From 5f8de423f190bbb79a62f804151bc24824fa32d8 Mon Sep 17 00:00:00 2001 From: "Matt A. Tobin" Date: Fri, 2 Feb 2018 04:16:08 -0500 Subject: Add m-esr52 at 52.6.0 --- python/altgraph/MANIFEST.in | 9 + python/altgraph/PKG-INFO | 216 +++++ python/altgraph/README.txt | 6 + python/altgraph/altgraph/Dot.py | 299 +++++++ python/altgraph/altgraph/Graph.py | 677 ++++++++++++++++ python/altgraph/altgraph/GraphAlgo.py | 147 ++++ python/altgraph/altgraph/GraphStat.py | 73 ++ python/altgraph/altgraph/GraphUtil.py | 137 ++++ python/altgraph/altgraph/ObjectGraph.py | 202 +++++ python/altgraph/altgraph/__init__.py | 135 ++++ python/altgraph/altgraph_tests/__init__.py | 1 + python/altgraph/altgraph_tests/test_altgraph.py | 45 ++ python/altgraph/altgraph_tests/test_dot.py | 370 +++++++++ python/altgraph/altgraph_tests/test_graph.py | 644 +++++++++++++++ python/altgraph/altgraph_tests/test_graphstat.py | 70 ++ python/altgraph/altgraph_tests/test_graphutil.py | 140 ++++ .../altgraph/altgraph_tests/test_object_graph.py | 349 +++++++++ python/altgraph/doc/Makefile | 89 +++ 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b/python/altgraph/MANIFEST.in @@ -0,0 +1,9 @@ +include ReadMe.txt +include *.txt MANIFEST.in *.py +graft doc +graft doc/_static +graft doc/_templates +graft altgraph_tests +global-exclude .DS_Store +global-exclude *.pyc +global-exclude *.so diff --git a/python/altgraph/PKG-INFO b/python/altgraph/PKG-INFO new file mode 100644 index 000000000..87b602f52 --- /dev/null +++ b/python/altgraph/PKG-INFO @@ -0,0 +1,216 @@ +Metadata-Version: 1.1 +Name: altgraph +Version: 0.12 +Summary: Python graph (network) package +Home-page: http://packages.python.org/altgraph +Author: Ronald Oussoren +Author-email: ronaldoussoren@mac.com +License: MIT +Download-URL: http://pypi.python.org/pypi/altgraph +Description: altgraph is a fork of graphlib: a graph (network) package for constructing + graphs, BFS and DFS traversals, topological sort, shortest paths, etc. with + graphviz output. + + altgraph includes some additional usage of Python 2.6+ features and + enhancements related to modulegraph and macholib. + + + Release history + =============== + + 0.12 + ---- + + - Added ``ObjectGraph.edgeData`` to retrieve the edge data + from a specific edge. + + - Added ``AltGraph.update_edge_data`` and ``ObjectGraph.updateEdgeData`` + to update the data associated with a graph edge. + + 0.11 + ---- + + - Stabilize the order of elements in dot file exports, + patch from bitbucket user 'pombredanne'. + + - Tweak setup.py file to remove dependency on distribute (but + keep the dependency on setuptools) + + + 0.10.2 + ------ + + - There where no classifiers in the package metadata due to a bug + in setup.py + + 0.10.1 + ------ + + This is a bugfix release + + Bug fixes: + + - Issue #3: The source archive contains a README.txt + while the setup file refers to ReadMe.txt. + + This is caused by a misfeature in distutils, as a + workaround I've renamed ReadMe.txt to README.txt + in the source tree and setup file. + + + 0.10 + ----- + + This is a minor feature release + + Features: + + - Do not use "2to3" to support Python 3. + + As a side effect of this altgraph now supports + Python 2.6 and later, and no longer supports + earlier releases of Python. + + - The order of attributes in the Dot output + is now always alphabetical. + + With this change the output will be consistent + between runs and Python versions. + + 0.9 + --- + + This is a minor bugfix release + + Features: + + - Added ``altgraph.ObjectGraph.ObjectGraph.nodes``, a method + yielding all nodes in an object graph. + + Bugfixes: + + - The 0.8 release didn't work with py2app when using + python 3.x. + + + 0.8 + ----- + + This is a minor feature release. The major new feature + is a extensive set of unittests, which explains almost + all other changes in this release. + + Bugfixes: + + - Installing failed with Python 2.5 due to using a distutils + class that isn't available in that version of Python + (issue #1 on the issue tracker) + + - ``altgraph.GraphStat.degree_dist`` now actually works + + - ``altgraph.Graph.add_edge(a, b, create_nodes=False)`` will + no longer create the edge when one of the nodes doesn't + exist. + + - ``altgraph.Graph.forw_topo_sort`` failed for some sparse graphs. + + - ``altgraph.Graph.back_topo_sort`` was completely broken in + previous releases. + + - ``altgraph.Graph.forw_bfs_subgraph`` now actually works. + + - ``altgraph.Graph.back_bfs_subgraph`` now actually works. + + - ``altgraph.Graph.iterdfs`` now returns the correct result + when the ``forward`` argument is ``False``. + + - ``altgraph.Graph.iterdata`` now returns the correct result + when the ``forward`` argument is ``False``. + + + Features: + + - The ``altgraph.Graph`` constructor now accepts an argument + that contains 2- and 3-tuples instead of requireing that + all items have the same size. The (optional) argument can now + also be any iterator. + + - ``altgraph.Graph.Graph.add_node`` has no effect when you + add a hidden node. + + - The private method ``altgraph.Graph._bfs`` is no longer + present. + + - The private method ``altgraph.Graph._dfs`` is no longer + present. + + - ``altgraph.ObjectGraph`` now has a ``__contains__`` methods, + which means you can use the ``in`` operator to check if a + node is part of a graph. + + - ``altgraph.GraphUtil.generate_random_graph`` will raise + ``GraphError`` instead of looping forever when it is + impossible to create the requested graph. + + - ``altgraph.Dot.edge_style`` raises ``GraphError`` when + one of the nodes is not present in the graph. The method + silently added the tail in the past, but without ensuring + a consistent graph state. + + - ``altgraph.Dot.save_img`` now works when the mode is + ``"neato"``. + + 0.7.2 + ----- + + This is a minor bugfix release + + Bugfixes: + + - distutils didn't include the documentation subtree + + 0.7.1 + ----- + + This is a minor feature release + + Features: + + - Documentation is now generated using `sphinx `_ + and can be viewed at . + + - The repository has moved to bitbucket + + - ``altgraph.GraphStat.avg_hops`` is no longer present, the function had no + implementation and no specified behaviour. + + - the module ``altgraph.compat`` is gone, which means altgraph will no + longer work with Python 2.3. + + + 0.7.0 + ----- + + This is a minor feature release. + + Features: + + - Support for Python 3 + + - It is now possible to run tests using 'python setup.py test' + + (The actual testsuite is still very minimal though) + +Keywords: graph +Platform: any +Classifier: Intended Audience :: Developers +Classifier: License :: OSI Approved :: MIT License +Classifier: Programming Language :: Python +Classifier: Programming Language :: Python :: 2 +Classifier: Programming Language :: Python :: 2.7 +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3.3 +Classifier: Programming Language :: Python :: 3.4 +Classifier: Topic :: Software Development :: Libraries :: Python Modules +Classifier: Topic :: Scientific/Engineering :: Mathematics +Classifier: Topic :: Scientific/Engineering :: Visualization diff --git a/python/altgraph/README.txt b/python/altgraph/README.txt new file mode 100644 index 000000000..904a14be5 --- /dev/null +++ b/python/altgraph/README.txt @@ -0,0 +1,6 @@ +altgraph is a fork of graphlib: a graph (network) package for constructing +graphs, BFS and DFS traversals, topological sort, shortest paths, etc. with +graphviz output. + +altgraph includes some additional usage of Python 2.6+ features and +enhancements related to modulegraph and macholib. diff --git a/python/altgraph/altgraph/Dot.py b/python/altgraph/altgraph/Dot.py new file mode 100644 index 000000000..49a471e4d --- /dev/null +++ b/python/altgraph/altgraph/Dot.py @@ -0,0 +1,299 @@ +''' +altgraph.Dot - Interface to the dot language +============================================ + +The :py:mod:`~altgraph.Dot` module provides a simple interface to the +file format used in the `graphviz `_ +program. The module is intended to offload the most tedious part of the process +(the **dot** file generation) while transparently exposing most of its features. + +To display the graphs or to generate image files the `graphviz `_ +package needs to be installed on the system, moreover the :command:`dot` and :command:`dotty` programs must +be accesible in the program path so that they can be ran from processes spawned +within the module. + +Example usage +------------- + +Here is a typical usage:: + + from altgraph import Graph, Dot + + # create a graph + edges = [ (1,2), (1,3), (3,4), (3,5), (4,5), (5,4) ] + graph = Graph.Graph(edges) + + # create a dot representation of the graph + dot = Dot.Dot(graph) + + # display the graph + dot.display() + + # save the dot representation into the mydot.dot file + dot.save_dot(file_name='mydot.dot') + + # save dot file as gif image into the graph.gif file + dot.save_img(file_name='graph', file_type='gif') + +Directed graph and non-directed graph +------------------------------------- + +Dot class can use for both directed graph and non-directed graph +by passing ``graphtype`` parameter. + +Example:: + + # create directed graph(default) + dot = Dot.Dot(graph, graphtype="digraph") + + # create non-directed graph + dot = Dot.Dot(graph, graphtype="graph") + +Customizing the output +---------------------- + +The graph drawing process may be customized by passing +valid :command:`dot` parameters for the nodes and edges. For a list of all +parameters see the `graphviz `_ +documentation. + +Example:: + + # customizing the way the overall graph is drawn + dot.style(size='10,10', rankdir='RL', page='5, 5' , ranksep=0.75) + + # customizing node drawing + dot.node_style(1, label='BASE_NODE',shape='box', color='blue' ) + dot.node_style(2, style='filled', fillcolor='red') + + # customizing edge drawing + dot.edge_style(1, 2, style='dotted') + dot.edge_style(3, 5, arrowhead='dot', label='binds', labelangle='90') + dot.edge_style(4, 5, arrowsize=2, style='bold') + + +.. note:: + + dotty (invoked via :py:func:`~altgraph.Dot.display`) may not be able to + display all graphics styles. To verify the output save it to an image file + and look at it that way. + +Valid attributes +---------------- + + - dot styles, passed via the :py:meth:`Dot.style` method:: + + rankdir = 'LR' (draws the graph horizontally, left to right) + ranksep = number (rank separation in inches) + + - node attributes, passed via the :py:meth:`Dot.node_style` method:: + + style = 'filled' | 'invisible' | 'diagonals' | 'rounded' + shape = 'box' | 'ellipse' | 'circle' | 'point' | 'triangle' + + - edge attributes, passed via the :py:meth:`Dot.edge_style` method:: + + style = 'dashed' | 'dotted' | 'solid' | 'invis' | 'bold' + arrowhead = 'box' | 'crow' | 'diamond' | 'dot' | 'inv' | 'none' | 'tee' | 'vee' + weight = number (the larger the number the closer the nodes will be) + + - valid `graphviz colors `_ + + - for more details on how to control the graph drawing process see the + `graphviz reference `_. +''' +import os +import warnings + +from altgraph import GraphError + + +class Dot(object): + ''' + A class providing a **graphviz** (dot language) representation + allowing a fine grained control over how the graph is being + displayed. + + If the :command:`dot` and :command:`dotty` programs are not in the current system path + their location needs to be specified in the contructor. + ''' + + def __init__(self, graph=None, nodes=None, edgefn=None, nodevisitor=None, edgevisitor=None, name="G", dot='dot', dotty='dotty', neato='neato', graphtype="digraph"): + ''' + Initialization. + ''' + self.name, self.attr = name, {} + + assert graphtype in ['graph', 'digraph'] + self.type = graphtype + + self.temp_dot = "tmp_dot.dot" + self.temp_neo = "tmp_neo.dot" + + self.dot, self.dotty, self.neato = dot, dotty, neato + + # self.nodes: node styles + # self.edges: edge styles + self.nodes, self.edges = {}, {} + + if graph is not None and nodes is None: + nodes = graph + if graph is not None and edgefn is None: + def edgefn(node, graph=graph): + return graph.out_nbrs(node) + if nodes is None: + nodes = () + + seen = set() + for node in nodes: + if nodevisitor is None: + style = {} + else: + style = nodevisitor(node) + if style is not None: + self.nodes[node] = {} + self.node_style(node, **style) + seen.add(node) + if edgefn is not None: + for head in seen: + for tail in (n for n in edgefn(head) if n in seen): + if edgevisitor is None: + edgestyle = {} + else: + edgestyle = edgevisitor(head, tail) + if edgestyle is not None: + if head not in self.edges: + self.edges[head] = {} + self.edges[head][tail] = {} + self.edge_style(head, tail, **edgestyle) + + def style(self, **attr): + ''' + Changes the overall style + ''' + self.attr = attr + + def display(self, mode='dot'): + ''' + Displays the current graph via dotty + ''' + + if mode == 'neato': + self.save_dot(self.temp_neo) + neato_cmd = "%s -o %s %s" % (self.neato, self.temp_dot, self.temp_neo) + os.system(neato_cmd) + else: + self.save_dot(self.temp_dot) + + plot_cmd = "%s %s" % (self.dotty, self.temp_dot) + os.system(plot_cmd) + + def node_style(self, node, **kwargs): + ''' + Modifies a node style to the dot representation. + ''' + if node not in self.edges: + self.edges[node] = {} + self.nodes[node] = kwargs + + def all_node_style(self, **kwargs): + ''' + Modifies all node styles + ''' + for node in self.nodes: + self.node_style(node, **kwargs) + + def edge_style(self, head, tail, **kwargs): + ''' + Modifies an edge style to the dot representation. + ''' + if tail not in self.nodes: + raise GraphError("invalid node %s" % (tail,)) + + try: + if tail not in self.edges[head]: + self.edges[head][tail]= {} + self.edges[head][tail] = kwargs + except KeyError: + raise GraphError("invalid edge %s -> %s " % (head, tail) ) + + def iterdot(self): + # write graph title + if self.type == 'digraph': + yield 'digraph %s {\n' % (self.name,) + elif self.type == 'graph': + yield 'graph %s {\n' % (self.name,) + + else: + raise GraphError("unsupported graphtype %s" % (self.type,)) + + # write overall graph attributes + for attr_name, attr_value in sorted(self.attr.items()): + yield '%s="%s";' % (attr_name, attr_value) + yield '\n' + + # some reusable patterns + cpatt = '%s="%s",' # to separate attributes + epatt = '];\n' # to end attributes + + # write node attributes + for node_name, node_attr in sorted(self.nodes.items()): + yield '\t"%s" [' % (node_name,) + for attr_name, attr_value in sorted(node_attr.items()): + yield cpatt % (attr_name, attr_value) + yield epatt + + # write edge attributes + for head in sorted(self.edges): + for tail in sorted(self.edges[head]): + if self.type == 'digraph': + yield '\t"%s" -> "%s" [' % (head, tail) + else: + yield '\t"%s" -- "%s" [' % (head, tail) + for attr_name, attr_value in sorted(self.edges[head][tail].items()): + yield cpatt % (attr_name, attr_value) + yield epatt + + # finish file + yield '}\n' + + def __iter__(self): + return self.iterdot() + + def save_dot(self, file_name=None): + ''' + Saves the current graph representation into a file + ''' + + if not file_name: + warnings.warn(DeprecationWarning, "always pass a file_name") + file_name = self.temp_dot + + fp = open(file_name, "w") + try: + for chunk in self.iterdot(): + fp.write(chunk) + finally: + fp.close() + + def save_img(self, file_name=None, file_type="gif", mode='dot'): + ''' + Saves the dot file as an image file + ''' + + if not file_name: + warnings.warn(DeprecationWarning, "always pass a file_name") + file_name = "out" + + if mode == 'neato': + self.save_dot(self.temp_neo) + neato_cmd = "%s -o %s %s" % (self.neato, self.temp_dot, self.temp_neo) + os.system(neato_cmd) + plot_cmd = self.dot + else: + self.save_dot(self.temp_dot) + plot_cmd = self.dot + + file_name = "%s.%s" % (file_name, file_type) + create_cmd = "%s -T%s %s -o %s" % (plot_cmd, file_type, self.temp_dot, file_name) + os.system(create_cmd) diff --git a/python/altgraph/altgraph/Graph.py b/python/altgraph/altgraph/Graph.py new file mode 100644 index 000000000..491e5c228 --- /dev/null +++ b/python/altgraph/altgraph/Graph.py @@ -0,0 +1,677 @@ +""" +altgraph.Graph - Base Graph class +================================= + +.. + #--Version 2.1 + #--Bob Ippolito October, 2004 + + #--Version 2.0 + #--Istvan Albert June, 2004 + + #--Version 1.0 + #--Nathan Denny, May 27, 1999 +""" + +from altgraph import GraphError +from collections import deque + +class Graph(object): + """ + The Graph class represents a directed graph with *N* nodes and *E* edges. + + Naming conventions: + + - the prefixes such as *out*, *inc* and *all* will refer to methods + that operate on the outgoing, incoming or all edges of that node. + + For example: :py:meth:`inc_degree` will refer to the degree of the node + computed over the incoming edges (the number of neighbours linking to + the node). + + - the prefixes such as *forw* and *back* will refer to the + orientation of the edges used in the method with respect to the node. + + For example: :py:meth:`forw_bfs` will start at the node then use the outgoing + edges to traverse the graph (goes forward). + """ + + def __init__(self, edges=None): + """ + Initialization + """ + + self.next_edge = 0 + self.nodes, self.edges = {}, {} + self.hidden_edges, self.hidden_nodes = {}, {} + + if edges is not None: + for item in edges: + if len(item) == 2: + head, tail = item + self.add_edge(head, tail) + elif len(item) == 3: + head, tail, data = item + self.add_edge(head, tail, data) + else: + raise GraphError("Cannot create edge from %s"%(item,)) + + + def __repr__(self): + return '' % ( + self.number_of_nodes(), self.number_of_edges()) + + def add_node(self, node, node_data=None): + """ + Adds a new node to the graph. Arbitrary data can be attached to the + node via the node_data parameter. Adding the same node twice will be + silently ignored. + + The node must be a hashable value. + """ + # + # the nodes will contain tuples that will store incoming edges, + # outgoing edges and data + # + # index 0 -> incoming edges + # index 1 -> outgoing edges + + if node in self.hidden_nodes: + # Node is present, but hidden + return + + if node not in self.nodes: + self.nodes[node] = ([], [], node_data) + + def add_edge(self, head_id, tail_id, edge_data=1, create_nodes=True): + """ + Adds a directed edge going from head_id to tail_id. + Arbitrary data can be attached to the edge via edge_data. + It may create the nodes if adding edges between nonexisting ones. + + :param head_id: head node + :param tail_id: tail node + :param edge_data: (optional) data attached to the edge + :param create_nodes: (optional) creates the head_id or tail_id node in case they did not exist + """ + # shorcut + edge = self.next_edge + + # add nodes if on automatic node creation + if create_nodes: + self.add_node(head_id) + self.add_node(tail_id) + + # update the corresponding incoming and outgoing lists in the nodes + # index 0 -> incoming edges + # index 1 -> outgoing edges + + try: + self.nodes[tail_id][0].append(edge) + self.nodes[head_id][1].append(edge) + except KeyError: + raise GraphError('Invalid nodes %s -> %s' % (head_id, tail_id)) + + # store edge information + self.edges[edge] = (head_id, tail_id, edge_data) + + + self.next_edge += 1 + + def hide_edge(self, edge): + """ + Hides an edge from the graph. The edge may be unhidden at some later + time. + """ + try: + head_id, tail_id, edge_data = self.hidden_edges[edge] = self.edges[edge] + self.nodes[tail_id][0].remove(edge) + self.nodes[head_id][1].remove(edge) + del self.edges[edge] + except KeyError: + raise GraphError('Invalid edge %s' % edge) + + def hide_node(self, node): + """ + Hides a node from the graph. The incoming and outgoing edges of the + node will also be hidden. The node may be unhidden at some later time. + """ + try: + all_edges = self.all_edges(node) + self.hidden_nodes[node] = (self.nodes[node], all_edges) + for edge in all_edges: + self.hide_edge(edge) + del self.nodes[node] + except KeyError: + raise GraphError('Invalid node %s' % node) + + def restore_node(self, node): + """ + Restores a previously hidden node back into the graph and restores + all of its incoming and outgoing edges. + """ + try: + self.nodes[node], all_edges = self.hidden_nodes[node] + for edge in all_edges: + self.restore_edge(edge) + del self.hidden_nodes[node] + except KeyError: + raise GraphError('Invalid node %s' % node) + + def restore_edge(self, edge): + """ + Restores a previously hidden edge back into the graph. + """ + try: + head_id, tail_id, data = self.hidden_edges[edge] + self.nodes[tail_id][0].append(edge) + self.nodes[head_id][1].append(edge) + self.edges[edge] = head_id, tail_id, data + del self.hidden_edges[edge] + except KeyError: + raise GraphError('Invalid edge %s' % edge) + + def restore_all_edges(self): + """ + Restores all hidden edges. + """ + for edge in list(self.hidden_edges.keys()): + try: + self.restore_edge(edge) + except GraphError: + pass + + def restore_all_nodes(self): + """ + Restores all hidden nodes. + """ + for node in list(self.hidden_nodes.keys()): + self.restore_node(node) + + def __contains__(self, node): + """ + Test whether a node is in the graph + """ + return node in self.nodes + + def edge_by_id(self, edge): + """ + Returns the edge that connects the head_id and tail_id nodes + """ + try: + head, tail, data = self.edges[edge] + except KeyError: + head, tail = None, None + raise GraphError('Invalid edge %s' % edge) + + return (head, tail) + + def edge_by_node(self, head, tail): + """ + Returns the edge that connects the head_id and tail_id nodes + """ + for edge in self.out_edges(head): + if self.tail(edge) == tail: + return edge + return None + + def number_of_nodes(self): + """ + Returns the number of nodes + """ + return len(self.nodes) + + def number_of_edges(self): + """ + Returns the number of edges + """ + return len(self.edges) + + def __iter__(self): + """ + Iterates over all nodes in the graph + """ + return iter(self.nodes) + + def node_list(self): + """ + Return a list of the node ids for all visible nodes in the graph. + """ + return list(self.nodes.keys()) + + def edge_list(self): + """ + Returns an iterator for all visible nodes in the graph. + """ + return list(self.edges.keys()) + + def number_of_hidden_edges(self): + """ + Returns the number of hidden edges + """ + return len(self.hidden_edges) + + def number_of_hidden_nodes(self): + """ + Returns the number of hidden nodes + """ + return len(self.hidden_nodes) + + def hidden_node_list(self): + """ + Returns the list with the hidden nodes + """ + return list(self.hidden_nodes.keys()) + + def hidden_edge_list(self): + """ + Returns a list with the hidden edges + """ + return list(self.hidden_edges.keys()) + + def describe_node(self, node): + """ + return node, node data, outgoing edges, incoming edges for node + """ + incoming, outgoing, data = self.nodes[node] + return node, data, outgoing, incoming + + def describe_edge(self, edge): + """ + return edge, edge data, head, tail for edge + """ + head, tail, data = self.edges[edge] + return edge, data, head, tail + + def node_data(self, node): + """ + Returns the data associated with a node + """ + return self.nodes[node][2] + + def edge_data(self, edge): + """ + Returns the data associated with an edge + """ + return self.edges[edge][2] + + def update_edge_data(self, edge, edge_data): + """ + Replace the edge data for a specific edge + """ + self.edges[edge] = self.edges[edge][0:2] + (edge_data,) + + def head(self, edge): + """ + Returns the node of the head of the edge. + """ + return self.edges[edge][0] + + def tail(self, edge): + """ + Returns node of the tail of the edge. + """ + return self.edges[edge][1] + + def out_nbrs(self, node): + """ + List of nodes connected by outgoing edges + """ + l = [self.tail(n) for n in self.out_edges(node)] + return l + + def inc_nbrs(self, node): + """ + List of nodes connected by incoming edges + """ + l = [self.head(n) for n in self.inc_edges(node)] + return l + + def all_nbrs(self, node): + """ + List of nodes connected by incoming and outgoing edges + """ + l = dict.fromkeys( self.inc_nbrs(node) + self.out_nbrs(node) ) + return list(l) + + def out_edges(self, node): + """ + Returns a list of the outgoing edges + """ + try: + return list(self.nodes[node][1]) + except KeyError: + raise GraphError('Invalid node %s' % node) + + return None + + def inc_edges(self, node): + """ + Returns a list of the incoming edges + """ + try: + return list(self.nodes[node][0]) + except KeyError: + raise GraphError('Invalid node %s' % node) + + return None + + def all_edges(self, node): + """ + Returns a list of incoming and outging edges. + """ + return set(self.inc_edges(node) + self.out_edges(node)) + + def out_degree(self, node): + """ + Returns the number of outgoing edges + """ + return len(self.out_edges(node)) + + def inc_degree(self, node): + """ + Returns the number of incoming edges + """ + return len(self.inc_edges(node)) + + def all_degree(self, node): + """ + The total degree of a node + """ + return self.inc_degree(node) + self.out_degree(node) + + def _topo_sort(self, forward=True): + """ + Topological sort. + + Returns a list of nodes where the successors (based on outgoing and + incoming edges selected by the forward parameter) of any given node + appear in the sequence after that node. + """ + topo_list = [] + queue = deque() + indeg = {} + + # select the operation that will be performed + if forward: + get_edges = self.out_edges + get_degree = self.inc_degree + get_next = self.tail + else: + get_edges = self.inc_edges + get_degree = self.out_degree + get_next = self.head + + for node in self.node_list(): + degree = get_degree(node) + if degree: + indeg[node] = degree + else: + queue.append(node) + + while queue: + curr_node = queue.popleft() + topo_list.append(curr_node) + for edge in get_edges(curr_node): + tail_id = get_next(edge) + if tail_id in indeg: + indeg[tail_id] -= 1 + if indeg[tail_id] == 0: + queue.append(tail_id) + + if len(topo_list) == len(self.node_list()): + valid = True + else: + # the graph has cycles, invalid topological sort + valid = False + + return (valid, topo_list) + + def forw_topo_sort(self): + """ + Topological sort. + + Returns a list of nodes where the successors (based on outgoing edges) + of any given node appear in the sequence after that node. + """ + return self._topo_sort(forward=True) + + def back_topo_sort(self): + """ + Reverse topological sort. + + Returns a list of nodes where the successors (based on incoming edges) + of any given node appear in the sequence after that node. + """ + return self._topo_sort(forward=False) + + def _bfs_subgraph(self, start_id, forward=True): + """ + Private method creates a subgraph in a bfs order. + + The forward parameter specifies whether it is a forward or backward + traversal. + """ + if forward: + get_bfs = self.forw_bfs + get_nbrs = self.out_nbrs + else: + get_bfs = self.back_bfs + get_nbrs = self.inc_nbrs + + g = Graph() + bfs_list = get_bfs(start_id) + for node in bfs_list: + g.add_node(node) + + for node in bfs_list: + for nbr_id in get_nbrs(node): + g.add_edge(node, nbr_id) + + return g + + def forw_bfs_subgraph(self, start_id): + """ + Creates and returns a subgraph consisting of the breadth first + reachable nodes based on their outgoing edges. + """ + return self._bfs_subgraph(start_id, forward=True) + + def back_bfs_subgraph(self, start_id): + """ + Creates and returns a subgraph consisting of the breadth first + reachable nodes based on the incoming edges. + """ + return self._bfs_subgraph(start_id, forward=False) + + def iterdfs(self, start, end=None, forward=True): + """ + Collecting nodes in some depth first traversal. + + The forward parameter specifies whether it is a forward or backward + traversal. + """ + visited, stack = set([start]), deque([start]) + + if forward: + get_edges = self.out_edges + get_next = self.tail + else: + get_edges = self.inc_edges + get_next = self.head + + while stack: + curr_node = stack.pop() + yield curr_node + if curr_node == end: + break + for edge in sorted(get_edges(curr_node)): + tail = get_next(edge) + if tail not in visited: + visited.add(tail) + stack.append(tail) + + def iterdata(self, start, end=None, forward=True, condition=None): + """ + Perform a depth-first walk of the graph (as ``iterdfs``) + and yield the item data of every node where condition matches. The + condition callback is only called when node_data is not None. + """ + + visited, stack = set([start]), deque([start]) + + if forward: + get_edges = self.out_edges + get_next = self.tail + else: + get_edges = self.inc_edges + get_next = self.head + + get_data = self.node_data + + while stack: + curr_node = stack.pop() + curr_data = get_data(curr_node) + if curr_data is not None: + if condition is not None and not condition(curr_data): + continue + yield curr_data + if curr_node == end: + break + for edge in get_edges(curr_node): + tail = get_next(edge) + if tail not in visited: + visited.add(tail) + stack.append(tail) + + def _iterbfs(self, start, end=None, forward=True): + """ + The forward parameter specifies whether it is a forward or backward + traversal. Returns a list of tuples where the first value is the hop + value the second value is the node id. + """ + queue, visited = deque([(start, 0)]), set([start]) + + # the direction of the bfs depends on the edges that are sampled + if forward: + get_edges = self.out_edges + get_next = self.tail + else: + get_edges = self.inc_edges + get_next = self.head + + while queue: + curr_node, curr_step = queue.popleft() + yield (curr_node, curr_step) + if curr_node == end: + break + for edge in get_edges(curr_node): + tail = get_next(edge) + if tail not in visited: + visited.add(tail) + queue.append((tail, curr_step + 1)) + + + def forw_bfs(self, start, end=None): + """ + Returns a list of nodes in some forward BFS order. + + Starting from the start node the breadth first search proceeds along + outgoing edges. + """ + return [node for node, step in self._iterbfs(start, end, forward=True)] + + def back_bfs(self, start, end=None): + """ + Returns a list of nodes in some backward BFS order. + + Starting from the start node the breadth first search proceeds along + incoming edges. + """ + return [node for node, step in self._iterbfs(start, end, forward=False)] + + def forw_dfs(self, start, end=None): + """ + Returns a list of nodes in some forward DFS order. + + Starting with the start node the depth first search proceeds along + outgoing edges. + """ + return list(self.iterdfs(start, end, forward=True)) + + def back_dfs(self, start, end=None): + """ + Returns a list of nodes in some backward DFS order. + + Starting from the start node the depth first search proceeds along + incoming edges. + """ + return list(self.iterdfs(start, end, forward=False)) + + def connected(self): + """ + Returns :py:data:`True` if the graph's every node can be reached from every + other node. + """ + node_list = self.node_list() + for node in node_list: + bfs_list = self.forw_bfs(node) + if len(bfs_list) != len(node_list): + return False + return True + + def clust_coef(self, node): + """ + Computes and returns the local clustering coefficient of node. The + local cluster coefficient is proportion of the actual number of edges between + neighbours of node and the maximum number of edges between those neighbours. + + See + for a formal definition. + """ + num = 0 + nbr_set = set(self.out_nbrs(node)) + + if node in nbr_set: + nbr_set.remove(node) # loop defense + + for nbr in nbr_set: + sec_set = set(self.out_nbrs(nbr)) + if nbr in sec_set: + sec_set.remove(nbr) # loop defense + num += len(nbr_set & sec_set) + + nbr_num = len(nbr_set) + if nbr_num: + clust_coef = float(num) / (nbr_num * (nbr_num - 1)) + else: + clust_coef = 0.0 + return clust_coef + + def get_hops(self, start, end=None, forward=True): + """ + Computes the hop distance to all nodes centered around a specified node. + + First order neighbours are at hop 1, their neigbours are at hop 2 etc. + Uses :py:meth:`forw_bfs` or :py:meth:`back_bfs` depending on the value of the forward + parameter. If the distance between all neighbouring nodes is 1 the hop + number corresponds to the shortest distance between the nodes. + + :param start: the starting node + :param end: ending node (optional). When not specified will search the whole graph. + :param forward: directionality parameter (optional). If C{True} (default) it uses L{forw_bfs} otherwise L{back_bfs}. + :return: returns a list of tuples where each tuple contains the node and the hop. + + Typical usage:: + + >>> print (graph.get_hops(1, 8)) + >>> [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)] + # node 1 is at 0 hops + # node 2 is at 1 hop + # ... + # node 8 is at 5 hops + """ + if forward: + return list(self._iterbfs(start=start, end=end, forward=True)) + else: + return list(self._iterbfs(start=start, end=end, forward=False)) diff --git a/python/altgraph/altgraph/GraphAlgo.py b/python/altgraph/altgraph/GraphAlgo.py new file mode 100644 index 000000000..9e6fff2b1 --- /dev/null +++ b/python/altgraph/altgraph/GraphAlgo.py @@ -0,0 +1,147 @@ +''' +altgraph.GraphAlgo - Graph algorithms +===================================== +''' +from altgraph import GraphError + +def dijkstra(graph, start, end=None): + """ + Dijkstra's algorithm for shortest paths + + `David Eppstein, UC Irvine, 4 April 2002 `_ + + `Python Cookbook Recipe `_ + + Find shortest paths from the start node to all nodes nearer than or equal to the end node. + + Dijkstra's algorithm is only guaranteed to work correctly when all edge lengths are positive. + This code does not verify this property for all edges (only the edges examined until the end + vertex is reached), but will correctly compute shortest paths even for some graphs with negative + edges, and will raise an exception if it discovers that a negative edge has caused it to make a mistake. + + *Adapted to altgraph by Istvan Albert, Pennsylvania State University - June, 9 2004* + + """ + D = {} # dictionary of final distances + P = {} # dictionary of predecessors + Q = _priorityDictionary() # estimated distances of non-final vertices + Q[start] = 0 + + for v in Q: + D[v] = Q[v] + if v == end: break + + for w in graph.out_nbrs(v): + edge_id = graph.edge_by_node(v,w) + vwLength = D[v] + graph.edge_data(edge_id) + if w in D: + if vwLength < D[w]: + raise GraphError("Dijkstra: found better path to already-final vertex") + elif w not in Q or vwLength < Q[w]: + Q[w] = vwLength + P[w] = v + + return (D,P) + +def shortest_path(graph, start, end): + """ + Find a single shortest path from the given start node to the given end node. + The input has the same conventions as dijkstra(). The output is a list of the nodes + in order along the shortest path. + + **Note that the distances must be stored in the edge data as numeric data** + """ + + D,P = dijkstra(graph, start, end) + Path = [] + while 1: + Path.append(end) + if end == start: break + end = P[end] + Path.reverse() + return Path + +# +# Utility classes and functions +# +class _priorityDictionary(dict): + ''' + Priority dictionary using binary heaps (internal use only) + + David Eppstein, UC Irvine, 8 Mar 2002 + + Implements a data structure that acts almost like a dictionary, with two modifications: + 1. D.smallest() returns the value x minimizing D[x]. For this to work correctly, + all values D[x] stored in the dictionary must be comparable. + 2. iterating "for x in D" finds and removes the items from D in sorted order. + Each item is not removed until the next item is requested, so D[x] will still + return a useful value until the next iteration of the for-loop. + Each operation takes logarithmic amortized time. + ''' + def __init__(self): + ''' + Initialize priorityDictionary by creating binary heap of pairs (value,key). + Note that changing or removing a dict entry will not remove the old pair from the heap + until it is found by smallest() or until the heap is rebuilt. + ''' + self.__heap = [] + dict.__init__(self) + + def smallest(self): + ''' + Find smallest item after removing deleted items from front of heap. + ''' + if len(self) == 0: + raise IndexError("smallest of empty priorityDictionary") + heap = self.__heap + while heap[0][1] not in self or self[heap[0][1]] != heap[0][0]: + lastItem = heap.pop() + insertionPoint = 0 + while 1: + smallChild = 2*insertionPoint+1 + if smallChild+1 < len(heap) and heap[smallChild] > heap[smallChild+1] : + smallChild += 1 + if smallChild >= len(heap) or lastItem <= heap[smallChild]: + heap[insertionPoint] = lastItem + break + heap[insertionPoint] = heap[smallChild] + insertionPoint = smallChild + return heap[0][1] + + def __iter__(self): + ''' + Create destructive sorted iterator of priorityDictionary. + ''' + def iterfn(): + while len(self) > 0: + x = self.smallest() + yield x + del self[x] + return iterfn() + + def __setitem__(self,key,val): + ''' + Change value stored in dictionary and add corresponding pair to heap. + Rebuilds the heap if the number of deleted items gets large, to avoid memory leakage. + ''' + dict.__setitem__(self,key,val) + heap = self.__heap + if len(heap) > 2 * len(self): + self.__heap = [(v,k) for k,v in self.iteritems()] + self.__heap.sort() # builtin sort probably faster than O(n)-time heapify + else: + newPair = (val,key) + insertionPoint = len(heap) + heap.append(None) + while insertionPoint > 0 and newPair < heap[(insertionPoint-1)//2]: + heap[insertionPoint] = heap[(insertionPoint-1)//2] + insertionPoint = (insertionPoint-1)//2 + heap[insertionPoint] = newPair + + def setdefault(self,key,val): + ''' + Reimplement setdefault to pass through our customized __setitem__. + ''' + if key not in self: + self[key] = val + return self[key] diff --git a/python/altgraph/altgraph/GraphStat.py b/python/altgraph/altgraph/GraphStat.py new file mode 100644 index 000000000..25fc46c2d --- /dev/null +++ b/python/altgraph/altgraph/GraphStat.py @@ -0,0 +1,73 @@ +''' +altgraph.GraphStat - Functions providing various graph statistics +================================================================= +''' +import sys + +def degree_dist(graph, limits=(0,0), bin_num=10, mode='out'): + ''' + Computes the degree distribution for a graph. + + Returns a list of tuples where the first element of the tuple is the center of the bin + representing a range of degrees and the second element of the tuple are the number of nodes + with the degree falling in the range. + + Example:: + + .... + ''' + + deg = [] + if mode == 'inc': + get_deg = graph.inc_degree + else: + get_deg = graph.out_degree + + for node in graph: + deg.append( get_deg(node) ) + + if not deg: + return [] + + results = _binning(values=deg, limits=limits, bin_num=bin_num) + + return results + +_EPS = 1.0/(2.0**32) +def _binning(values, limits=(0,0), bin_num=10): + ''' + Bins data that falls between certain limits, if the limits are (0, 0) the + minimum and maximum values are used. + + Returns a list of tuples where the first element of the tuple is the center of the bin + and the second element of the tuple are the counts. + ''' + if limits == (0, 0): + min_val, max_val = min(values) - _EPS, max(values) + _EPS + else: + min_val, max_val = limits + + # get bin size + bin_size = (max_val - min_val)/float(bin_num) + bins = [0] * (bin_num) + + # will ignore these outliers for now + out_points = 0 + for value in values: + try: + if (value - min_val) < 0: + out_points += 1 + else: + index = int((value - min_val)/float(bin_size)) + bins[index] += 1 + except IndexError: + out_points += 1 + + # make it ready for an x,y plot + result = [] + center = (bin_size/2) + min_val + for i, y in enumerate(bins): + x = center + bin_size * i + result.append( (x,y) ) + + return result diff --git a/python/altgraph/altgraph/GraphUtil.py b/python/altgraph/altgraph/GraphUtil.py new file mode 100644 index 000000000..d3b6acd74 --- /dev/null +++ b/python/altgraph/altgraph/GraphUtil.py @@ -0,0 +1,137 @@ +''' +altgraph.GraphUtil - Utility classes and functions +================================================== +''' + +import random +from collections import deque +from altgraph import Graph +from altgraph import GraphError + +def generate_random_graph(node_num, edge_num, self_loops=False, multi_edges=False): + ''' + Generates and returns a :py:class:`~altgraph.Graph.Graph` instance with *node_num* nodes + randomly connected by *edge_num* edges. + ''' + g = Graph.Graph() + + if not multi_edges: + if self_loops: + max_edges = node_num * node_num + else: + max_edges = node_num * (node_num-1) + + if edge_num > max_edges: + raise GraphError("inconsistent arguments to 'generate_random_graph'") + + nodes = range(node_num) + + for node in nodes: + g.add_node(node) + + while 1: + head = random.choice(nodes) + tail = random.choice(nodes) + + # loop defense + if head == tail and not self_loops: + continue + + # multiple edge defense + if g.edge_by_node(head,tail) is not None and not multi_edges: + continue + + # add the edge + g.add_edge(head, tail) + if g.number_of_edges() >= edge_num: + break + + return g + +def generate_scale_free_graph(steps, growth_num, self_loops=False, multi_edges=False): + ''' + Generates and returns a :py:class:`~altgraph.Graph.Graph` instance that will have *steps* \* *growth_num* nodes + and a scale free (powerlaw) connectivity. Starting with a fully connected graph with *growth_num* nodes + at every step *growth_num* nodes are added to the graph and are connected to existing nodes with + a probability proportional to the degree of these existing nodes. + ''' + # FIXME: The code doesn't seem to do what the documentation claims. + graph = Graph.Graph() + + # initialize the graph + store = [] + for i in range(growth_num): + #store += [ i ] * (growth_num - 1) + for j in range(i + 1, growth_num): + store.append(i) + store.append(j) + graph.add_edge(i,j) + + # generate + for node in range(growth_num, steps * growth_num): + graph.add_node(node) + while ( graph.out_degree(node) < growth_num ): + nbr = random.choice(store) + + # loop defense + if node == nbr and not self_loops: + continue + + # multi edge defense + if graph.edge_by_node(node, nbr) and not multi_edges: + continue + + graph.add_edge(node, nbr) + + + for nbr in graph.out_nbrs(node): + store.append(node) + store.append(nbr) + + return graph + +def filter_stack(graph, head, filters): + """ + Perform a walk in a depth-first order starting + at *head*. + + Returns (visited, removes, orphans). + + * visited: the set of visited nodes + * removes: the list of nodes where the node + data does not all *filters* + * orphans: tuples of (last_good, node), + where node is not in removes, is directly + reachable from a node in *removes* and + *last_good* is the closest upstream node that is not + in *removes*. + """ + + visited, removes, orphans = set([head]), set(), set() + stack = deque([(head, head)]) + get_data = graph.node_data + get_edges = graph.out_edges + get_tail = graph.tail + + while stack: + last_good, node = stack.pop() + data = get_data(node) + if data is not None: + for filtfunc in filters: + if not filtfunc(data): + removes.add(node) + break + else: + last_good = node + for edge in get_edges(node): + tail = get_tail(edge) + if last_good is not node: + orphans.add((last_good, tail)) + if tail not in visited: + visited.add(tail) + stack.append((last_good, tail)) + + orphans = [(last_good, tail) for (last_good, tail) in orphans if tail not in removes] + #orphans.sort() + + return visited, removes, orphans diff --git a/python/altgraph/altgraph/ObjectGraph.py b/python/altgraph/altgraph/ObjectGraph.py new file mode 100644 index 000000000..d07f51b68 --- /dev/null +++ b/python/altgraph/altgraph/ObjectGraph.py @@ -0,0 +1,202 @@ +""" +altgraph.ObjectGraph - Graph of objects with an identifier +========================================================== + +A graph of objects that have a "graphident" attribute. +graphident is the key for the object in the graph +""" + +from altgraph import GraphError +from altgraph.Graph import Graph +from altgraph.GraphUtil import filter_stack + +class ObjectGraph(object): + """ + A graph of objects that have a "graphident" attribute. + graphident is the key for the object in the graph + """ + def __init__(self, graph=None, debug=0): + if graph is None: + graph = Graph() + self.graphident = self + self.graph = graph + self.debug = debug + self.indent = 0 + graph.add_node(self, None) + + def __repr__(self): + return '<%s>' % (type(self).