CVS commit: pkgsrc/math/py-networkx

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Wed Jun  4 12:32:02 UTC 2025

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

Log Message:
py-networkx: updated to 3.5

networkx 3.5

API Changes

- Save Layouts on Graphs
- Expire d_separated and minimum_d_separator functions
- Expire all_triplets deprecation
- Expire random_triad deprecation
- DEP: Raise an exception for k_core functions with multigraphs
- Deprecate graph_could_be_isomorphic
- Expire total_spanning_tree_weight deprecation
- Expire deprecation of create kwarg in nonisomorphic_trees
- New draw API

Enhancements

- perf: optimise ``random_k_out_graph``
- Clausets local community detection algorithm
- ``find_asteroidal_triple`` improvement
- Add ``weight`` to harmonic_diameter
- Densest Subgraph Problem: Greedy Peeling and Greedy++ Implementations
- single_source_all_shortest_paths: don't loop over all nodes
- Error message improvement for nbunch_iter ( NetworkXError raised with specific message on TypeError with "iter" in msg )
- Faster computation of energy in Laplacian centrality
- Make ``forceatlas2_layout`` dispatchable
- Update dispatchable for ``forceatlas2_layout``
- Enable backend-only functions where NetworkX is just an API
- Steinertree kou enhancement in response to issue 5889 type:Enhancements
- Add Leiden as a backend-only algorithm
- Bipartite layout nodes optional
- Densest Subgraph Problem: FISTA based algorithm + Large scale tests
- Dispatch ``get_node_attributes`` and a few more from ``nx.classes.function``
- Faster ``could_be_isomorphic`` and ``number_of_cliques``
- Add square_clustering to algorithm benchmarks
- Faster Implementation of Structural Holes
- Improve runtime of number_of_nonisomorphic_trees()
- Fix write_gexf timeformat for dynamic Graphs
- Consolidate could_be_isomorphic
- Improving rooted_tree_isomorphism for deep trees
- Fixing nx.diameter inconsistent results with usebounds=True
- Faster ``square_clustering``
- Avoid repeated cache conversion failures for backends
- Improve _sparse_fruchterman_reingold with L-BFGS
- Improve Performance of Tree Isomorphism and Center Calculation
- Add option for ``biadjacency_matrix`` to be returned as a dense NumPy array
- Add Functions for Finding Connected Dominating Sets
- Add feature to make storing node contraction data optional
- Added "initial_node" param to generate_random_paths() to allow a starting node to be specified for generated walks
- Fix behavior for iterable ``sources`` argument in ``bfs_layers``
- Speed up ``connected_components`` and ``weakly_connected_components``
- BiRank Algorithm Implementation
- Enforce correct graph types for graph matchers

Bug Fixes

- Update ``_raise_on_directed`` to work with ``create_using`` pos arg
- trophic_levels now checks for paths from each node to a basal node
- Fix TSP weight parameter issues
- Fix for filtered MultiGraph views from ``edge_subgraph``
- BUG: fixed the ``if`` condition in ``asadpour_atsp``
- Implement Bar ConnectionStyle for labels
- Fixed a divide by zero error in forceatlas2
- Fix for issue 7645: Do not preserve 'cw' and 'ccw' attributes in PlanarEmbedding.to_undirected()
- fix typo in ramanujan branch
- Fix ``with nx.config(backend_priority=backends):``
- Fix handling of faux_infinite values in network_simplex
- Fixed the return type from an empty dict to an empty set
- Add ``edge_attrs="weight"`` to ``forceatlas2_layout`` dispatch decorator
- Fix graph_hash iteration counts and DiGraph handling
- Refactored the working of chordless_cycles to handle self loops
- Fix bc scale with k endpoints
- Fix BC scaling for source nodes with k and endpoints=False
- BUG: graph6 format invariant to trailing newline
- Fix ``random_degree_sequence_graph`` when input is an iterator
- Improve special cases in dispatch testing (paying off tech debt)
- Fix bug when assigning list to ``nx.config.backend_priority``
- A minimal fix for ``is_aperiodic``
- fix bug of _sparse_fruchterman_reingold and remove try/except idiom
- Fix edge case in ISMAGS symmetry detection

