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CVS commit: pkgsrc/math/py-networkx
Module Name: pkgsrc
Committed By: wiz
Date: Mon May 20 10:21:50 UTC 2024
Modified Files:
pkgsrc/math/py-networkx: Makefile PLIST distinfo
Log Message:
py-networkx: update to 3.3.
API Changes
-----------
- Disallow negative number of nodes in ``complete_multipartite_graph``
- DEP: Deprecate the all_triplets one-liner
- [A-star] Added expansion pruning via cutoff if cutoff is provided
- Make HITS raise exceptions consistent with power iterations
- DEP: Deprecate random_triad
- Added feature modular graph product
- ENH: Speed up common/non_neighbors by using _adj dict operations
- Deprecate the ``create`` argument of ``nonisomorphic_trees``
- Improve total_spanning_tree_weight
- Update __init__.py
- add **kwargs to traveling_salesman_problem
Enhancements
------------
- Add Tadpole graph
- [A-star] Added expansion pruning via cutoff if cutoff is provided
- Implementation of $S^1$ model
- [Feat] Random expanders utilities
- Compare graphs for generator functions when running tests with backend
- Add Kirchhoff index / Effective graph resistance
- Changed return types of shortest path methods to improve consistency
- New PR for Fixes minimal d-separator function failing to handle cases where no d-separators exist
- ENH : Provide non-normalized and normalized directed laplacian matrix calculation
- feat: drop the use of node attribute "first_nbr" in PlanarEmbedding
- Add functions to compute Schultz and Gutman Index
- Divisive community algorithms
- Added feature modular graph product
- ENH : added ``sort_neighbors`` to all functions in ``depth_first_search.py``
- New graph generator for the Kneser graph
- Draw MultiDiGraph edges and labels qa7008
- Use github actions to run a comparison benchmark
- BFS layout implementation
- Add ``max_level=`` argument to ``louvain_communities`` to limit macro-iterations
- Review and update ``@nx._dispatchable`` usage since 3.2.1
- Transmogrify ``_dispatchable`` objects into functions
- fix: make ``PlanarEmbedding.copy()`` use ``add_edges_from()`` from parent
- Allow seed of np.random instance to exactly produce arbitrarily large integers
- Improve total_spanning_tree_weight
- add seed to ``nx.generate_random_paths``
- Allow backends to implement ``should_run``
- Adding tree broadcasting algorithm in a new module
- Option to include initial labels in ``weisfeiler_lehman_subgraph_hashes``
- Add better error message when trying to get edge that is not present
- Make ``is_negatively_weighted`` dispatchable
- Add option to hide or show tick labels
- ENH: Cache graphs objects when converting to a backend
Bug Fixes
---------
- Fix listing of release notes on Releases page
- Fix syntax warning from bad escape sequence
- Fix triangles to avoid using ``is`` to compare nodes
- Fix error message for ``nx.mycielski_graph(0)``
- Disallow negative number of nodes in ``complete_multipartite_graph``
- Handle edge cases for greedy_modularity_communities
- FIX: Match the doc description while copying over data
- fix: Include singleton/trivial paths in all_simple_paths & other functions
- Dinitz correction
- Modify GML test to fix invalid octal character warning
- Fix random_spanning_tree() for single node and empty graphs
- PlanarEmbedding.remove_edge() now updates removed edge's neighbors
- add seed to graph creation
- add seed to tests of fast_label_propatation_communities
- Fix rich_club_coefficient() for single node and empty graphs
- Fix minimum_spanning_arborescence regression