__name__,) + + def flatten(self, condition=None, start=None): + """ + Iterate over the subgraph that is entirely reachable by condition + starting from the given start node or the ObjectGraph root + """ + if start is None: + start = self + start = self.getRawIdent(start) + return self.graph.iterdata(start=start, condition=condition) + + def nodes(self): + for ident in self.graph: + node = self.graph.node_data(ident) + if node is not None: + yield self.graph.node_data(ident) + + + def get_edges(self, node): + start = self.getRawIdent(node) + _, _, outraw, incraw = self.graph.describe_node(start) + def iter_edges(lst, n): + seen = set() + for tpl in (self.graph.describe_edge(e) for e in lst): + ident = tpl[n] + if ident not in seen: + yield self.findNode(ident) + seen.add(ident) + return iter_edges(outraw, 3), iter_edges(incraw, 2) + + def edgeData(self, fromNode, toNode): + start = self.getRawIdent(fromNode) + stop = self.getRawIdent(toNode) + edge = self.graph.edge_by_node(start, stop) + return self.graph.edge_data(edge) + + def updateEdgeData(self, fromNode, toNode, edgeData): + start = self.getRawIdent(fromNode) + stop = self.getRawIdent(toNode) + edge = self.graph.edge_by_node(start, stop) + self.graph.update_edge_data(edge, edgeData) + + def filterStack(self, filters): + """ + Filter the ObjectGraph in-place by removing all edges to nodes that + do not match every filter in the given filter list + + Returns a tuple containing the number of: (nodes_visited, nodes_removed, nodes_orphaned) + """ + visited, removes, orphans = filter_stack(self.graph, self, filters) + + for last_good, tail in orphans: + self.graph.add_edge(last_good, tail, edge_data='orphan') + + for node in removes: + self.graph.hide_node(node) + + return len(visited)-1, len(removes), len(orphans) + + def removeNode(self, node): + """ + Remove the given node from the graph if it exists + """ + ident = self.getIdent(node) + if ident is not None: + self.graph.hide_node(ident) + + def removeReference(self, fromnode, tonode): + """ + Remove all edges from fromnode to tonode + """ + if fromnode is None: + fromnode = self + fromident = self.getIdent(fromnode) + toident = self.getIdent(tonode) + if fromident is not None and toident is not None: + while True: + edge = self.graph.edge_by_node(fromident, toident) + if edge is None: + break + self.graph.hide_edge(edge) + + def getIdent(self, node): + """ + Get the graph identifier for a node + """ + ident = self.getRawIdent(node) + if ident is not None: + return ident + node = self.findNode(node) + if node is None: + return None + return node.graphident + + def getRawIdent(self, node): + """ + Get the identifier for a node object + """ + if node is self: + return node + ident = getattr(node, 'graphident', None) + return ident + + def __contains__(self, node): + return self.findNode(node) is not None + + def findNode(self, node): + """ + Find the node on the graph + """ + ident = self.getRawIdent(node) + if ident is None: + ident = node + try: + return self.graph.node_data(ident) + except KeyError: + return None + + def addNode(self, node): + """ + Add a node to the graph referenced by the root + """ + self.msg(4, "addNode", node) + + try: + self.graph.restore_node(node.graphident) + except GraphError: + self.graph.add_node(node.graphident, node) + + def createReference(self, fromnode, tonode, edge_data=None): + """ + Create a reference from fromnode to tonode + """ + if fromnode is None: + fromnode = self + fromident, toident = self.getIdent(fromnode), self.getIdent(tonode) + if fromident is None or toident is None: + return + self.msg(4, "createReference", fromnode, tonode, edge_data) + self.graph.add_edge(fromident, toident, edge_data=edge_data) + + def createNode(self, cls, name, *args, **kw): + """ + Add a node of type cls to the graph if it does not already exist + by the given name + """ + m = self.findNode(name) + if m is None: + m = cls(name, *args, **kw) + self.addNode(m) + return m + + def msg(self, level, s, *args): + """ + Print a debug message with the given level + """ + if s and level <= self.debug: + print ("%s%s %s" % (" " * self.indent, s, ' '.join(map(repr, args)))) + + def msgin(self, level, s, *args): + """ + Print a debug message and indent + """ + if level <= self.debug: + self.msg(level, s, *args) + self.indent = self.indent + 1 + + def msgout(self, level, s, *args): + """ + Dedent and print a debug message + """ + if level <= self.debug: + self.indent = self.indent - 1 + self.msg(level, s, *args) diff --git a/python/altgraph/altgraph/__init__.py b/python/altgraph/altgraph/__init__.py new file mode 100644 index 000000000..9f72c18e5 --- /dev/null +++ b/python/altgraph/altgraph/__init__.py @@ -0,0 +1,135 @@ +''' +altgraph - a python graph library +================================= + +altgraph is a fork of `graphlib `_ tailored +to use newer Python 2.3+ features, including additional support used by the +py2app suite (modulegraph and macholib, specifically). + +altgraph is a python based graph (network) representation and manipulation package. +It has started out as an extension to the `graph_lib module `_ +written by Nathan Denny it has been significantly optimized and expanded. + +The :class:`altgraph.Graph.Graph` class is loosely modeled after the `LEDA `_ +(Library of Efficient Datatypes) representation. The library +includes methods for constructing graphs, BFS and DFS traversals, +topological sort, finding connected components, shortest paths as well as a number +graph statistics functions. The library can also visualize graphs +via `graphviz `_. + +The package contains the following modules: + + - the :py:mod:`altgraph.Graph` module contains the :class:`~altgraph.Graph.Graph` class that stores the graph data + + - the :py:mod:`altgraph.GraphAlgo` module implements graph algorithms operating on graphs (:py:class:`~altgraph.Graph.Graph`} instances) + + - the :py:mod:`altgraph.GraphStat` module contains functions for computing statistical measures on graphs + + - the :py:mod:`altgraph.GraphUtil` module contains functions for generating, reading and saving graphs + + - the :py:mod:`altgraph.Dot` module contains functions for displaying graphs via `graphviz `_ + + - the :py:mod:`altgraph.ObjectGraph` module implements a graph of objects with a unique identifier + +Installation +------------ + +Download and unpack the archive then type:: + + python setup.py install + +This will install the library in the default location. For instructions on +how to customize the install procedure read the output of:: + + python setup.py --help install + +To verify that the code works run the test suite:: + + python setup.py test + +Example usage +------------- + +Lets assume that we want to analyze the graph below (links to the full picture) GRAPH_IMG. +Our script then might look the following way:: + + from altgraph import Graph, GraphAlgo, Dot + + # these are the edges + edges = [ (1,2), (2,4), (1,3), (2,4), (3,4), (4,5), (6,5), + (6,14), (14,15), (6, 15), (5,7), (7, 8), (7,13), (12,8), + (8,13), (11,12), (11,9), (13,11), (9,13), (13,10) ] + + # creates the graph + graph = Graph.Graph() + for head, tail in edges: + graph.add_edge(head, tail) + + # do a forward bfs from 1 at most to 20 + print(graph.forw_bfs(1)) + +This will print the nodes in some breadth first order:: + + [1, 2, 3, 4, 5, 7, 8, 13, 11, 10, 12, 9] + +If we wanted to get the hop-distance from node 1 to node 8 +we coud write:: + + print(graph.get_hops(1, 8)) + +This will print the following:: + + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)] + +Node 1 is at 0 hops since it is the starting node, nodes 2,3 are 1 hop away ... +node 8 is 5 hops away. To find the shortest distance between two nodes you +can use:: + + print(GraphAlgo.shortest_path(graph, 1, 12)) + +It will print the nodes on one (if there are more) the shortest paths:: + + [1, 2, 4, 5, 7, 13, 11, 12] + +To display the graph we can use the GraphViz backend:: + + dot = Dot.Dot(graph) + + # display the graph on the monitor + dot.display() + + # save it in an image file + dot.save_img(file_name='graph', file_type='gif') + + + +.. + @author: U{Istvan Albert} + + @license: MIT License + + Copyright (c) 2004 Istvan Albert unless otherwise noted. + + Permission is hereby granted, free of charge, to any person obtaining a copy of this software + and associated documentation files (the "Software"), to deal in the Software without restriction, + including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, + and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do + so. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, + INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR + PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE + FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, + ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. + @requires: Python 2.3 or higher + + @newfield contributor: Contributors: + @contributor: U{Reka Albert } + +''' +import pkg_resources +__version__ = pkg_resources.require('altgraph')[0].version + +class GraphError(ValueError): + pass diff --git a/python/altgraph/altgraph_tests/__init__.py b/python/altgraph/altgraph_tests/__init__.py new file mode 100644 index 000000000..6890389df --- /dev/null +++ b/python/altgraph/altgraph_tests/__init__.py @@ -0,0 +1 @@ +""" altgraph tests """ diff --git a/python/altgraph/altgraph_tests/test_altgraph.py b/python/altgraph/altgraph_tests/test_altgraph.py new file mode 100644 index 000000000..2ca6b251e --- /dev/null +++ b/python/altgraph/altgraph_tests/test_altgraph.py @@ -0,0 +1,45 @@ +#!/usr/bin/env py.test +import os +import sys + +from altgraph import Graph, GraphAlgo +import unittest + +class BasicTests (unittest.TestCase): + def setUp(self): + self.edges = [ + (1,2), (2,4), (1,3), (2,4), (3,4), (4,5), (6,5), (6,14), (14,15), + (6, 15), (5,7), (7, 8), (7,13), (12,8), (8,13), (11,12), (11,9), + (13,11), (9,13), (13,10) + ] + + # these are the edges + self.store = {} + self.g = Graph.Graph() + for head, tail in self.edges: + self.store[head] = self.store[tail] = None + self.g.add_edge(head, tail) + + def test_num_edges(self): + # check the parameters + self.assertEqual(self.g.number_of_nodes(), len(self.store)) + self.assertEqual(self.g.number_of_edges(), len(self.edges)) + + def test_forw_bfs(self): + # do a forward bfs + self.assertEqual( self.g.forw_bfs(1), + [1, 2, 3, 4, 5, 7, 8, 13, 11, 10, 12, 9]) + + + def test_get_hops(self): + # diplay the hops and hop numbers between nodes + self.assertEqual(self.g.get_hops(1, 8), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)]) + + def test_shortest_path(self): + self.assertEqual(GraphAlgo.shortest_path(self.g, 1, 12), + [1, 2, 4, 5, 7, 13, 11, 12]) + + +if __name__ == "__main__": # pragma: no cover + unittest.main() diff --git a/python/altgraph/altgraph_tests/test_dot.py b/python/altgraph/altgraph_tests/test_dot.py new file mode 100644 index 000000000..83993dad5 --- /dev/null +++ b/python/altgraph/altgraph_tests/test_dot.py @@ -0,0 +1,370 @@ +import unittest +import os + +from altgraph import Dot +from altgraph import Graph +from altgraph import GraphError + + +class TestDot (unittest.TestCase): + + def test_constructor(self): + g = Graph.Graph([ + (1,2), + (1,3), + (1,4), + (2,4), + (2,6), + (2,7), + (7,4), + (6,1), + ] + ) + + dot = Dot.Dot(g) + + self.assertEqual(dot.name, 'G') + self.assertEqual(dot.attr, {}) + self.assertEqual(dot.temp_dot, 'tmp_dot.dot') + self.assertEqual(dot.temp_neo, 'tmp_neo.dot') + self.assertEqual(dot.dot, 'dot') + self.assertEqual(dot.dotty, 'dotty') + self.assertEqual(dot.neato, 'neato') + self.assertEqual(dot.type, 'digraph') + + self.assertEqual(dot.nodes, dict([(x, {}) for x in g])) + + edges = {} + for head in g: + edges[head] = {} + for tail in g.out_nbrs(head): + edges[head][tail] = {} + + self.assertEqual(dot.edges[1], edges[1]) + self.assertEqual(dot.edges, edges) + + + dot = Dot.Dot(g, nodes=[1,2], + edgefn=lambda node: list(sorted(g.out_nbrs(node)))[:-1], + nodevisitor=lambda node: {'label': node}, + edgevisitor=lambda head, tail: {'label': (head, tail) }, + name="testgraph", + dot='/usr/local/bin/dot', + dotty='/usr/local/bin/dotty', + neato='/usr/local/bin/neato', + graphtype="graph") + + self.assertEqual(dot.name, 'testgraph') + self.assertEqual(dot.attr, {}) + self.assertEqual(dot.temp_dot, 'tmp_dot.dot') + self.assertEqual(dot.temp_neo, 'tmp_neo.dot') + self.assertEqual(dot.dot, '/usr/local/bin/dot') + self.assertEqual(dot.dotty, '/usr/local/bin/dotty') + self.assertEqual(dot.neato, '/usr/local/bin/neato') + self.assertEqual(dot.type, 'graph') + + self.assertEqual(dot.nodes, dict([(x, {'label': x}) for x in [1,2]])) + + edges = {} + for head in [1,2]: + edges[head] = {} + for tail in list(sorted(g.out_nbrs(head)))[:-1]: + if tail not in [1,2]: continue + edges[head][tail] = {'label': (head, tail) } + + self.assertEqual(dot.edges[1], edges[1]) + self.assertEqual(dot.edges, edges) + + self.assertRaises(GraphError, Dot.Dot, g, nodes=[1,2, 9]) + + def test_style(self): + g = Graph.Graph([]) + + dot = Dot.Dot(g) + + self.assertEqual(dot.attr, {}) + + dot.style(key='value') + self.assertEqual(dot.attr, {'key': 'value'}) + + dot.style(key2='value2') + self.assertEqual(dot.attr, {'key2': 'value2'}) + + def test_node_style(self): + g = Graph.Graph([ + (1,2), + (1,3), + (1,4), + (2,4), + (2,6), + (2,7), + (7,4), + (6,1), + ] + ) + + dot = Dot.Dot(g) + + self.assertEqual(dot.nodes[1], {}) + + dot.node_style(1, key='value') + self.assertEqual(dot.nodes[1], {'key': 'value'}) + + dot.node_style(1, key2='value2') + self.assertEqual(dot.nodes[1], {'key2': 'value2'}) + self.assertEqual(dot.nodes[2], {}) + + dot.all_node_style(key3='value3') + for n in g: + self.assertEqual(dot.nodes[n], {'key3': 'value3'}) + + self.assertTrue(9 not in dot.nodes) + dot.node_style(9, key='value') + self.assertEqual(dot.nodes[9], {'key': 'value'}) + + def test_edge_style(self): + g = Graph.Graph([ + (1,2), + (1,3), + (1,4), + (2,4), + (2,6), + (2,7), + (7,4), + (6,1), + ] + ) + + dot = Dot.Dot(g) + + self.assertEqual(dot.edges[1][2], {}) + dot.edge_style(1,2, foo='bar') + self.assertEqual(dot.edges[1][2], {'foo': 'bar'}) + + dot.edge_style(1,2, foo2='2bar') + self.assertEqual(dot.edges[1][2], {'foo2': '2bar'}) + + self.assertEqual(dot.edges[1][3], {}) + + self.assertFalse(6 in dot.edges[1]) + dot.edge_style(1,6, foo2='2bar') + self.assertEqual(dot.edges[1][6], {'foo2': '2bar'}) + + self.assertRaises(GraphError, dot.edge_style, 1, 9, a=1) + self.assertRaises(GraphError, dot.edge_style, 9, 1, a=1) + + + def test_iter(self): + g = Graph.Graph([ + (1,2), + (1,3), + (1,4), + (2,4), + (2,6), + (2,7), + (7,4), + (6,1), + ] + ) + + dot = Dot.Dot(g) + dot.style(graph="foobar") + dot.node_style(1, key='value') + dot.node_style(2, key='another', key2='world') + dot.edge_style(1,4, key1='value1', key2='value2') + dot.edge_style(2,4, key1='valueA') + + self.assertEqual(list(iter(dot)), list(dot.iterdot())) + + for item in dot.iterdot(): + self.assertTrue(isinstance(item, str)) + + first = list(dot.iterdot())[0] + self.assertEqual(first, "digraph %s {\n"%(dot.name,)) + + dot.type = 'graph' + first = list(dot.iterdot())[0] + self.assertEqual(first, "graph %s {\n"%(dot.name,)) + + dot.type = 'foo' + self.assertRaises(GraphError, list, dot.iterdot()) + dot.type = 'digraph' + + self.assertEqual(list(dot), [ + 'digraph G {\n', + 'graph="foobar";', + '\n', + + '\t"1" [', + 'key="value",', + '];\n', + + '\t"2" [', + 'key="another",', + 'key2="world",', + '];\n', + + '\t"3" [', + '];\n', + + '\t"4" [', + '];\n', + + '\t"6" [', + '];\n', + + '\t"7" [', + '];\n', + + '\t"1" -> "2" [', + '];\n', + + '\t"1" -> "3" [', + '];\n', + + '\t"1" -> "4" [', + 'key1="value1",', + 'key2="value2",', + '];\n', + + '\t"2" -> "4" [', + 'key1="valueA",', + '];\n', + + '\t"2" -> "6" [', + '];\n', + + '\t"2" -> "7" [', + '];\n', + + '\t"6" -> "1" [', + '];\n', + + '\t"7" -> "4" [', + '];\n', + '}\n']) + + + def test_save(self): + g = Graph.Graph([ + (1,2), + (1,3), + (1,4), + (2,4), + (2,6), + (2,7), + (7,4), + (6,1), + ] + ) + + dot = Dot.Dot(g) + dot.style(graph="foobar") + dot.node_style(1, key='value') + dot.node_style(2, key='another', key2='world') + dot.edge_style(1,4, key1='value1', key2='value2') + dot.edge_style(2,4, key1='valueA') + + fn = 'test_dot.dot' + self.assertTrue(not os.path.exists(fn)) + + try: + dot.save_dot(fn) + + fp = open(fn, 'r') + data = fp.read() + fp.close() + self.assertEqual(data, ''.join(dot)) + + finally: + if os.path.exists(fn): + os.unlink(fn) + + + def test_img(self): + g = Graph.Graph([ + (1,2), + (1,3), + (1,4), + (2,4), + (2,6), + (2,7), + (7,4), + (6,1), + ] + ) + + dot = Dot.Dot(g, dot='/usr/local/bin/!!dot', dotty='/usr/local/bin/!!dotty', neato='/usr/local/bin/!!neato') + dot.style(size='10,10', rankdir='RL', page='5, 5' , ranksep=0.75) + dot.node_style(1, label='BASE_NODE',shape='box', color='blue') + dot.node_style(2, style='filled', fillcolor='red') + dot.edge_style(1,4, style='dotted') + dot.edge_style(2,4, arrowhead='dot', label='binds', labelangle='90') + + system_cmds = [] + def fake_system(cmd): + system_cmds.append(cmd) + return None + + try: + real_system = os.system + os.system = fake_system + + system_cmds = [] + dot.save_img('foo') + self.assertEqual(system_cmds, ['/usr/local/bin/!!dot -Tgif tmp_dot.dot -o foo.gif']) + + system_cmds = [] + dot.save_img('foo', file_type='jpg') + self.assertEqual(system_cmds, ['/usr/local/bin/!!dot -Tjpg tmp_dot.dot -o foo.jpg']) + + system_cmds = [] + dot.save_img('bar', file_type='jpg', mode='neato') + self.assertEqual(system_cmds, [ + '/usr/local/bin/!!neato -o tmp_dot.dot tmp_neo.dot', + '/usr/local/bin/!!dot -Tjpg tmp_dot.dot -o bar.jpg', + ]) + + system_cmds = [] + dot.display() + self.assertEqual(system_cmds, [ + '/usr/local/bin/!!dotty tmp_dot.dot' + ]) + + system_cmds = [] + dot.display(mode='neato') + self.assertEqual(system_cmds, [ + '/usr/local/bin/!!neato -o tmp_dot.dot tmp_neo.dot', + '/usr/local/bin/!!dotty tmp_dot.dot' + ]) + + finally: + if os.path.exists(dot.temp_dot): + os.unlink(dot.temp_dot) + if os.path.exists(dot.temp_neo): + os.unlink(dot.temp_neo) + os.system = real_system + + if os.path.exists('/usr/local/bin/dot') and os.path.exists('/usr/local/bin/neato'): + try: + dot.dot='/usr/local/bin/dot' + dot.neato='/usr/local/bin/neato' + self.assertFalse(os.path.exists('foo.gif')) + dot.save_img('foo') + self.assertTrue(os.path.exists('foo.gif')) + os.unlink('foo.gif') + + self.assertFalse(os.path.exists('foo.gif')) + dot.save_img('foo', mode='neato') + self.assertTrue(os.path.exists('foo.gif')) + os.unlink('foo.gif') + + finally: + if os.path.exists(dot.temp_dot): + os.unlink(dot.temp_dot) + if os.path.exists(dot.temp_neo): + os.unlink(dot.temp_neo) + + +if __name__ == "__main__": # pragma: no cover + unittest.main() diff --git a/python/altgraph/altgraph_tests/test_graph.py b/python/altgraph/altgraph_tests/test_graph.py new file mode 100644 index 000000000..553549f5a --- /dev/null +++ b/python/altgraph/altgraph_tests/test_graph.py @@ -0,0 +1,644 @@ +import unittest + +from altgraph import GraphError +from altgraph.Graph import Graph + +class TestGraph (unittest.TestCase): + + def test_nodes(self): + graph = Graph() + + self.assertEqual(graph.node_list(), []) + + o1 = object() + o1b = object() + o2 = object() + graph.add_node(1, o1) + graph.add_node(1, o1b) + graph.add_node(2, o2) + graph.add_node(3) + + self.assertRaises(TypeError, graph.add_node, []) + + self.assertTrue(graph.node_data(1) is o1) + self.assertTrue(graph.node_data(2) is o2) + self.assertTrue(graph.node_data(3) is None) + + self.assertTrue(1 in graph) + self.assertTrue(2 in graph) + self.assertTrue(3 in graph) + + self.assertEqual(graph.number_of_nodes(), 3) + self.assertEqual(graph.number_of_hidden_nodes(), 0) + self.assertEqual(graph.hidden_node_list(), []) + self.assertEqual(list(sorted(graph)), [1, 2, 3]) + + graph.hide_node(1) + graph.hide_node(2) + graph.hide_node(3) + + + self.assertEqual(graph.number_of_nodes(), 0) + self.assertEqual(graph.number_of_hidden_nodes(), 3) + self.assertEqual(list(sorted(graph.hidden_node_list())), [1, 2, 3]) + + self.assertFalse(1 in graph) + self.assertFalse(2 in graph) + self.assertFalse(3 in graph) + + graph.add_node(1) + self.assertFalse(1 in graph) + + graph.restore_node(1) + self.assertTrue(1 in graph) + self.assertFalse(2 in graph) + self.assertFalse(3 in graph) + + graph.restore_all_nodes() + self.assertTrue(1 in graph) + self.assertTrue(2 in graph) + self.assertTrue(3 in graph) + + self.assertEqual(list(sorted(graph.node_list())), [1, 2, 3]) + + v = graph.describe_node(1) + self.assertEqual(v, (1, o1, [], [])) + + def test_edges(self): + graph = Graph() + graph.add_node(1) + graph.add_node(2) + graph.add_node(3) + graph.add_node(4) + graph.add_node(5) + + self.assertTrue(isinstance(graph.edge_list(), list)) + + graph.add_edge(1, 2) + graph.add_edge(4, 5, 'a') + + self.assertRaises(GraphError, graph.add_edge, 'a', 'b', create_nodes=False) + + self.assertEqual(graph.number_of_hidden_edges(), 0) + self.assertEqual(graph.number_of_edges(), 2) + e = graph.edge_by_node(1, 2) + self.assertTrue(isinstance(e, int)) + graph.hide_edge(e) + self.assertEqual(graph.number_of_hidden_edges(), 1) + self.assertEqual(graph.number_of_edges(), 1) + e2 = graph.edge_by_node(1, 2) + self.assertTrue(e2 is None) + + graph.restore_edge(e) + e2 = graph.edge_by_node(1, 2) + self.assertEqual(e, e2) + self.assertEqual(graph.number_of_hidden_edges(), 0) + + self.assertEqual(graph.number_of_edges(), 2) + + e1 = graph.edge_by_node(1, 2) + e2 = graph.edge_by_node(4, 5) + graph.hide_edge(e1) + graph.hide_edge(e2) + + self.assertEqual(graph.number_of_edges(), 0) + graph.restore_all_edges() + self.assertEqual(graph.number_of_edges(), 2) + + self.assertEqual(graph.edge_by_id(e1), (1,2)) + self.assertRaises(GraphError, graph.edge_by_id, (e1+1)*(e2+1)+1) + + self.assertEqual(list(sorted(graph.edge_list())), [e1, e2]) + + self.assertEqual(graph.describe_edge(e1), (e1, 1, 1, 2)) + self.assertEqual(graph.describe_edge(e2), (e2, 'a', 4, 5)) + + self.assertEqual(graph.edge_data(e1), 1) + self.assertEqual(graph.edge_data(e2), 'a') + + self.assertEqual(graph.head(e2), 4) + self.assertEqual(graph.tail(e2), 5) + + graph.add_edge(1, 3) + graph.add_edge(1, 5) + graph.add_edge(4, 1) + + self.assertEqual(list(sorted(graph.out_nbrs(1))), [2, 3, 5]) + self.assertEqual(list(sorted(graph.inc_nbrs(1))), [4]) + self.assertEqual(list(sorted(graph.inc_nbrs(5))), [1, 4]) + self.assertEqual(list(sorted(graph.all_nbrs(1))), [2, 3, 4, 5]) + + graph.add_edge(5, 1) + self.assertEqual(list(sorted(graph.all_nbrs(5))), [1, 4]) + + self.assertEqual(graph.out_degree(1), 3) + self.assertEqual(graph.inc_degree(2), 1) + self.assertEqual(graph.inc_degree(5), 2) + self.assertEqual(graph.all_degree(5), 3) + + v = graph.out_edges(4) + self.assertTrue(isinstance(v, list)) + self.assertEqual(graph.edge_by_id(v[0]), (4, 5)) + + v = graph.out_edges(1) + for e in v: + self.assertEqual(graph.edge_by_id(e)[0], 1) + + v = graph.inc_edges(1) + self.assertTrue(isinstance(v, list)) + self.assertEqual(graph.edge_by_id(v[0]), (4, 1)) + + v = graph.inc_edges(5) + for e in v: + self.assertEqual(graph.edge_by_id(e)[1], 5) + + v = graph.all_edges(5) + for e in v: + self.assertTrue(graph.edge_by_id(e)[1] == 5 or graph.edge_by_id(e)[0] == 5) + + e1 = graph.edge_by_node(1, 2) + self.assertTrue(isinstance(e1, int)) + graph.hide_node(1) + self.assertRaises(GraphError, graph.edge_by_node, 1, 2) + graph.restore_node(1) + e2 = graph.edge_by_node(1, 2) + self.assertEqual(e1, e2) + + + + def test_toposort(self): + graph = Graph() + graph.add_node(1) + graph.add_node(2) + graph.add_node(3) + graph.add_node(4) + graph.add_node(5) + + graph.add_edge(1, 2) + graph.add_edge(1, 3) + graph.add_edge(2, 4) + graph.add_edge(3, 5) + + ok, result = graph.forw_topo_sort() + self.assertTrue(ok) + for idx in range(1, 6): + self.assertTrue(idx in result) + + self.assertTrue(result.index(1) < result.index(2)) + self.assertTrue(result.index(1) < result.index(3)) + self.assertTrue(result.index(2) < result.index(4)) + self.assertTrue(result.index(3) < result.index(5)) + + ok, result = graph.back_topo_sort() + self.assertTrue(ok) + for idx in range(1, 6): + self.assertTrue(idx in result) + self.assertTrue(result.index(2) < result.index(1)) + self.assertTrue(result.index(3) < result.index(1)) + self.assertTrue(result.index(4) < result.index(2)) + self.assertTrue(result.index(5) < result.index(3)) + + + # Same graph as before, but with edges + # reversed, which means we should get + # the same results as before if using + # back_topo_sort rather than forw_topo_sort + # (and v.v.) + + graph = Graph() + graph.add_node(1) + graph.add_node(2) + graph.add_node(3) + graph.add_node(4) + graph.add_node(5) + + graph.add_edge(2, 1) + graph.add_edge(3, 1) + graph.add_edge(4, 2) + graph.add_edge(5, 3) + + ok, result = graph.back_topo_sort() + self.assertTrue(ok) + for idx in range(1, 6): + self.assertTrue(idx in result) + + self.assertTrue(result.index(1) < result.index(2)) + self.assertTrue(result.index(1) < result.index(3)) + self.assertTrue(result.index(2) < result.index(4)) + self.assertTrue(result.index(3) < result.index(5)) + + ok, result = graph.forw_topo_sort() + self.assertTrue(ok) + for idx in range(1, 6): + self.assertTrue(idx in result) + self.assertTrue(result.index(2) < result.index(1)) + self.assertTrue(result.index(3) < result.index(1)) + self.assertTrue(result.index(4) < result.index(2)) + self.assertTrue(result.index(5) < result.index(3)) + + + # Create a cycle + graph.add_edge(1, 5) + ok, result = graph.forw_topo_sort() + self.assertFalse(ok) + ok, result = graph.back_topo_sort() + self.assertFalse(ok) + + def test_bfs_subgraph(self): + graph = Graph() + graph.add_edge(1, 2) + graph.add_edge(1, 4) + graph.add_edge(2, 4) + graph.add_edge(4, 8) + graph.add_edge(4, 9) + graph.add_edge(4, 10) + graph.add_edge(8, 10) + + subgraph = graph.forw_bfs_subgraph(10) + self.assertTrue(isinstance(subgraph, Graph)) + self.assertEqual(subgraph.number_of_nodes(), 1) + self.assertTrue(10 in subgraph) + self.assertEqual(subgraph.number_of_edges(), 0) + + subgraph = graph.forw_bfs_subgraph(4) + self.assertTrue(isinstance(subgraph, Graph)) + self.assertEqual(subgraph.number_of_nodes(), 4) + self.assertTrue(4 in subgraph) + self.assertTrue(8 in subgraph) + self.assertTrue(9 in subgraph) + self.assertTrue(10 in subgraph) + self.assertEqual(subgraph.number_of_edges(), 4) + e = subgraph.edge_by_node(4, 8) + e = subgraph.edge_by_node(4, 9) + e = subgraph.edge_by_node(4, 10) + e = subgraph.edge_by_node(8, 10) + + # same graph as before, but switch around + # edges. This results in the same test results + # but now for back_bfs_subgraph rather than + # forw_bfs_subgraph + + graph = Graph() + graph.add_edge(2, 1) + graph.add_edge(4, 1) + graph.add_edge(4, 2) + graph.add_edge(8, 4) + graph.add_edge(9, 4) + graph.add_edge(10, 4) + graph.add_edge(10, 8) + + subgraph = graph.back_bfs_subgraph(10) + self.assertTrue(isinstance(subgraph, Graph)) + self.assertEqual(subgraph.number_of_nodes(), 1) + self.assertTrue(10 in subgraph) + self.assertEqual(subgraph.number_of_edges(), 0) + + subgraph = graph.back_bfs_subgraph(4) + self.assertTrue(isinstance(subgraph, Graph)) + self.assertEqual(subgraph.number_of_nodes(), 4) + self.assertTrue(4 in subgraph) + self.assertTrue(8 in subgraph) + self.assertTrue(9 in subgraph) + self.assertTrue(10 in subgraph) + self.assertEqual(subgraph.number_of_edges(), 4) + e = subgraph.edge_by_node(4, 8) + e = subgraph.edge_by_node(4, 9) + e = subgraph.edge_by_node(4, 10) + e = subgraph.edge_by_node(8, 10) + + def test_iterdfs(self): + graph = Graph() + graph.add_edge("1", "1.1") + graph.add_edge("1", "1.2") + graph.add_edge("1", "1.3") + graph.add_edge("1.1", "1.1.1") + graph.add_edge("1.1", "1.1.2") + graph.add_edge("1.2", "1.2.1") + graph.add_edge("1.2", "1.2.2") + graph.add_edge("1.2.2", "1.2.2.1") + graph.add_edge("1.2.2", "1.2.2.2") + graph.add_edge("1.2.2", "1.2.2.3") + + result = list(graph.iterdfs("1")) + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1', '1.1', '1.1.2', '1.1.1' + ]) + result = list(graph.iterdfs("1", "1.2.1")) + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1' + ]) + + result = graph.forw_dfs("1") + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1', '1.1', '1.1.2', '1.1.1' + ]) + result = graph.forw_dfs("1", "1.2.1") + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1' + ]) + + graph = Graph() + graph.add_edge("1.1", "1") + graph.add_edge("1.2", "1") + graph.add_edge("1.3", "1") + graph.add_edge("1.1.1", "1.1") + graph.add_edge("1.1.2", "1.1") + graph.add_edge("1.2.1", "1.2") + graph.add_edge("1.2.2", "1.2") + graph.add_edge("1.2.2.1", "1.2.2") + graph.add_edge("1.2.2.2", "1.2.2") + graph.add_edge("1.2.2.3", "1.2.2") + + result = list(graph.iterdfs("1", forward=False)) + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1', '1.1', '1.1.2', '1.1.1' + ]) + result = list(graph.iterdfs("1", "1.2.1", forward=False)) + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1' + ]) + result = graph.back_dfs("1") + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1', '1.1', '1.1.2', '1.1.1' + ]) + result = graph.back_dfs("1", "1.2.1") + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1' + ]) + + + # Introduce cyle: + graph.add_edge("1", "1.2") + result = list(graph.iterdfs("1", forward=False)) + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1', '1.1', '1.1.2', '1.1.1' + ]) + + result = graph.back_dfs("1") + self.assertEqual(result, [ + '1', '1.3', '1.2', '1.2.2', '1.2.2.3', '1.2.2.2', + '1.2.2.1', '1.2.1', '1.1', '1.1.2', '1.1.1' + ]) + + + def test_iterdata(self): + graph = Graph() + graph.add_node("1", "I") + graph.add_node("1.1", "I.I") + graph.add_node("1.2", "I.II") + graph.add_node("1.3", "I.III") + graph.add_node("1.1.1", "I.I.I") + graph.add_node("1.1.2", "I.I.II") + graph.add_node("1.2.1", "I.II.I") + graph.add_node("1.2.2", "I.II.II") + graph.add_node("1.2.2.1", "I.II.II.I") + graph.add_node("1.2.2.2", "I.II.II.II") + graph.add_node("1.2.2.3", "I.II.II.III") + + graph.add_edge("1", "1.1") + graph.add_edge("1", "1.2") + graph.add_edge("1", "1.3") + graph.add_edge("1.1", "1.1.1") + graph.add_edge("1.1", "1.1.2") + graph.add_edge("1.2", "1.2.1") + graph.add_edge("1.2", "1.2.2") + graph.add_edge("1.2.2", "1.2.2.1") + graph.add_edge("1.2.2", "1.2.2.2") + graph.add_edge("1.2.2", "1.2.2.3") + + result = list(graph.iterdata("1", forward=True)) + self.assertEqual(result, [ + 'I', 'I.III', 'I.II', 'I.II.II', 'I.II.II.III', 'I.II.II.II', + 'I.II.II.I', 'I.II.I', 'I.I', 'I.I.II', 'I.I.I' + ]) + + result = list(graph.iterdata("1", end="1.2.1", forward=True)) + self.assertEqual(result, [ + 'I', 'I.III', 'I.II', 'I.II.II', 'I.II.II.III', 'I.II.II.II', + 'I.II.II.I', 'I.II.I' + ]) + + result = list(graph.iterdata("1", condition=lambda n: len(n) < 6, forward=True)) + self.assertEqual(result, [ + 'I', 'I.III', 'I.II', + 'I.I', 'I.I.I' + ]) + + + # And the revese option: + graph = Graph() + graph.add_node("1", "I") + graph.add_node("1.1", "I.I") + graph.add_node("1.2", "I.II") + graph.add_node("1.3", "I.III") + graph.add_node("1.1.1", "I.I.I") + graph.add_node("1.1.2", "I.I.II") + graph.add_node("1.2.1", "I.II.I") + graph.add_node("1.2.2", "I.II.II") + graph.add_node("1.2.2.1", "I.II.II.I") + graph.add_node("1.2.2.2", "I.II.II.II") + graph.add_node("1.2.2.3", "I.II.II.III") + + graph.add_edge("1.1", "1") + graph.add_edge("1.2", "1") + graph.add_edge("1.3", "1") + graph.add_edge("1.1.1", "1.1") + graph.add_edge("1.1.2", "1.1") + graph.add_edge("1.2.1", "1.2") + graph.add_edge("1.2.2", "1.2") + graph.add_edge("1.2.2.1", "1.2.2") + graph.add_edge("1.2.2.2", "1.2.2") + graph.add_edge("1.2.2.3", "1.2.2") + + result = list(graph.iterdata("1", forward=False)) + self.assertEqual(result, [ + 'I', 'I.III', 'I.II', 'I.II.II', 'I.II.II.III', 'I.II.II.II', + 'I.II.II.I', 'I.II.I', 'I.I', 'I.I.II', 'I.I.I' + ]) + + result = list(graph.iterdata("1", end="1.2.1", forward=False)) + self.assertEqual(result, [ + 'I', 'I.III', 'I.II', 'I.II.II', 'I.II.II.III', 'I.II.II.II', + 'I.II.II.I', 'I.II.I' + ]) + + result = list(graph.iterdata("1", condition=lambda n: len(n) < 6, forward=False)) + self.assertEqual(result, [ + 'I', 'I.III', 'I.II', + 'I.I', 'I.I.I' + ]) + + def test_bfs(self): + graph = Graph() + graph.add_edge("1", "1.1") + graph.add_edge("1.1", "1.1.1") + graph.add_edge("1.1", "1.1.2") + graph.add_edge("1.1.2", "1.1.2.1") + graph.add_edge("1.1.2", "1.1.2.2") + graph.add_edge("1", "1.2") + graph.add_edge("1", "1.3") + graph.add_edge("1.2", "1.2.1") + + self.assertEqual(graph.forw_bfs("1"), + ['1', '1.1', '1.2', '1.3', '1.1.1', '1.1.2', '1.2.1', '1.1.2.1', '1.1.2.2']) + self.assertEqual(graph.forw_bfs("1", "1.1.1"), + ['1', '1.1', '1.2', '1.3', '1.1.1']) + + + # And the "reverse" graph + graph = Graph() + graph.add_edge("1.1", "1") + graph.add_edge("1.1.1", "1.1") + graph.add_edge("1.1.2", "1.1") + graph.add_edge("1.1.2.1", "1.1.2") + graph.add_edge("1.1.2.2", "1.1.2") + graph.add_edge("1.2", "1") + graph.add_edge("1.3", "1") + graph.add_edge("1.2.1", "1.2") + + self.assertEqual(graph.back_bfs("1"), + ['1', '1.1', '1.2', '1.3', '1.1.1', '1.1.2', '1.2.1', '1.1.2.1', '1.1.2.2']) + self.assertEqual(graph.back_bfs("1", "1.1.1"), + ['1', '1.1', '1.2', '1.3', '1.1.1']) + + + + # check cycle handling + graph.add_edge("1", "1.2.1") + self.assertEqual(graph.back_bfs("1"), + ['1', '1.1', '1.2', '1.3', '1.1.1', '1.1.2', '1.2.1', '1.1.2.1', '1.1.2.2']) + + + def test_connected(self): + graph = Graph() + graph.add_node(1) + graph.add_node(2) + graph.add_node(3) + graph.add_node(4) + + self.assertFalse(graph.connected()) + + graph.add_edge(1, 2) + graph.add_edge(3, 4) + self.assertFalse(graph.connected()) + + graph.add_edge(2, 3) + graph.add_edge(4, 1) + self.assertTrue(graph.connected()) + + def test_edges_complex(self): + g = Graph() + g.add_edge(1, 2) + e = g.edge_by_node(1,2) + g.hide_edge(e) + g.hide_node(2) + self.assertRaises(GraphError, g.restore_edge, e) + + g.restore_all_edges() + self.assertRaises(GraphError, g.edge_by_id, e) + + def test_clust_coef(self): + g = Graph() + g.add_edge(1, 2) + g.add_edge(1, 3) + g.add_edge(1, 4) + self.assertEqual(g.clust_coef(1), 0) + + g.add_edge(2, 5) + g.add_edge(3, 5) + g.add_edge(4, 5) + self.assertEqual(g.clust_coef(1), 0) + + g.add_edge(2, 3) + self.assertEqual(g.clust_coef(1), 1./6) + g.add_edge(2, 4) + self.assertEqual(g.clust_coef(1), 2./6) + g.add_edge(4, 2) + self.assertEqual(g.clust_coef(1), 3./6) + + g.add_edge(2, 3) + g.add_edge(2, 4) + g.add_edge(3, 4) + g.add_edge(3, 2) + g.add_edge(4, 2) + g.add_edge(4, 3) + self.assertEqual(g.clust_coef(1), 1) + + + def test_get_hops(self): + graph = Graph() + graph.add_edge(1, 2) + graph.add_edge(1, 3) + graph.add_edge(2, 4) + graph.add_edge(4, 5) + graph.add_edge(5, 7) + graph.add_edge(7, 8) + + self.assertEqual(graph.get_hops(1), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)]) + + self.assertEqual(graph.get_hops(1, 5), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3)]) + + graph.add_edge(5, 1) + graph.add_edge(7, 1) + graph.add_edge(7, 4) + + self.assertEqual(graph.get_hops(1), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)]) + + # And the reverse graph + graph = Graph() + graph.add_edge(2, 1) + graph.add_edge(3, 1) + graph.add_edge(4, 2) + graph.add_edge(5, 4) + graph.add_edge(7, 5) + graph.add_edge(8, 7) + + self.assertEqual(graph.get_hops(1, forward=False), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)]) + + self.assertEqual(graph.get_hops(1, 5, forward=False), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3)]) + + graph.add_edge(1, 5) + graph.add_edge(1, 7) + graph.add_edge(4, 7) + + self.assertEqual(graph.get_hops(1, forward=False), + [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)]) + + + def test_constructor(self): + graph = Graph(iter([ + (1, 2), + (2, 3, 'a'), + (1, 3), + (3, 4), + ])) + self.assertEqual(graph.number_of_nodes(), 4) + self.assertEqual(graph.number_of_edges(), 4) + try: + graph.edge_by_node(1,2) + graph.edge_by_node(2,3) + graph.edge_by_node(1,3) + graph.edge_by_node(3,4) + except GraphError: + self.fail("Incorrect graph") + + self.assertEqual(graph.edge_data(graph.edge_by_node(2, 3)), 'a') + + self.assertRaises(GraphError, Graph, [(1,2,3,4)]) + +if __name__ == "__main__": # pragma: no cover + unittest.main() diff --git a/python/altgraph/altgraph_tests/test_graphstat.py b/python/altgraph/altgraph_tests/test_graphstat.py new file mode 100644 index 000000000..b628b6f24 --- /dev/null +++ b/python/altgraph/altgraph_tests/test_graphstat.py @@ -0,0 +1,70 @@ +import unittest + +from altgraph import GraphStat +from altgraph import Graph +import sys + +class TestDegreesDist (unittest.TestCase): + + def test_simple(self): + a = Graph.Graph() + self.assertEqual(GraphStat.degree_dist(a), []) + + a.add_node(1) + a.add_node(2) + a.add_node(3) + + self.assertEqual(GraphStat.degree_dist(a), GraphStat._binning([0, 0, 0])) + + for x in range(100): + a.add_node(x) + + for x in range(1, 100): + for y in range(1, 50): + if x % y == 0: + a.add_edge(x, y) + + counts_inc = [] + counts_out = [] + for n in a: + counts_inc.append(a.inc_degree(n)) + counts_out.append(a.out_degree(n)) + + self.assertEqual(GraphStat.degree_dist(a), GraphStat._binning(counts_out)) + self.assertEqual(GraphStat.degree_dist(a, mode='inc'), GraphStat._binning(counts_inc)) + +class TestBinning (unittest.TestCase): + def test_simple(self): + + # Binning [0, 100) into 10 bins + a = list(range(100)) + out = GraphStat._binning(a, limits=(0, 100), bin_num=10) + + self.assertEqual(out, + [ (x*1.0, 10) for x in range(5, 100, 10) ]) + + + # Check that outliers are ignored. + a = list(range(100)) + out = GraphStat._binning(a, limits=(0, 90), bin_num=9) + + self.assertEqual(out, + [ (x*1.0, 10) for x in range(5, 90, 10) ]) + + + out = GraphStat._binning(a, limits=(0, 100), bin_num=15) + binSize = 100 / 15.0 + result = [0]*15 + for i in range(100): + bin = int(i/binSize) + try: + result[bin] += 1 + except IndexError: + pass + + result = [ (i * binSize + binSize/2, result[i]) for i in range(len(result))] + + self.assertEqual(result, out) + +if __name__ == "__main__": # pragma: no cover + unittest.main() diff --git a/python/altgraph/altgraph_tests/test_graphutil.py b/python/altgraph/altgraph_tests/test_graphutil.py new file mode 100644 index 000000000..c1166237c --- /dev/null +++ b/python/altgraph/altgraph_tests/test_graphutil.py @@ -0,0 +1,140 @@ +import unittest +from altgraph import GraphUtil +from altgraph import Graph, GraphError + +class TestGraphUtil (unittest.TestCase): + + def test_generate_random(self): + g = GraphUtil.generate_random_graph(10, 50) + self.assertEqual(g.number_of_nodes(), 10) + self.assertEqual(g.number_of_edges(), 50) + + seen = set() + + for e in g.edge_list(): + h, t = g.edge_by_id(e) + self.assertFalse(h == t) + self.assertTrue((h, t) not in seen) + seen.add((h, t)) + + g = GraphUtil.generate_random_graph(5, 30, multi_edges=True) + self.assertEqual(g.number_of_nodes(), 5) + self.assertEqual(g.number_of_edges(), 30) + + seen = set() + + for e in g.edge_list(): + h, t = g.edge_by_id(e) + self.assertFalse(h == t) + if (h, t) in seen: + break + seen.add((h, t)) + + else: + self.fail("no duplicates?") + + g = GraphUtil.generate_random_graph(5, 21, self_loops=True) + self.assertEqual(g.number_of_nodes(), 5) + self.assertEqual(g.number_of_edges(), 21) + + seen = set() + + for e in g.edge_list(): + h, t = g.edge_by_id(e) + self.assertFalse((h, t) in seen) + if h == t: + break + seen.add((h, t)) + + else: + self.fail("no self loops?") + + self.assertRaises(GraphError, GraphUtil.generate_random_graph, 5, 21) + g = GraphUtil.generate_random_graph(5, 21, True) + self.assertRaises(GraphError, GraphUtil.generate_random_graph, 5, 26, True) + + def test_generate_scale_free(self): + graph = GraphUtil.generate_scale_free_graph(50, 10) + self.assertEqual(graph.number_of_nodes(), 500) + + counts = {} + for node in graph: + degree = graph.inc_degree(node) + try: + counts[degree] += 1 + except KeyError: + counts[degree] = 1 + + total_counts = sum(counts.values()) + P = {} + for degree, count in counts.items(): + P[degree] = count * 1.0 / total_counts + + # XXX: use algoritm + # to check if P[degree] ~ degree ** G (for some G) + + #print sorted(P.items()) + + #print sorted([(count, degree) for degree, count in counts.items()]) + + #self.fail("missing tests for GraphUtil.generate_scale_free_graph") + + def test_filter_stack(self): + g = Graph.Graph() + g.add_node("1", "N.1") + g.add_node("1.1", "N.1.1") + g.add_node("1.1.1", "N.1.1.1") + g.add_node("1.1.2", "N.1.1.2") + g.add_node("1.1.3", "N.1.1.3") + g.add_node("1.1.1.1", "N.1.1.1.1") + g.add_node("1.1.1.2", "N.1.1.1.2") + g.add_node("1.1.2.1", "N.1.1.2.1") + g.add_node("1.1.2.2", "N.1.1.2.2") + g.add_node("1.1.2.3", "N.1.1.2.3") + g.add_node("2", "N.2") + + g.add_edge("1", "1.1") + g.add_edge("1.1", "1.1.1") + g.add_edge("1.1", "1.1.2") + g.add_edge("1.1", "1.1.3") + g.add_edge("1.1.1", "1.1.1.1") + g.add_edge("1.1.1", "1.1.1.2") + g.add_edge("1.1.2", "1.1.2.1") + g.add_edge("1.1.2", "1.1.2.2") + g.add_edge("1.1.2", "1.1.2.3") + + v, r, o = GraphUtil.filter_stack(g, "1", [ + lambda n: n != "N.1.1.1", lambda n: n != "N.1.1.2.3" ]) + + self.assertEqual(v, + set(["1", "1.1", "1.1.1", "1.1.2", "1.1.3", + "1.1.1.1", "1.1.1.2", "1.1.2.1", "1.1.2.2", + "1.1.2.3"])) + self.assertEqual(r, set([ + "1.1.1", "1.1.2.3"])) + + o.sort() + self.assertEqual(o, + [ + ("1.1", "1.1.1.1"), + ("1.1", "1.1.1.2") + ]) + + v, r, o = GraphUtil.filter_stack(g, "1", [ + lambda n: n != "N.1.1.1", lambda n: n != "N.1.1.1.2" ]) + + self.assertEqual(v, + set(["1", "1.1", "1.1.1", "1.1.2", "1.1.3", + "1.1.1.1", "1.1.1.2", "1.1.2.1", "1.1.2.2", + "1.1.2.3"])) + self.assertEqual(r, set([ + "1.1.1", "1.1.1.2"])) + + self.assertEqual(o, + [ + ("1.1", "1.1.1.1"), + ]) + + +if __name__ == "__main__": # pragma: no cover + unittest.main() diff --git a/python/altgraph/altgraph_tests/test_object_graph.py b/python/altgraph/altgraph_tests/test_object_graph.py new file mode 100644 index 000000000..9035607e7 --- /dev/null +++ b/python/altgraph/altgraph_tests/test_object_graph.py @@ -0,0 +1,349 @@ +import unittest +import sys +from altgraph.ObjectGraph import ObjectGraph +from altgraph.Graph import Graph + +try: + from StringIO import StringIO +except ImportError: + from io import StringIO + + +class Node (object): + def __init__(self, graphident): + self.graphident = graphident + +class SubNode (Node): + pass + +class ArgNode (object): + def __init__(self, graphident, *args, **kwds): + self.graphident = graphident + self.args = args + self.kwds = kwds + + def __repr__(self): + return ''%(self.graphident,) + +class TestObjectGraph (unittest.TestCase): + + def test_constructor(self): + graph = ObjectGraph() + self.assertTrue(isinstance(graph, ObjectGraph)) + + g = Graph() + graph = ObjectGraph(g) + self.assertTrue(graph.graph is g) + self.assertEqual(graph.debug, 0) + self.assertEqual(graph.indent, 0) + + graph = ObjectGraph(debug=5) + self.assertEqual(graph.debug, 5) + + def test_repr(self): + graph = ObjectGraph() + self.assertEqual(repr(graph), '') + + + def testNodes(self): + graph = ObjectGraph() + n1 = Node("n1") + n2 = Node("n2") + n3 = Node("n3") + n4 = Node("n4") + + n1b = Node("n1") + + self.assertTrue(graph.getIdent(graph) is graph) + self.assertTrue(graph.getRawIdent(graph) is graph) + + graph.addNode(n1) + graph.addNode(n2) + graph.addNode(n3) + + self.assertTrue(n1 in graph) + self.assertFalse(n4 in graph) + self.assertTrue("n1" in graph) + self.assertFalse("n4" in graph) + + self.assertTrue(graph.findNode(n1) is n1) + self.assertTrue(graph.findNode(n1b) is n1) + self.assertTrue(graph.findNode(n2) is n2) + self.assertTrue(graph.findNode(n4) is None) + self.assertTrue(graph.findNode("n1") is n1) + self.assertTrue(graph.findNode("n2") is n2) + self.assertTrue(graph.findNode("n4") is None) + + self.assertEqual(graph.getRawIdent(n1), "n1") + self.assertEqual(graph.getRawIdent(n1b), "n1") + self.assertEqual(graph.getRawIdent(n4), "n4") + self.assertEqual(graph.getRawIdent("n1"), None) + + self.assertEqual(graph.getIdent(n1), "n1") + self.assertEqual(graph.getIdent(n1b), "n1") + self.assertEqual(graph.getIdent(n4), "n4") + self.assertEqual(graph.getIdent("n1"), "n1") + + self.assertTrue(n3 in graph) + graph.removeNode(n3) + self.assertTrue(n3 