[pkgsrc/trunk]: pkgsrc/math/py-networkx py-networkx: updated to 2.2

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/math/py-networkx py-networkx: updated to 2.2
From: adam <adam%pkgsrc.org@localhost>
Date: Sun, 19 May 2019 16:40:26 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/145df0832be7
branches:  trunk
changeset: 326066:145df0832be7
user:      adam <adam%pkgsrc.org@localhost>
date:      Fri Nov 30 10:37:07 2018 +0000

description:
py-networkx: updated to 2.2

2.2:
This release is the result of 8 months of work with over 149 commits by
58 contributors. Highlights include:
- Add support for Python 3.7. This is the last release to support Python 2.
- Uniform random number generator (RNG) handling which defaults to global
  RNGs but allows specification of a single RNG for all random numbers in NX.
- Improved GraphViews to ease subclassing and remove cyclic references
  which caused trouble with deepcopy and pickle.
- New Graph method `G.update(H)`

diffstat:

 math/py-networkx/Makefile               |   42 +-------
 math/py-networkx/PLIST                  |  154 ++++++++++++++++++-------------
 math/py-networkx/distinfo               |   11 +-
 math/py-networkx/patches/patch-setup.py |   14 ++
 4 files changed, 114 insertions(+), 107 deletions(-)

diffs (truncated from 404 to 300 lines):

diff -r 131175460eca -r 145df0832be7 math/py-networkx/Makefile
--- a/math/py-networkx/Makefile Fri Nov 30 09:59:40 2018 +0000
+++ b/math/py-networkx/Makefile Fri Nov 30 10:37:07 2018 +0000
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.26 2018/05/07 15:27:09 khorben Exp $
+# $NetBSD: Makefile,v 1.27 2018/11/30 10:37:07 adam Exp $
 
-DISTNAME=      networkx-2.1
+DISTNAME=      networkx-2.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=n/networkx/}
 EXTRACT_SUFX=  .zip
@@ -12,42 +11,13 @@
 COMMENT=       Python package for creating and manipulating graphs and networks
 LICENSE=       modified-bsd
 
-DEPENDS+=      ${PYPKGPREFIX}-decorator>=4.1.0:../../devel/py-decorator
+DEPENDS+=      ${PYPKGPREFIX}-decorator>=4.3.0:../../devel/py-decorator
+TEST_DEPENDS+= ${PYPKGPREFIX}-nose>=1.3.7:../../devel/py-nose
 
 USE_LANGUAGES= # none
 
-REPLACE_INTERPRETER+=  python
-REPLACE.python.old=    /usr/bin/env python
-REPLACE.python.new=    ${PYTHONBIN}
-REPLACE_FILES.python=  \
-examples/drawing/*.py \
-examples/advanced/*.py \
-examples/graph/*.py \
-examples/applications/*.py \
-examples/algorithms/*.py \
-examples/pygraphviz/*.py \
-examples/basic/*.py \
-examples/jit/*.py \
-doc/release/*.py \
-networkx/readwrite/tests/*.py \
-networkx/utils/tests/*.py \
-networkx/generators/tests/*.py \
-networkx/classes/tests/*.py \
-networkx/algorithms/components/tests/*.py \
-networkx/algorithms/isomorphism/tests/*.py \
-networkx/algorithms/link_analysis/tests/*.py \
-networkx/algorithms/centrality/tests/*.py \
-networkx/algorithms/bipartite/tests/*.py \
-networkx/algorithms/traversal/tests/*.py \
-networkx/algorithms/approximation/tests/*.py \
-networkx/algorithms/assortativity/tests/*.py \
-networkx/algorithms/shortest_paths/tests/*.py \
-networkx/algorithms/tests/*.py \
-networkx/tests/*.py
-
-post-install:
-       ${RM} -f -r ${DESTDIR}${PREFIX}/share/doc/${PKGBASE}
-       ${MV} ${DESTDIR}${PREFIX}/share/doc/${DISTNAME} ${DESTDIR}${PREFIX}/share/doc/${PKGBASE}
+post-extract:
+       find ${WRKSRC} -type f -exec chmod 644 {} +
 
