CVS commit: pkgsrc/math/py-networkx

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Sun Nov  1 09:58:28 UTC 2015

Modified Files:
        pkgsrc/math/py-networkx: Makefile PLIST distinfo

Log Message:
Update py-networkx to 1.10, based on PR 50383 by Derouiche.

API changes

    [#1501] connected_components, weakly_connected_components, and strongly_connected_components return now a generator of sets of nodes. Previously the generator was of lists of nodes. This PR also 
refactored the connected_components and weakly_connected_components implementations making them faster, especially for large graphs.
    [#1547] The func_iter functions in Di/Multi/Graphs classes are slated for removal in NetworkX 2.0 release. func will behave like func_iter and return an iterator instead of list. These functions 
are deprecated in NetworkX 1.10 release.

New functionalities

    [#823] A enumerate_all_cliques function is added in the clique package (networkx.algorithms.clique) for enumerating all cliques (including nonmaximal ones) of undirected graphs.
    [#1105] A coloring package (networkx.algorithms.coloring) is created for graph coloring algorithms. Initially, a greedy_color function is provided for coloring graphs using various greedy 
heuristics.
    [#1193] A new generator edge_dfs, added to networkx.algorithms.traversal, implements a depth-first traversal of the edges in a graph. This complements functionality provided by a depth-first 
traversal of the nodes in a graph. For multigraphs, it allows the user to know precisely which edges were followed in a traversal. All NetworkX graph types are supported. A traversal can also reverse 
edge orientations or ignore them.
    [#1194] A find_cycle function is added to the networkx.algorithms.cycles package to find a cycle in a graph. Edge orientations can be optionally reversed or ignored.
    [#1210] Add a random generator for the duplication-divergence model.
    [#1241] A new networkx.algorithms.dominance package is added for dominance/dominator algorithms on directed graphs. It contains a immediate_dominators function for computing immediate 
dominators/dominator trees and a dominance_frontiers function for computing dominance frontiers.
    [#1269] The GML reader/parser and writer/generator are rewritten to remove the dependence on pyparsing and enable handling of arbitrary graph data.
    [#1280] The network simplex method in the networkx.algorithms.flow package is rewritten to improve its performance and support multi- and disconnected networks. For some cases, the new 
implementation is two or three orders of magnitude faster than the old implementation.
    [#1286] Added the Margulis–Gabber–Galil graph to networkx.generators.
    [#1306] Added the chordal p-cycle graph, a mildly explicit algebraic construction of a family of 3-regular expander graphs. Also, moves both the existing expander graph generator function (for 
the Margulis-Gabber-Galil expander) and the new chordal cycle graph function to a new module, networkx.generators.expanders.
    [#1314] Allow overwriting of base class dict with dict-like: OrderedGraph, ThinGraph, LogGraph, etc.
    [#1321] Added to_pandas_dataframe and from_pandas_dataframe.
    [#1322] Added the Hopcroft–Karp algorithm for finding a maximum cardinality matching in bipartite graphs.
    [#1336] Expanded data keyword in G.edges and added default keyword.
    [#1338] Added support for finding optimum branchings and arborescences.
    [#1340] Added a from_pandas_dataframe function that accepts Pandas DataFrames and returns a new graph object. At a minimum, the DataFrame must have two columns, which define the nodes that make 
up an edge. However, the function can also process an arbitrary number of additional columns as edge attributes, such as ‘weight’.
    [#1354] Expanded layout functions to add flexibility for drawing subsets of nodes with distinct layouts and for centering each layout around given coordinates.
    [#1356] Added ordered variants of default graph class.
    [#1360] Added harmonic centrality to network.algorithms.centrality.
    [#1390] The generators.bipartite have been moved to algorithms.bipartite.generators. The functions are not imported in the main namespace, so to use it, the bipartite package has to be imported.
    [#1391] Added Kanevsky’s algorithm for finding all minimum-size separating node sets in an undirected graph. It is implemented as a generator of node cut sets.
    [#1399] Added power function for simple graphs
    [#1405] Added fast approximation for node connectivity based on White and Newman’s approximation algorithm for finding node independent paths between two nodes.
    [#1413] Added transitive closure and antichains function for directed acyclic graphs in algorithms.dag. The antichains function was contributed by Peter Jipsen and Franco Saliola and originally 
developed for the SAGE project.
    [#1425] Added generator function for the complete multipartite graph.
    [#1427] Added nonisomorphic trees generator.
    [#1436] Added a generator function for circulant graphs to the networkx.generators.classic module.
    [#1437] Added function for computing quotient graphs; also created a new module, networkx.algorithms.minors.
    [#1438] Added longest_path and longest_path_length for DAG.
    [#1439] Added node and edge contraction functions to networkx.algorithms.minors.
    [#1445] Added a new modularity matrix module to networkx.linalg, and associated spectrum functions to the networkx.linalg.spectrum module.
    [#1447] Added function to generate all simple paths starting with the shortest ones based on Yen’s algorithm for finding k shortest paths at algorithms.simple_paths.
    [#1455] Added the directed modularity matrix to the networkx.linalg.modularity_matrix module.
    [#1474] Adds triadic_census function; also creates a new module, networkx.algorithms.triads.
    [#1476] Adds functions for testing if a graph has weighted or negatively weighted edges. Also adds a function for testing if a graph is empty. These are is_weighted, is_negatively_weighted, and 
is_empty.
    [#1481] Added Johnson’s algorithm; one more algorithm for shortest paths. It solves all pairs shortest path problem. This is johnson at algorithms.shortest_paths
    [#1414] Added Moody and White algorithm for identifying k_components in a graph, which is based on Kanevsky’s algorithm for finding all minimum-size node cut-sets (implemented in all_node_cuts 
#1391).
    [#1415] Added fast approximation for k_components to the networkx.approximation package. This is based on White and Newman approximation algorithm for finding node independent paths between two 
nodes (see #1405).

Removed functionalities

    [#1236] The legacy ford_fulkerson maximum flow function is removed. Use edmonds_karp instead.

Miscellaneous changes

    [#1192] Support for Python 2.6 is dropped.


To generate a diff of this commit:
cvs rdiff -u -r1.15 -r1.16 pkgsrc/math/py-networkx/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/math/py-networkx/PLIST
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/py-networkx/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.