py-networkx: updated to 2.5

NetworkX 2.5

Highlights
----------
This release is the result of 10 months of work with over 200 commits by
92 contributors. Highlights include:

- Dropped support for Python 3.5.
- add Pathlib support to work with files.
- improve performance.
- Updated docs and tests.
- Removed code designed to work with Python 2.

New Functions:
- lukes_partitioning
- triadic analysis functions
- functions for trophic levels analysis
- d_separated
- is_regular and other regular graph measures
- graph_hash using Weisfeiler Lehman methods
- common_neighbor_centrality (CCPA link prediction)
- max_weight_clique
- path_weight and is_path
- rescale_layout_dict
- junction_tree

New generators:
- paley_graph
- interval_graph

New layouts:
- multipartite_layout

Improvements
------------
- Add governance documents, developer guide and community structures
- Implement explicit deprecation policy.
- Initiate an NX Enhancement Proposal (NXEP) system
- optimize single_source_shortest_path
- improved consistent "weight" specification in shortest_path routines
- Reduce numpy.matrix usage which is discouraged by numpy.
- improved line color
- better search engine treatment of docs
- lattice and grid_graph and grid_2d_graph can use dim=tuple
- fix initializer of kamada_kawai_layout algorithm
- moral and threshold functions now included in namespace and docs
- scale arrows better when drawing
- more uniform creation of random lobster graphs
- allow editing graph during iteration over connected_components
- better column handling in coversion of pandas DataFrame
- allow simrank_similarity with directed graph input
- ensure VoteRank ability is nonnegative
- speedup kernighan_lin_bisection
- speedup negative weight cycle detection
- tree_isomorphism
- rooted_tree_isomorphism
- Gexf edge attribute "label" is available

API Changes
-----------
- enabled "copy" flag parameter in `contracted_nodes`
- allow partially periodic lattices
- return value for minimum_st_node_cut now always a set
- removed unused "has_numpy" argument from create_py_random_state
- fixed return values when drawing empty nodes and edges
- allow sets and frozensets of edges as input to nx.Graph()
- "weight" can be function for astar, directional_dijksta, all_shortest_path
- allow named key ids for GraphML edge writing
- all keywords are now checked for validity in nx.draw and friends
- EdgeDataView "in" operator checks if nodes are "in nbunch"
- remove completeness condition from minimum weight full matching
- option to sort neighbors in bfs traversal
- draw_networkx accepts numpy array for edgelist
- relabel_nodes with 2 nodes mapped to same node can now create multiedge
- steiner_tree works with MultiGraph
- Add `show` kwarg to view_pygraphviz
- Prepare for turning chordal_graph_cliques into a generator
- GraphML reader keyword force_multigraph creates MultiGraph even w/o multiedges

3 files changed, 72 insertions, 10 deletions

diff --git a/math/py-networkx/Makefile b/math/py-networkx/Makefile
index df38820a9f2..8e98a92f974 100644
--- a/math/py-networkx/Makefile
+++ b/math/py-networkx/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.32 2020/08/18 20:15:04 riastradh Exp $
+# $NetBSD: Makefile,v 1.33 2020/12/09 16:56:19 adam Exp $
 
-DISTNAME=	networkx-2.4
+DISTNAME=	networkx-2.5
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=	math python
 MASTER_SITES=	${MASTER_SITE_PYPI:=n/networkx/}
@@ -18,8 +18,7 @@ USE_LANGUAGES=	# none
 PYTHON_VERSIONS_INCOMPATIBLE=	27
 
 do-test:
-	${RUN} cd ${WRKSRC} && \
-	${SETENV} ${TEST_ENV} \
+	cd ${WRKSRC} && ${SETENV} ${TEST_ENV} \
 	pytest-${PYVERSSUFFIX} --pyargs networkx
 