Documentation

- set nx-arangodb link to github
- Re-submission of gh-7087 with better file provenance
- Fix code formatting of some examples
- Add examples for custom graph in the doc of ``soft_random_geometric_graph`` and ``thresholded_random_geometric_graph``
- Gallery example: bipartite a/b-core motif
- Add blurb about pytest-mpl dependency to contributing guide
- Minor updates to ``single_source_shortest_path_length`` docstring
- Added a note to the contributor guideline to avoid numpy scalars as a…
- Correcting the example given under subgraph_is_monomorphic.py
- [easy] Add to Contributor List
- doc: mention the second major update
- DOC: Add details about more grants
- Refactor: Moving backend docs from ``backends.py`` to ``backends.rst``
- Update readwrite docstrings for the ``path`` parameter
- Fix docstring example of ``nx.generate_random_paths(index_map=...)``
- Adds NVIDIA Corporation to list of supporters
- Fix use of triple backticks in docstrings
- Add paragraph about university classes to mentored projects
- Fix pygraphviz_layout example
- Add test-extras to optional dependencies
- doc: hash size are in bytes
- DOC: Clean up mentored projects page: move visualization project to completed section
- added 2 projects for GSoC 2025
- Add missing usebounds param descr to distance docstrings
- Add examples to graph_atlas_g docstring
- Add missing ``weight`` and ``gravity`` attribute to ``forceatlas2_layout`` docstring
- DOC: Update first docstring example and add a serialization example
- DOC: Remove myself from the mentor list for projects
- Fix typo in forceatlas2_layout
- Add ``tournament_matrix`` to docs
- Add function descriptions in the threshold.py file
- bugfix: use supergraph to compute superpos in plot_clusters example
- More ``random_paths`` docstring improvements
- Add nx-guides link to navbar without dropdown
- Clarifying backend graph class interface is_directed+is_multigraph
- Fix all sphinx build warnings
- Add a new gallery spring layout
- Add note about cycles in ``maximum_flow()``
- Clarify subgraph node/edge order is not preserved
- Fix typo in ``min_edge_cover`` docstring

Maintenance
-----------

- MAINT: wrapping ``partial`` with ``staticmethod()`` in ``test_link_prediction.py``
- Updating ``pip install``s in benchmarking workflow
- Mv changelist to release deps
- Drop support for Python 3.10
- Update minimum dependencies (SPEC 0)
- Remove print statements and comments from test suite
- Refactor closeness centrality tests
- Add Python fallback to random_k_out_graph + document dependencies
- Fix sphinx warnings from numpydoc parsing
- MAINT: Updating geospatial example to be compatible with ``osmnx=2.0.0``
- Add more tests for ``nx.lowest_common_ancestor``
- Update ``shortest_path`` and ``single_target_shortest_path_length`` for 3.5
- Parametrize edge_subgraph multigraph test
- Add filters for LOBPCG convergence warnings
- MAINT: Close mpl figures in tests to clear up test env
- Update pre-commit linting
- Small dispatching refactor: simple ``__call__`` when no backends
- Benchmarking: graph atlas
- Improve square clustering test derived from Zhang paper (reference 2)
- Fix exception for backend-only functions
- Add a subplot fixture to automate test cleanup
- MAINT: use nx.layout instead of importing layouts
- MAINT: Move stub func in the correct scope for pickle test
- Ensure standard import conventions are used
- Clean up pygrep pre-commit for import convention checks
- Add a few more square clustering test cases
- Don't use ``assert`` when using ``pytest.raises``
- Update doc requirements
- Update developer requirements
- MAINT: Minus not underscore in the dep package name
- Update readwrite docstrings for the ``path`` parameter
- Fix docstring example of ``nx.generate_random_paths(index_map=...)``
- Fix use of triple backticks in docstrings
- Add .mailmap file to consilidate contributors
- TST: Refactor example test case generation functions
- Refactor network_simplex test of faux_infinity
- Change CRLF format of two files
- Fix some typos
- Pre commit hooks to check line endings and trailing whitespace
- MAINT: replace the SHAs for blame and move the changes within pre-commit
- Rm stray instances of sparse matrices from test suite
- Remove unused imports
- Remove unnecessary ``dict(...)`` for SSSP algos that return dicts
- Change function calls to address pandas linting
- Activate pycodestyle in linting pre-commit
- Correct sphinx warnings from doc build
- ``effective_size`` of nodes with only self-loop edges is undefined
- DOC: docstring changes to ``to_dict_of_dicts`` and ``attr_matrix`` and input name change in ``min_fill_in_heuristic``
- Update layout.py
- Tree isomorphism input validation
- Tweaks and notes from a dive into backends.py
- MAINT: Follow-up to 7945 - rm helper function
- Some light refactoring to make the tree isomorphism tests more readable
- new try at will_call_mutate_inputs
- MAINT: rm debug print from similarity module
- Improve special cases in dispatch testing (paying off tech debt)
- Remove unused import in convert_matrix.py (networkx.utils.not_implemented_for)
- Use ``-n auto`` from pytest-xdist for dispatch and coverage CI jobs
- Make test file names unique to be threadsafe
- Update pre-commit repos
- Minor follow-up to gh-8002 tests
- Add linting for line length in docstrings and comments
- Add sg_execution_times.rst to gitignore
- Support both pydot v3 and pydot v4
- Update copyright license years
- Fix all sphinx build warnings
- Fix intermittent test failures in expander graph generator tests
- Refactor tree_isomorphism to improve code reuse and readability
- STY: Rm local variable remapping of heappush and heappop
- TST: Minor improvements to layout test suite
- Minor refactor to cleanup/improve matching test suite


