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* codespell: pre-commit, config, typos fixed (#6662)Yaroslav Halchenko2023-05-0311-26/+26
| | | | | | | | | | | | | | | | | | | | | | | | * One ambigous typo * one more ambigous typo * [DATALAD RUNCMD] run codespell throughout === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ For this to work -- it would require configuration files which were abandoned. See https://github.com/networkx/networkx/pull/6662 for more discussion etc. * Manual reversion of perform... "fix"
* Remove `topo_order` kwarg from `is_semiconnected` without deprecation. (#6651)Ross Barnowski2023-05-031-0/+4
| | | | | | | | | | | * Remove topo_order kwarg without deprecation. * Add release note about semiconnected removing the topo_order kwarg. * Add to doc_string the method used to find semiconnected --------- Co-authored-by: Dan Schult <dschult@colgate.edu>
* Make cycle_basis() deterministic (#6654)Efrem Braun2023-04-211-0/+3
| | | | | | Replace sets with dict keys to make cycle_basis deterministic with respect to node ordering. Co-authored-by: Dan Schult <dschult@colgate.edu>
* Designate 3.1 releasenetworkx-3.1Jarrod Millman2023-04-042-8/+130
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* Prep 3.1 releaseJarrod Millman2023-04-042-22/+66
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* Draft release notes (#6621)Jarrod Millman2023-04-041-8/+21
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* Deprecate shortest_path functions to have consistent return values in v3.3 ↵Dan Schult2023-03-281-0/+3
| | | | | | | (#6567) * Deprecate single_target..._length to channge to return a dict in v3.3 * deprecate shortest_path in case of all_pairs
* Lint using Ruff (#6371)danieleades2023-02-191-1/+1
| | | | | | | | | | | | | | | * lint and fix using ruff * add flake8-pie lints * remove useless import alias * bump version * bump deps --------- Co-authored-by: daniel.eades <daniel.eades@hotmail.com>
* Update developer requirements (#6429)Jarrod Millman2023-02-141-1/+1
| | | | | * Update developer requirements * Run linter
* Update release_3.0 authors (add Jim and Erik) (#6356)Erik Welch2023-01-111-0/+2
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* add OrderedGraph removal as an API change in release_3.0.rst (#6354)Dan Schult2023-01-101-0/+3
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* Add dev release notes templateJarrod Millman2023-01-071-0/+44
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* Designate 3.0 releasenetworkx-3.0Jarrod Millman2023-01-072-5/+6
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* Update release notes (#6341)Jarrod Millman2023-01-071-88/+152
| | | | | | | | | | | | | | | * Update release notes * Update doc/release/release_dev.rst Co-authored-by: Dan Schult <dschult@colgate.edu> * Update doc/release/release_dev.rst Co-authored-by: Dan Schult <dschult@colgate.edu> * Update highlights Co-authored-by: Dan Schult <dschult@colgate.edu>
* Fix links to migration guide (#6331)Jarrod Millman2023-01-041-2/+2
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* Correctly point towards 2.8.8 in release notes (#6298)Mridul Seth2022-12-251-1/+1
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* Fix links in release notes (#6281)Jarrod Millman2022-12-152-22/+10
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* Add 2.8.x release notes (#6255)Jarrod Millman2022-12-054-0/+199
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* Draft 3.0 release notes (#6232)Mridul Seth2022-12-012-11/+220
| | | | | | | | | | | | | | | | | | | | | | | | | * First go through release notes for 3.0 * Add release notes for 2.8.6, 2.8.7 and 2.8.8 * Update doc/release/release_3.0.rst Co-authored-by: Dan Schult <dschult@colgate.edu> * Apply suggestions from code review Co-authored-by: Dan Schult <dschult@colgate.edu> * use contribs.py to find commits b/w any 2 release tags * Update release notes * Remove 2.8.6 through 2.8.8 release notes They were inconsistent with existing release notes, which I will grab from the old releases. Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com>
* Designate 3.0rc1 releasenetworkx-3.0rc1Jarrod Millman2022-11-111-1/+1
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* Remove deprecated `find_cores` (#6139)Ross Barnowski2022-10-311-1/+0
| | | Remove deprecated find_cores.
