py-networkx: updated to 2.1

NetworkX 2.1

Highlights
This release is the result of four months of work with 75 pull requests by
37 contributors. Highlights include:

  - Arrows for drawing DiGraph edges are vastly improved!
    And an example to show them.

  - More than 12 new functions for graph generation, manipulation and/or
    new graph algorithms.

    - Add a large clique size heuristic function
    - Add rooted product function
    - Label Propagation Community Detection
    - Minimum cycle basis
    - Add Mycielski Operator
    - Adds prefix_tree, dag_to_branching, and example.
    - Add inverse_line_graph generator
    - Steiner tree and metric closure.
    - Add flow based node and edge disjoint paths.
    - Update geometric networks with new models
    - Graph edit distance
    - Added function for finding a k-edge-augmentation

  - G.name is no longer processed by graph operators. It remains as a
    property mechanism to access ``G.graph['name']`` but the user is in
    charge of updating or changing it for copies, subgraphs, unions and
    other graph operations.

Improvements
  - Many bug fixes, documentation changes.
  - Speed improvements especially for subgraphs.
  - Changed input variable names for functions using ``**kwds``
    to avoid name collisions -- especially ``add_node``
  - New examples for arrows and spectral embedding of the grid graph.

3 files changed, 54 insertions, 41 deletions

diff --git a/math/py-networkx/Makefile b/math/py-networkx/Makefile
index d60894c2c01..3eef9888c79 100644
--- a/math/py-networkx/Makefile
+++ b/math/py-networkx/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.24 2017/11/15 23:22:28 markd Exp $
+# $NetBSD: Makefile,v 1.25 2018/02/01 21:00:25 adam Exp $
 
-DISTNAME=	networkx-2.0
+DISTNAME=	networkx-2.1
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=	1
 CATEGORIES=	math python
 MASTER_SITES=	${MASTER_SITE_PYPI:=n/networkx/}
 EXTRACT_SUFX=	.zip
@@ -16,27 +15,9 @@ DEPENDS+=	${PYPKGPREFIX}-decorator>=4.1.0:../../devel/py-decorator
 
 USE_LANGUAGES=	# none
 
-REPLACE_PYTHON+=	networkx/algorithms/approximation/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/assortativity/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/bipartite/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/centrality/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/chordal/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/community/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/components/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/isomorphism/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/link_analysis/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/shortest_paths/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/tests/*.py
-REPLACE_PYTHON+=	networkx/algorithms/traversal/tests/*.py
-REPLACE_PYTHON+=	networkx/classes/tests/*.py
-REPLACE_PYTHON+=	networkx/generators/tests/*.py
-REPLACE_PYTHON+=	networkx/readwrite/tests/*.py
-REPLACE_PYTHON+=	networkx/tests/*.py
-REPLACE_PYTHON+=	networkx/utils/tests/*.py
-
 post-install:
-	mv ${DESTDIR}${PREFIX}/share/doc/${DISTNAME} ${DESTDIR}${PREFIX}/share/doc/${PKGBASE}
+	${RM} -f -r ${DESTDIR}${PREFIX}/share/doc/${PKGBASE}
+	${MV} ${DESTDIR}${PREFIX}/share/doc/${DISTNAME} ${DESTDIR}${PREFIX}/share/doc/${PKGBASE}
 
