Update dependency networkx to v3.3

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
networkx	==3.2.1 -> ==3.3

---

Release Notes

networkx/networkx (networkx)

v3.3: NetworkX 3.3

Compare Source

networkx 3.3

We're happy to announce the release of networkx 3.3!

API Changes

• Disallow negative number of nodes in complete_multipartite_graph (#​7057).
• DEP: Deprecate the all_triplets one-liner (#​7060).
• [A-star] Added expansion pruning via cutoff if cutoff is provided (#​7073).
• Make HITS raise exceptions consistent with power iterations (#​7084).
• DEP: Deprecate random_triad (#​7061).
• Added feature modular graph product (#​7227).
• ENH: Speed up common/non_neighbors by using _adj dict operations (#​7244).
• Deprecate the create argument of nonisomorphic_trees (#​7316).
• Improve total_spanning_tree_weight (#​7100).
• Update init.py (#​7320).
• add **kwargs to traveling_salesman_problem (#​7371).

Enhancements

• Add Tadpole graph (#​6999).
• [A-star] Added expansion pruning via cutoff if cutoff is provided (#​7073).
• Implementation of $S^1$ model (#​6858).
• [Feat] Random expanders utilities (#​6761).
• Compare graphs for generator functions when running tests with backend (#​7066).
• Add Kirchhoff index / Effective graph resistance (#​6926).
• Changed return types of shortest path methods to improve consistency (#​6584).
• New PR for Fixes minimal d-separator function failing to handle cases where no d-separators exist (#​7019).
• ENH : Provide non-normalized and normalized directed laplacian matrix calculation (#​7199).
• feat: drop the use of node attribute "first_nbr" in PlanarEmbedding (#​7202).
• Add functions to compute Schultz and Gutman Index (#​3709).
• Divisive community algorithms (#​5830).
• Added feature modular graph product (#​7227).
• ENH : added sort_neighbors to all functions in depth_first_search.py (#​7196).
• New graph generator for the Kneser graph (#​7146).
• Draw MultiDiGraph edges and labels qa7008 (#​7010).
• Use github actions to run a comparison benchmark (#​7268).
• BFS layout implementation (#​5179).
• Add max_level= argument to louvain_communities to limit macro-iterations (#​6909).
• Review and update @nx._dispatchable usage since 3.2.1 (#​7302).
• Transmogrify _dispatchable objects into functions (#​7298).
• fix: make PlanarEmbedding.copy() use add_edges_from() from parent (closes #​7223) (#​7224).
• Allow seed of np.random instance to exactly produce arbitrarily large integers (#​6869).
• Improve total_spanning_tree_weight (#​7100).
• add seed to nx.generate_random_paths (#​7332).
• Allow backends to implement should_run (#​7257).
• Adding tree broadcasting algorithm in a new module (#​6928).
• Option to include initial labels in weisfeiler_lehman_subgraph_hashes (#​6601).
• Add better error message when trying to get edge that is not present (#​7245).
• Make is_negatively_weighted dispatchable (#​7352).
• Add option to hide or show tick labels (#​6018).
• ENH: Cache graphs objects when converting to a backend (#​7345).

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).
• Handle edge cases for greedy_modularity_communities (#​6973).
• FIX: Match the doc description while copying over data (#​7092).
• fix: Include singleton/trivial paths in all_simple_paths & other functions (#​6694).
• Dinitz correction (#​6968).
• Modify GML test to fix invalid octal character warning (#​7159).
• Fix random_spanning_tree() for single node and empty graphs (#​7211).
• PlanarEmbedding.remove_edge() now updates removed edge's neighbors (#​6798).
• add seed to graph creation (#​7241).
• add seed to tests of fast_label_propatation_communities (#​7242).
• Fix rich_club_coefficient() for single node and empty graphs (#​7212).
• Fix minimum_spanning_arborescence regression (#​7280).
• Move arrowstyle input munging after intput validation (#​7293).
• Fix empty GraphML attribute is not parsed (#​7319).
• Add new test result to test_asadpour_tsp and change linprog method (#​7335).
• Fix custom weight attribute for Mehlhorn (#​6681).