* Fixed test for average shortest path in the case of directed graphs (#6003)Sebastiano Vigna2022-10-091-0/+4
| | | | | | | | | | | | | | | | | | | * Fixed test for average shortest path in the case of directed graphs * Fixed order * Update networkx/algorithms/shortest_paths/tests/test_generic.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Release bullet; added versionchanged * Add brief description to versionchanged directive. * Fixed definition * Using \substack Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Minor docstring touchups and test refactor for `is_path` (#5967)Ross Barnowski2022-09-081-0/+4
| | | | | | | | | | | | | | | * Touch up docstring. * Condense conditional. * Minor refactor of ispath test - parametrize and rm redundant. * Add release note. * Update networkx/classes/function.py Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Dan Schult <dschult@colgate.edu>
* [ENH] Find and verify a minimal D-separating set in DAG (#5898)Adam Li2022-08-231-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Ran black * Add unit tests * Rename and fix citation * Black * Fix unite tests * Isort * Add algo description * Update networkx/algorithms/tests/test_d_separation.py * Update networkx/algorithms/traversal/breadth_first_search.py * Address dans comments * Fix unit tests * Update networkx/algorithms/tests/test_d_separation.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Apply suggestions from code review Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/dag.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/dag.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Fix comments * Clean up the docs a bit more * Merge Co-authored-by: Dan Schult <dschult@colgate.edu>
* Update mapping logic in `relabel_nodes` (#5912)Ross Barnowski2022-08-171-1/+8
| | | | | | | | | | | | | | | | | * Use mapping ABC instead of hasattr introspection. * Test exception for non-mapping non-callables. * Switch logic to check for callable instead of not mapping. * Apply comment from code review. * Use built-in callable instead of abc. Co-authored-by: Dan Schult <dschult@colgate.edu> * Add release note. Co-authored-by: Dan Schult <dschult@colgate.edu>
* Replace LCA with naive implementations (#5883)Ross Barnowski2022-08-131-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | * WIP: Replace functions to evaluate tests. * Raise prompt exceptions by wrapping generator. * Fix erroneous ground-truth self-ancestor in tests. * Move pair creation outside of generator and validate. * Convert input with fromkeys to preserve order and rm duplicates. * Replace LCA implementations & update tests. * Test cleanup: move new tests into old class. Allows us to get rid of duplication/another test setup. * Rm naive fns from refguide. * Add release note. * Remove unused imports. * Remove missed duplicate function (bad rebase). Co-authored-by: Dilara Tekinoglu <dilaranurtuncturk@gmail.com>
* Add 2.8.5 release notesJarrod Millman2022-07-182-0/+59
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* Attempt to reverse slowdown from hasattr needed for cached_property (#5836)Dan Schult2022-07-161-0/+19
| | | | | | | | | | | | | | | | | * Automate reset of cache for _adj,_pred,_succ * Make G._adj a data descriptor that resets G.adj when needed. * update places in the code where both G._succ and G._adj are changed This is no longer needed since G._succ and G._adj are synced during __set__ * testing hasattr(G, `_adj`) no longer ensures an instance. * Make mypy happy * Switch to hardcode attribute names in the data descriptors * Improve doc_strings for the data descriptors
* Implement directed edge swap (#5663)Ben Heil2022-06-241-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add tests for directed edge swap * Add directed edge swap algorithm * Allow more swaps in directed tests * Fix errors in swap.py to meet test criteria * Remove TODOs * Update documentation for directed_edge_swap and run black * Fix incosistent spacing * Add references * Added PR to release docs * Fix reference formatting * Improve documentation * An -> A * Update networkx/algorithms/swap.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Add 'Raises' section to documentation * Update tests to use keyword arguments for directed_edge_swap * Fix references to 'triple-edge' swap * Use not_implemented_for decorator for directed_edge_swap * Rename n to tries and remove unnecessary updates * Rename e to msg * Use 'succ' instead of 'out_edges' for getting successors * Update networkx/algorithms/swap.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/tests/test_swap.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/tests/test_swap.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/tests/test_swap.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/swap.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Convert gnp graphs to path graphs for clarity * Use seed when testing directed edge swap * Check node equality sooner * Add directed_edge_swap to documentation Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Dan Schult <dschult@colgate.edu>
