 0 pattern = "%4d %s" while i > base: pattern = "%7.2f %s" i
python
{ "resource": "" }
q9980
pp_timestamp
train
def pp_timestamp(t): """ Get a friendly timestamp represented as a string. """ if t is None: return ''
python
{ "resource": "" }
q9981
GarbageGraph.print_stats
train
def print_stats(self, stream=None): """ Log annotated garbage objects to console or file. :param stream: open file, uses sys.stdout if not given """ if not stream: # pragma: no cover stream = sys.stdout self.metadata.sort(key=lambda x: -x.size) stream.write('%-10s %8s %-12s %-46s\n' % ('id', 'size', 'type', 'representation')) for g in self.metadata:
python
{ "resource": "" }
q9982
Profile.disable
train
def disable(self, threads=True): """ Disable profiling. """ if self.enabled_start: sys.settrace(None)
python
{ "resource": "" }
q9983
Tee.flush
train
def flush(self): """ Force commit changes to the file and stdout """ if not self.nostdout:
python
{ "resource": "" }
q9984
PStatsAdapter.parents
train
def parents(self, node): """Determine all parents of node in our tree""" return [
python
{ "resource": "" }
q9985
PStatsAdapter.filename
train
def filename( self, node ): """Extension to squaremap api to provide "what file is this" information""" if not node.directory: # TODO: any cases other than built-ins? return None if node.filename == '~':
python
{ "resource": "" }
q9986
get_obj
train
def get_obj(ref): """Get object from string reference.""" oid = int(ref)
python
{ "resource": "" }
q9987
process
train
def process(): """Get process overview.""" pmi = ProcessMemoryInfo()
python
{ "resource": "" }
q9988
tracker_index
train
def tracker_index(): """Get tracker overview.""" stats = server.stats if stats and stats.snapshots: stats.annotate() timeseries = [] for cls in stats.tracked_classes: series = [] for snapshot in stats.snapshots: series.append(snapshot.classes.get(cls, {}).get('sum', 0)) timeseries.append((cls, series)) series = [s.overhead for s in stats.snapshots] timeseries.append(("Profiling overhead", series)) if stats.snapshots[0].system_total.data_segment: # Assume tracked data resides in the data segment
python
{ "resource": "" }
q9989
tracker_class
train
def tracker_class(clsname): """Get class instance details.""" stats = server.stats if not stats: bottle.redirect('/tracker')
python
{ "resource": "" }
q9990
garbage_cycle
train
def garbage_cycle(index): """Get reference cycle details.""" graph = _compute_garbage_graphs()[int(index)]
python
{ "resource": "" }
q9991
_get_graph
train
def _get_graph(graph, filename): """Retrieve or render a graph.""" try: rendered = graph.rendered_file except AttributeError:
python
{ "resource": "" }
q9992
garbage_graph
train
def garbage_graph(index): """Get graph representation of reference cycle.""" graph = _compute_garbage_graphs()[int(index)] reduce_graph = bottle.request.GET.get('reduce', '') if reduce_graph: graph = graph.reduce_to_cycles() if not graph: return None filename = 'garbage%so%s.png' %
python
{ "resource": "" }
q9993
_winreg_getShellFolder
train
def _winreg_getShellFolder( name ): """Get a shell folder by string name from the registry""" k = _winreg.OpenKey( _winreg.HKEY_CURRENT_USER, r"Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders" )
python
{ "resource": "" }
q9994
appdatadirectory
train
def appdatadirectory( ): """Attempt to retrieve the current user's app-data directory This is the location where application-specific files should be stored. On *nix systems, this will be the ${HOME}/.config directory. On Win32 systems, it will be the "Application Data" directory. Note that for Win32 systems it is normal to create a sub-directory for storing data in the Application Data directory. """ if shell: # on Win32 and have Win32all extensions, best-case return shell_getShellFolder(shellcon.CSIDL_APPDATA) if _winreg: # on Win32, but no Win32 shell com available, this uses # a direct registry access, likely to fail on Win98/Me return _winreg_getShellFolder( 'AppData' ) # okay, what if for some reason _winreg is missing? would we want to
python
{ "resource": "" }
q9995
get_objects
train
def get_objects(remove_dups=True, include_frames=False): """Return a list of all known objects excluding frame objects. If (outer) frame objects shall be included, pass `include_frames=True`. In order to prevent building reference cycles, the current frame object (of the caller of get_objects) is ignored. This will not prevent creating reference cycles if the object list is passed up the call-stack. Therefore, frame objects are not included by default. Keyword arguments: remove_dups -- if True, all duplicate objects will be removed. include_frames -- if True, includes frame objects. """ gc.collect() # Do not initialize local variables before calling gc.get_objects or those # will be included in the list. Furthermore, ignore frame objects to # prevent reference cycles. tmp = gc.get_objects() tmp = [o for o in
python
{ "resource": "" }
q9996
get_size
train
def get_size(objects): """Compute the total size of all elements in objects.""" res = 0 for o in objects:
python
{ "resource": "" }
q9997
get_diff
train
def get_diff(left, right): """Get the difference of both lists. The result will be a dict with this form {'+': [], '-': []}. Items listed in '+' exist only in the right list, items listed in '-' exist only in the left list. """ res = {'+': [], '-': []} def partition(objects): """Partition the passed object list.""" res = {} for o in objects: t = type(o) if type(o) not in res: res[t] = [] res[t].append(o) return res def get_not_included(foo,
python
{ "resource": "" }
q9998
filter
train
def filter(objects, Type=None, min=-1, max=-1): #PYCHOK muppy filter """Filter objects. The filter can be by type, minimum size, and/or maximum size. Keyword arguments: Type -- object type to filter by min -- minimum object size
python
{ "resource": "" }
q9999
get_referents
train
def get_referents(object, level=1): """Get all referents of an object up to a certain level. The referents will not be returned in a specific order and will not contain duplicate objects. Duplicate objects will be removed. Keyword arguments: level -- level of indirection to which referents considered. This function is recursive.
python
{ "resource": "" }