not in graph) + graph.addNode(n3) + self.assertTrue(n3 in graph) + + n = graph.createNode(SubNode, "n1") + self.assertTrue(n is n1) + + n = graph.createNode(SubNode, "n8") + self.assertTrue(isinstance(n, SubNode)) + self.assertTrue(n in graph) + self.assertTrue(graph.findNode("n8") is n) + + n = graph.createNode(ArgNode, "args", 1, 2, 3, a='a', b='b') + self.assertTrue(isinstance(n, ArgNode)) + self.assertTrue(n in graph) + self.assertTrue(graph.findNode("args") is n) + self.assertEqual(n.args, (1, 2, 3)) + self.assertEqual(n.kwds, {'a':'a', 'b':'b'}) + + def testEdges(self): + graph = ObjectGraph() + n1 = graph.createNode(ArgNode, "n1", 1) + n2 = graph.createNode(ArgNode, "n2", 1) + n3 = graph.createNode(ArgNode, "n3", 1) + n4 = graph.createNode(ArgNode, "n4", 1) + + graph.createReference(n1, n2, "n1-n2") + graph.createReference("n1", "n3", "n1-n3") + graph.createReference("n2", n3) + + g = graph.graph + e = g.edge_by_node("n1", "n2") + self.assertTrue(e is not None) + self.assertEqual(g.edge_data(e), "n1-n2") + + e = g.edge_by_node("n1", "n3") + self.assertTrue(e is not None) + self.assertEqual(g.edge_data(e), "n1-n3") + + e = g.edge_by_node("n2", "n3") + self.assertTrue(e is not None) + self.assertEqual(g.edge_data(e), None) + + e = g.edge_by_node("n1", "n4") + self.assertTrue(e is None) + + graph.removeReference(n1, n2) + e = g.edge_by_node("n1", "n2") + self.assertTrue(e is None) + + graph.removeReference("n1", "n3") + e = g.edge_by_node("n1", "n3") + self.assertTrue(e is None) + + graph.createReference(n1, n2, "foo") + e = g.edge_by_node("n1", "n2") + self.assertTrue(e is not None) + self.assertEqual(g.edge_data(e), "foo") + + + def test_flatten(self): + graph = ObjectGraph() + n1 = graph.createNode(ArgNode, "n1", 1) + n2 = graph.createNode(ArgNode, "n2", 2) + n3 = graph.createNode(ArgNode, "n3", 3) + n4 = graph.createNode(ArgNode, "n4", 4) + n5 = graph.createNode(ArgNode, "n5", 5) + n6 = graph.createNode(ArgNode, "n6", 6) + n7 = graph.createNode(ArgNode, "n7", 7) + n8 = graph.createNode(ArgNode, "n8", 8) + + graph.createReference(graph, n1) + graph.createReference(graph, n7) + graph.createReference(n1, n2) + graph.createReference(n1, n4) + graph.createReference(n2, n3) + graph.createReference(n2, n5) + graph.createReference(n5, n6) + graph.createReference(n4, n6) + graph.createReference(n4, n2) + + self.assertFalse(isinstance(graph.flatten(), list)) + + fl = list(graph.flatten()) + self.assertTrue(n1 in fl) + self.assertTrue(n2 in fl) + self.assertTrue(n3 in fl) + self.assertTrue(n4 in fl) + self.assertTrue(n5 in fl) + self.assertTrue(n6 in fl) + self.assertTrue(n7 in fl) + self.assertFalse(n8 in fl) + + fl = list(graph.flatten(start=n2)) + self.assertFalse(n1 in fl) + self.assertTrue(n2 in fl) + self.assertTrue(n3 in fl) + self.assertFalse(n4 in fl) + self.assertTrue(n5 in fl) + self.assertTrue(n6 in fl) + self.assertFalse(n7 in fl) + self.assertFalse(n8 in fl) + + graph.createReference(n1, n5) + fl = list(graph.flatten(lambda n: n.args[0] % 2 != 0)) + self.assertTrue(n1 in fl) + self.assertFalse(n2 in fl) + self.assertFalse(n3 in fl) + self.assertFalse(n4 in fl) + self.assertTrue(n5 in fl) + self.assertFalse(n6 in fl) + self.assertTrue(n7 in fl) + self.assertFalse(n8 in fl) + + def test_iter_nodes(self): + graph = ObjectGraph() + n1 = graph.createNode(ArgNode, "n1", 1) + n2 = graph.createNode(ArgNode, "n2", 2) + n3 = graph.createNode(ArgNode, "n3", 3) + n4 = graph.createNode(ArgNode, "n4", 4) + n5 = graph.createNode(ArgNode, "n5", 5) + n6 = graph.createNode(ArgNode, "n6", 5) + + nodes = graph.nodes() + if sys.version[0] == '2': + self.assertTrue(hasattr(nodes, 'next')) + else: + self.assertTrue(hasattr(nodes, '__next__')) + self.assertTrue(hasattr(nodes, '__iter__')) + + nodes = list(nodes) + self.assertEqual(len(nodes), 6) + self.assertTrue(n1 in nodes) + self.assertTrue(n2 in nodes) + self.assertTrue(n3 in nodes) + self.assertTrue(n4 in nodes) + self.assertTrue(n5 in nodes) + self.assertTrue(n6 in nodes) + + def test_get_edges(self): + graph = ObjectGraph() + n1 = graph.createNode(ArgNode, "n1", 1) + n2 = graph.createNode(ArgNode, "n2", 2) + n3 = graph.createNode(ArgNode, "n3", 3) + n4 = graph.createNode(ArgNode, "n4", 4) + n5 = graph.createNode(ArgNode, "n5", 5) + n6 = graph.createNode(ArgNode, "n6", 5) + + graph.createReference(n1, n2) + graph.createReference(n1, n3) + graph.createReference(n3, n1) + graph.createReference(n5, n1) + graph.createReference(n2, n4) + graph.createReference(n2, n5) + graph.createReference(n6, n2) + + outs, ins = graph.get_edges(n1) + + self.assertFalse(isinstance(outs, list)) + self.assertFalse(isinstance(ins, list)) + + ins = list(ins) + outs = list(outs) + + + self.assertTrue(n1 not in outs) + self.assertTrue(n2 in outs) + self.assertTrue(n3 in outs) + self.assertTrue(n4 not in outs) + self.assertTrue(n5 not in outs) + self.assertTrue(n6 not in outs) + + self.assertTrue(n1 not in ins) + self.assertTrue(n2 not in ins) + self.assertTrue(n3 in ins) + self.assertTrue(n4 not in ins) + self.assertTrue(n5 in ins) + self.assertTrue(n6 not in ins) + + def test_filterStack(self): + graph = ObjectGraph() + n1 = graph.createNode(ArgNode, "n1", 0) + n11 = graph.createNode(ArgNode, "n1.1", 1) + n12 = graph.createNode(ArgNode, "n1.2", 0) + n111 = graph.createNode(ArgNode, "n1.1.1", 0) + n112 = graph.createNode(ArgNode, "n1.1.2",2) + n2 = graph.createNode(ArgNode, "n2", 0) + n3 = graph.createNode(ArgNode, "n2", 0) + + graph.createReference(None, n1) + graph.createReference(None, n2) + graph.createReference(n1, n11) + graph.createReference(n1, n12) + graph.createReference(n11, n111) + graph.createReference(n11, n112) + + self.assertTrue(n1 in graph) + self.assertTrue(n2 in graph) + self.assertTrue(n11 in graph) + self.assertTrue(n12 in graph) + self.assertTrue(n111 in graph) + self.assertTrue(n112 in graph) + self.assertTrue(n2 in graph) + self.assertTrue(n3 in graph) + + visited, removes, orphans = graph.filterStack( + [lambda n: n.args[0] != 1, lambda n: n.args[0] != 2]) + + self.assertEqual(visited, 6) + self.assertEqual(removes, 2) + self.assertEqual(orphans, 1) + + e = graph.graph.edge_by_node(n1.graphident, n111.graphident) + self.assertEqual(graph.graph.edge_data(e), "orphan") + + self.assertTrue(n1 in graph) + self.assertTrue(n2 in graph) + self.assertTrue(n11 not in graph) + self.assertTrue(n12 in graph) + self.assertTrue(n111 in graph) + self.assertTrue(n112 not in graph) + self.assertTrue(n2 in graph) + self.assertTrue(n3 in graph) + + +class TestObjectGraphIO (unittest.TestCase): + def setUp(self): + self._stdout = sys.stdout + + def tearDown(self): + sys.stdout = self._stdout + + def test_msg(self): + graph = ObjectGraph() + + sys.stdout = fp = StringIO() + graph.msg(0, "foo") + self.assertEqual(fp.getvalue(), "foo \n") + + sys.stdout = fp = StringIO() + graph.msg(5, "foo") + self.assertEqual(fp.getvalue(), "") + + sys.stdout = fp = StringIO() + graph.debug = 10 + graph.msg(5, "foo") + self.assertEqual(fp.getvalue(), "foo \n") + + sys.stdout = fp = StringIO() + graph.msg(0, "foo", 1, "a") + self.assertEqual(fp.getvalue(), "foo 1 'a'\n") + + sys.stdout = fp = StringIO() + graph.msgin(0, "hello", "world") + graph.msg(0, "test me") + graph.msgout(0, "bye bye") + self.assertEqual(fp.getvalue(), "hello 'world'\n test me \nbye bye \n") + + +if __name__ == "__main__": # pragma: no cover + unittest.main() diff --git a/python/altgraph/doc/Makefile b/python/altgraph/doc/Makefile new file mode 100644 index 000000000..b91ac8142 --- /dev/null +++ b/python/altgraph/doc/Makefile @@ -0,0 +1,89 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/altgraph.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/altgraph.qhc" + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \ + "run these through (pdf)latex." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/python/altgraph/doc/_build/doctrees/changelog.doctree b/python/altgraph/doc/_build/doctrees/changelog.doctree new file mode 100644 index 000000000..b78e2f235 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/changelog.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/core.doctree b/python/altgraph/doc/_build/doctrees/core.doctree new file mode 100644 index 000000000..367409313 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/core.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/dot.doctree b/python/altgraph/doc/_build/doctrees/dot.doctree new file mode 100644 index 000000000..f2bd9ea89 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/dot.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/environment.pickle b/python/altgraph/doc/_build/doctrees/environment.pickle new file mode 100644 index 000000000..4e7b4ea03 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/environment.pickle differ diff --git a/python/altgraph/doc/_build/doctrees/graph.doctree b/python/altgraph/doc/_build/doctrees/graph.doctree new file mode 100644 index 000000000..5c9aef42c Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/graph.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/graphalgo.doctree b/python/altgraph/doc/_build/doctrees/graphalgo.doctree new file mode 100644 index 000000000..e22ca572d Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/graphalgo.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/graphstat.doctree b/python/altgraph/doc/_build/doctrees/graphstat.doctree new file mode 100644 index 000000000..2e0503615 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/graphstat.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/graphutil.doctree b/python/altgraph/doc/_build/doctrees/graphutil.doctree new file mode 100644 index 000000000..eb9fa2c65 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/graphutil.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/index.doctree b/python/altgraph/doc/_build/doctrees/index.doctree new file mode 100644 index 000000000..f3241e5e3 Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/index.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/license.doctree b/python/altgraph/doc/_build/doctrees/license.doctree new file mode 100644 index 000000000..ba3ce378a Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/license.doctree differ diff --git a/python/altgraph/doc/_build/doctrees/objectgraph.doctree b/python/altgraph/doc/_build/doctrees/objectgraph.doctree new file mode 100644 index 000000000..802396b9c Binary files /dev/null and b/python/altgraph/doc/_build/doctrees/objectgraph.doctree differ diff --git a/python/altgraph/doc/_build/html/.buildinfo b/python/altgraph/doc/_build/html/.buildinfo new file mode 100644 index 000000000..003a04976 --- /dev/null +++ b/python/altgraph/doc/_build/html/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 84aa655833f036f5ba0f6f2dbd1945fa +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/python/altgraph/doc/_build/html/_sources/changelog.txt b/python/altgraph/doc/_build/html/_sources/changelog.txt new file mode 100644 index 000000000..e491c9544 --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/changelog.txt @@ -0,0 +1,176 @@ +Release history +=============== + +0.11 +---- + +- Stabilize the order of elements in dot file exports, + patch from bitbucket user 'pombredanne'. + +- Tweak setup.py file to remove dependency on distribute (but + keep the dependency on setuptools) + + +0.10.2 +------ + +- There where no classifiers in the package metadata due to a bug + in setup.py + +0.10.1 +------ + +This is a bugfix release + +Bug fixes: + +- Issue #3: The source archive contains a README.txt + while the setup file refers to ReadMe.txt. + + This is caused by a misfeature in distutils, as a + workaround I've renamed ReadMe.txt to README.txt + in the source tree and setup file. + + +0.10 +----- + +This is a minor feature release + +Features: + +- Do not use "2to3" to support Python 3. + + As a side effect of this altgraph now supports + Python 2.6 and later, and no longer supports + earlier releases of Python. + +- The order of attributes in the Dot output + is now always alphabetical. + + With this change the output will be consistent + between runs and Python versions. + +0.9 +--- + +This is a minor bugfix release + +Features: + +- Added ``altgraph.ObjectGraph.ObjectGraph.nodes``, a method + yielding all nodes in an object graph. + +Bugfixes: + +- The 0.8 release didn't work with py2app when using + python 3.x. + + +0.8 +----- + +This is a minor feature release. The major new feature +is a extensive set of unittests, which explains almost +all other changes in this release. + +Bugfixes: + +- Installing failed with Python 2.5 due to using a distutils + class that isn't available in that version of Python + (issue #1 on the issue tracker) + +- ``altgraph.GraphStat.degree_dist`` now actually works + +- ``altgraph.Graph.add_edge(a, b, create_nodes=False)`` will + no longer create the edge when one of the nodes doesn't + exist. + +- ``altgraph.Graph.forw_topo_sort`` failed for some sparse graphs. + +- ``altgraph.Graph.back_topo_sort`` was completely broken in + previous releases. + +- ``altgraph.Graph.forw_bfs_subgraph`` now actually works. + +- ``altgraph.Graph.back_bfs_subgraph`` now actually works. + +- ``altgraph.Graph.iterdfs`` now returns the correct result + when the ``forward`` argument is ``False``. + +- ``altgraph.Graph.iterdata`` now returns the correct result + when the ``forward`` argument is ``False``. + + +Features: + +- The ``altgraph.Graph`` constructor now accepts an argument + that contains 2- and 3-tuples instead of requireing that + all items have the same size. The (optional) argument can now + also be any iterator. + +- ``altgraph.Graph.Graph.add_node`` has no effect when you + add a hidden node. + +- The private method ``altgraph.Graph._bfs`` is no longer + present. + +- The private method ``altgraph.Graph._dfs`` is no longer + present. + +- ``altgraph.ObjectGraph`` now has a ``__contains__`` methods, + which means you can use the ``in`` operator to check if a + node is part of a graph. + +- ``altgraph.GraphUtil.generate_random_graph`` will raise + ``GraphError`` instead of looping forever when it is + impossible to create the requested graph. + +- ``altgraph.Dot.edge_style`` raises ``GraphError`` when + one of the nodes is not present in the graph. The method + silently added the tail in the past, but without ensuring + a consistent graph state. + +- ``altgraph.Dot.save_img`` now works when the mode is + ``"neato"``. + +0.7.2 +----- + +This is a minor bugfix release + +Bugfixes: + +- distutils didn't include the documentation subtree + +0.7.1 +----- + +This is a minor feature release + +Features: + +- Documentation is now generated using `sphinx `_ + and can be viewed at . + +- The repository has moved to bitbucket + +- ``altgraph.GraphStat.avg_hops`` is no longer present, the function had no + implementation and no specified behaviour. + +- the module ``altgraph.compat`` is gone, which means altgraph will no + longer work with Python 2.3. + + +0.7.0 +----- + +This is a minor feature release. + +Features: + +- Support for Python 3 + +- It is now possible to run tests using 'python setup.py test' + + (The actual testsuite is still very minimal though) diff --git a/python/altgraph/doc/_build/html/_sources/core.txt b/python/altgraph/doc/_build/html/_sources/core.txt new file mode 100644 index 000000000..8288f6a94 --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/core.txt @@ -0,0 +1,26 @@ +:mod:`altgraph` --- A Python Graph Library +================================================== + +.. module:: altgraph + :synopsis: A directional graph for python + +altgraph is a fork of `graphlib `_ tailored +to use newer Python 2.3+ features, including additional support used by the +py2app suite (modulegraph and macholib, specifically). + +altgraph is a python based graph (network) representation and manipulation package. +It has started out as an extension to the `graph_lib module `_ +written by Nathan Denny it has been significantly optimized and expanded. + +The :class:`altgraph.Graph.Graph` class is loosely modeled after the `LEDA `_ +(Library of Efficient Datatypes) representation. The library +includes methods for constructing graphs, BFS and DFS traversals, +topological sort, finding connected components, shortest paths as well as a number +graph statistics functions. The library can also visualize graphs +via `graphviz `_. + + +.. exception:: GraphError + + Exception raised when methods are called with bad values of + an inconsistent state. diff --git a/python/altgraph/doc/_build/html/_sources/dot.txt b/python/altgraph/doc/_build/html/_sources/dot.txt new file mode 100644 index 000000000..3848c488a --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/dot.txt @@ -0,0 +1,224 @@ +:mod:`altgraph.Dot` --- Interface to the dot language +===================================================== + +.. module:: altgraph.Dot + :synopsis: Interface to the dot language as used by Graphviz.. + +The :py:mod:`~altgraph.Dot` module provides a simple interface to the +file format used in the `graphviz`_ program. The module is intended to +offload the most tedious part of the process (the **dot** file generation) +while transparently exposing most of its features. + +.. _`graphviz`: `_ + +To display the graphs or to generate image files the `graphviz`_ +package needs to be installed on the system, moreover the :command:`dot` and :command:`dotty` programs must +be accesible in the program path so that they can be ran from processes spawned +within the module. + +Example usage +------------- + +Here is a typical usage:: + + from altgraph import Graph, Dot + + # create a graph + edges = [ (1,2), (1,3), (3,4), (3,5), (4,5), (5,4) ] + graph = Graph.Graph(edges) + + # create a dot representation of the graph + dot = Dot.Dot(graph) + + # display the graph + dot.display() + + # save the dot representation into the mydot.dot file + dot.save_dot(file_name='mydot.dot') + + # save dot file as gif image into the graph.gif file + dot.save_img(file_name='graph', file_type='gif') + + +Directed graph and non-directed graph +------------------------------------- + +Dot class can use for both directed graph and non-directed graph +by passing *graphtype* parameter. + +Example:: + + # create directed graph(default) + dot = Dot.Dot(graph, graphtype="digraph") + + # create non-directed graph + dot = Dot.Dot(graph, graphtype="graph") + + +Customizing the output +---------------------- + +The graph drawing process may be customized by passing +valid :command:`dot` parameters for the nodes and edges. For a list of all +parameters see the `graphviz`_ documentation. + +Example:: + + # customizing the way the overall graph is drawn + dot.style(size='10,10', rankdir='RL', page='5, 5' , ranksep=0.75) + + # customizing node drawing + dot.node_style(1, label='BASE_NODE',shape='box', color='blue' ) + dot.node_style(2, style='filled', fillcolor='red') + + # customizing edge drawing + dot.edge_style(1, 2, style='dotted') + dot.edge_style(3, 5, arrowhead='dot', label='binds', labelangle='90') + dot.edge_style(4, 5, arrowsize=2, style='bold') + + + .. note:: + + dotty (invoked via :py:func:`~altgraph.Dot.display`) may not be able to + display all graphics styles. To verify the output save it to an image + file and look at it that way. + +Valid attributes +---------------- + +- dot styles, passed via the :py:meth:`Dot.style` method:: + + rankdir = 'LR' (draws the graph horizontally, left to right) + ranksep = number (rank separation in inches) + +- node attributes, passed via the :py:meth:`Dot.node_style` method:: + + style = 'filled' | 'invisible' | 'diagonals' | 'rounded' + shape = 'box' | 'ellipse' | 'circle' | 'point' | 'triangle' + +- edge attributes, passed via the :py:meth:`Dot.edge_style` method:: + + style = 'dashed' | 'dotted' | 'solid' | 'invis' | 'bold' + arrowhead = 'box' | 'crow' | 'diamond' | 'dot' | 'inv' | 'none' | 'tee' | 'vee' + weight = number (the larger the number the closer the nodes will be) + +- valid `graphviz colors `_ + +- for more details on how to control the graph drawing process see the + `graphviz reference `_. + + +Class interface +--------------- + +.. class:: Dot(graph[, nodes[, edgefn[, nodevisitor[, edgevisitor[, name[, dot[, dotty[, neato[, graphtype]]]]]]]]]) + + Creates a new Dot generator based on the specified + :class:`Graph `. The Dot generator won't reference + the *graph* once it is constructed. + + If the *nodes* argument is present it is the list of nodes to include + in the graph, otherwise all nodes in *graph* are included. + + If the *edgefn* argument is present it is a function that yields the + nodes connected to another node, this defaults to + :meth:`graph.out_nbr `. The constructor won't + add edges to the dot file unless both the head and tail of the edge + are in *nodes*. + + If the *name* is present it specifies the name of the graph in the resulting + dot file. The default is ``"G"``. + + The functions *nodevisitor* and *edgevisitor* return the default style + for a given edge or node (both default to functions that return an empty + style). + + The arguments *dot*, *dotty* and *neato* are used to pass the path to + the corresponding `graphviz`_ command. + + +Updating graph attributes +......................... + +.. method:: Dot.style(\**attr) + + Sets the overall style (graph attributes) to the given attributes. + + See `Valid Attributes`_ for more information about the attributes. + +.. method:: Dot.node_style(node, \**attr) + + Sets the style for *node* to the given attributes. + + This method will add *node* to the graph when it isn't already + present. + + See `Valid Attributes`_ for more information about the attributes. + +.. method:: Dot.all_node_style(\**attr) + + Replaces the current style for all nodes + + +.. method:: edge_style(head, tail, \**attr) + + Sets the style of an edge to the given attributes. The edge will + be added to the graph when it isn't already present, but *head* + and *tail* must both be valid nodes. + + See `Valid Attributes`_ for more information about the attributes. + + + +Emitting output +............... + +.. method:: Dot.display([mode]) + + Displays the current graph via dotty. + + If the *mode* is ``"neato"`` the dot file is processed with + the neato command before displaying. + + This method won't return until the dotty command exits. + +.. method:: save_dot(filename) + + Saves the current graph representation into the given file. + + .. note:: + + For backward compatibility reasons this method can also + be called without an argument, it will then write the graph + into a fixed filename (present in the attribute :data:`Graph.temp_dot`). + + This feature is deprecated and should not be used. + + +.. method:: save_image(file_name[, file_type[, mode]]) + + Saves the current graph representation as an image file. The output + is written into a file whose basename is *file_name* and whose suffix + is *file_type*. + + The *file_type* specifies the type of file to write, the default + is ``"gif"``. + + If the *mode* is ``"neato"`` the dot file is processed with + the neato command before displaying. + + .. note:: + + For backward compatibility reasons this method can also + be called without an argument, it will then write the graph + with a fixed basename (``"out"``). + + This feature is deprecated and should not be used. + +.. method:: iterdot() + + Yields all lines of a `graphviz`_ input file (including line endings). + +.. method:: __iter__() + + Alias for the :meth:`iterdot` method. diff --git a/python/altgraph/doc/_build/html/_sources/graph.txt b/python/altgraph/doc/_build/html/_sources/graph.txt new file mode 100644 index 000000000..72e36bbc1 --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/graph.txt @@ -0,0 +1,299 @@ +:mod:`altgraph.Graph` --- Basic directional graphs +================================================== + +.. module:: altgraph.Graph + :synopsis: Basic directional graphs. + +The module :mod:`altgraph.Graph` provides a class :class:`Graph` that +represents a directed graph with *N* nodes and *E* edges. + +.. class:: Graph([edges]) + + Constructs a new empty :class:`Graph` object. If the optional + *edges* parameter is supplied, updates the graph by adding the + specified edges. + + All of the elements in *edges* should be tuples with two or three + elements. The first two elements of the tuple are the source and + destination node of the edge, the optional third element is the + edge data. The source and destination nodes are added to the graph + when the aren't already present. + + +Node related methods +-------------------- + +.. method:: Graph.add_node(node[, node_data]) + + Adds a new node to the graph if it is not already present. The new + node must be a hashable object. + + Arbitrary data can be attached to the node via the optional *node_data* + argument. + + .. note:: the node also won't be added to the graph when it is + present but currently hidden. + + +.. method:: Graph.hide_node(node) + + Hides a *node* from the graph. The incoming and outgoing edges of + the node will also be hidden. + + Raises :class:`altgraph.GraphError` when the node is not (visible) + node of the graph. + + +.. method:: Graph.restore_node(node) + + Restores a previously hidden *node*. The incoming and outgoing + edges of the node are also restored. + + Raises :class:`altgraph.GraphError` when the node is not a hidden + node of the graph. + +.. method:: Graph.restore_all_nodes() + + Restores all hidden nodes. + +.. method:: Graph.number_of_nodes() + + Return the number of visible nodes in the graph. + +.. method:: Graph.number_of_hidden_nodes() + + Return the number of hidden nodes in the graph. + +.. method:: Graph.node_list() + + Return a list with all visible nodes in the graph. + +.. method:: Graph.hidden_node_list() + + Return a list with all hidden nodes in the graph. + +.. method:: node_data(node) + + Return the data associated with the *node* when it was + added. + +.. method:: Graph.describe_node(node) + + Returns *node*, the node's data and the lists of outgoing + and incoming edges for the node. + + .. note:: + + the edge lists should not be modified, doing so + can result in unpredicatable behavior. + +.. method:: Graph.__contains__(node) + + Returns True iff *node* is a node in the graph. This + method is accessed through the *in* operator. + +.. method:: Graph.__iter__() + + Yield all nodes in the graph. + +.. method:: Graph.out_edges(node) + + Return the list of outgoing edges for *node* + +.. method:: Graph.inc_edges(node) + + Return the list of incoming edges for *node* + +.. method:: Graph.all_edges(node) + + Return the list of incoming and outgoing edges for *node* + +.. method:: Graph.out_degree(node) + + Return the number of outgoing edges for *node*. + +.. method:: Graph.inc_degree(node) + + Return the number of incoming edges for *node*. + +.. method:: Graph.all_degree(node) + + Return the number of edges (incoming or outgoing) for *node*. + +Edge related methods +-------------------- + +.. method:: Graph.add_edge(head_id, tail_id [, edge data [, create_nodes]]) + + Adds a directed edge from *head_id* to *tail_id*. Arbitrary data can + be added via *edge_data*. When *create_nodes* is *True* (the default), + *head_id* and *tail_id* will be added to the graph when the aren't + already present. + +.. method:: Graph.hide_edge(edge) + + Hides an edge from the graph. The edge may be unhidden at some later + time. + +.. method:: Graph.restore_edge(edge) + + Restores a previously hidden *edge*. + +.. method:: Graph.restore_all_edges() + + Restore all edges that were hidden before, except for edges + referring to hidden nodes. + +.. method:: Graph.edge_by_node(head, tail) + + Return the edge ID for an edge from *head* to *tail*, + or :data:`None` when no such edge exists. + +.. method:: Graph.edge_by_id(edge) + + Return the head and tail of the *edge* + +.. method:: Graph.edge_data(edge) + + Return the data associated with the *edge*. + + +.. method:: Graph.head(edge) + + Return the head of an *edge* + +.. method:: Graph.tail(edge) + + Return the tail of an *edge* + +.. method:: Graph.describe_edge(edge) + + Return the *edge*, the associated data, its head and tail. + +.. method:: Graph.number_of_edges() + + Return the number of visible edges. + +.. method:: Graph.number_of_hidden_edges() + + Return the number of hidden edges. + +.. method:: Graph.edge_list() + + Returns a list with all visible edges in the graph. + +.. method:: Graph.hidden_edge_list() + + Returns a list with all hidden edges in the graph. + +Graph traversal +--------------- + +.. method:: Graph.out_nbrs(node) + + Return a list of all nodes connected by outgoing edges. + +.. method:: Graph.inc_nbrs(node) + + Return a list of all nodes connected by incoming edges. + +.. method:: Graph.all_nbrs(node) + + Returns a list of nodes connected by an incoming or outgoing edge. + +.. method:: Graph.forw_topo_sort() + + Return a list of nodes where the successors (based on outgoing + edges) of any given node apear in the sequence after that node. + +.. method:: Graph.back_topo_sort() + + Return a list of nodes where the successors (based on incoming + edges) of any given node apear in the sequence after that node. + +.. method:: Graph.forw_bfs_subgraph(start_id) + + Return a subgraph consisting of the breadth first + reachable nodes from *start_id* based on their outgoing edges. + + +.. method:: Graph.back_bfs_subgraph(start_id) + + Return a subgraph consisting of the breadth first + reachable nodes from *start_id* based on their incoming edges. + +.. method:: Graph.iterdfs(start[, end[, forward]]) + + Yield nodes in a depth first traversal starting at the *start* + node. + + If *end* is specified traversal stops when reaching that node. + + If forward is True (the default) edges are traversed in forward + direction, otherwise they are traversed in reverse direction. + +.. method:: Graph.iterdata(start[, end[, forward[, condition]]]) + + Yield the associated data for nodes in a depth first traversal + starting at the *start* node. This method will not yield values for nodes + without associated data. + + If *end* is specified traversal stops when reaching that node. + + If *condition* is specified and the condition callable returns + False for the associated data this method will not yield the + associated data and will not follow the edges for the node. + + If forward is True (the default) edges are traversed in forward + direction, otherwise they are traversed in reverse direction. + +.. method:: Graph.forw_bfs(start[, end]) + + Returns a list of nodes starting at *start* in some bread first + search order (following outgoing edges). + + When *end* is specified iteration stops at that node. + +.. method:: Graph.back_bfs(start[, end]) + + Returns a list of nodes starting at *start* in some bread first + search order (following incoming edges). + + When *end* is specified iteration stops at that node. + +.. method:: Graph.get_hops(start[, end[, forward]]) + + Computes the hop distance to all nodes centered around a specified node. + + First order neighbours are at hop 1, their neigbours are at hop 2 etc. + Uses :py:meth:`forw_bfs` or :py:meth:`back_bfs` depending on the value of + the forward parameter. + + If the distance between all neighbouring nodes is 1 the hop number + corresponds to the shortest distance between the nodes. + + Typical usage:: + + >>> print graph.get_hops(1, 8) + >>> [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)] + # node 1 is at 0 hops + # node 2 is at 1 hop + # ... + # node 8 is at 5 hops + + +Graph statistics +---------------- + +.. method:: Graph.connected() + + Returns True iff every node in the graph can be reached from + every other node. + +.. method:: Graph.clust_coef(node) + + Returns the local clustering coefficient of node. + + The local cluster coefficient is the proportion of the actual number + of edges between neighbours of node and the maximum number of + edges between those nodes. diff --git a/python/altgraph/doc/_build/html/_sources/graphalgo.txt b/python/altgraph/doc/_build/html/_sources/graphalgo.txt new file mode 100644 index 000000000..84d492f44 --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/graphalgo.txt @@ -0,0 +1,26 @@ +:mod:`altgraph.GraphAlgo` --- Graph algorithms +================================================== + +.. module:: altgraph.GraphAlgo + :synopsis: Basic graphs algoritms + +.. function:: dijkstra(graph, start[, end]) + + Dijkstra's algorithm for shortest paths. + + Find shortest paths from the start node to all nodes nearer + than or equal to the *end* node. The edge data is assumed to be the edge length. + + .. note:: + + Dijkstra's algorithm is only guaranteed to work correctly when all edge lengths are positive. + This code does not verify this property for all edges (only the edges examined until the end + vertex is reached), but will correctly compute shortest paths even for some graphs with negative + edges, and will raise an exception if it discovers that a negative edge has caused it to make a mistake. + + +.. function:: shortest_path(graph, start, end) + + Find a single shortest path from the given start node to the given end node. + The input has the same conventions as :func:`dijkstra`. The output is a list + of the nodes in order along the shortest path. diff --git a/python/altgraph/doc/_build/html/_sources/graphstat.txt b/python/altgraph/doc/_build/html/_sources/graphstat.txt new file mode 100644 index 000000000..0931a12dd --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/graphstat.txt @@ -0,0 +1,25 @@ +:mod:`altgraph.GraphStat` --- Functions providing various graph statistics +========================================================================== + +.. module:: altgraph.GraphStat + :synopsis: Functions providing various graph statistics + +The module :mod:`altgraph.GraphStat` provides function that calculate +graph statistics. Currently there is only one such function, more may +be added later. + +.. function:: degree_dist(graph[, limits[, bin_num[, mode]]]) + + Groups the number of edges per node into *bin_num* bins + and returns the list of those bins. Every item in the result + is a tuple with the center of the bin and the number of items + in that bin. + + When the *limits* argument is present it must be a tuple with + the mininum and maximum number of edges that get binned (that + is, when *limits* is ``(4, 10)`` only nodes with between 4 + and 10 edges get counted. + + The *mode* argument is used to count incoming (``'inc'``) or + outgoing (``'out'``) edges. The default is to count the outgoing + edges. diff --git a/python/altgraph/doc/_build/html/_sources/graphutil.txt b/python/altgraph/doc/_build/html/_sources/graphutil.txt new file mode 100644 index 000000000..c07836df8 --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/graphutil.txt @@ -0,0 +1,55 @@ +:mod:`altgraph.GraphUtil` --- Utility functions +================================================ + +.. module:: altgraph.GraphUtil + :synopsis: Utility functions + +The module :mod:`altgraph.GraphUtil` performs a number of more +or less useful utility functions. + +.. function:: generate_random_graph(node_num, edge_num[, self_loops[, multi_edges]) + + Generates and returns a :class:`Graph ` instance + with *node_num* nodes randomly connected by *edge_num* edges. + + When *self_loops* is present and True there can be edges that point from + a node to itself. + + When *multi_edge* is present and True there can be duplicate edges. + + This method raises :class:`GraphError `_ + +.. function:: filter_stack(graph, head, filters) + + Perform a depth-first oder walk of the graph starting at *head* and + apply all filter functions in *filters* on the node data of the nodes + found. + + Returns (*visited*, *removes*, *orphans*), where + + * *visited*: the set of visited nodes + + * *removes*: the list of nodes where the node data doesn't match + all *filters*. + + * *orphans*: list of tuples (*last_good*, *node*), where + node is not in *removes* and one of the nodes that is connected + by an incoming edge is in *removes*. *Last_good* is the + closest upstream node that is not in *removes*. diff --git a/python/altgraph/doc/_build/html/_sources/index.txt b/python/altgraph/doc/_build/html/_sources/index.txt new file mode 100644 index 000000000..1e8d504ed --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/index.txt @@ -0,0 +1,41 @@ +.. altgraph documentation master file, created by + sphinx-quickstart on Tue Aug 31 11:04:49 2010. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Altgraph - A basic graph library +================================ + +altgraph is a fork of graphlib: a graph (network) package for constructing +graphs, BFS and DFS traversals, topological sort, shortest paths, etc. with +graphviz output. + +The primary users of this package are `macholib `_ and `modulegraph `_. + +.. toctree:: + :maxdepth: 1 + + changelog + license + core + graph + objectgraph + graphalgo + graphstat + graphutil + dot + +Online Resources +---------------- + +* `Sourcecode repository on bitbucket `_ + +* `The issue tracker `_ + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/python/altgraph/doc/_build/html/_sources/license.txt b/python/altgraph/doc/_build/html/_sources/license.txt new file mode 100644 index 000000000..498e60be0 --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/license.txt @@ -0,0 +1,25 @@ +License +======= + +Copyright (c) 2004 Istvan Albert unless otherwise noted. + +Parts are copyright (c) Bob Ippolito + +Parts are copyright (c) 2010-2014 Ronald Oussoren + +MIT License +........... + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software +and associated documentation files (the "Software"), to deal in the Software without restriction, +including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do +so. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, +INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR +PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE +FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, +ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + diff --git a/python/altgraph/doc/_build/html/_sources/objectgraph.txt b/python/altgraph/doc/_build/html/_sources/objectgraph.txt new file mode 100644 index 000000000..87485255f --- /dev/null +++ b/python/altgraph/doc/_build/html/_sources/objectgraph.txt @@ -0,0 +1,134 @@ +:mod:`altgraph.ObjectGraph` --- Graphs of objecs with an identifier +=================================================================== + +.. module:: altgraph.ObjectGraph + :synopsis: A graph of objects that have a "graphident" attribute. + +.. class:: ObjectGraph([graph[, debug]]) + + A graph of objects that have a "graphident" attribute. The + value of this attribute is the key for the object in the + graph. + + The optional *graph* is a previously constructed + :class:`Graph `. + + The optional *debug* level controls the amount of debug output + (see :meth:`msg`, :meth:`msgin` and :meth:`msgout`). + + .. note:: the altgraph library does not generate output, the + debug attribute and message methods are present for use + by subclasses. + +.. data:: ObjectGraph.graph + + An :class:`Graph ` object that contains + the graph data. + + +.. method:: ObjectGraph.addNode(node) + + Adds a *node* to the graph. + + .. note:: re-adding a node that was previously removed + using :meth:`removeNode` will reinstate the previously + removed node. + +.. method:: ObjectGraph.createNode(self, cls, name, \*args, \**kwds) + + Creates a new node using ``cls(*args, **kwds)`` and adds that + node using :meth:`addNode`. + + Returns the newly created node. + +.. method:: ObjectGraph.removeNode(node) + + Removes a *node* from the graph when it exists. The *node* argument + is either a node object, or the graphident of a node. + +.. method:: ObjectGraph.createReferences(fromnode, tonode[, edge_data]) + + Creates a reference from *fromnode* to *tonode*. The optional + *edge_data* is associated with the edge. + + *Fromnode* and *tonode* can either be node objects or the graphident + values for nodes. + +.. method:: removeReference(fromnode, tonode) + + Removes the reference from *fromnode* to *tonode* if it exists. + +.. method:: ObjectGraph.getRawIdent(node) + + Returns the *graphident* attribute of *node*, or the graph itself + when *node* is :data:`None`. + +.. method:: getIdent(node) + + Same as :meth:`getRawIdent`, but only if the node is part + of the graph. + + *Node* can either be an actual node object or the graphident of + a node. + +.. method:: ObjectGraph.findNode(node) + + Returns a given node in the graph, or :data:`Node` when it cannot + be found. + + *Node* is either an object with a *graphident* attribute or + the *graphident* attribute itself. + +.. method:: ObjectGraph.__contains__(node) + + Returns True if *node* is a member of the graph. *Node* is either an + object with a *graphident* attribute or the *graphident* attribute itself. + +.. method:: ObjectGraph.flatten([condition[, start]]) + + Yield all nodes that are entirely reachable by *condition* + starting fromt he given *start* node or the graph root. + + .. note:: objects are only reachable from the graph root + when there is a reference from the root to the node + (either directly or through another node) + +.. method:: ObjectGraph.nodes() + + Yield all nodes in the graph. + +.. method:: ObjectGraph.get_edges(node) + + Returns two iterators that yield the nodes reaching by + outgoing and incoming edges. + +.. method:: ObjectGraph.filterStack(filters) + + Filter the ObjectGraph in-place by removing all edges to nodes that + do not match every filter in the given filter list + + Returns a tuple containing the number of: + (*nodes_visited*, *nodes_removed*, *nodes_orphaned*) + + +Debug output +------------ + +.. data:: ObjectGraph.debug + + The current debug level. + +.. method:: ObjectGraph.msg(level, text, \*args) + + Print a debug message at the current indentation level when the current + debug level is *level* or less. + +.. method:: ObjectGraph.msgin(level, text, \*args) + + Print a debug message when the current debug level is *level* or less, + and increase the indentation level. + +.. method:: ObjectGraph.msgout(level, text, \*args) + + Decrease the indentation level and print a debug message when the + current debug level is *level* or less. diff --git a/python/altgraph/doc/_build/html/_static/ajax-loader.gif b/python/altgraph/doc/_build/html/_static/ajax-loader.gif new file mode 100644 index 000000000..61faf8cab Binary files /dev/null and b/python/altgraph/doc/_build/html/_static/ajax-loader.gif differ diff --git a/python/altgraph/doc/_build/html/_static/basic.css b/python/altgraph/doc/_build/html/_static/basic.css new file mode 100644 index 000000000..c959cf0db --- /dev/null +++ b/python/altgraph/doc/_build/html/_static/basic.css @@ -0,0 +1,537 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; 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font-style: italic } /* Literal.String.Interpol */ +.highlight .sx { color: #c65d09 } /* Literal.String.Other */ +.highlight .sr { color: #235388 } /* Literal.String.Regex */ +.highlight .s1 { color: #4070a0 } /* Literal.String.Single */ +.highlight .ss { color: #517918 } /* Literal.String.Symbol */ +.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */ +.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */ +.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */ +.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */ +.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/_static/searchtools.js b/python/altgraph/doc/_build/html/_static/searchtools.js new file mode 100644 index 000000000..f5c7e5fee --- /dev/null +++ b/python/altgraph/doc/_build/html/_static/searchtools.js @@ -0,0 +1,622 @@ +/* + * searchtools.js_t + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilties for the full-text search. + * + * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + +/** + * Simple result scoring code. + */ +var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 +}; + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, + dataType: "script", cache: true, + complete: function(jqxhr, textstatus) { + if (textstatus != "success") { + document.getElementById("searchindexloader").src = url; + } + }}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + var i; + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + } + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('