 .include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"
diff -r 131175460eca -r 145df0832be7 math/py-networkx/PLIST
--- a/math/py-networkx/PLIST    Fri Nov 30 09:59:40 2018 +0000
+++ b/math/py-networkx/PLIST    Fri Nov 30 10:37:07 2018 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.15 2018/02/01 21:00:25 adam Exp $
+@comment $NetBSD: PLIST,v 1.16 2018/11/30 10:37:07 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -68,9 +68,15 @@
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_steinertree.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_steinertree.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_steinertree.pyo
+${PYSITELIB}/networkx/algorithms/approximation/tests/test_treewidth.py
+${PYSITELIB}/networkx/algorithms/approximation/tests/test_treewidth.pyc
+${PYSITELIB}/networkx/algorithms/approximation/tests/test_treewidth.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_vertex_cover.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_vertex_cover.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_vertex_cover.pyo
+${PYSITELIB}/networkx/algorithms/approximation/treewidth.py
+${PYSITELIB}/networkx/algorithms/approximation/treewidth.pyc
+${PYSITELIB}/networkx/algorithms/approximation/treewidth.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/vertex_cover.py
 ${PYSITELIB}/networkx/algorithms/approximation/vertex_cover.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/vertex_cover.pyo
@@ -227,9 +233,15 @@
 ${PYSITELIB}/networkx/algorithms/centrality/load.py
 ${PYSITELIB}/networkx/algorithms/centrality/load.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/load.pyo
+${PYSITELIB}/networkx/algorithms/centrality/percolation.py
+${PYSITELIB}/networkx/algorithms/centrality/percolation.pyc
+${PYSITELIB}/networkx/algorithms/centrality/percolation.pyo
 ${PYSITELIB}/networkx/algorithms/centrality/reaching.py
 ${PYSITELIB}/networkx/algorithms/centrality/reaching.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/reaching.pyo
+${PYSITELIB}/networkx/algorithms/centrality/second_order.py
+${PYSITELIB}/networkx/algorithms/centrality/second_order.pyc
+${PYSITELIB}/networkx/algorithms/centrality/second_order.pyo
 ${PYSITELIB}/networkx/algorithms/centrality/subgraph_alg.py
 ${PYSITELIB}/networkx/algorithms/centrality/subgraph_alg.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/subgraph_alg.pyo
@@ -269,9 +281,15 @@
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_load_centrality.py
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_load_centrality.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_load_centrality.pyo
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_percolation_centrality.py
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_percolation_centrality.pyc
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_percolation_centrality.pyo
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_reaching.py
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_reaching.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_reaching.pyo
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_second_order_centrality.py
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_second_order_centrality.pyc
+${PYSITELIB}/networkx/algorithms/centrality/tests/test_second_order_centrality.pyo
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_subgraph.py
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_subgraph.pyc
 ${PYSITELIB}/networkx/algorithms/centrality/tests/test_subgraph.pyo
@@ -305,9 +323,9 @@
 ${PYSITELIB}/networkx/algorithms/community/__init__.py
 ${PYSITELIB}/networkx/algorithms/community/__init__.pyc
 ${PYSITELIB}/networkx/algorithms/community/__init__.pyo
-${PYSITELIB}/networkx/algorithms/community/asyn_fluidc.py
-${PYSITELIB}/networkx/algorithms/community/asyn_fluidc.pyc
-${PYSITELIB}/networkx/algorithms/community/asyn_fluidc.pyo
+${PYSITELIB}/networkx/algorithms/community/asyn_fluid.py
+${PYSITELIB}/networkx/algorithms/community/asyn_fluid.pyc
+${PYSITELIB}/networkx/algorithms/community/asyn_fluid.pyo
 ${PYSITELIB}/networkx/algorithms/community/centrality.py
 ${PYSITELIB}/networkx/algorithms/community/centrality.pyc
 ${PYSITELIB}/networkx/algorithms/community/centrality.pyo
@@ -326,12 +344,15 @@
 ${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/modularity_max.py