- Move arrowstyle input munging after intput validation
- Fix empty GraphML attribute is not parsed
- Add new test result to ``test_asadpour_tsp`` and change ``linprog`` method
- Fix custom weight attribute for Mehlhorn
Documentation
-------------
- Update release process
- Update convert_matrix.py
- fix extendability function name in bipartite.rst
- Minor doc cleanups to remove doc build warnings
- DOC: Add example to generic_bfs_edges to demonstrate the ``neighbors`` param
- Hierarchical clustering layout gallery example
- Fixed an error in the documentation of the katz centrality
- Create 3d_rotation_anime.py
- DOC: Add docstrings to filter view functions
- DOC: Add docstrings to Filter mapping views
- DOCS: Fix internal links to other functions in isomorphvf2
- added note for the triangle inequality case in TSP
- Add note about importance of testing to contributor guide
- Proposal to add centrality overview to mentored projects
- Improve documentation of Component Algorithms
- Add dot io to readwrite
- Add Python versions to release notes
- DOC: Turn on inline plots in graph generators docstrings
- Fix duplicate numbering in contributor guide
- DOC: remove unnecessary 'or' in planted_partition_graph
- DOC: Link methods in functions to base Graph methods/properties
- Connect docs to doc_string for total_spanning_tree_weight
- Image
- update triadic_census documentation for undirected graphs - issue 4386
- added 3d and animation to plot_greedy_coloring.py
- DOC: fix URL econded links and doc references
- DOC: add reference to fast_label_propagation_communities
- updated See also sec of argmap class
- DOC : updated examples in mincost.py
- Document the walk_type argument default in directed_laplacian and similar functions
- DOC: Add plots to classic graph generators docs
- Fix a tiny typo in ``structuralholes.py::local_constraint`` docstring
- Added ``subgraph_is_monomorphic`` and ``subgraph_monomorphisms_iter`` in docs
- Fix online docs for ``_dispatch``
- DOC : Updated docs for panther_similarity
- Fix warnings when building docs
- Improve docs for optimal_edit_paths
- DOC: build with nx-parallel extra documentation information
- Fixed typo in tensor product documentation
- Add example for cycle detection
- Update general_k_edge_subgraphs docstring
- Update docstring of nonisomorphic_trees
- adding self loops related docs and tests for functions in ``cluster.py``
- Add minimum_cycle_basis to cycle_basis See Also
- Update CONTRIBUTING.rst
- Fix all sphinx warnings during doc build
- Doc infrastructure: replace ``nb2plot`` with ``myst-nb``
- Add explicit targets of missing modules for intersphinx
- DOC: add doc suggestions for arbitrarily large random integers tools
- Try/except intermittently failing basemaps in geospatial examples
- Update docstring example with future-proof pandas assignment
- Remove animation from spectral clustering example to improve performance
- Doc Improvements for Approximations Files
- Update ``LCF_graph`` docstring
- Option to include initial labels in ``weisfeiler_lehman_subgraph_hashes``
- Add eriknw as contributor
- [DOC, DISPATCH] : updated and added ``backend.py``'s docs
- add **kwargs to traveling_salesman_problem
- Move the backend docs and connect the config docs. Both in a single sidebar entry
Maintenance
-----------
- Drop Python 3.9 support
- fix: Explicitly check for None/False in edge_attr during import from np
- Add favicon
- Remove unused code resistance_distance
- Fix names of small graphs
- Improve error messages for misconfigured backend treatment
- MAINT: Fixup union exception message