Documentation

• Update release process (#​7029).
• Update convert_matrix.py (#​7018).
• fix extendability function name in bipartite.rst (#​7042).
• Minor doc cleanups to remove doc build warnings (#​7048).
• DOC: Add example to generic_bfs_edges to demonstrate the neighbors param (#​7072).
• Hierarchical clustering layout gallery example (#​7058).
• Fixed an error in the documentation of the katz centrality (#​6294).
• Create 3d_rotation_anime.py (#​7025).
• DOC: Add docstrings to filter view functions (#​7086).
• DOC: Add docstrings to Filter mapping views (#​7075).
• DOCS: Fix internal links to other functions in isomorphvf2 (#​6706).
• added note for the triangle inequality case in TSP (#​6995).
• Add note about importance of testing to contributor guide (#​7103).
• Proposal to add centrality overview to mentored projects (#​7104).
• Improve documentation of Component Algorithms (#​5473).
• Add dot io to readwrite (#​5061).
• Add Python versions to release notes (#​7113).
• DOC: Turn on inline plots in graph generators docstrings (#​6401).
• Fix duplicate numbering in contributor guide (#​7116).
• DOC: remove unnecessary 'or' in planted_partition_graph (#​7115).
• DOC: Link methods in functions to base Graph methods/properties (#​7125).
• Connect docs to doc_string for total_spanning_tree_weight (#​7098).
• Image (3D RGB data) segmentation by spectral clustering with 3D illustrations (#​7040).
• update triadic_census documentation for undirected graphs - issue 4386 (#​7141).
• added 3d and animation to plot_greedy_coloring.py (#​7090).
• DOC: fix URL econded links and doc references (#​7152).
• DOC: add reference to fast_label_propagation_communities (#​7167).
• updated See also sec of argmap class (#​7163).
• DOC : updated examples in mincost.py (#​7169).
• Document the walk_type argument default in directed_laplacian and similar functions (#​7171).
• DOC: Add plots to classic graph generators docs (#​7114).
• Fix a tiny typo in structuralholes.py::local_constraint docstring (#​7198).
• Added subgraph_is_monomorphic and subgraph_monomorphisms_iter in docs (#​7197).
• Fix online docs for _dispatch (#​7194).
• DOC : Updated docs for panther_similarity (#​7175).
• Fix warnings when building docs (#​7195).
• Improve docs for optimal_edit_paths (#​7130).
• DOC: build with nx-parallel extra documentation information (#​7220).
• Fixed typo in tensor product documentation (Fixes #​7228) (#​7229).
• Add example for cycle detection (#​6560).
• Update general_k_edge_subgraphs docstring (#​7254).
• Update docstring of nonisomorphic_trees (#​7255).
• adding self loops related docs and tests for functions in cluster.py (#​7261).
• Add minimum_cycle_basis to cycle_basis See Also (#​7274).
• Update CONTRIBUTING.rst (#​7270).
• Fix all sphinx warnings during doc build (#​7289).
• Doc infrastructure: replace nb2plot with myst-nb (#​7237).
• Add explicit targets of missing modules for intersphinx (#​7313).
• DOC: add doc suggestions for arbitrarily large random integers tools (#​7322).
• Try/except intermittently failing basemaps in geospatial examples (#​7324).
• Update docstring example with future-proof pandas assignment (#​7323).
• Remove animation from spectral clustering example to improve performance (#​7328).
• Doc Improvements for Approximations Files (#​7338).
• Update LCF_graph docstring (#​7262).
• Option to include initial labels in weisfeiler_lehman_subgraph_hashes (#​6601).
• Add eriknw as contributor (#​7343).
• [DOC, DISPATCH] : updated and added backend.py's docs (#​7305).
• add **kwargs to traveling_salesman_problem (#​7371).
• Move the backend docs and connect the config docs. Both in a single sidebar entry (#​7389).