 .include "../../lang/python/egg.mk"
diff --git a/math/py-networkx/PLIST b/math/py-networkx/PLIST
index 9570e6c61bd..b93dca03a92 100644
--- a/math/py-networkx/PLIST
+++ b/math/py-networkx/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.18 2020/04/11 07:45:41 adam Exp $
+@comment $NetBSD: PLIST,v 1.19 2020/12/09 16:56:19 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -314,9 +314,15 @@ ${PYSITELIB}/networkx/algorithms/centrality/tests/test_second_order_centrality.p
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_subgraph.py
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_subgraph.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_subgraph.pyo
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_trophic.py
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_trophic.pyc
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_trophic.pyo
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_voterank.py
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_voterank.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_voterank.pyo
+${PYSITELIB}/networkx/algorithms/centrality/trophic.py
+${PYSITELIB}/networkx/algorithms/centrality/trophic.pyc
+${PYSITELIB}/networkx/algorithms/centrality/trophic.pyo
 ${PYSITELIB}/networkx/algorithms/centrality/voterank_alg.py
 ${PYSITELIB}/networkx/algorithms/centrality/voterank_alg.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/voterank_alg.pyo
@@ -374,6 +380,9 @@ ${PYSITELIB}/networkx/algorithms/community/kernighan_lin.pyo
 ${PYSITELIB}/networkx/algorithms/community/label_propagation.py
 ${PYSITELIB}/networkx/algorithms/community/label_propagation.pyc
 ${PYSITELIB}/networkx/algorithms/community/label_propagation.pyo
+${PYSITELIB}/networkx/algorithms/community/lukes.py
+${PYSITELIB}/networkx/algorithms/community/lukes.pyc
+${PYSITELIB}/networkx/algorithms/community/lukes.pyo
 ${PYSITELIB}/networkx/algorithms/community/modularity_max.py
 ${PYSITELIB}/networkx/algorithms/community/modularity_max.pyc
 ${PYSITELIB}/networkx/algorithms/community/modularity_max.pyo
@@ -398,6 +407,9 @@ ${PYSITELIB}/networkx/algorithms/community/tests/test_kernighan_lin.pyo
 ${PYSITELIB}/networkx/algorithms/community/tests/test_label_propagation.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_label_propagation.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_label_propagation.pyo
+${PYSITELIB}/networkx/algorithms/community/tests/test_lukes.py
+${PYSITELIB}/networkx/algorithms/community/tests/test_lukes.pyc
+${PYSITELIB}/networkx/algorithms/community/tests/test_lukes.pyo
 ${PYSITELIB}/networkx/algorithms/community/tests/test_modularity_max.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_modularity_max.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_modularity_max.pyo
@@ -518,6 +530,9 @@ ${PYSITELIB}/networkx/algorithms/cuts.pyo
 ${PYSITELIB}/networkx/algorithms/cycles.py
 ${PYSITELIB}/networkx/algorithms/cycles.pyc
 ${PYSITELIB}/networkx/algorithms/cycles.pyo
+${PYSITELIB}/networkx/algorithms/d_separation.py
+${PYSITELIB}/networkx/algorithms/d_separation.pyc
+${PYSITELIB}/networkx/algorithms/d_separation.pyo
 ${PYSITELIB}/networkx/algorithms/dag.py
 ${PYSITELIB}/networkx/algorithms/dag.pyc
 ${PYSITELIB}/networkx/algorithms/dag.pyo
@@ -594,6 +609,9 @@ ${PYSITELIB}/networkx/algorithms/flow/tests/wlm3.gpickle.bz2
 ${PYSITELIB}/networkx/algorithms/flow/utils.py
 ${PYSITELIB}/networkx/algorithms/flow/utils.pyc
 ${PYSITELIB}/networkx/algorithms/flow/utils.pyo
+${PYSITELIB}/networkx/algorithms/graph_hashing.py
+${PYSITELIB}/networkx/algorithms/graph_hashing.pyc
+${PYSITELIB}/networkx/algorithms/graph_hashing.pyo
 ${PYSITELIB}/networkx/algorithms/graphical.py
 ${PYSITELIB}/networkx/algorithms/graphical.pyc
 ${PYSITELIB}/networkx/algorithms/graphical.pyo
@@ -646,9 +664,15 @@ ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_match_helpers.pyo
 ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_temporalisomorphvf2.py
 ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_temporalisomorphvf2.pyc
 ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_temporalisomorphvf2.pyo
+${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_tree_isomorphism.py
+${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_tree_isomorphism.pyc