To generate a diff of this commit:
cvs rdiff -u -r1.45 -r1.46 pkgsrc/math/py-networkx/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/math/py-networkx/PLIST \
    pkgsrc/math/py-networkx/distinfo

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

Modified files:

Index: pkgsrc/math/py-networkx/Makefile
diff -u pkgsrc/math/py-networkx/Makefile:1.45 pkgsrc/math/py-networkx/Makefile:1.46
--- pkgsrc/math/py-networkx/Makefile:1.45       Tue Apr 15 16:31:38 2025
+++ pkgsrc/math/py-networkx/Makefile    Wed Jun  4 12:32:02 2025
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.45 2025/04/15 16:31:38 adam Exp $
+# $NetBSD: Makefile,v 1.46 2025/06/04 12:32:02 adam Exp $
 
-DISTNAME=      networkx-3.4.2
+DISTNAME=      networkx-3.5
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=n/networkx/}
 

Index: pkgsrc/math/py-networkx/PLIST
diff -u pkgsrc/math/py-networkx/PLIST:1.23 pkgsrc/math/py-networkx/PLIST:1.24
--- pkgsrc/math/py-networkx/PLIST:1.23  Tue Apr 15 16:31:38 2025
+++ pkgsrc/math/py-networkx/PLIST       Wed Jun  4 12:32:02 2025
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.23 2025/04/15 16:31:38 adam Exp $
+@comment $NetBSD: PLIST,v 1.24 2025/06/04 12:32:02 adam Exp $
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
@@ -23,6 +23,9 @@ ${PYSITELIB}/networkx/algorithms/approxi
 ${PYSITELIB}/networkx/algorithms/approximation/connectivity.py
 ${PYSITELIB}/networkx/algorithms/approximation/connectivity.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/connectivity.pyo
+${PYSITELIB}/networkx/algorithms/approximation/density.py
+${PYSITELIB}/networkx/algorithms/approximation/density.pyc
+${PYSITELIB}/networkx/algorithms/approximation/density.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/distance_measures.py
 ${PYSITELIB}/networkx/algorithms/approximation/distance_measures.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/distance_measures.pyo
@@ -56,6 +59,9 @@ ${PYSITELIB}/networkx/algorithms/approxi
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_connectivity.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_connectivity.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_connectivity.pyo
+${PYSITELIB}/networkx/algorithms/approximation/tests/test_density.py
+${PYSITELIB}/networkx/algorithms/approximation/tests/test_density.pyc
+${PYSITELIB}/networkx/algorithms/approximation/tests/test_density.pyo
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_distance_measures.py
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_distance_measures.pyc
 ${PYSITELIB}/networkx/algorithms/approximation/tests/test_distance_measures.pyo
@@ -161,6 +167,9 @@ ${PYSITELIB}/networkx/algorithms/biparti
 ${PYSITELIB}/networkx/algorithms/bipartite/generators.py
 ${PYSITELIB}/networkx/algorithms/bipartite/generators.pyc
 ${PYSITELIB}/networkx/algorithms/bipartite/generators.pyo
+${PYSITELIB}/networkx/algorithms/bipartite/link_analysis.py
+${PYSITELIB}/networkx/algorithms/bipartite/link_analysis.pyc
+${PYSITELIB}/networkx/algorithms/bipartite/link_analysis.pyo
 ${PYSITELIB}/networkx/algorithms/bipartite/matching.py
 ${PYSITELIB}/networkx/algorithms/bipartite/matching.pyc
 ${PYSITELIB}/networkx/algorithms/bipartite/matching.pyo
@@ -200,6 +209,9 @@ ${PYSITELIB}/networkx/algorithms/biparti
 ${PYSITELIB}/networkx/algorithms/bipartite/tests/test_generators.py
 ${PYSITELIB}/networkx/algorithms/bipartite/tests/test_generators.pyc
 ${PYSITELIB}/networkx/algorithms/bipartite/tests/test_generators.pyo
