Update dependency networkx to v3.3
This MR contains the following updates:
Package | Update | Change |
---|---|---|
networkx | minor |
==3.2.1 -> ==3.3
|
Release Notes
networkx/networkx (networkx)
v3.3
: NetworkX 3.3
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 ofnonisomorphic_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 MR 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 indepth_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 tolouvain_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()
useadd_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 changelinprog
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
andsubgraph_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
withmyst-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")
tonumber_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 onTypeError
exception (#7109). - updated functions in
core.py
(#7027). - label check on push and change check name (#7111).
- DEP : adding
not_implemented_for("multigraph”)
tok_core
,k_shell
,k_crust
andk_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
andsimrank
, and ignored isolated nodes inpanther_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
tognm_random_graph
incommunity/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
withmyst-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=
andreturns_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
totest_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.
Configuration
-
If you want to rebase/retry this MR, check this box
This MR has been generated by Renovate Bot.