Log message:
py-networkx: add missing tools

Log message:
py-networkx: Update to 3.2.1

Changelog:
3.2.1:

Release date: 28 October 2023

Supports Python 3.9, 3.10, 3.11, and 3.12.

NetworkX is a Python package for the creation, manipulation, and study of the
structure, dynamics, and functions of complex networks.

For more information, please visit our website and our gallery of examples.
Please send comments and questions to the networkx-discuss mailing list.

API Changes#

  * Disallow negative number of nodes in complete_multipartite_graph (#7057).

Enhancements#

  * Add Tadpole graph (#6999).

Bug Fixes#

  * Fix listing of release notes on Releases page (#7030).

  * Fix syntax warning from bad escape sequence (#7034).

  * Fix triangles to avoid using is to compare nodes (#7041).

  * Fix error message for nx.mycielski_graph(0) (#7056).

  * Disallow negative number of nodes in complete_multipartite_graph (#7057).

Documentation#

  * Update release process (#7029).

  * fix extendability function name in bipartite.rst (#7042).

  * Minor doc cleanups to remove doc build warnings (#7048).

Maintenance#

  * fix: Explicitly check for None/False in edge_attr during import from np (#
    6825).

  * Add favicon (#7043).

  * Remove unused code resistance_distance (#7053).

  * Fix names of small graphs (#7055).

  * Improve error messages for misconfigured backend treatment (#7062).

Other#

  * Update convert_matrix.py (#7018).

3.2:

Release date: 18 October 2023

Supports Python 3.9, 3.10, 3.11, and 3.12.

NetworkX is a Python package for the creation, manipulation, and study of the
structure, dynamics, and functions of complex networks.

For more information, please visit our website and our gallery of examples.
Please send comments and questions to the networkx-discuss mailing list.

Highlights#

  * Add @nx._dispatch decorator to most algorithms (#6688).

API Changes#

  * Remove topo_order kwarg from is_semiconnected without deprecation (#6651).

  * deprecate Edmonds class (#6785).

  * Make weight part of the API for functions which had default assumptions (#
    6814).

  * ENH: let users set a default value in get_attr methods (#6887).

  * Rename function join as join_trees (#6908).

  * API: Add a decorator to deprecate positional args (#6905).

  * Expire deprecation for attrs kwarg in node_link module (#6939).

  * Minor touchup to the sort_neighbors deprecation (#6942).

  * Rm deprecated create_using kwarg from scale_free_graph (#6940).

  * Make position part of the API for geometric_edges (#6816).

  * Undeprecate literal_(de)stringizer (#6943).

  * Make new dtype param for incidence_matrix kwarg-only (#6954).

  * Make weight and seed for fast_label_propagation_communities kwarg only (#
    6955).

  * API: Rm default value from time_delta for cd_index (#6953).

  * Deprecate strongly_connected_components_recursive (#6957).

  * Rm deprecated clique helper functions (#6941).

Enhancements#

  * Update calculation of triangles (#6258).

  * Add single_source_all_shortest_paths and all_pairs_all_shortest_paths (#
    5959).

  * Add @nx._dispatch decorator to most algorithms (#6688).

  * Move benchmarks inside main repo (#6835).

  * ENH ?? Replaced for-loops in :function:rescale_layout with numpy vectorized
    methods (#6879).

  * Fast label propagation algorithm for community detection (#6843).

  * Add time series Visibility Graph generator (#6880).

  * Random trees & forests (#6758).

  * Add support for tuple-nodes to default gml parser (#6950).

  * Add Kemeny??s constant (#6929).

  * Speedup resistance_distance (#6925).

  * Allow graph generators and conversion functions to be dispatched (#6876).

  * adding extendability problem (2nd try) (#4890).

Bug Fixes#

  * Fixing DOT format for to_agraph() (#6474).

  * Remove topo_order kwarg from is_semiconnected without deprecation (#6651).

  * Stabilize test of approximation.connected_components (#6715).

  * Fix minimum_cycle_basis and change to return cycle instead of set (#6788).

  * Refix minimum_cycle_basis and scipy.sparse conversions and add tests (#6789
    ).

  * number_of_walks might use a weighted edge attribute (#6815).

  * GML: added support for reading multi-line values (#6837).

  * Avoid directed_laplacian_matrix causing nans in some cases (#6866).

  * Add test about zero weight cycles and fix goldberg-radzik (#6892).