+${PYSITELIB}/networkx/algorithms/community/modularity_max.pyc
+${PYSITELIB}/networkx/algorithms/community/modularity_max.pyo
 ${PYSITELIB}/networkx/algorithms/community/quality.py
 ${PYSITELIB}/networkx/algorithms/community/quality.pyc
 ${PYSITELIB}/networkx/algorithms/community/quality.pyo
-${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_fluidc.py
-${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_fluidc.pyc
-${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_fluidc.pyo
+${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_fluid.py
+${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_fluid.pyc
+${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_fluid.pyo
 ${PYSITELIB}/networkx/algorithms/community/tests/test_centrality.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_centrality.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_centrality.pyo
@@ -347,6 +368,9 @@
 ${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_modularity_max.py
+${PYSITELIB}/networkx/algorithms/community/tests/test_modularity_max.pyc
+${PYSITELIB}/networkx/algorithms/community/tests/test_modularity_max.pyo
 ${PYSITELIB}/networkx/algorithms/community/tests/test_quality.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_quality.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_quality.pyo
@@ -613,6 +637,24 @@
 ${PYSITELIB}/networkx/algorithms/mis.py
 ${PYSITELIB}/networkx/algorithms/mis.pyc
 ${PYSITELIB}/networkx/algorithms/mis.pyo
+${PYSITELIB}/networkx/algorithms/node_classification/__init__.py
+${PYSITELIB}/networkx/algorithms/node_classification/__init__.pyc
+${PYSITELIB}/networkx/algorithms/node_classification/__init__.pyo
+${PYSITELIB}/networkx/algorithms/node_classification/hmn.py
+${PYSITELIB}/networkx/algorithms/node_classification/hmn.pyc
+${PYSITELIB}/networkx/algorithms/node_classification/hmn.pyo
+${PYSITELIB}/networkx/algorithms/node_classification/lgc.py
+${PYSITELIB}/networkx/algorithms/node_classification/lgc.pyc
+${PYSITELIB}/networkx/algorithms/node_classification/lgc.pyo
+${PYSITELIB}/networkx/algorithms/node_classification/tests/test_harmonic_function.py
+${PYSITELIB}/networkx/algorithms/node_classification/tests/test_harmonic_function.pyc
+${PYSITELIB}/networkx/algorithms/node_classification/tests/test_harmonic_function.pyo
+${PYSITELIB}/networkx/algorithms/node_classification/tests/test_local_and_global_consistency.py
+${PYSITELIB}/networkx/algorithms/node_classification/tests/test_local_and_global_consistency.pyc
+${PYSITELIB}/networkx/algorithms/node_classification/tests/test_local_and_global_consistency.pyo
+${PYSITELIB}/networkx/algorithms/node_classification/utils.py
+${PYSITELIB}/networkx/algorithms/node_classification/utils.pyc
+${PYSITELIB}/networkx/algorithms/node_classification/utils.pyo
 ${PYSITELIB}/networkx/algorithms/operators/__init__.py
 ${PYSITELIB}/networkx/algorithms/operators/__init__.pyc
 ${PYSITELIB}/networkx/algorithms/operators/__init__.pyo
@@ -640,6 +682,9 @@
 ${PYSITELIB}/networkx/algorithms/operators/unary.py
 ${PYSITELIB}/networkx/algorithms/operators/unary.pyc
 ${PYSITELIB}/networkx/algorithms/operators/unary.pyo
+${PYSITELIB}/networkx/algorithms/planarity.py
+${PYSITELIB}/networkx/algorithms/planarity.pyc
+${PYSITELIB}/networkx/algorithms/planarity.pyo
 ${PYSITELIB}/networkx/algorithms/reciprocity.py
 ${PYSITELIB}/networkx/algorithms/reciprocity.pyc
 ${PYSITELIB}/networkx/algorithms/reciprocity.pyo
@@ -688,9 +733,15 @@
 ${PYSITELIB}/networkx/algorithms/simple_paths.py
 ${PYSITELIB}/networkx/algorithms/simple_paths.pyc
 ${PYSITELIB}/networkx/algorithms/simple_paths.pyo
+${PYSITELIB}/networkx/algorithms/smallworld.py
+${PYSITELIB}/networkx/algorithms/smallworld.pyc
+${PYSITELIB}/networkx/algorithms/smallworld.pyo
 ${PYSITELIB}/networkx/algorithms/smetric.py
 ${PYSITELIB}/networkx/algorithms/smetric.pyc
 ${PYSITELIB}/networkx/algorithms/smetric.pyo
+${PYSITELIB}/networkx/algorithms/sparsifiers.py
+${PYSITELIB}/networkx/algorithms/sparsifiers.pyc
+${PYSITELIB}/networkx/algorithms/sparsifiers.pyo
 ${PYSITELIB}/networkx/algorithms/structuralholes.py
 ${PYSITELIB}/networkx/algorithms/structuralholes.pyc
 ${PYSITELIB}/networkx/algorithms/structuralholes.pyo
@@ -778,6 +829,9 @@
 ${PYSITELIB}/networkx/algorithms/tests/test_mis.py