' + _('Searching') + '

').appendTo(this.out); + this.dots = $('').appendTo(this.title); + this.status = $('

').appendTo(this.out); + this.output = $('
'); + } + // Prettify the comment rating. + comment.pretty_rating = comment.rating + ' point' + + (comment.rating == 1 ? '' : 's'); + // Make a class (for displaying not yet moderated comments differently) + comment.css_class = comment.displayed ? '' : ' moderate'; + // Create a div for this comment. + var context = $.extend({}, opts, comment); + var div = $(renderTemplate(commentTemplate, context)); + + // If the user has voted on this comment, highlight the correct arrow. + if (comment.vote) { + var direction = (comment.vote == 1) ? 'u' : 'd'; + div.find('#' + direction + 'v' + comment.id).hide(); + div.find('#' + direction + 'u' + comment.id).show(); + } + + if (opts.moderator || comment.text != '[deleted]') { + div.find('a.reply').show(); + if (comment.proposal_diff) + div.find('#sp' + comment.id).show(); + if (opts.moderator && !comment.displayed) + div.find('#cm' + comment.id).show(); + if (opts.moderator || (opts.username == comment.username)) + div.find('#dc' + comment.id).show(); + } + return div; + } + + /** + * A simple template renderer. Placeholders such as <%id%> are replaced + * by context['id'] with items being escaped. Placeholders such as <#id#> + * are not escaped. + */ + function renderTemplate(template, context) { + var esc = $(document.createElement('div')); + + function handle(ph, escape) { + var cur = context; + $.each(ph.split('.'), function() { + cur = cur[this]; + }); + return escape ? esc.text(cur || "").html() : cur; + } + + return template.replace(/<([%#])([\w\.]*)\1>/g, function() { + return handle(arguments[2], arguments[1] == '%' ? true : false); + }); + } + + /** Flash an error message briefly. */ + function showError(message) { + $(document.createElement('div')).attr({'class': 'popup-error'}) + .append($(document.createElement('div')) + .attr({'class': 'error-message'}).text(message)) + .appendTo('body') + .fadeIn("slow") + .delay(2000) + .fadeOut("slow"); + } + + /** Add a link the user uses to open the comments popup. */ + $.fn.comment = function() { + return this.each(function() { + var id = $(this).attr('id').substring(1); + var count = COMMENT_METADATA[id]; + var title = count + ' comment' + (count == 1 ? '' : 's'); + var image = count > 0 ? opts.commentBrightImage : opts.commentImage; + var addcls = count == 0 ? ' nocomment' : ''; + $(this) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-open' + addcls, + id: 'ao' + id + }) + .append($(document.createElement('img')).attr({ + src: image, + alt: 'comment', + title: title + })) + .click(function(event) { + event.preventDefault(); + show($(this).attr('id').substring(2)); + }) + ) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-close hidden', + id: 'ah' + id + }) + .append($(document.createElement('img')).attr({ + src: opts.closeCommentImage, + alt: 'close', + title: 'close' + })) + .click(function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }) + ); + }); + }; + + var opts = { + processVoteURL: '/_process_vote', + addCommentURL: '/_add_comment', + getCommentsURL: '/_get_comments', + acceptCommentURL: '/_accept_comment', + deleteCommentURL: '/_delete_comment', + commentImage: '/static/_static/comment.png', + closeCommentImage: '/static/_static/comment-close.png', + loadingImage: '/static/_static/ajax-loader.gif', + commentBrightImage: '/static/_static/comment-bright.png', + upArrow: '/static/_static/up.png', + downArrow: '/static/_static/down.png', + upArrowPressed: '/static/_static/up-pressed.png', + downArrowPressed: '/static/_static/down-pressed.png', + voting: false, + moderator: false + }; + + if (typeof COMMENT_OPTIONS != "undefined") { + opts = jQuery.extend(opts, COMMENT_OPTIONS); + } + + var popupTemplate = '\ +
\ +