  * Modify s_metric normalized default so function doesn??t raise (#6841).

  * Error handling for invalid prufer sequence from_prufer_sequence: issue #
    6420 (#6457).

  * FIX: Better default behaviour for percolation centrality with no node attrs
    (#6894).

  * FIX: MultiDiGraphs keys got lost in weighted shortest paths (#6963).

  * Handle edge cases in Laplacian centrality (#6938).

  * adding a formula that ignores self-loops at the each level of directed
    louvain algorithm (#6630).

  * Fix ````is_k_edge_connected```` for case of k=2 (#7024).

Documentation#

  * Fix links in laplacian_centrality and laplacian_matrix (#6623).

  * Add Greedy Coloring Example to Gallery (#6647).

  * Add linting to contributor guide (#6692).

  * Minor fixups to equitable_coloring docstring (#6673).

  * Remove survey banner (#6818).

  * fix: make messages readable (#6860).

  * add docs for source input of dfs_predecessor and dfs_successor (#6867).

  * Clarify that basis generates simple cycles only (#6882).

  * Revert ??Clarify that basis generates simple cycles only?? (#6885).

  * updating TSP example docs (#6794).

  * MAINT: Point the PR template to pre-commit (#6902).

  * fix doc build errors/warnings (#6907).

  * DOC: stray backtick and double instead of simple backtick (#6917).

  * DOC: Add example for self loop multidigraph in contraction (#6901).

  * Fix sphinx docs rendering of dispatched functions (#6895).

  * added more examples on graphical degree sequence (#5634).

  * Minor touchup to the sort_neighbors deprecation (#6942).

  * Warning comment for float weights in betweenness.py (#5171).

  * DOC: Misc typos (#6959).

  * Fixing typo in effective_size documentation (#6967).

  * fix examples in tournament.py (#6964).

  * Fix a reference (#6977).

  * Add missing parameter to snap_aggregation docstring (#6978).

  * Update developer deprecation todo list (#6985).

  * Add ??networkx.plugin_info?? entry point and update docstring (#6911).

  * document graph type; add links; rm unused import (#6992).

  * Add GraphBLAS backend to online docs (#6998).

  * Add 3.2rc0 release notes (#6997).

  * Update release process for changelist (#7005).

  * Update contributing guide for changelist workflow (#7004).

  * Fix definition of \(m\) parameter in docstring of modularity function (#
    6990).

  * updated docs of SA_tsp and TA_tsp (#7013).

  * Update katz_centrality missing default alpha value (#7015).

Maintenance#

  * Replacing codecov Python CLI with gh action (#6635).

  * Bump pyupgrade minimum Python version to 3.9 (#6634).

  * MAINT: minor coverage cleanup (#6674).

  * Rm unreachable code for validating input (#6675).

  * Pin sphinx<7 as temporary fix for doc CI failures (#6680).

  * Example of improving test granularity related to #5092 (#5094).

  * MAINT: Bump scipy version and take advantage of lazy loading (#6704).

  * Drop support for Python 3.8 per SPEC0 (#6733).

  * Update pygraphviz (#6724).

  * Update core dependencies per SPEC0 (#6734).

  * Test on Python 3.12-beta2 (#6737).

  * update the OSMnx example (#6775).

  * Minor fixups to clear up numpy deprecation warnings (#6776).

  * Add label-check workflow (#6797).

  * Use dependabot (#6799).

  * Bump webfactory/ssh-agent from 0.7.0 to 0.8.0 (#6800).

  * Attach milestone to merged PRs (#6802).

  * Add preserve_all_attrs to convert_from_nx to make it concise (#6812).

  * Bump scientific-python/attach-next-milestone-action from
    f94a5235518d4d34911c41e19d780b8e79d42238 to
    bc07be829f693829263e57d5e8489f4e57d3d420 (#6830).

  * Relax threshold in test of betweenness_centrality (#6827).

  * Add @nx._dispatch to {single_source,all_pairs}_all_shortest_paths, cd_index
    (#6832).

  * ci: Add distribution verification checks to nightly wheel upload (#6831).

  * MAINT: fix link to nightly releases wheels (#6845).

  * Don??t test numpy2 nightlies (#6852).

  * MAINT: replace numpy aliases in scipy namespace (#6857).

  * Unpin scipy upperbound for tests (#6727).

  * Temporary work-around for NEP 51 numpy scalar reprs + NX doctests (#6856).