-.include "../../lang/python/application.mk"
 .include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-networkx/PLIST b/math/py-networkx/PLIST
index 185587e3c9d..301da3f6644 100644
--- a/math/py-networkx/PLIST
+++ b/math/py-networkx/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.14 2017/11/15 23:22:28 markd Exp $
+@comment $NetBSD: PLIST,v 1.15 2018/02/01 21:00:25 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -38,6 +38,9 @@ ${PYSITELIB}/networkx/algorithms/approximation/matching.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/ramsey.py
 ${PYSITELIB}/networkx/algorithms/approximation/ramsey.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/ramsey.pyo
+${PYSITELIB}/networkx/algorithms/approximation/steinertree.py
+${PYSITELIB}/networkx/algorithms/approximation/steinertree.pyc
+${PYSITELIB}/networkx/algorithms/approximation/steinertree.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_approx_clust_coeff.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_approx_clust_coeff.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_approx_clust_coeff.pyo
@@ -62,6 +65,9 @@ ${PYSITELIB}/networkx/algorithms/approximation/tests/test_matching.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_ramsey.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_ramsey.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_ramsey.pyo
+${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_vertex_cover.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_vertex_cover.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_vertex_cover.pyo
@@ -302,9 +308,6 @@ ${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_lpa.py
-${PYSITELIB}/networkx/algorithms/community/asyn_lpa.pyc
-${PYSITELIB}/networkx/algorithms/community/asyn_lpa.pyo
 ${PYSITELIB}/networkx/algorithms/community/centrality.py
 ${PYSITELIB}/networkx/algorithms/community/centrality.pyc
 ${PYSITELIB}/networkx/algorithms/community/centrality.pyo
@@ -320,15 +323,15 @@ ${PYSITELIB}/networkx/algorithms/community/kclique.pyo
 ${PYSITELIB}/networkx/algorithms/community/kernighan_lin.py
 ${PYSITELIB}/networkx/algorithms/community/kernighan_lin.pyc
 ${PYSITELIB}/networkx/algorithms/community/kernighan_lin.pyo
+${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/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_lpa.py
-${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_lpa.pyc
-${PYSITELIB}/networkx/algorithms/community/tests/test_asyn_lpa.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
@@ -341,6 +344,9 @@ ${PYSITELIB}/networkx/algorithms/community/tests/test_kclique.pyo
 ${PYSITELIB}/networkx/algorithms/community/tests/test_kernighan_lin.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_kernighan_lin.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_kernighan_lin.pyo
+${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_quality.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_quality.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_quality.pyo
@@ -398,6 +404,12 @@ ${PYSITELIB}/networkx/algorithms/connectivity/connectivity.pyo
 ${PYSITELIB}/networkx/algorithms/connectivity/cuts.py
 ${PYSITELIB}/networkx/algorithms/connectivity/cuts.pyc
 ${PYSITELIB}/networkx/algorithms/connectivity/cuts.pyo
+${PYSITELIB}/networkx/algorithms/connectivity/disjoint_paths.py
+${PYSITELIB}/networkx/algorithms/connectivity/disjoint_paths.pyc
+${PYSITELIB}/networkx/algorithms/connectivity/disjoint_paths.pyo
+${PYSITELIB}/networkx/algorithms/connectivity/edge_augmentation.py
+${PYSITELIB}/networkx/algorithms/connectivity/edge_augmentation.pyc
+${PYSITELIB}/networkx/algorithms/connectivity/edge_augmentation.pyo
 ${PYSITELIB}/networkx/algorithms/connectivity/edge_kcomponents.py
 ${PYSITELIB}/networkx/algorithms/connectivity/edge_kcomponents.pyc
 ${PYSITELIB}/networkx/algorithms/connectivity/edge_kcomponents.pyo
@@ -416,6 +428,12 @@ ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_connectivity.pyo
 ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_cuts.py
 ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_cuts.pyc
 ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_cuts.pyo
+${PYSITELIB}/networkx/algorithms/connectivity/tests/test_disjoint_paths.py
+${PYSITELIB}/networkx/algorithms/connectivity/tests/test_disjoint_paths.pyc
+${PYSITELIB}/networkx/algorithms/connectivity/tests/test_disjoint_paths.pyo
+${PYSITELIB}/networkx/algorithms/connectivity/tests/test_edge_augmentation.py
+${PYSITELIB}/networkx/algorithms/connectivity/tests/test_edge_augmentation.pyc
+${PYSITELIB}/networkx/algorithms/connectivity/tests/test_edge_augmentation.pyo
 ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_edge_kcomponents.py
 ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_edge_kcomponents.pyc
 ${PYSITELIB}/networkx/algorithms/connectivity/tests/test_edge_kcomponents.pyo
@@ -664,6 +682,9 @@ ${PYSITELIB}/networkx/algorithms/shortest_paths/unweighted.pyo
 ${PYSITELIB}/networkx/algorithms/shortest_paths/weighted.py
 ${PYSITELIB}/networkx/algorithms/shortest_paths/weighted.pyc