+${PYSITELIB}/networkx/algorithms/bipartite/tests/test_link_analysis.py
+${PYSITELIB}/networkx/algorithms/bipartite/tests/test_link_analysis.pyc
+${PYSITELIB}/networkx/algorithms/bipartite/tests/test_link_analysis.pyo
 ${PYSITELIB}/networkx/algorithms/bipartite/tests/test_matching.py
 ${PYSITELIB}/networkx/algorithms/bipartite/tests/test_matching.pyc
 ${PYSITELIB}/networkx/algorithms/bipartite/tests/test_matching.pyo
@@ -407,6 +419,12 @@ ${PYSITELIB}/networkx/algorithms/communi
 ${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/leiden.py
+${PYSITELIB}/networkx/algorithms/community/leiden.pyc
+${PYSITELIB}/networkx/algorithms/community/leiden.pyo
+${PYSITELIB}/networkx/algorithms/community/local.py
+${PYSITELIB}/networkx/algorithms/community/local.pyc
+${PYSITELIB}/networkx/algorithms/community/local.pyo
 ${PYSITELIB}/networkx/algorithms/community/louvain.py
 ${PYSITELIB}/networkx/algorithms/community/louvain.pyc
 ${PYSITELIB}/networkx/algorithms/community/louvain.pyo
@@ -440,6 +458,12 @@ ${PYSITELIB}/networkx/algorithms/communi
 ${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_leiden.py
+${PYSITELIB}/networkx/algorithms/community/tests/test_leiden.pyc
+${PYSITELIB}/networkx/algorithms/community/tests/test_leiden.pyo
+${PYSITELIB}/networkx/algorithms/community/tests/test_local.py
+${PYSITELIB}/networkx/algorithms/community/tests/test_local.pyc
+${PYSITELIB}/networkx/algorithms/community/tests/test_local.pyo
 ${PYSITELIB}/networkx/algorithms/community/tests/test_louvain.py
 ${PYSITELIB}/networkx/algorithms/community/tests/test_louvain.pyc
 ${PYSITELIB}/networkx/algorithms/community/tests/test_louvain.pyo
@@ -1264,6 +1288,11 @@ ${PYSITELIB}/networkx/drawing/nx_pylab.p
 ${PYSITELIB}/networkx/drawing/tests/__init__.py
 ${PYSITELIB}/networkx/drawing/tests/__init__.pyc
 ${PYSITELIB}/networkx/drawing/tests/__init__.pyo
+${PYSITELIB}/networkx/drawing/tests/baseline/test_display_complex.png
+${PYSITELIB}/networkx/drawing/tests/baseline/test_display_empty_graph.png
+${PYSITELIB}/networkx/drawing/tests/baseline/test_display_house_with_colors.png
+${PYSITELIB}/networkx/drawing/tests/baseline/test_display_labels_and_colors.png
+${PYSITELIB}/networkx/drawing/tests/baseline/test_display_shortest_path.png
 ${PYSITELIB}/networkx/drawing/tests/baseline/test_house_with_colors.png
 ${PYSITELIB}/networkx/drawing/tests/test_agraph.py
 ${PYSITELIB}/networkx/drawing/tests/test_agraph.pyc
Index: pkgsrc/math/py-networkx/distinfo
diff -u pkgsrc/math/py-networkx/distinfo:1.23 pkgsrc/math/py-networkx/distinfo:1.24
--- pkgsrc/math/py-networkx/distinfo:1.23       Thu Oct 24 06:50:47 2024
+++ pkgsrc/math/py-networkx/distinfo    Wed Jun  4 12:32:02 2025
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.23 2024/10/24 06:50:47 adam Exp $
+$NetBSD: distinfo,v 1.24 2025/06/04 12:32:02 adam Exp $
 
-BLAKE2s (networkx-3.4.2.tar.gz) = ffd5280eae814a3871fb871c09a3abed42ebf9d63887ca1a7a4356f43e86ad69
-SHA512 (networkx-3.4.2.tar.gz) = 910e1400ad18711761c715896c3238b9c7d8914c571ab4db3aaf18a772b5fef90e5378ca435fbfce55b5821f1ddd3863a3cd65030086e80a971df91d9203c637
-Size (networkx-3.4.2.tar.gz) = 2151368 bytes
+BLAKE2s (networkx-3.5.tar.gz) = 5327aeaff4b1d7f0ff32d10a85c61d908b3474caf7e533df95211cf4b5573f84
+SHA512 (networkx-3.5.tar.gz) = 9c060385913cfe67126e71eb9e53c032faa51c9609336ce78333d22e5f73078eb5b4826e0709cae0bd448fef2a5b2fb6f4c29be28c70d34a936d1cf6a00e83a1
+Size (networkx-3.5.tar.gz) = 2471065 bytes