 ${PYSITELIB}/networkx/algorithms/tests/test_mis.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_mis.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_planarity.py
+${PYSITELIB}/networkx/algorithms/tests/test_planarity.pyc
+${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
@@ -790,9 +844,15 @@
 ${PYSITELIB}/networkx/algorithms/tests/test_simple_paths.py
 ${PYSITELIB}/networkx/algorithms/tests/test_simple_paths.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_simple_paths.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_smallworld.py
+${PYSITELIB}/networkx/algorithms/tests/test_smallworld.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_smallworld.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_smetric.py
 ${PYSITELIB}/networkx/algorithms/tests/test_smetric.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_smetric.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_sparsifiers.py
+${PYSITELIB}/networkx/algorithms/tests/test_sparsifiers.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_sparsifiers.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_structuralholes.py
 ${PYSITELIB}/networkx/algorithms/tests/test_structuralholes.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_structuralholes.pyo
@@ -835,6 +895,9 @@
 ${PYSITELIB}/networkx/algorithms/traversal/depth_first_search.py
 ${PYSITELIB}/networkx/algorithms/traversal/depth_first_search.pyc
 ${PYSITELIB}/networkx/algorithms/traversal/depth_first_search.pyo
+${PYSITELIB}/networkx/algorithms/traversal/edgebfs.py
+${PYSITELIB}/networkx/algorithms/traversal/edgebfs.pyc
+${PYSITELIB}/networkx/algorithms/traversal/edgebfs.pyo
 ${PYSITELIB}/networkx/algorithms/traversal/edgedfs.py
 ${PYSITELIB}/networkx/algorithms/traversal/edgedfs.pyc
 ${PYSITELIB}/networkx/algorithms/traversal/edgedfs.pyo
@@ -847,6 +910,9 @@
 ${PYSITELIB}/networkx/algorithms/traversal/tests/test_dfs.py
 ${PYSITELIB}/networkx/algorithms/traversal/tests/test_dfs.pyc
 ${PYSITELIB}/networkx/algorithms/traversal/tests/test_dfs.pyo
+${PYSITELIB}/networkx/algorithms/traversal/tests/test_edgebfs.py
+${PYSITELIB}/networkx/algorithms/traversal/tests/test_edgebfs.pyc
+${PYSITELIB}/networkx/algorithms/traversal/tests/test_edgebfs.pyo
 ${PYSITELIB}/networkx/algorithms/traversal/tests/test_edgedfs.py
 ${PYSITELIB}/networkx/algorithms/traversal/tests/test_edgedfs.pyc
 ${PYSITELIB}/networkx/algorithms/traversal/tests/test_edgedfs.pyo
@@ -1070,6 +1136,9 @@
 ${PYSITELIB}/networkx/generators/social.py
 ${PYSITELIB}/networkx/generators/social.pyc
 ${PYSITELIB}/networkx/generators/social.pyo
+${PYSITELIB}/networkx/generators/spectral_graph_forge.py
+${PYSITELIB}/networkx/generators/spectral_graph_forge.pyc
+${PYSITELIB}/networkx/generators/spectral_graph_forge.pyo
 ${PYSITELIB}/networkx/generators/stochastic.py
 ${PYSITELIB}/networkx/generators/stochastic.pyc
 ${PYSITELIB}/networkx/generators/stochastic.pyo
@@ -1127,6 +1196,9 @@
 ${PYSITELIB}/networkx/generators/tests/test_small.py
 ${PYSITELIB}/networkx/generators/tests/test_small.pyc
 ${PYSITELIB}/networkx/generators/tests/test_small.pyo
+${PYSITELIB}/networkx/generators/tests/test_spectral_graph_forge.py
+${PYSITELIB}/networkx/generators/tests/test_spectral_graph_forge.pyc
+${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
@@ -1316,6 +1388,9 @@
 ${PYSITELIB}/networkx/tests/test.py
 ${PYSITELIB}/networkx/tests/test.pyc
 ${PYSITELIB}/networkx/tests/test.pyo
+${PYSITELIB}/networkx/tests/test_all_random_functions.py
+${PYSITELIB}/networkx/tests/test_all_random_functions.pyc
+${PYSITELIB}/networkx/tests/test_all_random_functions.pyo
 ${PYSITELIB}/networkx/tests/test_convert.py
 ${PYSITELIB}/networkx/tests/test_convert.pyc
 ${PYSITELIB}/networkx/tests/test_convert.pyo
@@ -1346,6 +1421,9 @@
 ${PYSITELIB}/networkx/utils/heaps.py
 ${PYSITELIB}/networkx/utils/heaps.pyc
 ${PYSITELIB}/networkx/utils/heaps.pyo
+${PYSITELIB}/networkx/utils/mapped_queue.py
+${PYSITELIB}/networkx/utils/mapped_queue.pyc
+${PYSITELIB}/networkx/utils/mapped_queue.pyo
 ${PYSITELIB}/networkx/utils/misc.py
 ${PYSITELIB}/networkx/utils/misc.pyc
 ${PYSITELIB}/networkx/utils/misc.pyo
@@ -1364,6 +1442,9 @@
 ${PYSITELIB}/networkx/utils/tests/test_heaps.py
 ${PYSITELIB}/networkx/utils/tests/test_heaps.pyc
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