- MAINT: Minor touchups to tadpole and lollipop graph
- Add ``@not_implemented_for("directed")`` to ``number_connected_components``
- remove unused code
- Minor touchups to the beamsearch module
- Fix annoying split strings on same line
- Update dispatch decorator for ``hits`` to use ``"weight"`` edge weight
- Remove nbconvert upper pin
- Add a step to CI to check for warnings at import time
- Added few tests for /generators/duplication.py and /generators/geomet…
- Test on Python 3.13-dev
- Changed arguments list of GraphMLWriterLxml.dump()
- ``write_graphml``: Small fix for object type description on ``TypeError`` exception
- updated functions in ``core.py``
- label check on push and change check name
- DEP : adding ``not_implemented_for("multigraph”)`` to ``k_core``, ``k_shell``, ``k_crust`` and ``k_corona``
- Add label check when pull request is edited instead of push
- Add label workflow pull_request type synchronize and echo message
- adding test coverage for isomorphism when using digraphs
- Remove usage of ``__networkx_plugin__``
- DOC: consistent spelling of neighbor and rename vars
- MAINT: use ruff format instead of black
- Ensure warnings related to changes in shortest_path returns are visible to users
- Sync up behavior of is_{type} for empty graphs
- Added ``NodeNotFound`` exceptions to ``_apply_prediction`` and ``simrank``, and ignored isolated nodes in ``panther_similarity``
- Fix not_implemented_for decorator for is_regular and related functions
- Fix all_node_cuts output for complete graphs
- Remove ``"networkx.plugins"`` and ``"networkx.plugin_info"`` entry-points
- Bump actions/setup-python from 4 to 5
- Update test suite for Pytest v8
- Undeprecate ````nx_pydot```` now that pydot is actively maintained again
- Future-proofing and improve tests
- Drop old dependencies per SPEC 0
- Update pygraphviz
- Refactor geometric_soft_configuration_model tests for performance
- Rename ``_dispatch`` to ``_dispatchable``
- Replace tempfile with tmp_path fixture in test suite
- updated test_directed_edge_swap #5814
- Bump copyright year for 2024
- Improving test coverage for Small.py
- Test for symmetric edge flow betweenness partition
- MAINT : added ``seed`` to ``gnm_random_graph`` in ``community/tests/test_label_propagation.py``
- Bump scientific-python/upload-nightly-action from 0.2.0 to 0.3.0
- adding self loops related docs and tests for functions in ``cluster.py``
- Improving test coverage for Mycielsky.py
- Use ruff's docstring formatting
- Add docstring formatting change to blame-ignore-revs
- Improve test coverage for random_clustered and update function names
- Doc infrastructure: replace ``nb2plot`` with ``myst-nb``
- Temporarily rm geospatial examples to fix CI
- Improve test coverage for bipartite extendability
- CI: Update scientific-python/upload-nightly-action from 0.3.0 to 0.4.0
- CI: Group dependabot updates
- CI: update upload-nightly-action to 0.5.0
- renaming backend ``func_info`` dictionary's keys
- Add ``mutates_input=`` and ``returns_graph=`` to ``_dispatchable``
- Avoid creating results with numpy scalars
- Bump changelist from 0.4 to 0.5
- Improve test coverage for bipartite matrix.py
- Un-dispatch coloring strategies
- Undo change in return type of ``single_target_shortest_path_length``
- Remove animation from spectral clustering example to improve performance
- Expire steinertree mehlhorn futurewarning
- Update louvain test modularity comparison to leq
- Add aaronzo as contributor
- Fix #7339. ``shortest_path`` inconsisitent with warning
- Add ``nx.config`` dict for configuring dispatching and backends