+${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_tree_isomorphism.pyo
 ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_vf2userfunc.py
 ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_vf2userfunc.pyc
 ${PYSITELIB}/networkx/algorithms/isomorphism/tests/test_vf2userfunc.pyo
+${PYSITELIB}/networkx/algorithms/isomorphism/tree_isomorphism.py
+${PYSITELIB}/networkx/algorithms/isomorphism/tree_isomorphism.pyc
+${PYSITELIB}/networkx/algorithms/isomorphism/tree_isomorphism.pyo
 ${PYSITELIB}/networkx/algorithms/isomorphism/vf2userfunc.py
 ${PYSITELIB}/networkx/algorithms/isomorphism/vf2userfunc.pyc
 ${PYSITELIB}/networkx/algorithms/isomorphism/vf2userfunc.pyo
@@ -751,6 +775,9 @@ ${PYSITELIB}/networkx/algorithms/planarity.pyo
 ${PYSITELIB}/networkx/algorithms/reciprocity.py
 ${PYSITELIB}/networkx/algorithms/reciprocity.pyc
 ${PYSITELIB}/networkx/algorithms/reciprocity.pyo
+${PYSITELIB}/networkx/algorithms/regular.py
+${PYSITELIB}/networkx/algorithms/regular.pyc
+${PYSITELIB}/networkx/algorithms/regular.pyo
 ${PYSITELIB}/networkx/algorithms/richclub.py
 ${PYSITELIB}/networkx/algorithms/richclub.pyc
 ${PYSITELIB}/networkx/algorithms/richclub.pyo
@@ -853,6 +880,9 @@ ${PYSITELIB}/networkx/algorithms/tests/test_cuts.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_cycles.py
 ${PYSITELIB}/networkx/algorithms/tests/test_cycles.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_cycles.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_d_separation.py
+${PYSITELIB}/networkx/algorithms/tests/test_d_separation.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_d_separation.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_dag.py
 ${PYSITELIB}/networkx/algorithms/tests/test_dag.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_dag.pyo
@@ -874,6 +904,9 @@ ${PYSITELIB}/networkx/algorithms/tests/test_efficiency.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_euler.py
 ${PYSITELIB}/networkx/algorithms/tests/test_euler.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_euler.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_graph_hashing.py
+${PYSITELIB}/networkx/algorithms/tests/test_graph_hashing.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_graph_hashing.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_graphical.py
 ${PYSITELIB}/networkx/algorithms/tests/test_graphical.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_graphical.pyo
@@ -895,6 +928,9 @@ ${PYSITELIB}/networkx/algorithms/tests/test_lowest_common_ancestors.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_matching.py
 ${PYSITELIB}/networkx/algorithms/tests/test_matching.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_matching.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_max_weight_clique.py
+${PYSITELIB}/networkx/algorithms/tests/test_max_weight_clique.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_max_weight_clique.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_minors.py
 ${PYSITELIB}/networkx/algorithms/tests/test_minors.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_minors.pyo
@@ -916,6 +952,9 @@ ${PYSITELIB}/networkx/algorithms/tests/test_planarity.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_reciprocity.py
 ${PYSITELIB}/networkx/algorithms/tests/test_reciprocity.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_reciprocity.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_regular.py
+${PYSITELIB}/networkx/algorithms/tests/test_regular.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_regular.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_richclub.py
 ${PYSITELIB}/networkx/algorithms/tests/test_richclub.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_richclub.pyo
@@ -1009,6 +1048,9 @@ ${PYSITELIB}/networkx/algorithms/tree/branchings.pyo
 ${PYSITELIB}/networkx/algorithms/tree/coding.py
 ${PYSITELIB}/networkx/algorithms/tree/coding.pyc
 ${PYSITELIB}/networkx/algorithms/tree/coding.pyo
+${PYSITELIB}/networkx/algorithms/tree/decomposition.py
+${PYSITELIB}/networkx/algorithms/tree/decomposition.pyc
+${PYSITELIB}/networkx/algorithms/tree/decomposition.pyo
 ${PYSITELIB}/networkx/algorithms/tree/mst.py
 ${PYSITELIB}/networkx/algorithms/tree/mst.pyc
 ${PYSITELIB}/networkx/algorithms/tree/mst.pyo
@@ -1027,6 +1069,9 @@ ${PYSITELIB}/networkx/algorithms/tree/tests/test_branchings.pyo