\ + Sort by:\ + best rated\ + newest\ + oldest\ +

\ +
Comments
\ +
\ + loading comments...
\ +
    \ +
    \ +

    Add a comment\ + (markup):

    \ +
    \ + reStructured text markup: *emph*, **strong**, \ + ``code``, \ + code blocks: :: and an indented block after blank line
    \ +
    \ + \ +

    \ + \ + Propose a change ▹\ + \ + \ + Propose a change ▿\ + \ +

    \ + \ + \ + \ + \ + \ +
    \ +
    '; + + var commentTemplate = '\ +
    \ +
    \ +
    \ + \ + \ + \ + \ + \ + \ +
    \ +
    \ + \ + \ + \ + \ + \ + \ +
    \ +
    \ +
    \ +

    \ + <%username%>\ + <%pretty_rating%>\ + <%time.delta%>\ +

    \ +
    <#text#>
    \ +

    \ + \ + reply ▿\ + proposal ▹\ + proposal ▿\ + \ + \ +

    \ + 
    \
+<#proposal_diff#>\
+
    \ +
      \ +
      \ +
      \ +
      \ + '; + + var replyTemplate = '\ +
    • \ +
      \ +
      \ + \ + \ + \ + \ + \ + \ +
      \ +
      • '; + + $(document).ready(function() { + init(); + }); +})(jQuery); + +$(document).ready(function() { + // add comment anchors for all paragraphs that are commentable + $('.sphinx-has-comment').comment(); + + // highlight search words in search results + $("div.context").each(function() { + var params = $.getQueryParameters(); + var terms = (params.q) ? params.q[0].split(/\s+/) : []; + var result = $(this); + $.each(terms, function() { + result.highlightText(this.toLowerCase(), 'highlighted'); + }); + }); + + // directly open comment window if requested + var anchor = document.location.hash; + if (anchor.substring(0, 9) == '#comment-') { + $('#ao' + anchor.substring(9)).click(); + document.location.hash = '#s' + anchor.substring(9); + } +}); diff --git a/python/altgraph/doc/_build/html/changelog.html b/python/altgraph/doc/_build/html/changelog.html new file mode 100644 index 000000000..8f0f459ea --- /dev/null +++ b/python/altgraph/doc/_build/html/changelog.html @@ -0,0 +1,271 @@ + + + + + + + + Release history — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      Release history¶

      +
      +

      0.11¶

      +
        +
      • Stabilize the order of elements in dot file exports, +patch from bitbucket user ‘pombredanne’.
        • +
      • Tweak setup.py file to remove dependency on distribute (but +keep the dependency on setuptools)
        • +
      +
      +
      +

      0.10.2¶

      +
        +
      • There where no classifiers in the package metadata due to a bug +in setup.py
        • +
      +
      +
      +

      0.10.1¶

      +

      This is a bugfix release

      +

      Bug fixes:

      +
        +

      • Issue #3: The source archive contains a README.txt +while the setup file refers to ReadMe.txt.

        +

        This is caused by a misfeature in distutils, as a +workaround I’ve renamed ReadMe.txt to README.txt +in the source tree and setup file.

        +
        • +
      +
      +
      +

      0.10¶

      +

      This is a minor feature release

      +

      Features:

      +
        +

      • Do not use “2to3” to support Python 3.

        +

        As a side effect of this altgraph now supports +Python 2.6 and later, and no longer supports +earlier releases of Python.

        +
        • +

      • The order of attributes in the Dot output +is now always alphabetical.

        +

        With this change the output will be consistent +between runs and Python versions.