* Remove deprecated function edge_betweeness (#5765)Juanita Gomez2022-06-211-1/+0
| | | | | | | | * Remove deprecated function edge_betweeness * [ci skip] remove from release doc validation script. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
* Remove betweenness_centrality_source (#5786)Dilara Tekinoglu2022-06-161-1/+0
| | | | | | | Remove betweenness_centrality_source in favor of preferred name, betweenness_centrality_subset. Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* remove `adj_matrix` from `linalg/graphmatrix.py` (#5753)Dimitrios Papageorgiou2022-06-151-1/+0
| | | | | | | * remove adj_matrix from graphmatrix.py * [skip ci] Rm function from doc inspection list for release. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Bump release versionJarrod Millman2022-06-131-2/+2
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* Add 2.8.4 release notesJarrod Millman2022-06-132-0/+58
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* Fix link to 2.8.3 notesJarrod Millman2022-06-041-0/+1
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* Add 2.8.3 release notesJarrod Millman2022-06-041-0/+56
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* Fix old release notesJarrod Millman2022-06-042-4/+4
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* Update developer requirements (#5689)Jarrod Millman2022-06-021-1/+1
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* Designate 2.8.2 releasenetworkx-2.8.2Jarrod Millman2022-05-212-0/+37
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* Designate 2.8.1 releasenetworkx-2.8.1Jarrod Millman2022-05-183-96/+141
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* Update release notesJarrod Millman2022-05-181-14/+78
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* Disallow isolated nodes for Eulerian Path (#5616)Dilara Tekinoglu2022-05-121-0/+17
| | | | | | | | | | | | | | | | | | | | | | | * Disallow isolated nodes for Eulerian path & make related doc_string change * Remove test for directed graphs with isolated nodes * Fix syntax error in examples * Restore deleted tests for euler path * Fix assertion error * Fix typo * Update networkx/algorithms/euler.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update release_dev.rst Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu> Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Fixes #5403: Errors on non-distinct bipartite node sets (#5442)Aaron Z2022-05-081-0/+5
| | | | | | | | | | | * is_bipartite_node_set errors if nodes not distinct * weighted_projected_graph errors if nodeset too big * update release_dev.rst * Use sets instead of lists for collecting flowfuncs in tests. (#5589) Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* MAINT: Fix sphinx build errors and warnings (#5571)Mridul Seth2022-04-252-3/+4
| | | | | * Add polynomials to the algorithms toctree * fix indents for sphinx
* Fix release notesJarrod Millman2022-04-091-1/+1
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* Finalize release notesJarrod Millman2022-04-093-36/+147
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* Add notes about NumPy/SciPy integration to NX 2->3 migration guide (#5505)Ross Barnowski2022-04-091-4/+158
| | | | | | | | | | | | | | | | | | | | | * Add skeleton about numpy/scipy to migration guide. * Update release timeline. * Comment out todo and touchup text on random. * Finish recarray/structured dtypes section. * Add blurb about pagerank. * Add section about matrix->array. * Reorganize and link. * Fix rst. * Fix formatting Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com>
* Update release notesJarrod Millman2022-04-041-2/+2
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* Fix min_weight_matching to convert edge weights without reciprocal (#5394)Dan Schult2022-04-011-0/+4
| | | | | | | * Add test and then fix code and docs * Correct and improve docs. Change 1e-6 to 1 to maintain integers. Include argument in docstring for why adding the 1 doesn't impact the min
* Fix average_neighbor_degree calculations for directed graph (#5404)yusuf-csdev2022-03-271-0/+19
| | | | | | | | | | | | | | | | | Fixes #5383 * bugfix-for-issue-5383 * bugfix-for-issue-5383 * modify neighbor finding logic * recommit * Add release notes for new average_neoghbors_degree * shrink docs and comments. minor code order changes. Co-authored-by: Dan Schult <dschult@colgate.edu>
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