 ${PYSITELIB}/networkx/algorithms/tree/tests/test_coding.py
 ${PYSITELIB}/networkx/algorithms/tree/tests/test_coding.pyc
 ${PYSITELIB}/networkx/algorithms/tree/tests/test_coding.pyo
+${PYSITELIB}/networkx/algorithms/tree/tests/test_decomposition.py
+${PYSITELIB}/networkx/algorithms/tree/tests/test_decomposition.pyc
+${PYSITELIB}/networkx/algorithms/tree/tests/test_decomposition.pyo
 ${PYSITELIB}/networkx/algorithms/tree/tests/test_mst.py
 ${PYSITELIB}/networkx/algorithms/tree/tests/test_mst.pyc
 ${PYSITELIB}/networkx/algorithms/tree/tests/test_mst.pyo
@@ -1129,6 +1174,9 @@ ${PYSITELIB}/networkx/classes/tests/test_special.pyo
 ${PYSITELIB}/networkx/classes/tests/test_subgraphviews.py
 ${PYSITELIB}/networkx/classes/tests/test_subgraphviews.pyc
 ${PYSITELIB}/networkx/classes/tests/test_subgraphviews.pyo
+${PYSITELIB}/networkx/conftest.py
+${PYSITELIB}/networkx/conftest.pyc
+${PYSITELIB}/networkx/conftest.pyo
 ${PYSITELIB}/networkx/convert.py
 ${PYSITELIB}/networkx/convert.pyc
 ${PYSITELIB}/networkx/convert.pyo
@@ -1211,6 +1259,9 @@ ${PYSITELIB}/networkx/generators/internet_as_graphs.pyo
 ${PYSITELIB}/networkx/generators/intersection.py
 ${PYSITELIB}/networkx/generators/intersection.pyc
 ${PYSITELIB}/networkx/generators/intersection.pyo
+${PYSITELIB}/networkx/generators/interval_graph.py
+${PYSITELIB}/networkx/generators/interval_graph.pyc
+${PYSITELIB}/networkx/generators/interval_graph.pyo
 ${PYSITELIB}/networkx/generators/joint_degree_seq.py
 ${PYSITELIB}/networkx/generators/joint_degree_seq.pyc
 ${PYSITELIB}/networkx/generators/joint_degree_seq.pyo
@@ -1244,6 +1295,9 @@ ${PYSITELIB}/networkx/generators/spectral_graph_forge.pyo
 ${PYSITELIB}/networkx/generators/stochastic.py
 ${PYSITELIB}/networkx/generators/stochastic.pyc
 ${PYSITELIB}/networkx/generators/stochastic.pyo
+${PYSITELIB}/networkx/generators/sudoku.py
+${PYSITELIB}/networkx/generators/sudoku.pyc
+${PYSITELIB}/networkx/generators/sudoku.pyo
 ${PYSITELIB}/networkx/generators/tests/__init__.py
 ${PYSITELIB}/networkx/generators/tests/__init__.pyc
 ${PYSITELIB}/networkx/generators/tests/__init__.pyo
@@ -1286,6 +1340,9 @@ ${PYSITELIB}/networkx/generators/tests/test_internet_as_graphs.pyo
 ${PYSITELIB}/networkx/generators/tests/test_intersection.py
 ${PYSITELIB}/networkx/generators/tests/test_intersection.pyc
 ${PYSITELIB}/networkx/generators/tests/test_intersection.pyo
+${PYSITELIB}/networkx/generators/tests/test_interval_graph.py
+${PYSITELIB}/networkx/generators/tests/test_interval_graph.pyc
+${PYSITELIB}/networkx/generators/tests/test_interval_graph.pyo
 ${PYSITELIB}/networkx/generators/tests/test_joint_degree_seq.py
 ${PYSITELIB}/networkx/generators/tests/test_joint_degree_seq.pyc
 ${PYSITELIB}/networkx/generators/tests/test_joint_degree_seq.pyo
@@ -1316,6 +1373,9 @@ ${PYSITELIB}/networkx/generators/tests/test_spectral_graph_forge.pyo
 ${PYSITELIB}/networkx/generators/tests/test_stochastic.py
 ${PYSITELIB}/networkx/generators/tests/test_stochastic.pyc
 ${PYSITELIB}/networkx/generators/tests/test_stochastic.pyo
+${PYSITELIB}/networkx/generators/tests/test_sudoku.py
+${PYSITELIB}/networkx/generators/tests/test_sudoku.pyc
+${PYSITELIB}/networkx/generators/tests/test_sudoku.pyo
 ${PYSITELIB}/networkx/generators/tests/test_trees.py
 ${PYSITELIB}/networkx/generators/tests/test_trees.pyc
 ${PYSITELIB}/networkx/generators/tests/test_trees.pyo
@@ -1358,6 +1418,9 @@ ${PYSITELIB}/networkx/linalg/tests/__init__.pyo
 ${PYSITELIB}/networkx/linalg/tests/test_algebraic_connectivity.py
 ${PYSITELIB}/networkx/linalg/tests/test_algebraic_connectivity.pyc
 ${PYSITELIB}/networkx/linalg/tests/test_algebraic_connectivity.pyo
+${PYSITELIB}/networkx/linalg/tests/test_attrmatrix.py
+${PYSITELIB}/networkx/linalg/tests/test_attrmatrix.pyc
+${PYSITELIB}/networkx/linalg/tests/test_attrmatrix.pyo
 ${PYSITELIB}/networkx/linalg/tests/test_bethehessian.py
 ${PYSITELIB}/networkx/linalg/tests/test_bethehessian.pyc
 ${PYSITELIB}/networkx/linalg/tests/test_bethehessian.pyo
diff --git a/math/py-networkx/distinfo b/math/py-networkx/distinfo
index 435b1abccad..4ab7a66ff15 100644
--- a/math/py-networkx/distinfo
+++ b/math/py-networkx/distinfo
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.15 2020/04/11 07:45:41 adam Exp $
+$NetBSD: distinfo,v 1.16 2020/12/09 16:56:19 adam Exp $
 