Maintenance

• Drop Python 3.9 support (#​7028).
• 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).
• MAINT: Fixup union exception message (#​7071).
• MAINT: Minor touchups to tadpole and lollipop graph (#​7049).
• Add @not_implemented_for("directed") to number_connected_components (#​7074).
• remove unused code (#​7076).
• Minor touchups to the beamsearch module (#​7059).
• Fix annoying split strings on same line (#​7079).
• Update dispatch decorator for hits to use "weight" edge weight (#​7081).
• Remove nbconvert upper pin (revert #​6984) (#​7083).
• Add a step to CI to check for warnings at import time (#​7077).
• Added few tests for /generators/duplication.py and /generators/geomet… (#​6976).
• Test on Python 3.13-dev (#​7096).
• Changed arguments list of GraphMLWriterLxml.dump() (#​6261).
• write_graphml: Small fix for object type description on TypeError exception (#​7109).
• updated functions in core.py (#​7027).
• label check on push and change check name (#​7111).
• DEP : adding not_implemented_for("multigraph”) to k_core, k_shell, k_crust and k_corona (#​7121).
• Add label check when pull request is edited instead of push (#​7134).
• Add label workflow pull_request type synchronize and echo message (#​7135).
• adding test coverage for isomorphism when using digraphs (#​6417).
• Remove usage of __networkx_plugin__ (use __networkx_backend__ instead) (#​7157).
• DOC: consistent spelling of neighbor and rename vars (#​7162).
• MAINT: use ruff format instead of black (#​7160).
• Ensure warnings related to changes in shortest_path returns are visible to users (#​7161).
• Sync up behavior of is_{type} for empty graphs (#​5849).
• Added NodeNotFound exceptions to _apply_prediction and simrank, and ignored isolated nodes in panther_similarity (#​7110).
• Fix not_implemented_for decorator for is_regular and related functions (#​7182).
• Fix all_node_cuts output for complete graphs (#​6558).
• Remove "networkx.plugins" and "networkx.plugin_info" entry-points (#​7192).
• Bump actions/setup-python from 4 to 5 (#​7201).
• Update test suite for Pytest v8 (#​7203).
• Undeprecate nx_pydot now that pydot is actively maintained again (#​7204).
• Future-proofing and improve tests (#​7209).
• Drop old dependencies per SPEC 0 (#​7217).
• Update pygraphviz (#​7216).
• Refactor geometric_soft_configuration_model tests for performance (#​7210).
• Rename _dispatch to _dispatchable (#​7193).
• Replace tempfile with tmp_path fixture in test suite (#​7221).
• updated test_directed_edge_swap #​5814 (#​6426).
• Bump copyright year for 2024 (#​7232).
• Improving test coverage for Small.py (#​7260).
• Test for symmetric edge flow betweenness partition (#​7251).
• MAINT : added seed to gnm_random_graph in community/tests/test_label_propagation.py (#​7264).
• Bump scientific-python/upload-nightly-action from 0.2.0 to 0.3.0 (#​7266).
• adding self loops related docs and tests for functions in cluster.py (#​7261).
• Improving test coverage for Mycielsky.py (#​7271).
• Use ruff's docstring formatting (#​7276).
• Add docstring formatting change to blame-ignore-revs (#​7281).
• Improve test coverage for random_clustered and update function names (#​7273).
• Doc infrastructure: replace nb2plot with myst-nb (#​7237).
• Temporarily rm geospatial examples to fix CI (#​7299).
• Improve test coverage for bipartite extendability (#​7306).
• CI: Update scientific-python/upload-nightly-action from 0.3.0 to 0.4.0 (#​7309).
• CI: Group dependabot updates (#​7308).
• CI: update upload-nightly-action to 0.5.0 (#​7311).
• renaming backend func_info dictionary's keys (#​7219).
• Add mutates_input= and returns_graph= to _dispatchable (#​7191).
• Avoid creating results with numpy scalars (re: NEP 51) (#​7282).
• Bump changelist from 0.4 to 0.5 (#​7325).
• Improve test coverage for bipartite matrix.py (#​7312).
• Un-dispatch coloring strategies (#​7329).
• Undo change in return type of single_target_shortest_path_length (#​7327).
• Remove animation from spectral clustering example to improve performance (#​7328).
• Expire steinertree mehlhorn futurewarning (#​7337).
• Update louvain test modularity comparison to leq (#​7336).
• Add aaronzo as contributor (#​7342).
• Fix #​7339. shortest_path inconsisitent with warning (#​7341).
• Add nx.config dict for configuring dispatching and backends (#​7225).
• Improve test coverage for Steiner Tree & Docs (#​7348).
• added seed to test_richclub_normalized (#​7355).
• Add tests to link_prediction.py (#​7357).
• Fix pydot tests when testing backends (#​7356).
• Future proof xml parsing in graphml (#​7360).
• make doc_string examples order-independent by removing np.set_printoptions (#​7361).
• Close figures on test cleanup (#​7373).
• More numpy scalars cleanup for numpy 2.0 (#​7374).
• Update numpydoc (#​7364).
• Fix pygraphviz tests causing segmentation faults in backend test (#​7380).
• Add dispatching to broadcasting.py (#​7386).
• Update test suite to handle when scipy is not installed (#​7388).
• Rm deprecated np.row_stack in favor of vstack (#​7390).
• Fix exception for del config[key] (#​7391).
• Bump the GH actions with 3 updates (#​7310).