 ${PYSITELIB}/networkx/algorithms/shortest_paths/weighted.pyo
+${PYSITELIB}/networkx/algorithms/similarity.py
+${PYSITELIB}/networkx/algorithms/similarity.pyc
+${PYSITELIB}/networkx/algorithms/similarity.pyo
 ${PYSITELIB}/networkx/algorithms/simple_paths.py
 ${PYSITELIB}/networkx/algorithms/simple_paths.pyc
 ${PYSITELIB}/networkx/algorithms/simple_paths.pyo
@@ -763,6 +784,9 @@ ${PYSITELIB}/networkx/algorithms/tests/test_reciprocity.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_richclub.py
 ${PYSITELIB}/networkx/algorithms/tests/test_richclub.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_richclub.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_similarity.py
+${PYSITELIB}/networkx/algorithms/tests/test_similarity.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_similarity.pyo
 ${PYSITELIB}/networkx/algorithms/tests/test_simple_paths.py
 ${PYSITELIB}/networkx/algorithms/tests/test_simple_paths.pyc
 ${PYSITELIB}/networkx/algorithms/tests/test_simple_paths.pyo
@@ -1028,6 +1052,9 @@ ${PYSITELIB}/networkx/generators/lattice.pyo
 ${PYSITELIB}/networkx/generators/line.py
 ${PYSITELIB}/networkx/generators/line.pyc
 ${PYSITELIB}/networkx/generators/line.pyo
+${PYSITELIB}/networkx/generators/mycielski.py
+${PYSITELIB}/networkx/generators/mycielski.pyc
+${PYSITELIB}/networkx/generators/mycielski.pyo
 ${PYSITELIB}/networkx/generators/nonisomorphic_trees.py
 ${PYSITELIB}/networkx/generators/nonisomorphic_trees.pyc
 ${PYSITELIB}/networkx/generators/nonisomorphic_trees.pyo
@@ -1085,6 +1112,9 @@ ${PYSITELIB}/networkx/generators/tests/test_lattice.pyo
 ${PYSITELIB}/networkx/generators/tests/test_line.py
 ${PYSITELIB}/networkx/generators/tests/test_line.pyc
 ${PYSITELIB}/networkx/generators/tests/test_line.pyo
+${PYSITELIB}/networkx/generators/tests/test_mycielski.py
+${PYSITELIB}/networkx/generators/tests/test_mycielski.pyc
+${PYSITELIB}/networkx/generators/tests/test_mycielski.pyo
 ${PYSITELIB}/networkx/generators/tests/test_nonisomorphic_trees.py
 ${PYSITELIB}/networkx/generators/tests/test_nonisomorphic_trees.pyc
 ${PYSITELIB}/networkx/generators/tests/test_nonisomorphic_trees.pyo
@@ -1100,15 +1130,15 @@ ${PYSITELIB}/networkx/generators/tests/test_small.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_tree.py
-${PYSITELIB}/networkx/generators/tests/test_tree.pyc
-${PYSITELIB}/networkx/generators/tests/test_tree.pyo
+${PYSITELIB}/networkx/generators/tests/test_trees.py
+${PYSITELIB}/networkx/generators/tests/test_trees.pyc
+${PYSITELIB}/networkx/generators/tests/test_trees.pyo
 ${PYSITELIB}/networkx/generators/tests/test_triads.py
 ${PYSITELIB}/networkx/generators/tests/test_triads.pyc
 ${PYSITELIB}/networkx/generators/tests/test_triads.pyo
-${PYSITELIB}/networkx/generators/tree.py
-${PYSITELIB}/networkx/generators/tree.pyc
-${PYSITELIB}/networkx/generators/tree.pyo
+${PYSITELIB}/networkx/generators/trees.py
+${PYSITELIB}/networkx/generators/trees.pyc
+${PYSITELIB}/networkx/generators/trees.pyo
 ${PYSITELIB}/networkx/generators/triads.py
 ${PYSITELIB}/networkx/generators/triads.pyc
 ${PYSITELIB}/networkx/generators/triads.pyo
@@ -1374,6 +1404,7 @@ share/doc/${PKGBASE}/examples/drawing/plot_chess_masters.py
 share/doc/${PKGBASE}/examples/drawing/plot_circular_tree.py
 share/doc/${PKGBASE}/examples/drawing/plot_degree_histogram.py
 share/doc/${PKGBASE}/examples/drawing/plot_degree_rank.py
+share/doc/${PKGBASE}/examples/drawing/plot_directed.py
 share/doc/${PKGBASE}/examples/drawing/plot_edge_colormap.py
 share/doc/${PKGBASE}/examples/drawing/plot_ego_graph.py
 share/doc/${PKGBASE}/examples/drawing/plot_four_grids.py
@@ -1386,6 +1417,7 @@ share/doc/${PKGBASE}/examples/drawing/plot_node_colormap.py
 share/doc/${PKGBASE}/examples/drawing/plot_random_geometric_graph.py
 share/doc/${PKGBASE}/examples/drawing/plot_sampson.py
 share/doc/${PKGBASE}/examples/drawing/plot_simple_path.py
+share/doc/${PKGBASE}/examples/drawing/plot_spectral_grid.py
 share/doc/${PKGBASE}/examples/drawing/plot_unix_email.py
 share/doc/${PKGBASE}/examples/drawing/plot_weighted_graph.py
 share/doc/${PKGBASE}/examples/drawing/unix_email.mbox
diff --git a/math/py-networkx/distinfo b/math/py-networkx/distinfo
index 4724d47fcf7..79e110913a6 100644
--- a/math/py-networkx/distinfo
+++ b/math/py-networkx/distinfo
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.10 2017/09/27 13:25:54 adam Exp $
+$NetBSD: distinfo,v 1.11 2018/02/01 21:00:25 adam Exp $
 
-SHA1 (networkx-2.0.zip) = 423ebfdf77ce6268273115a3d1e653ea6c9d3eb2
-RMD160 (networkx-2.0.zip) = 2118e59b4614b7f83d9ac6673ec00a78bc5b849d
-SHA512 (networkx-2.0.zip) = 44d0d26c0ec5424a32e74ac514f2281d4aded83711fc32a2b88dfcbeb1f41826bae7f7f53af89231a9dda76675b660e93587d3553c487d6aa1a65f635ac0ad1c
-Size (networkx-2.0.zip) = 1549125 bytes
+SHA1 (networkx-2.1.zip) = a481bea7b41c0d6af191c7d2bcde56d75da20b3e
+RMD160 (networkx-2.1.zip) = 52295c8c57b4e6897244f0129f396af2c5114997
+SHA512 (networkx-2.1.zip) = 61b819ccfdd38e009e5b363f4bf551f2924bbf751b078aab1b41da9faf4c6b0841f38750b96bd359d3aebefef01e65e88b4c43a378ec25bbd45283d92bdae678
+Size (networkx-2.1.zip) = 1612593 bytes