  * Unpin numpy nightly wheels (#6854).

  * fix: make messages readable (#6860).

  * Revert ??Pin sphinx<7 as temporary fix for doc CI failures (#6680)?? (#6859
    ).

  * Change _dispatch to a class instead of a closure (#6840).

  * Move random_state decorators before @nx._dispatch (#6878).

  * MAINT: Make GEXF and graphml writer work with numpy 2.0 (#6900).

  * Rename function join as join_trees (#6908).

  * add missing join deprecation stuff to release_dev and conftest (#6933).

  * MAINT: move dispatch test workflow as an independent CI job (#6934).

  * MAINT: Use importlib.resources instead of file dunder to access files (#
    6936).

  * DOC, MAINT: Deduplicate docs instructions (#6937).

  * MAINT: Raise clean error with random_triad for graph with <3 nodes (#6962).

  * Update numpydoc (#6773).

  * MAINT: update pre-commit tools deps (#6965).

  * MAINT: Clean up commented out code in triads (#6961).

  * MAINT: Scipy nightly failing with np alias (#6969).

  * Bump actions/checkout from 3 to 4 (#6970).

  * Add for testing new pydata-sphinx-theme PR (#6982).

  * MAINT: Disable building delaunay geospatial example temporarily (#6981).

  * Revert ??MAINT: Disable building delaunay geospatial example temporarily??
    (#6984).

  * Enhancements change default join trees 6947 (#6948).

  * Update sphinx theme (#6930).

  * Generate requirements files from pyproject.toml (#6987).

  * Use trusted publisher (#6988).

  * Prefer ??backend?? instead of ??plugin?? (#6989).

  * CI: Pin scientific-python/upload-nightly-action to 0.2.0 (#6993).

  * Support Python 3.12 (#7009).

  * pip install nx-cugraph from git, not nightly wheels, for docs (#7011).

  * Fix typos (#7012).

Other#

  * Update release process (#6622).

  * Add Lowest Common Ancestor example to Gallery (#6542).

  * Add examples to bipartite centrality.py (#6613).

  * Remove Python 3.8 from CI (#6636).

  * Fix links in eigenvector.py and katz_centrality.py (#6640).

  * Use the correct namespace for girvan_newman examples (#6643).

  * Preserve node order in bipartite_layout (#6644).

  * Make cycle_basis() deterministic (#6654).

  * Added docstrings examples for clique.py (#6576).

  * Fix output of is_chordal for empty graphs (#6563).

  * Allow multiple graphs for @nx._dispatch (#6628).

  * Adding GitHub Links next to Dheeraj??s name in the contributors list (#6670
    ).

  * Adding is_tounament to main namespace (#6498).

  * Use unpacking operator on dicts to prevent constructing intermediate
    objects (#6040).

  * Added tests to test_correlation.py (#6590).

  * Improve test coverage for neighbor_degree.py (#6589).

  * Added docstring examples for nx_pylab.py (#6616).

  * Improve Test Coverage for current_flow_closeness.py (#6677).

  * try adding circleci artifact secret (#6679).

  * Improve test coverage for reaching.py (#6678).

  * added tests to euler.py (#6608).

  * codespell: pre-commit, config, typos fixed (#6662).

  * Improve test coverage for mst.py (#6540).

  * Handle weights as distance= in testing dispatch (#6671).

  * remove survey banner (#6687).

  * CircleCI: add token for image redirector (#6695).

  * MAINT: Add subgraph_view and reverse_view to nx namespace directly through
    graphviews (#6689).

  * Added docstring example for dense.py (#6669).

  * MAINT: Add a github action cron job to upload nightly wheels (#6701).

  * MAINT: fix file path in nightly build workflow (#6702).

  * Add example script for shortest path (#6534).

  * Added doctrings for generic_graph_view (#6697).

  * Doc: wrong underline length (#6708).

  * MAINT: cron job to test against nightly deps every week (#6705).

  * simplify stack in dfs (#6366).

  * optimize generic_bfs_edges function (#6359).

  * Optimize _plain_bfs functions (#6340).

  * Added girth computation function (#6633).

  * MAINT: Stop CI from uploading nightly on forks (#6717).

  * Performance improvement for astar_path (#6723).

  * Skip scipy-1.11.0rc1 due to known issue (#6726).

  * Add an optional argument to the incidence_matrix function to provide ?? (#
    6725).