        +
        • +
      +
      +
      +

      0.9¶

      +

      This is a minor bugfix release

      +

      Features:

      +
        +
      • Added altgraph.ObjectGraph.ObjectGraph.nodes, a method +yielding all nodes in an object graph.
        • +
      +

      Bugfixes:

      +
        +
      • The 0.8 release didn’t work with py2app when using +python 3.x.
        • +
      +
      +
      +

      0.8¶

      +

      This is a minor feature release. The major new feature +is a extensive set of unittests, which explains almost +all other changes in this release.

      +

      Bugfixes:

      +
        +
      • Installing failed with Python 2.5 due to using a distutils +class that isn’t available in that version of Python +(issue #1 on the issue tracker)
        • +
      • altgraph.GraphStat.degree_dist now actually works
        • +
      • altgraph.Graph.add_edge(a, b, create_nodes=False) will +no longer create the edge when one of the nodes doesn’t +exist.
        • +
      • altgraph.Graph.forw_topo_sort failed for some sparse graphs.
        • +
      • altgraph.Graph.back_topo_sort was completely broken in +previous releases.
        • +
      • altgraph.Graph.forw_bfs_subgraph now actually works.
        • +
      • altgraph.Graph.back_bfs_subgraph now actually works.
        • +
      • altgraph.Graph.iterdfs now returns the correct result +when the forward argument is False.
        • +
      • altgraph.Graph.iterdata now returns the correct result +when the forward argument is False.
        • +
      +

      Features:

      +
        +
      • The altgraph.Graph constructor now accepts an argument +that contains 2- and 3-tuples instead of requireing that +all items have the same size. The (optional) argument can now +also be any iterator.
        • +
      • altgraph.Graph.Graph.add_node has no effect when you +add a hidden node.
        • +
      • The private method altgraph.Graph._bfs is no longer +present.
        • +
      • The private method altgraph.Graph._dfs is no longer +present.
        • +
      • altgraph.ObjectGraph now has a __contains__ methods, +which means you can use the in operator to check if a +node is part of a graph.
        • +
      • altgraph.GraphUtil.generate_random_graph will raise +GraphError instead of looping forever when it is +impossible to create the requested graph.
        • +
      • altgraph.Dot.edge_style raises GraphError when +one of the nodes is not present in the graph. The method +silently added the tail in the past, but without ensuring +a consistent graph state.
        • +
      • altgraph.Dot.save_img now works when the mode is +"neato".
        • +
      +
      +
      +

      0.7.2¶

      +

      This is a minor bugfix release

      +

      Bugfixes:

      +
        +
      • distutils didn’t include the documentation subtree
        • +
      +
      +
      +

      0.7.1¶

      +

      This is a minor feature release

      +

      Features:

      +
        +
      • Documentation is now generated using sphinx +and can be viewed at <http://packages.python.org/altgraph>.
        • +
      • The repository has moved to bitbucket
        • +
      • altgraph.GraphStat.avg_hops is no longer present, the function had no +implementation and no specified behaviour.
        • +
      • the module altgraph.compat is gone, which means altgraph will no +longer work with Python 2.3.
        • +
      +
      +
      +

      0.7.0¶

      +

      This is a minor feature release.

      +

      Features:

      +
        +

      • Support for Python 3

        +
        • +

      • It is now possible to run tests using ‘python setup.py test’

        +

        (The actual testsuite is still very minimal though)

        +
        • +
      +
      +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Previous topic

      +

      Altgraph - A basic graph library

      +

      Next topic

      +

      License

      + + +
      +
      +
      +
      +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/core.html b/python/altgraph/doc/_build/html/core.html new file mode 100644 index 000000000..3d2ee1737 --- /dev/null +++ b/python/altgraph/doc/_build/html/core.html @@ -0,0 +1,130 @@ + + + + + + + + altgraph — A Python Graph Library — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph — A Python Graph Library¶

      +

      altgraph is a fork of graphlib tailored +to use newer Python 2.3+ features, including additional support used by the +py2app suite (modulegraph and macholib, specifically).

      +

      altgraph is a python based graph (network) representation and manipulation package. +It has started out as an extension to the graph_lib module +written by Nathan Denny it has been significantly optimized and expanded.

      +

      The altgraph.Graph.Graph class is loosely modeled after the LEDA +(Library of Efficient Datatypes) representation. The library +includes methods for constructing graphs, BFS and DFS traversals, +topological sort, finding connected components, shortest paths as well as a number +graph statistics functions. The library can also visualize graphs +via graphviz.

      +
      +
      +exception altgraph.GraphError¶
      +

      Exception raised when methods are called with bad values of +an inconsistent state.

      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      License

      +

      Next topic

      +

      altgraph.Graph — Basic directional graphs

      + + +
      +
      +
      +
      +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/dot.html b/python/altgraph/doc/_build/html/dot.html new file mode 100644 index 000000000..87fabc077 --- /dev/null +++ b/python/altgraph/doc/_build/html/dot.html @@ -0,0 +1,332 @@ + + + + + + + + altgraph.Dot — Interface to the dot language — altgraph 0.11 documentation + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph.Dot — Interface to the dot language¶

      +

      The Dot module provides a simple interface to the +file format used in the graphviz program. The module is intended to +offload the most tedious part of the process (the dot file generation) +while transparently exposing most of its features.

      +

      To display the graphs or to generate image files the graphviz +package needs to be installed on the system, moreover the dot and dotty programs must +be accesible in the program path so that they can be ran from processes spawned +within the module.

      +
      +

      Example usage¶

      +

      Here is a typical usage:

      +
      from altgraph import Graph, Dot
+
+# create a graph
+edges = [ (1,2), (1,3), (3,4), (3,5), (4,5), (5,4) ]
+graph = Graph.Graph(edges)
+
+# create a dot representation of the graph
+dot = Dot.Dot(graph)
+
+# display the graph
+dot.display()
+
+# save the dot representation into the mydot.dot file
+dot.save_dot(file_name='mydot.dot')
+
+# save dot file as gif image into the graph.gif file
+dot.save_img(file_name='graph', file_type='gif')
+
      +
      +
      +
      +

      Directed graph and non-directed graph¶

      +

      Dot class can use for both directed graph and non-directed graph +by passing graphtype parameter.

      +

      Example:

      +
      # create directed graph(default)
+dot = Dot.Dot(graph, graphtype="digraph")
+
+# create non-directed graph
+dot = Dot.Dot(graph, graphtype="graph")
+
      +
      +
      +
      +

      Customizing the output¶

      +

      The graph drawing process may be customized by passing +valid dot parameters for the nodes and edges. For a list of all +parameters see the graphviz documentation.

      +

      Example:

      +
      # customizing the way the overall graph is drawn
+dot.style(size='10,10', rankdir='RL', page='5, 5' , ranksep=0.75)
+
+# customizing node drawing
+dot.node_style(1, label='BASE_NODE',shape='box', color='blue' )
+dot.node_style(2, style='filled', fillcolor='red')
+
+# customizing edge drawing
+dot.edge_style(1, 2, style='dotted')
+dot.edge_style(3, 5, arrowhead='dot', label='binds', labelangle='90')
+dot.edge_style(4, 5, arrowsize=2, style='bold')
+
+
+.. note::
+
+   dotty (invoked via :py:func:`~altgraph.Dot.display`) may not be able to
+   display all graphics styles. To verify the output save it to an image
+   file and look at it that way.
+
      +
      +
      +
      +

      Valid attributes¶

      +
        +

      • dot styles, passed via the Dot.style() method:

        +
        rankdir = 'LR'   (draws the graph horizontally, left to right)
+ranksep = number (rank separation in inches)
+
        +
        +
        • +

      • node attributes, passed via the Dot.node_style() method:

        +
        style = 'filled' | 'invisible' | 'diagonals' | 'rounded'
+shape = 'box' | 'ellipse' | 'circle' | 'point' | 'triangle'
+
        +
        +
        • +

      • edge attributes, passed via the Dot.edge_style() method:

        +
        style     = 'dashed' | 'dotted' | 'solid' | 'invis' | 'bold'
+arrowhead = 'box' | 'crow' | 'diamond' | 'dot' | 'inv' | 'none' | 'tee' | 'vee'
+weight    = number (the larger the number the closer the nodes will be)
+
        +
        +
        • +

      • valid graphviz colors

        +
        • +

      • for more details on how to control the graph drawing process see the +graphviz reference.

        +
        • +
      +
      +
      +

      Class interface¶

      +
      +
      +class altgraph.Dot.Dot(graph[, nodes[, edgefn[, nodevisitor[, edgevisitor[, name[, dot[, dotty[, neato[, graphtype]]]]]]]]])¶
      +

      Creates a new Dot generator based on the specified +Graph. The Dot generator won’t reference +the graph once it is constructed.

      +

      If the nodes argument is present it is the list of nodes to include +in the graph, otherwise all nodes in graph are included.

      +

      If the edgefn argument is present it is a function that yields the +nodes connected to another node, this defaults to +graph.out_nbr. The constructor won’t +add edges to the dot file unless both the head and tail of the edge +are in nodes.

      +

      If the name is present it specifies the name of the graph in the resulting +dot file. The default is "G".

      +

      The functions nodevisitor and edgevisitor return the default style +for a given edge or node (both default to functions that return an empty +style).

      +

      The arguments dot, dotty and neato are used to pass the path to +the corresponding graphviz command.

      +
      + +
      +

      Updating graph attributes¶

      +
      +
      +Dot.style(**attr)¶
      +

      Sets the overall style (graph attributes) to the given attributes.

      +

      See Valid Attributes for more information about the attributes.

      +
      + +
      +
      +Dot.node_style(node, **attr)¶
      +

      Sets the style for node to the given attributes.

      +

      This method will add node to the graph when it isn’t already +present.

      +

      See Valid Attributes for more information about the attributes.

      +
      + +
      +
      +Dot.all_node_style(**attr)¶
      +

      Replaces the current style for all nodes

      +
      + +
      +
      +altgraph.Dot.edge_style(head, tail, **attr)¶
      +

      Sets the style of an edge to the given attributes. The edge will +be added to the graph when it isn’t already present, but head +and tail must both be valid nodes.

      +

      See Valid Attributes for more information about the attributes.

      +
      + +
      +
      +

      Emitting output¶

      +
      +
      +Dot.display([mode])¶
      +

      Displays the current graph via dotty.

      +

      If the mode is "neato" the dot file is processed with +the neato command before displaying.

      +

      This method won’t return until the dotty command exits.

      +
      + +
      +
      +altgraph.Dot.save_dot(filename)¶
      +

      Saves the current graph representation into the given file.

      +
      +

      Note

      +

      For backward compatibility reasons this method can also +be called without an argument, it will then write the graph +into a fixed filename (present in the attribute Graph.temp_dot).

      +

      This feature is deprecated and should not be used.

      +
      +
      + +
      +
      +altgraph.Dot.save_image(file_name[, file_type[, mode]])¶
      +

      Saves the current graph representation as an image file. The output +is written into a file whose basename is file_name and whose suffix +is file_type.

      +

      The file_type specifies the type of file to write, the default +is "gif".

      +

      If the mode is "neato" the dot file is processed with +the neato command before displaying.

      +
      +

      Note

      +

      For backward compatibility reasons this method can also +be called without an argument, it will then write the graph +with a fixed basename ("out").

      +

      This feature is deprecated and should not be used.

      +
      +
      + +
      +
      +altgraph.Dot.iterdot()¶
      +

      Yields all lines of a graphviz input file (including line endings).

      +
      + +
      +
      +altgraph.Dot.__iter__()¶
      +

      Alias for the iterdot() method.

      +
      + +
      +
      +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Previous topic

      +

      altgraph.GraphUtil — Utility functions

      + + +
      +
      +
      +
      +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/genindex.html b/python/altgraph/doc/_build/html/genindex.html new file mode 100644 index 000000000..16977c712 --- /dev/null +++ b/python/altgraph/doc/_build/html/genindex.html @@ -0,0 +1,604 @@ + + + + + + + + + Index — altgraph 0.11 documentation + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + + +

      Index

      + +
      + _ + | A + | B + | C + | D + | E + | F + | G + | H + | I + | M + | N + | O + | R + | S + | T + +
      +

      _

      +
      + + +
      + +
      __contains__() (altgraph.Graph.Graph method) +
      + +
      + +
      (altgraph.ObjectGraph.ObjectGraph method) +
      + +
      +
      + +
      __iter__() (altgraph.Graph.Graph method) +
      + +
      + +
      (in module altgraph.Dot) +
      + +
      +
      + +

      A

      + + + +
      + +
      add_edge() (altgraph.Graph.Graph method) +
      + + +
      add_node() (altgraph.Graph.Graph method) +
      + + +
      addNode() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      all_degree() (altgraph.Graph.Graph method) +
      + + +
      all_edges() (altgraph.Graph.Graph method) +
      + + +
      all_nbrs() (altgraph.Graph.Graph method) +
      + + +
      all_node_style() (altgraph.Dot.Dot method) +
      + +
      + +
      altgraph (module) +
      + + +
      altgraph.Dot (module) +
      + + +
      altgraph.Graph (module) +
      + + +
      altgraph.GraphAlgo (module) +
      + + +
      altgraph.GraphStat (module) +
      + + +
      altgraph.GraphUtil (module) +
      + + +
      altgraph.ObjectGraph (module) +
      + +
      + +

      B

      + + + +
      + +
      back_bfs() (altgraph.Graph.Graph method) +
      + + +
      back_bfs_subgraph() (altgraph.Graph.Graph method) +
      + +
      + +
      back_topo_sort() (altgraph.Graph.Graph method) +
      + +
      + +

      C

      + + + +
      + +
      clust_coef() (altgraph.Graph.Graph method) +
      + + +
      connected() (altgraph.Graph.Graph method) +
      + +
      + +
      createNode() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      createReferences() (altgraph.ObjectGraph.ObjectGraph method) +
      + +
      + +

      D

      + + + +
      + +
      degree_dist() (in module altgraph.GraphStat) +
      + + +
      describe_edge() (altgraph.Graph.Graph method) +
      + + +
      describe_node() (altgraph.Graph.Graph method) +
      + +
      + +
      dijkstra() (in module altgraph.GraphAlgo) +
      + + +
      display() (altgraph.Dot.Dot method) +
      + + +
      Dot (class in altgraph.Dot) +
      + +
      + +

      E

      + + + +
      + +
      edge_by_id() (altgraph.Graph.Graph method) +
      + + +
      edge_by_node() (altgraph.Graph.Graph method) +
      + + +
      edge_data() (altgraph.Graph.Graph method) +
      + +
      + +
      edge_list() (altgraph.Graph.Graph method) +
      + + +
      edge_style() (in module altgraph.Dot) +
      + +
      + +

      F

      + + + +
      + +
      filter_stack() (in module altgraph.GraphUtil) +
      + + +
      filterStack() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      findNode() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      flatten() (altgraph.ObjectGraph.ObjectGraph method) +
      + +
      + +
      forw_bfs() (altgraph.Graph.Graph method) +
      + + +
      forw_bfs_subgraph() (altgraph.Graph.Graph method) +
      + + +
      forw_topo_sort() (altgraph.Graph.Graph method) +
      + +
      + +

      G

      + + + +
      + +
      generate_random_graph() (in module altgraph.GraphUtil) +
      + + +
      generate_scale_free_graph() (in module altgraph.GraphUtil) +
      + + +
      get_edges() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      get_hops() (altgraph.Graph.Graph method) +
      + +
      + +
      getIdent() (in module altgraph.ObjectGraph) +
      + + +
      getRawIdent() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      Graph (class in altgraph.Graph) +
      + + +
      GraphError +
      + +
      + +

      H

      + + + +
      + +
      head() (altgraph.Graph.Graph method) +
      + + +
      hidden_edge_list() (altgraph.Graph.Graph method) +
      + + +
      hidden_node_list() (altgraph.Graph.Graph method) +
      + +
      + +
      hide_edge() (altgraph.Graph.Graph method) +
      + + +
      hide_node() (altgraph.Graph.Graph method) +
      + +
      + +

      I

      + + + +
      + +
      inc_degree() (altgraph.Graph.Graph method) +
      + + +
      inc_edges() (altgraph.Graph.Graph method) +
      + + +
      inc_nbrs() (altgraph.Graph.Graph method) +
      + +
      + +
      iterdata() (altgraph.Graph.Graph method) +
      + + +
      iterdfs() (altgraph.Graph.Graph method) +
      + + +
      iterdot() (in module altgraph.Dot) +
      + +
      + +

      M

      + + + +
      + +
      msg() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      msgin() (altgraph.ObjectGraph.ObjectGraph method) +
      + +
      + +
      msgout() (altgraph.ObjectGraph.ObjectGraph method) +
      + +
      + +

      N

      + + + +
      + +
      node_data() (in module altgraph.Graph) +
      + + +
      node_list() (altgraph.Graph.Graph method) +
      + + +
      node_style() (altgraph.Dot.Dot method) +
      + + +
      nodes() (altgraph.ObjectGraph.ObjectGraph method) +
      + +
      + +
      number_of_edges() (altgraph.Graph.Graph method) +
      + + +
      number_of_hidden_edges() (altgraph.Graph.Graph method) +
      + + +
      number_of_hidden_nodes() (altgraph.Graph.Graph method) +
      + + +
      number_of_nodes() (altgraph.Graph.Graph method) +
      + +
      + +

      O

      + + + +
      + +
      ObjectGraph (class in altgraph.ObjectGraph) +
      + + +
      ObjectGraph.debug (in module altgraph.ObjectGraph) +
      + + +
      ObjectGraph.graph (in module altgraph.ObjectGraph) +
      + +
      + +
      out_degree() (altgraph.Graph.Graph method) +
      + + +
      out_edges() (altgraph.Graph.Graph method) +
      + + +
      out_nbrs() (altgraph.Graph.Graph method) +
      + +
      + +

      R

      + + + +
      + +
      removeNode() (altgraph.ObjectGraph.ObjectGraph method) +
      + + +
      removeReference() (in module altgraph.ObjectGraph) +
      + + +
      restore_all_edges() (altgraph.Graph.Graph method) +
      + +
      + +
      restore_all_nodes() (altgraph.Graph.Graph method) +
      + + +
      restore_edge() (altgraph.Graph.Graph method) +
      + + +
      restore_node() (altgraph.Graph.Graph method) +
      + +
      + +

      S

      + + + +
      + +
      save_dot() (in module altgraph.Dot) +
      + + +
      save_image() (in module altgraph.Dot) +
      + +
      + +
      shortest_path() (in module altgraph.GraphAlgo) +
      + + +
      style() (altgraph.Dot.Dot method) +
      + +
      + +

      T

      + + +
      + +
      tail() (altgraph.Graph.Graph method) +
      + +
      + + + + + + +
      +
      + + + + + +
      +
      +
      + +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/graph.html b/python/altgraph/doc/_build/html/graph.html new file mode 100644 index 000000000..72dd1cdef --- /dev/null +++ b/python/altgraph/doc/_build/html/graph.html @@ -0,0 +1,491 @@ + + + + + + + + altgraph.Graph — Basic directional graphs — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph.Graph — Basic directional graphs¶

      +

      The module altgraph.Graph provides a class Graph that +represents a directed graph with N nodes and E edges.

      +
      +
      +class altgraph.Graph.Graph([edges])¶
      +

      Constructs a new empty Graph object. If the optional +edges parameter is supplied, updates the graph by adding the +specified edges.

      +

      All of the elements in edges should be tuples with two or three +elements. The first two elements of the tuple are the source and +destination node of the edge, the optional third element is the +edge data. The source and destination nodes are added to the graph +when the aren’t already present.

      +
      + + + +
      +

      Graph traversal¶

      +
      +
      +Graph.out_nbrs(node)¶
      +

      Return a list of all nodes connected by outgoing edges.

      +
      + +
      +
      +Graph.inc_nbrs(node)¶
      +

      Return a list of all nodes connected by incoming edges.

      +
      + +
      +
      +Graph.all_nbrs(node)¶
      +

      Returns a list of nodes connected by an incoming or outgoing edge.

      +
      + +
      +
      +Graph.forw_topo_sort()¶
      +

      Return a list of nodes where the successors (based on outgoing +edges) of any given node apear in the sequence after that node.

      +
      + +
      +
      +Graph.back_topo_sort()¶
      +

      Return a list of nodes where the successors (based on incoming +edges) of any given node apear in the sequence after that node.

      +
      + +
      +
      +Graph.forw_bfs_subgraph(start_id)¶
      +

      Return a subgraph consisting of the breadth first +reachable nodes from start_id based on their outgoing edges.

      +
      + +
      +
      +Graph.back_bfs_subgraph(start_id)¶
      +

      Return a subgraph consisting of the breadth first +reachable nodes from start_id based on their incoming edges.

      +
      + +
      +
      +Graph.iterdfs(start[, end[, forward]])¶
      +

      Yield nodes in a depth first traversal starting at the start +node.

      +

      If end is specified traversal stops when reaching that node.

      +

      If forward is True (the default) edges are traversed in forward +direction, otherwise they are traversed in reverse direction.

      +
      + +
      +
      +Graph.iterdata(start[, end[, forward[, condition]]])¶
      +

      Yield the associated data for nodes in a depth first traversal +starting at the start node. This method will not yield values for nodes +without associated data.

      +

      If end is specified traversal stops when reaching that node.

      +

      If condition is specified and the condition callable returns +False for the associated data this method will not yield the +associated data and will not follow the edges for the node.

      +

      If forward is True (the default) edges are traversed in forward +direction, otherwise they are traversed in reverse direction.

      +
      + +
      +
      +Graph.forw_bfs(start[, end])¶
      +

      Returns a list of nodes starting at start in some bread first +search order (following outgoing edges).

      +

      When end is specified iteration stops at that node.

      +
      + +
      +
      +Graph.back_bfs(start[, end])¶
      +

      Returns a list of nodes starting at start in some bread first +search order (following incoming edges).

      +

      When end is specified iteration stops at that node.

      +
      + +
      +
      +Graph.get_hops(start[, end[, forward]])¶
      +

      Computes the hop distance to all nodes centered around a specified node.

      +

      First order neighbours are at hop 1, their neigbours are at hop 2 etc. +Uses forw_bfs() or back_bfs() depending on the value of +the forward parameter.

      +

      If the distance between all neighbouring nodes is 1 the hop number +corresponds to the shortest distance between the nodes.

      +

      Typical usage:

      +
      >>> print graph.get_hops(1, 8)
+>>> [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)]
+# node 1 is at 0 hops
+# node 2 is at 1 hop
+# ...
+# node 8 is at 5 hops
+
      +
      +
      + +
      +
      +

      Graph statistics¶

      +
      +
      +Graph.connected()¶
      +

      Returns True iff every node in the graph can be reached from +every other node.

      +
      + +
      +
      +Graph.clust_coef(node)¶
      +

      Returns the local clustering coefficient of node.

      +

      The local cluster coefficient is the proportion of the actual number +of edges between neighbours of node and the maximum number of +edges between those nodes.

      +
      + +
      +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Previous topic

      +

      altgraph — A Python Graph Library

      +

      Next topic

      +

      altgraph.ObjectGraph — Graphs of objecs with an identifier

      + + +
      +
      +
      +
      +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/graphalgo.html b/python/altgraph/doc/_build/html/graphalgo.html new file mode 100644 index 000000000..07800d977 --- /dev/null +++ b/python/altgraph/doc/_build/html/graphalgo.html @@ -0,0 +1,134 @@ + + + + + + + + altgraph.GraphAlgo — Graph algorithms — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph.GraphAlgo — Graph algorithms¶

      +
      +
      +altgraph.GraphAlgo.dijkstra(graph, start[, end])¶
      +

      Dijkstra’s algorithm for shortest paths.

      +

      Find shortest paths from the start node to all nodes nearer +than or equal to the end node. The edge data is assumed to be the edge length.

      +
      +

      Note

      +

      Dijkstra’s algorithm is only guaranteed to work correctly when all edge lengths are positive. +This code does not verify this property for all edges (only the edges examined until the end +vertex is reached), but will correctly compute shortest paths even for some graphs with negative +edges, and will raise an exception if it discovers that a negative edge has caused it to make a mistake.

      +
      +
      + +
      +
      +altgraph.GraphAlgo.shortest_path(graph, start, end)¶
      +

      Find a single shortest path from the given start node to the given end node. +The input has the same conventions as dijkstra(). The output is a list +of the nodes in order along the shortest path.

      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      altgraph.ObjectGraph — Graphs of objecs with an identifier

      +

      Next topic

      +

      altgraph.GraphStat — Functions providing various graph statistics

      + + +
      +
      +
      +
      +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/graphstat.html b/python/altgraph/doc/_build/html/graphstat.html new file mode 100644 index 000000000..49a89bf51 --- /dev/null +++ b/python/altgraph/doc/_build/html/graphstat.html @@ -0,0 +1,130 @@ + + + + + + + + altgraph.GraphStat — Functions providing various graph statistics — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph.GraphStat — Functions providing various graph statistics¶

      +

      The module altgraph.GraphStat provides function that calculate +graph statistics. Currently there is only one such function, more may +be added later.

      +
      +
      +altgraph.GraphStat.degree_dist(graph[, limits[, bin_num[, mode]]])¶
      +

      Groups the number of edges per node into bin_num bins +and returns the list of those bins. Every item in the result +is a tuple with the center of the bin and the number of items +in that bin.

      +

      When the limits argument is present it must be a tuple with +the mininum and maximum number of edges that get binned (that +is, when limits is (4, 10) only nodes with between 4 +and 10 edges get counted.

      +

      The mode argument is used to count incoming ('inc') or +outgoing ('out') edges. The default is to count the outgoing +edges.

      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      altgraph.GraphAlgo — Graph algorithms

      +

      Next topic

      +

      altgraph.GraphUtil — Utility functions

      + + +
      +
      +
      +
      +
      +

      Navigation

      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/graphutil.html b/python/altgraph/doc/_build/html/graphutil.html new file mode 100644 index 000000000..774efcfdf --- /dev/null +++ b/python/altgraph/doc/_build/html/graphutil.html @@ -0,0 +1,162 @@ + + + + + + + + altgraph.GraphUtil — Utility functions — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph.GraphUtil — Utility functions¶

      +

      The module altgraph.GraphUtil performs a number of more +or less useful utility functions.

      +
      +
      +altgraph.GraphUtil.generate_random_graph(node_num, edge_num[, self_loops[, multi_edges])¶
      +

      Generates and returns a Graph instance +with node_num nodes randomly connected by edge_num edges.

      +

      When self_loops is present and True there can be edges that point from +a node to itself.

      +

      When multi_edge is present and True there can be duplicate edges.

      +

      This method raises GraphError <altgraph.GraphError when +a graph with the requested configuration cannot be created.

      +
      + +
      +
      +altgraph.GraphUtil.generate_scale_free_graph(steps, growth_num[, self_loops[, multi_edges]])¶
      +

      Generates and returns a Graph instance that +will have steps*growth_n um nodes and a scale free (powerlaw) +connectivity.

      +

      Starting with a fully connected graph with growth_num nodes +at every step growth_num nodes are added to the graph and are connected +to existing nodes with a probability proportional to the degree of these +existing nodes.

      +
      +

      Warning

      +

      The current implementation is basically untested, although +code inspection seems to indicate an implementation that is consistent +with the description at +Wolfram MathWorld

      +
      +
      + +
      +
      +altgraph.GraphUtil.filter_stack(graph, head, filters)¶
      +

      Perform a depth-first oder walk of the graph starting at head and +apply all filter functions in filters on the node data of the nodes +found.

      +

      Returns (visited, removes, orphans), where

      +
        +
      • visited: the set of visited nodes
        • +
      • removes: the list of nodes where the node data doesn’t match +all filters.
        • +
      • orphans: list of tuples (last_good, node), where +node is not in removes and one of the nodes that is connected +by an incoming edge is in removes. Last_good is the +closest upstream node that is not in removes.
        • +
      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      altgraph.GraphStat — Functions providing various graph statistics

      +

      Next topic

      +

      altgraph.Dot — Interface to the dot language

      + + +
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      + +
      +
      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/index.html b/python/altgraph/doc/_build/html/index.html new file mode 100644 index 000000000..83c8c9a25 --- /dev/null +++ b/python/altgraph/doc/_build/html/index.html @@ -0,0 +1,142 @@ + + + + + + + + Altgraph - A basic graph library — altgraph 0.11 documentation + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      Altgraph - A basic graph library¶

      +

      altgraph is a fork of graphlib: a graph (network) package for constructing +graphs, BFS and DFS traversals, topological sort, shortest paths, etc. with +graphviz output.

      +

      The primary users of this package are macholib and modulegraph.

      +
      + +
      + +
      +

      Indices and tables¶

      + +
      +
      + + +
      +
      +
      +
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      Table Of Contents

      + + +

      Next topic

      +

      Release history

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      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
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      License¶

      +

      Copyright (c) 2004 Istvan Albert unless otherwise noted.

      +

      Parts are copyright (c) Bob Ippolito

      +

      Parts are copyright (c) 2010-2014 Ronald Oussoren

      +
      +

      MIT License¶

      +

      Permission is hereby granted, free of charge, to any person obtaining a copy of this software +and associated documentation files (the “Software”), to deal in the Software without restriction, +including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do +so.