-SHA1 (networkx-2.4.tar.gz) = ffed34d57b2a758e30c02d2730bf0eefef5ed0a8
-RMD160 (networkx-2.4.tar.gz) = dd24447411f7a8ec05bcad713255109a9ead3dfd
-SHA512 (networkx-2.4.tar.gz) = 38eabef56e3667b7fa85206ae01a0a8f5c71bfa2f324bc2490c433cb973508a03955183a0c58ae40390f86d6a4741135cdb426c4c15e53e2f123072f0cac1b89
-Size (networkx-2.4.tar.gz) = 1462338 bytes
+SHA1 (networkx-2.5.tar.gz) = 439af030cbfdc2c4cbdef5dc423d5ea8e527d02a
+RMD160 (networkx-2.5.tar.gz) = fd5549bc788c32e6d2681f2ec9d460b8d63b5f5d
+SHA512 (networkx-2.5.tar.gz) = ab51198072d20bdba7c9ceb6856631a20a7e9527a7cadb41271a999f57bf60da5488269c6e4e1f3f4f33420ec6493af665386842c216ea1cfadd1792ccb6444e
+Size (networkx-2.5.tar.gz) = 1542085 bytes
 SHA1 (patch-setup.py) = 9859c3102492d4f9afd41533c3b1bf45cbc6850d