- Improve test coverage for Steiner Tree & Docs
- added ``seed`` to ``test_richclub_normalized``
- Add tests to link_prediction.py
- Fix pydot tests when testing backends
- Future proof xml parsing in graphml
- make doc_string examples order-independent by removing np.set_printoptions
- Close figures on test cleanup
- More numpy scalars cleanup for numpy 2.0
- Update numpydoc
- Fix pygraphviz tests causing segmentation faults in backend test
- Add dispatching to broadcasting.py
- Update test suite to handle when scipy is not installed
- Rm deprecated np.row_stack in favor of vstack
- Fix exception for ``del config[key]``
- Bump the GH actions with 3 updates
To generate a diff of this commit:
cvs rdiff -u -r1.39 -r1.40 pkgsrc/math/py-networkx/Makefile
cvs rdiff -u -r1.21 -r1.22 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:1.39 pkgsrc/math/py-networkx/Makefile:1.40
--- pkgsrc/math/py-networkx/Makefile:1.39 Sun Jan 7 21:15:46 2024
+++ pkgsrc/math/py-networkx/Makefile Mon May 20 10:21:50 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.39 2024/01/07 21:15:46 wiz Exp $
+# $NetBSD: Makefile,v 1.40 2024/05/20 10:21:50 wiz Exp $
-DISTNAME= networkx-3.2.1
+DISTNAME= networkx-3.3
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=n/networkx/}
@@ -18,8 +18,5 @@ USE_LANGUAGES= # none
PYTHON_VERSIONS_INCOMPATIBLE= 27
-do-test:
- cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest-${PYVERSSUFFIX} networkx
-
.include "../../lang/python/wheel.mk"
.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/math/py-networkx/PLIST
diff -u pkgsrc/math/py-networkx/PLIST:1.21 pkgsrc/math/py-networkx/PLIST:1.22
--- pkgsrc/math/py-networkx/PLIST:1.21 Tue Jan 2 00:37:37 2024
+++ pkgsrc/math/py-networkx/PLIST Mon May 20 10:21:50 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.21 2024/01/02 00:37:37 ryoon Exp $
+@comment $NetBSD: PLIST,v 1.22 2024/05/20 10:21:50 wiz Exp $
${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.txt
${PYSITELIB}/${WHEEL_INFODIR}/METADATA
${PYSITELIB}/${WHEEL_INFODIR}/RECORD
@@ -221,6 +221,9 @@ ${PYSITELIB}/networkx/algorithms/boundar
${PYSITELIB}/networkx/algorithms/bridges.py
${PYSITELIB}/networkx/algorithms/bridges.pyc
${PYSITELIB}/networkx/algorithms/bridges.pyo
+${PYSITELIB}/networkx/algorithms/broadcasting.py
+${PYSITELIB}/networkx/algorithms/broadcasting.pyc
+${PYSITELIB}/networkx/algorithms/broadcasting.pyo
${PYSITELIB}/networkx/algorithms/centrality/__init__.py
${PYSITELIB}/networkx/algorithms/centrality/__init__.pyc
${PYSITELIB}/networkx/algorithms/centrality/__init__.pyo
@@ -392,6 +395,9 @@ ${PYSITELIB}/networkx/algorithms/communi
${PYSITELIB}/networkx/algorithms/community/community_utils.py
${PYSITELIB}/networkx/algorithms/community/community_utils.pyc
${PYSITELIB}/networkx/algorithms/community/community_utils.pyo
+${PYSITELIB}/networkx/algorithms/community/divisive.py
+${PYSITELIB}/networkx/algorithms/community/divisive.pyc
+${PYSITELIB}/networkx/algorithms/community/divisive.pyo
${PYSITELIB}/networkx/algorithms/community/kclique.py
${PYSITELIB}/networkx/algorithms/community/kclique.pyc
${PYSITELIB}/networkx/algorithms/community/kclique.pyo
@@ -422,6 +428,9 @@ ${PYSITELIB}/networkx/algorithms/communi
${PYSITELIB}/networkx/algorithms/community/tests/test_centrality.py
${PYSITELIB}/networkx/algorithms/community/tests/test_centrality.pyc
${PYSITELIB}/networkx/algorithms/community/tests/test_centrality.pyo
+${PYSITELIB}/networkx/algorithms/community/tests/test_divisive.py
+${PYSITELIB}/networkx/algorithms/community/tests/test_divisive.pyc