      +

      THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, +INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR +PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE +FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, +ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.

      +
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      altgraph — A Python Graph Library

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      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/objectgraph.html b/python/altgraph/doc/_build/html/objectgraph.html new file mode 100644 index 000000000..c9879f656 --- /dev/null +++ b/python/altgraph/doc/_build/html/objectgraph.html @@ -0,0 +1,283 @@ + + + + + + + + altgraph.ObjectGraph — Graphs of objecs with an identifier — altgraph 0.11 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      altgraph.ObjectGraph — Graphs of objecs with an identifier¶

      +
      +
      +class altgraph.ObjectGraph.ObjectGraph([graph[, debug]])¶
      +

      A graph of objects that have a “graphident” attribute. The +value of this attribute is the key for the object in the +graph.

      +

      The optional graph is a previously constructed +Graph.

      +

      The optional debug level controls the amount of debug output +(see msg(), msgin() and msgout()).

      +
      +

      Note

      +

      the altgraph library does not generate output, the +debug attribute and message methods are present for use +by subclasses.

      +
      +
      + +
      +
      +ObjectGraph.graph¶
      +

      An Graph object that contains +the graph data.

      +
      + +
      +
      +ObjectGraph.addNode(node)¶
      +

      Adds a node to the graph.

      +
      +

      Note

      +

      re-adding a node that was previously removed +using removeNode() will reinstate the previously +removed node.

      +
      +
      + +
      +
      +ObjectGraph.createNode(self, cls, name, *args, **kwds)¶
      +

      Creates a new node using cls(*args, **kwds) and adds that +node using addNode().

      +

      Returns the newly created node.

      +
      + +
      +
      +ObjectGraph.removeNode(node)¶
      +

      Removes a node from the graph when it exists. The node argument +is either a node object, or the graphident of a node.

      +
      + +
      +
      +ObjectGraph.createReferences(fromnode, tonode[, edge_data])¶
      +

      Creates a reference from fromnode to tonode. The optional +edge_data is associated with the edge.

      +

      Fromnode and tonode can either be node objects or the graphident +values for nodes.

      +
      + +
      +
      +altgraph.ObjectGraph.removeReference(fromnode, tonode)¶
      +

      Removes the reference from fromnode to tonode if it exists.

      +
      + +
      +
      +ObjectGraph.getRawIdent(node)¶
      +

      Returns the graphident attribute of node, or the graph itself +when node is None.

      +
      + +
      +
      +altgraph.ObjectGraph.getIdent(node)¶
      +

      Same as getRawIdent(), but only if the node is part +of the graph.

      +

      Node can either be an actual node object or the graphident of +a node.

      +
      + +
      +
      +ObjectGraph.findNode(node)¶
      +

      Returns a given node in the graph, or Node when it cannot +be found.

      +

      Node is either an object with a graphident attribute or +the graphident attribute itself.

      +
      + +
      +
      +ObjectGraph.__contains__(node)¶
      +

      Returns True if node is a member of the graph. Node is either an +object with a graphident attribute or the graphident attribute itself.

      +
      + +
      +
      +ObjectGraph.flatten([condition[, start]])¶
      +

      Yield all nodes that are entirely reachable by condition +starting fromt he given start node or the graph root.

      +
      +

      Note

      +

      objects are only reachable from the graph root +when there is a reference from the root to the node +(either directly or through another node)

      +
      +
      + +
      +
      +ObjectGraph.nodes()¶
      +

      Yield all nodes in the graph.

      +
      + +
      +
      +ObjectGraph.get_edges(node)¶
      +

      Returns two iterators that yield the nodes reaching by +outgoing and incoming edges.

      +
      + +
      +
      +ObjectGraph.filterStack(filters)¶
      +

      Filter the ObjectGraph in-place by removing all edges to nodes that +do not match every filter in the given filter list

      +

      Returns a tuple containing the number of: +(nodes_visited, nodes_removed, nodes_orphaned)

      +
      + +
      +

      Debug output¶

      +
      +
      +ObjectGraph.debug¶
      +

      The current debug level.

      +
      + +
      +
      +ObjectGraph.msg(level, text, *args)¶
      +

      Print a debug message at the current indentation level when the current +debug level is level or less.

      +
      + +
      +
      +ObjectGraph.msgin(level, text, *args)¶
      +

      Print a debug message when the current debug level is level or less, +and increase the indentation level.

      +
      + +
      +
      +ObjectGraph.msgout(level, text, *args)¶
      +

      Decrease the indentation level and print a debug message when the +current debug level is level or less.

      +
      + +
      +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Previous topic