Contributors

54 authors added to this release (alphabetically):

• @​BucketHeadP65
• @​dependabot[bot]
• @​nelsonaloysio
• @​YVWX
• Aaron Z. (@​aaronzo)
• Aditi Juneja (@​Schefflera-Arboricola)
• AKSHAYA MADHURI (@​akshayamadhuri)
• Alex Markham (@​Alex-Markham)
• Anders Rydbirk (@​anders-rydbirk)
• Andrew Knyazev (@​lobpcg)
• Ayooluwa (@​Ay-slim)
• Baldo (@​BrunoBaldissera)
• Benjamin Edwards (@​bjedwards)
• Chiranjeevi Karthik Kuruganti (@​karthikchiru12)
• Chris Pryer (@​cnpryer)
• d.grigonis (@​dgrigonis)
• Dan Schult (@​dschult)
• Daniel V. Egdal (@​DanielEgdal)
• Dilara Tekinoglu (@​dtekinoglu)
• Dishie Vinchhi (@​Dishie2498)
• Erik Welch (@​eriknw)
• Frédéric Crozatier (@​fcrozatier)
• Henrik Finsberg (@​finsberg)
• Jangwon Yie (@​jangwon-yie)
• Jaron Lee (@​jaron-lee)
• Jarrod Millman (@​jarrodmillman)
• Jon Crall (@​Erotemic)
• Jonas Otto (@​ottojo)
• Jordan Matelsky (@​j6k4m8)
• Koen van den Berk (@​kalkoen)
• Luigi Sciarretta (@​LuigiSciar)
• Luigi Sciarretta (@​LuigiSciarretta)
• Matt Schwennesen (@​mjschwenne)
• Matthew Feickert (@​matthewfeickert)
• Matthieu Gouel (@​matthieugouel)
• Mauricio Souza de Alencar (@​mdealencar)
• Maximilian Seeliger (@​max-seeli)
• Mridul Seth (@​MridulS)
• Navya Agarwal (@​navyagarwal)
• Neil Botelho (@​NeilBotelho)
• Nihal John George (@​nihalgeorge01)
• Paolo Lammens (@​plammens)
• Patrick Nicodemus (@​patrick-nicodemus)
• Paula Pérez Bianchi (@​paulitapb)
• Purvi Chaurasia (@​PurviChaurasia)
• Robert (@​ImHereForTheCookies)
• Robert Jankowski (@​robertjankowski)
• Ross Barnowski (@​rossbar)
• Sadra Barikbin (@​sadra-barikbin)
• Salim BELHADDAD (@​salym)
• Till Hoffmann (@​tillahoffmann)
• Vanshika Mishra (@​vanshika230)
• William Black (@​smokestacklightnin)
• William Zijie Zhang (@​Transurgeon)

29 reviewers added to this release (alphabetically):

• @​YVWX
• Aaron Z. (@​aaronzo)
• Aditi Juneja (@​Schefflera-Arboricola)
• AKSHAYA MADHURI (@​akshayamadhuri)
• Andrew Knyazev (@​lobpcg)
• Ayooluwa (@​Ay-slim)
• Chiranjeevi Karthik Kuruganti (@​karthikchiru12)
• Chris Pryer (@​cnpryer)
• d.grigonis (@​dgrigonis)
• Dan Schult (@​dschult)
• Erik Welch (@​eriknw)
• Frédéric Crozatier (@​fcrozatier)
• Henrik Finsberg (@​finsberg)
• Jarrod Millman (@​jarrodmillman)
• Kyle Sunden (@​ksunden)
• Matt Schwennesen (@​mjschwenne)
• Mauricio Souza de Alencar (@​mdealencar)
• Maximilian Seeliger (@​max-seeli)
• Mridul Seth (@​MridulS)
• Nihal John George (@​nihalgeorge01)
• Paolo Lammens (@​plammens)
• Paula Pérez Bianchi (@​paulitapb)
• Rick Ratzel (@​rlratzel)
• Robert Jankowski (@​robertjankowski)
• Ross Barnowski (@​rossbar)
• Stefan van der Walt (@​stefanv)
• Vanshika Mishra (@​vanshika230)
• William Black (@​smokestacklightnin)
• William Zijie Zhang (@​Transurgeon)

These lists are automatically generated, and may not be complete or may contain duplicates.

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this change requires to drop support for python 3.9

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