+${PYSITELIB}/networkx/algorithms/community/tests/test_divisive.pyo
${PYSITELIB}/networkx/algorithms/community/tests/test_kclique.py
${PYSITELIB}/networkx/algorithms/community/tests/test_kclique.pyc
${PYSITELIB}/networkx/algorithms/community/tests/test_kclique.pyo
@@ -886,6 +895,9 @@ ${PYSITELIB}/networkx/algorithms/tests/t
${PYSITELIB}/networkx/algorithms/tests/test_bridges.py
${PYSITELIB}/networkx/algorithms/tests/test_bridges.pyc
${PYSITELIB}/networkx/algorithms/tests/test_bridges.pyo
+${PYSITELIB}/networkx/algorithms/tests/test_broadcasting.py
+${PYSITELIB}/networkx/algorithms/tests/test_broadcasting.pyc
+${PYSITELIB}/networkx/algorithms/tests/test_broadcasting.pyo
${PYSITELIB}/networkx/algorithms/tests/test_chains.py
${PYSITELIB}/networkx/algorithms/tests/test_chains.pyc
${PYSITELIB}/networkx/algorithms/tests/test_chains.pyo
@@ -1183,9 +1195,6 @@ ${PYSITELIB}/networkx/classes/tests/disp
${PYSITELIB}/networkx/classes/tests/historical_tests.py
${PYSITELIB}/networkx/classes/tests/historical_tests.pyc
${PYSITELIB}/networkx/classes/tests/historical_tests.pyo
-${PYSITELIB}/networkx/classes/tests/test_backends.py
-${PYSITELIB}/networkx/classes/tests/test_backends.pyc
-${PYSITELIB}/networkx/classes/tests/test_backends.pyo
${PYSITELIB}/networkx/classes/tests/test_coreviews.py
${PYSITELIB}/networkx/classes/tests/test_coreviews.pyc
${PYSITELIB}/networkx/classes/tests/test_coreviews.pyo
@@ -1647,6 +1656,9 @@ ${PYSITELIB}/networkx/utils/__init__.pyo
${PYSITELIB}/networkx/utils/backends.py
${PYSITELIB}/networkx/utils/backends.pyc
${PYSITELIB}/networkx/utils/backends.pyo
+${PYSITELIB}/networkx/utils/configs.py
+${PYSITELIB}/networkx/utils/configs.pyc
+${PYSITELIB}/networkx/utils/configs.pyo
${PYSITELIB}/networkx/utils/decorators.py
${PYSITELIB}/networkx/utils/decorators.pyc
${PYSITELIB}/networkx/utils/decorators.pyo
@@ -1671,6 +1683,12 @@ ${PYSITELIB}/networkx/utils/tests/__init
${PYSITELIB}/networkx/utils/tests/test__init.py
${PYSITELIB}/networkx/utils/tests/test__init.pyc
${PYSITELIB}/networkx/utils/tests/test__init.pyo
+${PYSITELIB}/networkx/utils/tests/test_backends.py
+${PYSITELIB}/networkx/utils/tests/test_backends.pyc
+${PYSITELIB}/networkx/utils/tests/test_backends.pyo
+${PYSITELIB}/networkx/utils/tests/test_config.py
+${PYSITELIB}/networkx/utils/tests/test_config.pyc
+${PYSITELIB}/networkx/utils/tests/test_config.pyo
${PYSITELIB}/networkx/utils/tests/test_decorators.py
${PYSITELIB}/networkx/utils/tests/test_decorators.pyc
${PYSITELIB}/networkx/utils/tests/test_decorators.pyo
Index: pkgsrc/math/py-networkx/distinfo
diff -u pkgsrc/math/py-networkx/distinfo:1.21 pkgsrc/math/py-networkx/distinfo:1.22
--- pkgsrc/math/py-networkx/distinfo:1.21 Tue Jan 2 00:37:37 2024
+++ pkgsrc/math/py-networkx/distinfo Mon May 20 10:21:50 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.21 2024/01/02 00:37:37 ryoon Exp $
+$NetBSD: distinfo,v 1.22 2024/05/20 10:21:50 wiz Exp $
-BLAKE2s (networkx-3.2.1.tar.gz) = 0dce230d3195ec644e8085d28de98cca3987bb36c3d03c47f482c004a2ae26fb
-SHA512 (networkx-3.2.1.tar.gz) = 579c54a4a016617f5260df01b821c3906c4f289e80ae7bd618c0ebb9e05ebe806e71f1f660e3012531d04572ac4e6670aa73117ed26da8248fbb8ef7228b5803
-Size (networkx-3.2.1.tar.gz) = 2073928 bytes
+BLAKE2s (networkx-3.3.tar.gz) = 6ec7268f800646c37db4bc7248575d78ef27ccee0d9325e88fbae95f15e0d238
+SHA512 (networkx-3.3.tar.gz) = 86306cabd7e15aa79cae4d84a42e8804b1e904fc2127725067a80e3ddf31f0fa72ebb9d21284018e72bdfc662c766a5be55564572aadaf7392dada7ea93d1ea4
+Size (networkx-3.3.tar.gz) = 2126579 bytes
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