      +

      altgraph.Graph — Basic directional graphs

      +

      Next topic

      +

      altgraph.GraphAlgo — Graph algorithms

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      + © Copyright 2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert. + Created using Sphinx 1.2.1. +
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      + altgraph + A directional graph for python
          + altgraph.Dot + Interface to the dot language as used by Graphviz..
          + altgraph.Graph + Basic directional graphs.
          + altgraph.GraphAlgo + Basic graphs algoritms
          + altgraph.GraphStat + Functions providing various graph statistics
          + altgraph.GraphUtil + Utility functions
          + altgraph.ObjectGraph + A graph of objects that have a "graphident" attribute.
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      + + \ No newline at end of file diff --git a/python/altgraph/doc/_build/html/searchindex.js b/python/altgraph/doc/_build/html/searchindex.js new file mode 100644 index 000000000..972760abe --- /dev/null +++ b/python/altgraph/doc/_build/html/searchindex.js @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/python/altgraph/doc/changelog.rst b/python/altgraph/doc/changelog.rst new file mode 100644 index 000000000..02fd412d6 --- /dev/null +++ b/python/altgraph/doc/changelog.rst @@ -0,0 +1,185 @@ +Release history +=============== + +0.12 +---- + +- Added ``ObjectGraph.edgeData`` to retrieve the edge data + from a specific edge. + +- Added ``AltGraph.update_edge_data`` and ``ObjectGraph.updateEdgeData`` + to update the data associated with a graph edge. + +0.11 +---- + +- Stabilize the order of elements in dot file exports, + patch from bitbucket user 'pombredanne'. + +- Tweak setup.py file to remove dependency on distribute (but + keep the dependency on setuptools) + + +0.10.2 +------ + +- There where no classifiers in the package metadata due to a bug + in setup.py + +0.10.1 +------ + +This is a bugfix release + +Bug fixes: + +- Issue #3: The source archive contains a README.txt + while the setup file refers to ReadMe.txt. + + This is caused by a misfeature in distutils, as a + workaround I've renamed ReadMe.txt to README.txt + in the source tree and setup file. + + +0.10 +----- + +This is a minor feature release + +Features: + +- Do not use "2to3" to support Python 3. + + As a side effect of this altgraph now supports + Python 2.6 and later, and no longer supports + earlier releases of Python. + +- The order of attributes in the Dot output + is now always alphabetical. + + With this change the output will be consistent + between runs and Python versions. + +0.9 +--- + +This is a minor bugfix release + +Features: + +- Added ``altgraph.ObjectGraph.ObjectGraph.nodes``, a method + yielding all nodes in an object graph. + +Bugfixes: + +- The 0.8 release didn't work with py2app when using + python 3.x. + + +0.8 +----- + +This is a minor feature release. The major new feature +is a extensive set of unittests, which explains almost +all other changes in this release. + +Bugfixes: + +- Installing failed with Python 2.5 due to using a distutils + class that isn't available in that version of Python + (issue #1 on the issue tracker) + +- ``altgraph.GraphStat.degree_dist`` now actually works + +- ``altgraph.Graph.add_edge(a, b, create_nodes=False)`` will + no longer create the edge when one of the nodes doesn't + exist. + +- ``altgraph.Graph.forw_topo_sort`` failed for some sparse graphs. + +- ``altgraph.Graph.back_topo_sort`` was completely broken in + previous releases. + +- ``altgraph.Graph.forw_bfs_subgraph`` now actually works. + +- ``altgraph.Graph.back_bfs_subgraph`` now actually works. + +- ``altgraph.Graph.iterdfs`` now returns the correct result + when the ``forward`` argument is ``False``. + +- ``altgraph.Graph.iterdata`` now returns the correct result + when the ``forward`` argument is ``False``. + + +Features: + +- The ``altgraph.Graph`` constructor now accepts an argument + that contains 2- and 3-tuples instead of requireing that + all items have the same size. The (optional) argument can now + also be any iterator. + +- ``altgraph.Graph.Graph.add_node`` has no effect when you + add a hidden node. + +- The private method ``altgraph.Graph._bfs`` is no longer + present. + +- The private method ``altgraph.Graph._dfs`` is no longer + present. + +- ``altgraph.ObjectGraph`` now has a ``__contains__`` methods, + which means you can use the ``in`` operator to check if a + node is part of a graph. + +- ``altgraph.GraphUtil.generate_random_graph`` will raise + ``GraphError`` instead of looping forever when it is + impossible to create the requested graph. + +- ``altgraph.Dot.edge_style`` raises ``GraphError`` when + one of the nodes is not present in the graph. The method + silently added the tail in the past, but without ensuring + a consistent graph state. + +- ``altgraph.Dot.save_img`` now works when the mode is + ``"neato"``. + +0.7.2 +----- + +This is a minor bugfix release + +Bugfixes: + +- distutils didn't include the documentation subtree + +0.7.1 +----- + +This is a minor feature release + +Features: + +- Documentation is now generated using `sphinx `_ + and can be viewed at . + +- The repository has moved to bitbucket + +- ``altgraph.GraphStat.avg_hops`` is no longer present, the function had no + implementation and no specified behaviour. + +- the module ``altgraph.compat`` is gone, which means altgraph will no + longer work with Python 2.3. + + +0.7.0 +----- + +This is a minor feature release. + +Features: + +- Support for Python 3 + +- It is now possible to run tests using 'python setup.py test' + + (The actual testsuite is still very minimal though) diff --git a/python/altgraph/doc/conf.py b/python/altgraph/doc/conf.py new file mode 100644 index 000000000..cd3fd9912 --- /dev/null +++ b/python/altgraph/doc/conf.py @@ -0,0 +1,209 @@ +# -*- coding: utf-8 -*- +# +# altgraph documentation build configuration file, created by +# sphinx-quickstart on Tue Aug 31 11:04:49 2010. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +def get_version(): + fn = os.path.join( + os.path.dirname(os.path.dirname(os.path.abspath(__file__))), + 'setup.cfg') + for ln in open(fn): + if ln.startswith('version'): + version = ln.split('=')[-1].strip() + return version + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.append(os.path.abspath('.')) +sys.path.insert(0, + os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) + +# -- General configuration ----------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.autodoc' ] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'altgraph' +copyright = u'2010-2011, Ronald Oussoren, Bob Ippolito, 2004 Istvan Albert' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = get_version() +# The full version, including alpha/beta/rc tags. +release = version + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of documents that shouldn't be included in the build. +#unused_docs = [] + +# List of directories, relative to source directory, that shouldn't be searched +# for source files. +exclude_trees = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. Major themes that come with +# Sphinx are currently 'default' and 'sphinxdoc'. +html_theme = 'nature' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_use_modindex = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +html_show_sourcelink = False + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = '' + +# Output file base name for HTML help builder. +htmlhelp_basename = 'altgraphdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +# The paper size ('letter' or 'a4'). +#latex_paper_size = 'letter' + +# The font size ('10pt', '11pt' or '12pt'). +#latex_font_size = '10pt' + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'altgraph.tex', u'altgraph Documentation', + u'Ronald Oussoren', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# Additional stuff for the LaTeX preamble. +#latex_preamble = '' + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_use_modindex = True + + +# Example configuration for intersphinx: refer to the Python standard library. +intersphinx_mapping = {'python': ('http://docs.python.org/', None) } diff --git a/python/altgraph/doc/core.rst b/python/altgraph/doc/core.rst new file mode 100644 index 000000000..8288f6a94 --- /dev/null +++ b/python/altgraph/doc/core.rst @@ -0,0 +1,26 @@ +:mod:`altgraph` --- A Python Graph Library +================================================== + +.. module:: altgraph + :synopsis: A directional graph for python + +altgraph is a fork of `graphlib `_ tailored +to use newer Python 2.3+ features, including additional support used by the +py2app suite (modulegraph and macholib, specifically). + +altgraph is a python based graph (network) representation and manipulation package. +It has started out as an extension to the `graph_lib module `_ +written by Nathan Denny it has been significantly optimized and expanded. + +The :class:`altgraph.Graph.Graph` class is loosely modeled after the `LEDA `_ +(Library of Efficient Datatypes) representation. The library +includes methods for constructing graphs, BFS and DFS traversals, +topological sort, finding connected components, shortest paths as well as a number +graph statistics functions. The library can also visualize graphs +via `graphviz `_. + + +.. exception:: GraphError + + Exception raised when methods are called with bad values of + an inconsistent state. diff --git a/python/altgraph/doc/dot.rst b/python/altgraph/doc/dot.rst new file mode 100644 index 000000000..3848c488a --- /dev/null +++ b/python/altgraph/doc/dot.rst @@ -0,0 +1,224 @@ +:mod:`altgraph.Dot` --- Interface to the dot language +===================================================== + +.. module:: altgraph.Dot + :synopsis: Interface to the dot language as used by Graphviz.. + +The :py:mod:`~altgraph.Dot` module provides a simple interface to the +file format used in the `graphviz`_ program. The module is intended to +offload the most tedious part of the process (the **dot** file generation) +while transparently exposing most of its features. + +.. _`graphviz`: `_ + +To display the graphs or to generate image files the `graphviz`_ +package needs to be installed on the system, moreover the :command:`dot` and :command:`dotty` programs must +be accesible in the program path so that they can be ran from processes spawned +within the module. + +Example usage +------------- + +Here is a typical usage:: + + from altgraph import Graph, Dot + + # create a graph + edges = [ (1,2), (1,3), (3,4), (3,5), (4,5), (5,4) ] + graph = Graph.Graph(edges) + + # create a dot representation of the graph + dot = Dot.Dot(graph) + + # display the graph + dot.display() + + # save the dot representation into the mydot.dot file + dot.save_dot(file_name='mydot.dot') + + # save dot file as gif image into the graph.gif file + dot.save_img(file_name='graph', file_type='gif') + + +Directed graph and non-directed graph +------------------------------------- + +Dot class can use for both directed graph and non-directed graph +by passing *graphtype* parameter. + +Example:: + + # create directed graph(default) + dot = Dot.Dot(graph, graphtype="digraph") + + # create non-directed graph + dot = Dot.Dot(graph, graphtype="graph") + + +Customizing the output +---------------------- + +The graph drawing process may be customized by passing +valid :command:`dot` parameters for the nodes and edges. For a list of all +parameters see the `graphviz`_ documentation. + +Example:: + + # customizing the way the overall graph is drawn + dot.style(size='10,10', rankdir='RL', page='5, 5' , ranksep=0.75) + + # customizing node drawing + dot.node_style(1, label='BASE_NODE',shape='box', color='blue' ) + dot.node_style(2, style='filled', fillcolor='red') + + # customizing edge drawing + dot.edge_style(1, 2, style='dotted') + dot.edge_style(3, 5, arrowhead='dot', label='binds', labelangle='90') + dot.edge_style(4, 5, arrowsize=2, style='bold') + + + .. note:: + + dotty (invoked via :py:func:`~altgraph.Dot.display`) may not be able to + display all graphics styles. To verify the output save it to an image + file and look at it that way. + +Valid attributes +---------------- + +- dot styles, passed via the :py:meth:`Dot.style` method:: + + rankdir = 'LR' (draws the graph horizontally, left to right) + ranksep = number (rank separation in inches) + +- node attributes, passed via the :py:meth:`Dot.node_style` method:: + + style = 'filled' | 'invisible' | 'diagonals' | 'rounded' + shape = 'box' | 'ellipse' | 'circle' | 'point' | 'triangle' + +- edge attributes, passed via the :py:meth:`Dot.edge_style` method:: + + style = 'dashed' | 'dotted' | 'solid' | 'invis' | 'bold' + arrowhead = 'box' | 'crow' | 'diamond' | 'dot' | 'inv' | 'none' | 'tee' | 'vee' + weight = number (the larger the number the closer the nodes will be) + +- valid `graphviz colors `_ + +- for more details on how to control the graph drawing process see the + `graphviz reference `_. + + +Class interface +--------------- + +.. class:: Dot(graph[, nodes[, edgefn[, nodevisitor[, edgevisitor[, name[, dot[, dotty[, neato[, graphtype]]]]]]]]]) + + Creates a new Dot generator based on the specified + :class:`Graph `. The Dot generator won't reference + the *graph* once it is constructed. + + If the *nodes* argument is present it is the list of nodes to include + in the graph, otherwise all nodes in *graph* are included. + + If the *edgefn* argument is present it is a function that yields the + nodes connected to another node, this defaults to + :meth:`graph.out_nbr `. The constructor won't + add edges to the dot file unless both the head and tail of the edge + are in *nodes*. + + If the *name* is present it specifies the name of the graph in the resulting + dot file. The default is ``"G"``. + + The functions *nodevisitor* and *edgevisitor* return the default style + for a given edge or node (both default to functions that return an empty + style). + + The arguments *dot*, *dotty* and *neato* are used to pass the path to + the corresponding `graphviz`_ command. + + +Updating graph attributes +......................... + +.. method:: Dot.style(\**attr) + + Sets the overall style (graph attributes) to the given attributes. + + See `Valid Attributes`_ for more information about the attributes. + +.. method:: Dot.node_style(node, \**attr) + + Sets the style for *node* to the given attributes. + + This method will add *node* to the graph when it isn't already + present. + + See `Valid Attributes`_ for more information about the attributes. + +.. method:: Dot.all_node_style(\**attr) + + Replaces the current style for all nodes + + +.. method:: edge_style(head, tail, \**attr) + + Sets the style of an edge to the given attributes. The edge will + be added to the graph when it isn't already present, but *head* + and *tail* must both be valid nodes. + + See `Valid Attributes`_ for more information about the attributes. + + + +Emitting output +............... + +.. method:: Dot.display([mode]) + + Displays the current graph via dotty. + + If the *mode* is ``"neato"`` the dot file is processed with + the neato command before displaying. + + This method won't return until the dotty command exits. + +.. method:: save_dot(filename) + + Saves the current graph representation into the given file. + + .. note:: + + For backward compatibility reasons this method can also + be called without an argument, it will then write the graph + into a fixed filename (present in the attribute :data:`Graph.temp_dot`). + + This feature is deprecated and should not be used. + + +.. method:: save_image(file_name[, file_type[, mode]]) + + Saves the current graph representation as an image file. The output + is written into a file whose basename is *file_name* and whose suffix + is *file_type*. + + The *file_type* specifies the type of file to write, the default + is ``"gif"``. + + If the *mode* is ``"neato"`` the dot file is processed with + the neato command before displaying. + + .. note:: + + For backward compatibility reasons this method can also + be called without an argument, it will then write the graph + with a fixed basename (``"out"``). + + This feature is deprecated and should not be used. + +.. method:: iterdot() + + Yields all lines of a `graphviz`_ input file (including line endings). + +.. method:: __iter__() + + Alias for the :meth:`iterdot` method. diff --git a/python/altgraph/doc/graph.rst b/python/altgraph/doc/graph.rst new file mode 100644 index 000000000..502a2186a --- /dev/null +++ b/python/altgraph/doc/graph.rst @@ -0,0 +1,305 @@ +:mod:`altgraph.Graph` --- Basic directional graphs +================================================== + +.. module:: altgraph.Graph + :synopsis: Basic directional graphs. + +The module :mod:`altgraph.Graph` provides a class :class:`Graph` that +represents a directed graph with *N* nodes and *E* edges. + +.. class:: Graph([edges]) + + Constructs a new empty :class:`Graph` object. If the optional + *edges* parameter is supplied, updates the graph by adding the + specified edges. + + All of the elements in *edges* should be tuples with two or three + elements. The first two elements of the tuple are the source and + destination node of the edge, the optional third element is the + edge data. The source and destination nodes are added to the graph + when the aren't already present. + + +Node related methods +-------------------- + +.. method:: Graph.add_node(node[, node_data]) + + Adds a new node to the graph if it is not already present. The new + node must be a hashable object. + + Arbitrary data can be attached to the node via the optional *node_data* + argument. + + .. note:: the node also won't be added to the graph when it is + present but currently hidden. + + +.. method:: Graph.hide_node(node) + + Hides a *node* from the graph. The incoming and outgoing edges of + the node will also be hidden. + + Raises :class:`altgraph.GraphError` when the node is not (visible) + node of the graph. + + +.. method:: Graph.restore_node(node) + + Restores a previously hidden *node*. The incoming and outgoing + edges of the node are also restored. + + Raises :class:`altgraph.GraphError` when the node is not a hidden + node of the graph. + +.. method:: Graph.restore_all_nodes() + + Restores all hidden nodes. + +.. method:: Graph.number_of_nodes() + + Return the number of visible nodes in the graph. + +.. method:: Graph.number_of_hidden_nodes() + + Return the number of hidden nodes in the graph. + +.. method:: Graph.node_list() + + Return a list with all visible nodes in the graph. + +.. method:: Graph.hidden_node_list() + + Return a list with all hidden nodes in the graph. + +.. method:: node_data(node) + + Return the data associated with the *node* when it was + added. + +.. method:: Graph.describe_node(node) + + Returns *node*, the node's data and the lists of outgoing + and incoming edges for the node. + + .. note:: + + the edge lists should not be modified, doing so + can result in unpredicatable behavior. + +.. method:: Graph.__contains__(node) + + Returns True iff *node* is a node in the graph. This + method is accessed through the *in* operator. + +.. method:: Graph.__iter__() + + Yield all nodes in the graph. + +.. method:: Graph.out_edges(node) + + Return the list of outgoing edges for *node* + +.. method:: Graph.inc_edges(node) + + Return the list of incoming edges for *node* + +.. method:: Graph.all_edges(node) + + Return the list of incoming and outgoing edges for *node* + +.. method:: Graph.out_degree(node) + + Return the number of outgoing edges for *node*. + +.. method:: Graph.inc_degree(node) + + Return the number of incoming edges for *node*. + +.. method:: Graph.all_degree(node) + + Return the number of edges (incoming or outgoing) for *node*. + +Edge related methods +-------------------- + +.. method:: Graph.add_edge(head_id, tail_id [, edge data [, create_nodes]]) + + Adds a directed edge from *head_id* to *tail_id*. Arbitrary data can + be added via *edge_data*. When *create_nodes* is *True* (the default), + *head_id* and *tail_id* will be added to the graph when the aren't + already present. + +.. method:: Graph.hide_edge(edge) + + Hides an edge from the graph. The edge may be unhidden at some later + time. + +.. method:: Graph.restore_edge(edge) + + Restores a previously hidden *edge*. + +.. method:: Graph.restore_all_edges() + + Restore all edges that were hidden before, except for edges + referring to hidden nodes. + +.. method:: Graph.edge_by_node(head, tail) + + Return the edge ID for an edge from *head* to *tail*, + or :data:`None` when no such edge exists. + +.. method:: Graph.edge_by_id(edge) + + Return the head and tail of the *edge* + +.. method:: Graph.edge_data(edge) + + Return the data associated with the *edge*. + +.. method:: Graph.update_edge_data(edge, data) + + Replace the edge data for *edge* by *data*. Raises + :exc:`KeyError` when the edge does not exist. + + .. versionadded:: 0.12 + +.. method:: Graph.head(edge) + + Return the head of an *edge* + +.. method:: Graph.tail(edge) + + Return the tail of an *edge* + +.. method:: Graph.describe_edge(edge) + + Return the *edge*, the associated data, its head and tail. + +.. method:: Graph.number_of_edges() + + Return the number of visible edges. + +.. method:: Graph.number_of_hidden_edges() + + Return the number of hidden edges. + +.. method:: Graph.edge_list() + + Returns a list with all visible edges in the graph. + +.. method:: Graph.hidden_edge_list() + + Returns a list with all hidden edges in the graph. + +Graph traversal +--------------- + +.. method:: Graph.out_nbrs(node) + + Return a list of all nodes connected by outgoing edges. + +.. method:: Graph.inc_nbrs(node) + + Return a list of all nodes connected by incoming edges. + +.. method:: Graph.all_nbrs(node) + + Returns a list of nodes connected by an incoming or outgoing edge. + +.. method:: Graph.forw_topo_sort() + + Return a list of nodes where the successors (based on outgoing + edges) of any given node apear in the sequence after that node. + +.. method:: Graph.back_topo_sort() + + Return a list of nodes where the successors (based on incoming + edges) of any given node apear in the sequence after that node. + +.. method:: Graph.forw_bfs_subgraph(start_id) + + Return a subgraph consisting of the breadth first + reachable nodes from *start_id* based on their outgoing edges. + + +.. method:: Graph.back_bfs_subgraph(start_id) + + Return a subgraph consisting of the breadth first + reachable nodes from *start_id* based on their incoming edges. + +.. method:: Graph.iterdfs(start[, end[, forward]]) + + Yield nodes in a depth first traversal starting at the *start* + node. + + If *end* is specified traversal stops when reaching that node. + + If forward is True (the default) edges are traversed in forward + direction, otherwise they are traversed in reverse direction. + +.. method:: Graph.iterdata(start[, end[, forward[, condition]]]) + + Yield the associated data for nodes in a depth first traversal + starting at the *start* node. This method will not yield values for nodes + without associated data. + + If *end* is specified traversal stops when reaching that node. + + If *condition* is specified and the condition callable returns + False for the associated data this method will not yield the + associated data and will not follow the edges for the node. + + If forward is True (the default) edges are traversed in forward + direction, otherwise they are traversed in reverse direction. + +.. method:: Graph.forw_bfs(start[, end]) + + Returns a list of nodes starting at *start* in some bread first + search order (following outgoing edges). + + When *end* is specified iteration stops at that node. + +.. method:: Graph.back_bfs(start[, end]) + + Returns a list of nodes starting at *start* in some bread first + search order (following incoming edges). + + When *end* is specified iteration stops at that node. + +.. method:: Graph.get_hops(start[, end[, forward]]) + + Computes the hop distance to all nodes centered around a specified node. + + First order neighbours are at hop 1, their neigbours are at hop 2 etc. + Uses :py:meth:`forw_bfs` or :py:meth:`back_bfs` depending on the value of + the forward parameter. + + If the distance between all neighbouring nodes is 1 the hop number + corresponds to the shortest distance between the nodes. + + Typical usage:: + + >>> print graph.get_hops(1, 8) + >>> [(1, 0), (2, 1), (3, 1), (4, 2), (5, 3), (7, 4), (8, 5)] + # node 1 is at 0 hops + # node 2 is at 1 hop + # ... + # node 8 is at 5 hops + + +Graph statistics +---------------- + +.. method:: Graph.connected() + + Returns True iff every node in the graph can be reached from + every other node. + +.. method:: Graph.clust_coef(node) + + Returns the local clustering coefficient of node. + + The local cluster coefficient is the proportion of the actual number + of edges between neighbours of node and the maximum number of + edges between those nodes. diff --git a/python/altgraph/doc/graphalgo.rst b/python/altgraph/doc/graphalgo.rst new file mode 100644 index 000000000..84d492f44 --- /dev/null +++ b/python/altgraph/doc/graphalgo.rst @@ -0,0 +1,26 @@ +:mod:`altgraph.GraphAlgo` --- Graph algorithms +================================================== + +.. module:: altgraph.GraphAlgo + :synopsis: Basic graphs algoritms + +.. function:: dijkstra(graph, start[, end]) + + Dijkstra's algorithm for shortest paths. + + Find shortest paths from the start node to all nodes nearer + than or equal to the *end* node. The edge data is assumed to be the edge length. + + .. note:: + + Dijkstra's algorithm is only guaranteed to work correctly when all edge lengths are positive. + This code does not verify this property for all edges (only the edges examined until the end + vertex is reached), but will correctly compute shortest paths even for some graphs with negative + edges, and will raise an exception if it discovers that a negative edge has caused it to make a mistake. + + +.. function:: shortest_path(graph, start, end) + + Find a single shortest path from the given start node to the given end node. + The input has the same conventions as :func:`dijkstra`. The output is a list + of the nodes in order along the shortest path. diff --git a/python/altgraph/doc/graphstat.rst b/python/altgraph/doc/graphstat.rst new file mode 100644 index 000000000..0931a12dd --- /dev/null +++ b/python/altgraph/doc/graphstat.rst @@ -0,0 +1,25 @@ +:mod:`altgraph.GraphStat` --- Functions providing various graph statistics +========================================================================== + +.. module:: altgraph.GraphStat + :synopsis: Functions providing various graph statistics + +The module :mod:`altgraph.GraphStat` provides function that calculate +graph statistics. Currently there is only one such function, more may +be added later. + +.. function:: degree_dist(graph[, limits[, bin_num[, mode]]]) + + Groups the number of edges per node into *bin_num* bins + and returns the list of those bins. Every item in the result + is a tuple with the center of the bin and the number of items + in that bin. + + When the *limits* argument is present it must be a tuple with + the mininum and maximum number of edges that get binned (that + is, when *limits* is ``(4, 10)`` only nodes with between 4 + and 10 edges get counted. + + The *mode* argument is used to count incoming (``'inc'``) or + outgoing (``'out'``) edges. The default is to count the outgoing + edges. diff --git a/python/altgraph/doc/graphutil.rst b/python/altgraph/doc/graphutil.rst new file mode 100644 index 000000000..c07836df8 --- /dev/null +++ b/python/altgraph/doc/graphutil.rst @@ -0,0 +1,55 @@ +:mod:`altgraph.GraphUtil` --- Utility functions +================================================ + +.. module:: altgraph.GraphUtil + :synopsis: Utility functions + +The module :mod:`altgraph.GraphUtil` performs a number of more +or less useful utility functions. + +.. function:: generate_random_graph(node_num, edge_num[, self_loops[, multi_edges]) + + Generates and returns a :class:`Graph ` instance + with *node_num* nodes randomly connected by *edge_num* edges. + + When *self_loops* is present and True there can be edges that point from + a node to itself. + + When *multi_edge* is present and True there can be duplicate edges. + + This method raises :class:`GraphError `_ + +.. function:: filter_stack(graph, head, filters) + + Perform a depth-first oder walk of the graph starting at *head* and + apply all filter functions in *filters* on the node data of the nodes + found. + + Returns (*visited*, *removes*, *orphans*), where + + * *visited*: the set of visited nodes + + * *removes*: the list of nodes where the node data doesn't match + all *filters*. + + * *orphans*: list of tuples (*last_good*, *node*), where + node is not in *removes* and one of the nodes that is connected + by an incoming edge is in *removes*. *Last_good* is the + closest upstream node that is not in *removes*. diff --git a/python/altgraph/doc/index.rst b/python/altgraph/doc/index.rst new file mode 100644 index 000000000..1e8d504ed --- /dev/null +++ b/python/altgraph/doc/index.rst @@ -0,0 +1,41 @@ +.. altgraph documentation master file, created by + sphinx-quickstart on Tue Aug 31 11:04:49 2010. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Altgraph - A basic graph library +================================ + +altgraph is a fork of graphlib: a graph (network) package for constructing +graphs, BFS and DFS traversals, topological sort, shortest paths, etc. with +graphviz output. + +The primary users of this package are `macholib `_ and `modulegraph `_. + +.. toctree:: + :maxdepth: 1 + + changelog + license + core + graph + objectgraph + graphalgo + graphstat + graphutil + dot + +Online Resources +---------------- + +* `Sourcecode repository on bitbucket `_ + +* `The issue tracker `_ + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/python/altgraph/doc/license.rst b/python/altgraph/doc/license.rst new file mode 100644 index 000000000..498e60be0 --- /dev/null +++ b/python/altgraph/doc/license.rst @@ -0,0 +1,25 @@ +License +======= + +Copyright (c) 2004 Istvan Albert unless otherwise noted. + +Parts are copyright (c) Bob Ippolito + +Parts are copyright (c) 2010-2014 Ronald Oussoren + +MIT License +........... + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software +and associated documentation files (the "Software"), to deal in the Software without restriction, +including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do +so. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, +INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR +PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE +FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, +ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + diff --git a/python/altgraph/doc/objectgraph.rst b/python/altgraph/doc/objectgraph.rst new file mode 100644 index 000000000..e3df396b1 --- /dev/null +++ b/python/altgraph/doc/objectgraph.rst @@ -0,0 +1,146 @@ +:mod:`altgraph.ObjectGraph` --- Graphs of objecs with an identifier +=================================================================== + +.. module:: altgraph.ObjectGraph + :synopsis: A graph of objects that have a "graphident" attribute. + +.. class:: ObjectGraph([graph[, debug]]) + + A graph of objects that have a "graphident" attribute. The + value of this attribute is the key for the object in the + graph. + + The optional *graph* is a previously constructed + :class:`Graph `. + + The optional *debug* level controls the amount of debug output + (see :meth:`msg`, :meth:`msgin` and :meth:`msgout`). + + .. note:: the altgraph library does not generate output, the + debug attribute and message methods are present for use + by subclasses. + +.. data:: ObjectGraph.graph + + An :class:`Graph ` object that contains + the graph data. + + +.. method:: ObjectGraph.addNode(node) + + Adds a *node* to the graph. + + .. note:: re-adding a node that was previously removed + using :meth:`removeNode` will reinstate the previously + removed node. + +.. method:: ObjectGraph.createNode(self, cls, name, \*args, \**kwds) + + Creates a new node using ``cls(*args, **kwds)`` and adds that + node using :meth:`addNode`. + + Returns the newly created node. + +.. method:: ObjectGraph.removeNode(node) + + Removes a *node* from the graph when it exists. The *node* argument + is either a node object, or the graphident of a node. + +.. method:: ObjectGraph.createReferences(fromnode, tonode[, edge_data]) + + Creates a reference from *fromnode* to *tonode*. The optional + *edge_data* is associated with the edge. + + *Fromnode* and *tonode* can either be node objects or the graphident + values for nodes. + +.. method:: removeReference(fromnode, tonode) + + Removes the reference from *fromnode* to *tonode* if it exists. + +.. method:: ObjectGraph.getRawIdent(node) + + Returns the *graphident* attribute of *node*, or the graph itself + when *node* is :data:`None`. + +.. method:: getIdent(node) + + Same as :meth:`getRawIdent`, but only if the node is part + of the graph. + + *Node* can either be an actual node object or the graphident of + a node. + +.. method:: ObjectGraph.findNode(node) + + Returns a given node in the graph, or :data:`Node` when it cannot + be found. + + *Node* is either an object with a *graphident* attribute or + the *graphident* attribute itself. + +.. method:: ObjectGraph.__contains__(node) + + Returns True if *node* is a member of the graph. *Node* is either an + object with a *graphident* attribute or the *graphident* attribute itself. + +.. method:: ObjectGraph.flatten([condition[, start]]) + + Yield all nodes that are entirely reachable by *condition* + starting fromt he given *start* node or the graph root. + + .. note:: objects are only reachable from the graph root + when there is a reference from the root to the node + (either directly or through another node) + +.. method:: ObjectGraph.nodes() + + Yield all nodes in the graph. + +.. method:: ObjectGraph.get_edges(node) + + Returns two iterators that yield the nodes reaching by + outgoing and incoming edges. + +.. method:: ObjectGraph.filterStack(filters) + + Filter the ObjectGraph in-place by removing all edges to nodes that + do not match every filter in the given filter list + + Returns a tuple containing the number of: + (*nodes_visited*, *nodes_removed*, *nodes_orphaned*) + +.. method:: ObjectGraph.edgeData(fromNode, toNode): + Return the edge data associated with the edge from *fromNode* + to *toNode*. Raises :exc:`KeyError` when no such edge exists. + + .. versionadded: 0.12 + +.. method:: ObjectGraph.updateEdgeData(fromNode, toNode, edgeData) + + Replace the data associated with the edge from *fromNode* to + *toNode* by *edgeData*. + + Raises :exc:`KeyError` when the edge does not exist. + +Debug output +------------ + +.. data:: ObjectGraph.debug + + The current debug level. + +.. method:: ObjectGraph.msg(level, text, \*args) + + Print a debug message at the current indentation level when the current + debug level is *level* or less. + +.. method:: ObjectGraph.msgin(level, text, \*args) + + Print a debug message when the current debug level is *level* or less, + and increase the indentation level. + +.. method:: ObjectGraph.msgout(level, text, \*args) + + Decrease the indentation level and print a debug message when the + current debug level is *level* or less. diff --git a/python/altgraph/setup.cfg b/python/altgraph/setup.cfg new file mode 100644 index 000000000..9c6880e3c --- /dev/null +++ b/python/altgraph/setup.cfg @@ -0,0 +1,36 @@ +[metadata] +name = altgraph +version = 0.12 +description = Python graph (network) package +long_description_file = + README.txt + doc/changelog.rst +author = Ronald Oussoren +author_email = ronaldoussoren@mac.com +maintainer = Ronald Oussoren +maintainer_email = ronaldoussoren@mac.com +url = http://packages.python.org/altgraph +download_url = http://pypi.python.org/pypi/altgraph +license = MIT +classifiers = + Intended Audience :: Developers + License :: OSI Approved :: MIT License + Programming Language :: Python + Programming Language :: Python :: 2 + Programming Language :: Python :: 2.7 + Programming Language :: Python :: 3 + Programming Language :: Python :: 3.3 + Programming Language :: Python :: 3.4 + Topic :: Software Development :: Libraries :: Python Modules + Topic :: Scientific/Engineering :: Mathematics + Topic :: Scientific/Engineering :: Visualization +keywords = graph +platforms = any +packages = altgraph +zip-safe = 1 + +[egg_info] +tag_build = +tag_date = 0 +tag_svn_revision = 0 + diff --git a/python/altgraph/setup.py b/python/altgraph/setup.py new file mode 100644 index 000000000..a1a4cb6eb --- /dev/null +++ b/python/altgraph/setup.py @@ -0,0 +1,867 @@ +""" +Shared setup file for simple python packages. Uses a setup.cfg that +is the same as the distutils2 project, unless noted otherwise. + +It exists for two reasons: +1) This makes it easier to reuse setup.py code between my own + projects + +2) Easier migration to distutils2 when that catches on. + +Additional functionality: + +* Section metadata: + requires-test: Same as 'tests_require' option for setuptools. + +""" + +import sys +import os +import re +import platform +from fnmatch import fnmatch +import os +import sys +import time +import tempfile +import tarfile +try: + import urllib.request as urllib +except ImportError: + import urllib +from distutils import log +try: + from hashlib import md5 + +except ImportError: + from md5 import md5 + +if sys.version_info[0] == 2: + from ConfigParser import RawConfigParser, NoOptionError, NoSectionError +else: + from configparser import RawConfigParser, NoOptionError, NoSectionError + +ROOTDIR = os.path.dirname(os.path.abspath(__file__)) + + +# +# +# +# Parsing the setup.cfg and converting it to something that can be +# used by setuptools.setup() +# +# +# + +def eval_marker(value): + """ + Evaluate an distutils2 environment marker. + + This code is unsafe when used with hostile setup.cfg files, + but that's not a problem for our own files. + """ + value = value.strip() + + class M: + def __init__(self, **kwds): + for k, v in kwds.items(): + setattr(self, k, v) + + variables = { + 'python_version': '%d.%d'%(sys.version_info[0], sys.version_info[1]), + 'python_full_version': sys.version.split()[0], + 'os': M( + name=os.name, + ), + 'sys': M( + platform=sys.platform, + ), + 'platform': M( + version=platform.version(), + machine=platform.machine(), + ), + } + + return bool(eval(value, variables, variables)) + + + return True + +def _opt_value(cfg, into, section, key, transform = None): + try: + v = cfg.get(section, key) + if transform != _as_lines and ';' in v: + v, marker = v.rsplit(';', 1) + if not eval_marker(marker): + return + + v = v.strip() + + if v: + if transform: + into[key] = transform(v.strip()) + else: + into[key] = v.strip() + + except (NoOptionError, NoSectionError): + pass + +def _as_bool(value): + if value.lower() in ('y', 'yes', 'on'): + return True + elif value.lower() in ('n', 'no', 'off'): + return False + elif value.isdigit(): + return bool(int(value)) + else: + raise ValueError(value) + +def _as_list(value): + return value.split() + +def _as_lines(value): + result = [] + for v in value.splitlines(): + if ';' in v: + v, marker = v.rsplit(';', 1) + if not eval_marker(marker): + continue + + v = v.strip() + if v: + result.append(v) + else: + result.append(v) + return result + +def _map_requirement(value): + m = re.search(r'(\S+)\s*(?:\((.*)\))?', value) + name = m.group(1) + version = m.group(2) + + if version is None: + return name + + else: + mapped = [] + for v in version.split(','): + v = v.strip() + if v[0].isdigit(): + # Checks for a specific version prefix + m = v.rsplit('.', 1) + mapped.append('>=%s,<%s.%s'%( + v, m[0], int(m[1])+1)) + + else: + mapped.append(v) + return '%s %s'%(name, ','.join(mapped),) + +def _as_requires(value): + requires = [] + for req in value.splitlines(): + if ';' in req: + req, marker = v.rsplit(';', 1) + if not eval_marker(marker): + continue + req = req.strip() + + if not req: + continue + requires.append(_map_requirement(req)) + return requires + +def parse_setup_cfg(): + cfg = RawConfigParser() + r = cfg.read([os.path.join(ROOTDIR, 'setup.cfg')]) + if len(r) != 1: + print("Cannot read 'setup.cfg'") + sys.exit(1) + + metadata = dict( + name = cfg.get('metadata', 'name'), + version = cfg.get('metadata', 'version'), + description = cfg.get('metadata', 'description'), + ) + + _opt_value(cfg, metadata, 'metadata', 'license') + _opt_value(cfg, metadata, 'metadata', 'maintainer') + _opt_value(cfg, metadata, 'metadata', 'maintainer_email') + _opt_value(cfg, metadata, 'metadata', 'author') + _opt_value(cfg, metadata, 'metadata', 'author_email') + _opt_value(cfg, metadata, 'metadata', 'url') + _opt_value(cfg, metadata, 'metadata', 'download_url') + _opt_value(cfg, metadata, 'metadata', 'classifiers', _as_lines) + _opt_value(cfg, metadata, 'metadata', 'platforms', _as_list) + _opt_value(cfg, metadata, 'metadata', 'packages', _as_list) + _opt_value(cfg, metadata, 'metadata', 'keywords', _as_list) + + try: + v = cfg.get('metadata', 'requires-dist') + + except (NoOptionError, NoSectionError): + pass + + else: + requires = _as_requires(v) + if requires: + metadata['install_requires'] = requires + + try: + v = cfg.get('metadata', 'requires-test') + + except (NoOptionError, NoSectionError): + pass + + else: + requires = _as_requires(v) + if requires: + metadata['tests_require'] = requires + + + try: + v = cfg.get('metadata', 'long_description_file') + except (NoOptionError, NoSectionError): + pass + + else: + parts = [] + for nm in v.split(): + fp = open(nm, 'rU') + parts.append(fp.read()) + fp.close() + + metadata['long_description'] = '\n\n'.join(parts) + + + try: + v = cfg.get('metadata', 'zip-safe') + except (NoOptionError, NoSectionError): + pass + + else: + metadata['zip_safe'] = _as_bool(v) + + try: + v = cfg.get('metadata', 'console_scripts') + except (NoOptionError, NoSectionError): + pass + + else: + if 'entry_points' not in metadata: + metadata['entry_points'] = {} + + metadata['entry_points']['console_scripts'] = v.splitlines() + + if sys.version_info[:2] <= (2,6): + try: + metadata['tests_require'] += ", unittest2" + except KeyError: + metadata['tests_require'] = "unittest2" + + return metadata + + +# +# +# +# Bootstrapping setuptools/distribute, based on +# a heavily modified version of distribute_setup.py +# +# +# + + +SETUPTOOLS_PACKAGE='setuptools' + + +try: + import subprocess + + def _python_cmd(*args): + args = (sys.executable,) + args + return subprocess.call(args) == 0 + +except ImportError: + def _python_cmd(*args): + args = (sys.executable,) + args + new_args = [] + for a in args: + new_args.append(a.replace("'", "'\"'\"'")) + os.system(' '.join(new_args)) == 0 + + +try: + import json + + def get_pypi_src_download(package): + url = 'https://pypi.python.org/pypi/%s/json'%(package,) + fp = urllib.urlopen(url) + try: + try: + data = fp.read() + + finally: + fp.close() + except urllib.error: + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + pkgdata = json.loads(data.decode('utf-8')) + if 'urls' not in pkgdata: + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + for info in pkgdata['urls']: + if info['packagetype'] == 'sdist' and info['url'].endswith('tar.gz'): + return (info.get('md5_digest'), info['url']) + + raise RuntimeError("Cannot determine downlink link for %s"%(package,)) + +except ImportError: + # Python 2.5 compatibility, no JSON in stdlib but luckily JSON syntax is + # simular enough to Python's syntax to be able to abuse the Python compiler + + import _ast as ast + + def get_pypi_src_download(package): + url = 'https://pypi.python.org/pypi/%s/json'%(package,) + fp = urllib.urlopen(url) + try: + try: + data = fp.read() + + finally: + fp.close() + except urllib.error: + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + + a = compile(data, '-', 'eval', ast.PyCF_ONLY_AST) + if not isinstance(a, ast.Expression): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + a = a.body + if not isinstance(a, ast.Dict): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + for k, v in zip(a.keys, a.values): + if not isinstance(k, ast.Str): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + k = k.s + if k == 'urls': + a = v + break + else: + raise RuntimeError("PyPI JSON for %s doesn't contain URLs section"%(package,)) + + if not isinstance(a, ast.List): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + for info in v.elts: + if not isinstance(info, ast.Dict): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + url = None + packagetype = None + chksum = None + + for k, v in zip(info.keys, info.values): + if not isinstance(k, ast.Str): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + + if k.s == 'url': + if not isinstance(v, ast.Str): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + url = v.s + + elif k.s == 'packagetype': + if not isinstance(v, ast.Str): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + packagetype = v.s + + elif k.s == 'md5_digest': + if not isinstance(v, ast.Str): + raise RuntimeError("Cannot determine download link for %s"%(package,)) + chksum = v.s + + if url is not None and packagetype == 'sdist' and url.endswith('.tar.gz'): + return (chksum, url) + + raise RuntimeError("Cannot determine download link for %s"%(package,)) + +def _build_egg(egg, tarball, to_dir): + # extracting the tarball + tmpdir = tempfile.mkdtemp() + log.warn('Extracting in %s', tmpdir) + old_wd = os.getcwd() + try: + os.chdir(tmpdir) + tar = tarfile.open(tarball) + _extractall(tar) + tar.close() + + # going in the directory + subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) + os.chdir(subdir) + log.warn('Now working in %s', subdir) + + # building an egg + log.warn('Building a %s egg in %s', egg, to_dir) + _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir) + + finally: + os.chdir(old_wd) + # returning the result + log.warn(egg) + if not os.path.exists(egg): + raise IOError('Could not build the egg.') + + +def _do_download(to_dir, packagename=SETUPTOOLS_PACKAGE): + tarball = download_setuptools(packagename, to_dir) + version = tarball.split('-')[-1][:-7] + egg = os.path.join(to_dir, '%s-%s-py%d.%d.egg' + % (packagename, version, sys.version_info[0], sys.version_info[1])) + if not os.path.exists(egg): + _build_egg(egg, tarball, to_dir) + sys.path.insert(0, egg) + import setuptools + setuptools.bootstrap_install_from = egg + + +def use_setuptools(): + # making sure we use the absolute path + return _do_download(os.path.abspath(os.curdir)) + +def download_setuptools(packagename, to_dir): + # making sure we use the absolute path + to_dir = os.path.abspath(to_dir) + try: + from urllib.request import urlopen + except ImportError: + from urllib2 import urlopen + + chksum, url = get_pypi_src_download(packagename) + tgz_name = os.path.basename(url) + saveto = os.path.join(to_dir, tgz_name) + + src = dst = None + if not os.path.exists(saveto): # Avoid repeated downloads + try: + log.warn("Downloading %s", url) + src = urlopen(url) + # Read/write all in one block, so we don't create a corrupt file + # if the download is interrupted. + data = src.read() + + if chksum is not None: + data_sum = md5(data).hexdigest() + if data_sum != chksum: + raise RuntimeError("Downloading %s failed: corrupt checksum"%(url,)) + + + dst = open(saveto, "wb") + dst.write(data) + finally: + if src: + src.close() + if dst: + dst.close() + return os.path.realpath(saveto) + + + +def _extractall(self, path=".", members=None): + """Extract all members from the archive to the current working + directory and set owner, modification time and permissions on + directories afterwards. `path' specifies a different directory + to extract to. `members' is optional and must be a subset of the + list returned by getmembers(). + """ + import copy + import operator + from tarfile import ExtractError + directories = [] + + if members is None: + members = self + + for tarinfo in members: + if tarinfo.isdir(): + # Extract directories with a safe mode. + directories.append(tarinfo) + tarinfo = copy.copy(tarinfo) + tarinfo.mode = 448 # decimal for oct 0700 + self.extract(tarinfo, path) + + # Reverse sort directories. + if sys.version_info < (2, 4): + def sorter(dir1, dir2): + return cmp(dir1.name, dir2.name) + directories.sort(sorter) + directories.reverse() + else: + directories.sort(key=operator.attrgetter('name'), reverse=True) + + # Set correct owner, mtime and filemode on directories. + for tarinfo in directories: + dirpath = os.path.join(path, tarinfo.name) + try: + self.chown(tarinfo, dirpath) + self.utime(tarinfo, dirpath) + self.chmod(tarinfo, dirpath) + except ExtractError: + e = sys.exc_info()[1] + if self.errorlevel > 1: + raise + else: + self._dbg(1, "tarfile: %s" % e) + + +# +# +# +# Definitions of custom commands +# +# +# + +try: + import setuptools + +except ImportError: + use_setuptools() + +from setuptools import setup + +try: + from distutils.core import PyPIRCCommand +except ImportError: + PyPIRCCommand = None # Ancient python version + +from distutils.core import Command +from distutils.errors import DistutilsError +from distutils import log + +if PyPIRCCommand is None: + class upload_docs (Command): + description = "upload sphinx documentation" + user_options = [] + + def initialize_options(self): + pass + + def finalize_options(self): + pass + + def run(self): + raise DistutilsError("not supported on this version of python") + +else: + class upload_docs (PyPIRCCommand): + description = "upload sphinx documentation" + user_options = PyPIRCCommand.user_options + + def initialize_options(self): + PyPIRCCommand.initialize_options(self) + self.username = '' + self.password = '' + + + def finalize_options(self): + PyPIRCCommand.finalize_options(self) + config = self._read_pypirc() + if config != {}: + self.username = config['username'] + self.password = config['password'] + + + def run(self): + import subprocess + import shutil + import zipfile + import os + import urllib + import StringIO + from base64 import standard_b64encode + import httplib + import urlparse + + # Extract the package name from distutils metadata + meta = self.distribution.metadata + name = meta.get_name() + + # Run sphinx + if os.path.exists('doc/_build'): + shutil.rmtree('doc/_build') + os.mkdir('doc/_build') + + p = subprocess.Popen(['make', 'html'], + cwd='doc') + exit = p.wait() + if exit != 0: + raise DistutilsError("sphinx-build failed") + + # Collect sphinx output + if not os.path.exists('dist'): + os.mkdir('dist') + zf = zipfile.ZipFile('dist/%s-docs.zip'%(name,), 'w', + compression=zipfile.ZIP_DEFLATED) + + for toplevel, dirs, files in os.walk('doc/_build/html'): + for fn in files: + fullname = os.path.join(toplevel, fn) + relname = os.path.relpath(fullname, 'doc/_build/html') + + print ("%s -> %s"%(fullname, relname)) + + zf.write(fullname, relname) + + zf.close() + + # Upload the results, this code is based on the distutils + # 'upload' command. + content = open('dist/%s-docs.zip'%(name,), 'rb').read() + + data = { + ':action': 'doc_upload', + 'name': name, + 'content': ('%s-docs.zip'%(name,), content), + } + auth = "Basic " + standard_b64encode(self.username + ":" + + self.password) + + + boundary = '--------------GHSKFJDLGDS7543FJKLFHRE75642756743254' + sep_boundary = '\n--' + boundary + end_boundary = sep_boundary + '--' + body = StringIO.StringIO() + for key, value in data.items(): + if not isinstance(value, list): + value = [value] + + for value in value: + if isinstance(value, tuple): + fn = ';filename="%s"'%(value[0]) + value = value[1] + else: + fn = '' + + body.write(sep_boundary) + body.write('\nContent-Disposition: form-data; name="%s"'%key) + body.write(fn) + body.write("\n\n") + body.write(value) + + body.write(end_boundary) + body.write('\n') + body = body.getvalue() + + self.announce("Uploading documentation to %s"%(self.repository,), log.INFO) + + schema, netloc, url, params, query, fragments = \ + urlparse.urlparse(self.repository) + + + if schema == 'http': + http = httplib.HTTPConnection(netloc) + elif schema == 'https': + http = httplib.HTTPSConnection(netloc) + else: + raise AssertionError("unsupported schema "+schema) + + data = '' + loglevel = log.INFO + try: + http.connect() + http.putrequest("POST", url) + http.putheader('Content-type', + 'multipart/form-data; boundary=%s'%boundary) + http.putheader('Content-length', str(len(body))) + http.putheader('Authorization', auth) + http.endheaders() + http.send(body) + except socket.error: + e = socket.exc_info()[1] + self.announce(str(e), log.ERROR) + return + + r = http.getresponse() + if r.status in (200, 301): + self.announce('Upload succeeded (%s): %s' % (r.status, r.reason), + log.INFO) + else: + self.announce('Upload failed (%s): %s' % (r.status, r.reason), + log.ERROR) + + print ('-'*75) + print (r.read()) + print ('-'*75) + + +def recursiveGlob(root, pathPattern): + """ + Recursively look for files matching 'pathPattern'. Return a list + of matching files/directories. + """ + result = [] + + for rootpath, dirnames, filenames in os.walk(root): + for fn in filenames: + if fnmatch(fn, pathPattern): + result.append(os.path.join(rootpath, fn)) + return result + + +def importExternalTestCases(unittest, + pathPattern="test_*.py", root=".", package=None): + """ + Import all unittests in the PyObjC tree starting at 'root' + """ + + testFiles = recursiveGlob(root, pathPattern) + testModules = map(lambda x:x[len(root)+1:-3].replace('/', '.'), testFiles) + if package is not None: + testModules = [(package + '.' + m) for m in testModules] + + suites = [] + + for modName in testModules: + try: + module = __import__(modName) + except ImportError: + print("SKIP %s: %s"%(modName, sys.exc_info()[1])) + continue + + if '.' in modName: + for elem in modName.split('.')[1:]: + module = getattr(module, elem) + + s = unittest.defaultTestLoader.loadTestsFromModule(module) + suites.append(s) + + return unittest.TestSuite(suites) + + + +class test (Command): + description = "run test suite" + user_options = [ + ('verbosity=', None, "print what tests are run"), + ] + + def initialize_options(self): + self.verbosity='1' + + def finalize_options(self): + if isinstance(self.verbosity, str): + self.verbosity = int(self.verbosity) + + + def cleanup_environment(self): + ei_cmd = self.get_finalized_command('egg_info') + egg_name = ei_cmd.egg_name.replace('-', '_') + + to_remove = [] + for dirname in sys.path: + bn = os.path.basename(dirname) + if bn.startswith(egg_name + "-"): + to_remove.append(dirname) + + for dirname in to_remove: + log.info("removing installed %r from sys.path before testing"%( + dirname,)) + sys.path.remove(dirname) + + def add_project_to_sys_path(self): + from pkg_resources import normalize_path, add_activation_listener + from pkg_resources import working_set, require + + self.reinitialize_command('egg_info') + self.run_command('egg_info') + self.reinitialize_command('build_ext', inplace=1) + self.run_command('build_ext') + + + # Check if this distribution is already on sys.path + # and remove that version, this ensures that the right + # copy of the package gets tested. + + self.__old_path = sys.path[:] + self.__old_modules = sys.modules.copy() + + + ei_cmd = self.get_finalized_command('egg_info') + sys.path.insert(0, normalize_path(ei_cmd.egg_base)) + sys.path.insert(1, os.path.dirname(__file__)) + + # Strip the namespace packages defined in this distribution + # from sys.modules, needed to reset the search path for + # those modules. + + nspkgs = getattr(self.distribution, 'namespace_packages') + if nspkgs is not None: + for nm in nspkgs: + del sys.modules[nm] + + # Reset pkg_resources state: + add_activation_listener(lambda dist: dist.activate()) + working_set.__init__() + require('%s==%s'%(ei_cmd.egg_name, ei_cmd.egg_version)) + + def remove_from_sys_path(self): + from pkg_resources import working_set + sys.path[:] = self.__old_path + sys.modules.clear() + sys.modules.update(self.__old_modules) + working_set.__init__() + + + def run(self): + import unittest + + # Ensure that build directory is on sys.path (py3k) + + self.cleanup_environment() + self.add_project_to_sys_path() + + try: + meta = self.distribution.metadata + name = meta.get_name() + test_pkg = name + "_tests" + suite = importExternalTestCases(unittest, + "test_*.py", test_pkg, test_pkg) + + runner = unittest.TextTestRunner(verbosity=self.verbosity) + result = runner.run(suite) + + # Print out summary. This is a structured format that + # should make it easy to use this information in scripts. + summary = dict( + count=result.testsRun, + fails=len(result.failures), + errors=len(result.errors), + xfails=len(getattr(result, 'expectedFailures', [])), + xpass=len(getattr(result, 'expectedSuccesses', [])), + skip=len(getattr(result, 'skipped', [])), + ) + print("SUMMARY: %s"%(summary,)) + + finally: + self.remove_from_sys_path() + +# +# +# +# And finally run the setuptools main entry point. +# +# +# + +metadata = parse_setup_cfg() + +setup( + cmdclass=dict( + upload_docs=upload_docs, + test=test, + ), + **metadata +) -- cgit v1.2.3