  * Graph walks implementation by jfinkels & dtekinoglu (#5908).

  * DOCS: Add walks to algorithms.index (#6736).

  * Add note about using latex formatting in docstring in the contributor guide
    (#6535).

  * Fix intersection_all method (#6744).

  * Fix Johnson method for unweighted graphs (#6760).

  * MAINT: Ignore SciPy v1.11 in requirements (#6769).

  * Replace deprecated numpy.alltrue method (#6768).

  * keep out scipy 1.11.1 (#6772).

  * Document additional imports required for building the documentation (#6766
    ).

  * modified max_weight_matching to be non-recursive (#6684).

  * Rewrite NXEP 3 (#6648).

  * Refactor edmonds algorithm (#6743).

  * Docstring improvement for nx_pylab.py (#6602).

  * Use pyproject.toml (#6774).

  * Include missing package_data (#6780).

  * [BUG] Patch doc and functionality for is_minimal_d_separator (#6427).

  * Update to the documentation of eigenvector centrality (#6009).

  * Fix typo in contributing page (#6784).

  * Fix empty graph zero division error for louvain (#6791).

  * Vertical chains for network text (#6759).

  * Time dependent module (#6682).

  * Allow user to opt out of edge attributes in from_numpy_array (#6259).

  * modifies ````bfs_edges```` and adds warning to ````generic_bfs_edges```` (#
    5925).

  * Spelling (#6752).

  * Added test cases for join operation and fixed join operation to handle
    label_attributes (#6503).

  * Remove serialisation artifacts on adjacency_graph (#6041).

  * Patch view signature (#6267).

  * Doc add nongraphical examples 6944 (#6946).

  * feat: docstring examples for algorithms/operators/all.py (#6974).

Log message:
*: remove more references to Python 3.7

Log message:
py-networkx: updated to 3.1

NetworkX 3.1

- Minor bug-fixes and speed-ups
- Improvements to plugin based backend infrastructure
- Minor documentation improvements
- Improved test coverage
- Last release supporting Python 3.8
- Stopped building PDF version of docs
- Use Ruff for linting

NetworkX 3.0

- Better syncing between G._succ and G._adj for directed G.
  And slightly better speed from all the core adjacency data structures.
  G.adj is now a cached_property while still having the cache reset when
  G._adj is set to a new dict (which doesn't happen very often).
  Note: We have always assumed that G._succ and G._adj point to the same
  object. But we did not enforce it well. If you have somehow worked
  around our attempts and are relying on these private attributes being
  allowed to be different from each other due to loopholes in our previous
  code, you will have to look for other loopholes in our new code
  (or subclass DiGraph to explicitly allow this).
- If your code sets G._succ or G._adj to new dictionary-like objects, you no longer
  have to set them both. Setting either will ensure the other is set as well.
  And the cached_properties G.adj and G.succ will be rest accordingly too.
- If you use the presence of the attribute `_adj` as a criteria for the object
  being a Graph instance, that code may need updating. The graph classes
  themselves now have an attribute `_adj`. So, it is possible that whatever you
  are checking might be a class rather than an instance. We suggest you check
  for attribute `_adj` to verify it is like a NetworkX graph object or type and
  then `type(obj) is type` to check if it is a class.
- We have added an `experimental plugin feature \ 
<https://github.com/networkx/networkx/pull/6000>`_,
  which let users choose alternate backends like GraphBLAS, CuGraph for \ 
computation. This is an
  opt-in feature and may change in future releases.
- Improved integration with the general `Scientific Python ecosystem \ 
<https://networkx.org/documentation/latest/release/migration_guide_from_2.x_to_3.0.html#improved-integration-with-scientific-python>`_.
- New drawing feature (module and tests) from NetworkX graphs to the TikZ \ 
library of TeX/LaTeX.
  The basic interface is ``nx.to_latex(G, pos, **options)`` to construct a \ 
string of latex code or
  ``nx.write_latex(G, filename, as_document=True, **options)`` to write the \ 
string to a file.
- Added an improved subgraph isomorphism algorithm called VF2++.

Log message:
*: bump PKGREVISION for egg.mk users

They now have a tool dependency on py-setuptools instead of a DEPENDS

Log message:
math: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

Log message:
math: Remove SHA1 hashes for distfiles

Log message:
py-networkx: updated to 2.5.1

2.5.1:
Bug fixes

Log message:
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

Log message:
math/py-networkx: Fix running tests.