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* Designate 2.8.6 releasenetworkx-2.8.6Jarrod Millman2022-08-222-3/+1
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* Update release notesJarrod Millman2022-08-222-5/+42
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* See matplotlb 3.6rc1 failure (#5937)Jarrod Millman2022-08-222-4/+4
| | | | | | | | | | | * See matplotlb 3.6rc1 failure * replace use of private class method to allow mpl v3.6 to work. * ensure ax exists before calling colorbar * Undo matplotlib pin Co-authored-by: Dan Schult <dschult@colgate.edu>
* docstring update to lexicographical_topological_sort issue 5681 (#5930)Kevin Brown2022-08-211-9/+52
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * docstring update to lex-topo-sort - explain effect and purpose for lexi sort - add hints for fixing non-sortable nodes - add hint to exception msg - Add examples * Shorten the first line of the doc_string Co-authored-by: Dan Schult <dschult@colgate.edu> * Generalize the description of sort failures Co-authored-by: Dan Schult <dschult@colgate.edu> * more succinct description of key function Co-authored-by: Dan Schult <dschult@colgate.edu> * improve description of key function Co-authored-by: Dan Schult <dschult@colgate.edu> * Black'd it. Co-authored-by: Dan Schult <dschult@colgate.edu>
* Update release notesJarrod Millman2022-08-211-0/+38
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* Replace LCA with naive implementations (#5883)Ross Barnowski2022-08-213-409/+50
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Improve LCA input validation (#5877)Ross Barnowski2022-08-211-8/+2
| | | | | | | * Remove explicit checks for None nodes. The graph objects already do not allow None nodes. * Change elif to if for raising branches.
* update all_pairs_lca docstrings (#5876)Tanmay Aeron2022-08-211-12/+50
| | | | | | | | | | | * update all_pairs_lca docstrings * typo * changed docstring acc to numpydoc format * Minor fixups. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Minor doc fixups (#5868)Ross Barnowski2022-08-214-8/+12
| | | | | | | | | * Fix examples section formatting in condensed docstr. * Rm stray reference to ordered grpahs. * Add naive LCA algs to reference guide. * Fix heading names in LCA docstrings.
* Add examples for the condensation function (#5452)kpetridis2022-08-211-0/+20
| | | | | * Add examples for the condensation function * Added comments and removed unnecessary operation
* Naive lowest common ancestor implementation (#5736)Dilara Tekinoglu2022-08-212-3/+227
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add naive lca methods * Naive algorithm implementation for LCA * Modify naive lca functions * Correct parameters of nx.ancestors * Update lowest_common_ancestors.py * Parametrize tests * Apply suggestions from code review Co-authored-by: Dan Schult <dschult@colgate.edu> * Yield instead of append * Tests for naive lca * Correct test cases for naive lca algorithms * Apply suggestions from code review Co-authored-by: Mridul Seth <mail@mriduls.com> * Fix function name -when calling * Make requested changes * Inlining _get_a_lowest_common_ancestor Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu> Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Mridul Seth <mail@mriduls.com>
* Add examples to lowest common ancestors algorithms (#5531)Dilara Tekinoglu2022-08-211-0/+41
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add examples to lowest common ancestors documentation * Fix output style of examples * Fix output style of example * Update pre-commit * Update networkx/algorithms/lowest_common_ancestors.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update networkx/algorithms/lowest_common_ancestors.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Indentation fix & pprint dictionary * Update networkx/algorithms/lowest_common_ancestors.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update networkx/algorithms/lowest_common_ancestors.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update networkx/algorithms/lowest_common_ancestors.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Move "import pprint" to the example Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Bump nodelink args deprecation expiration to v3.2 (#5933)Ross Barnowski2022-08-213-11/+10
| | | | | | * Bump deprecation expiration for nodelink params to v3.2. * Fixup warnings filter.
* Propose to make new node_link arguments keyword only. (#5928)Ross Barnowski2022-08-211-1/+9
| | | Propose to make new node_link args kwarg only.
* Add function bfs_layers to docs (#5932)Dan Schult2022-08-213-3/+4
| | | Add function bfs_layers to docs. fix two doc formatting typos
* Adds ```nx.bfs_layers``` method (#5879)Dhaval Kumar2022-08-212-17/+92
| | | | | | | | | | | | | * reformatted the files * reformatted the files * added final changes * changed descendants_at_distance * fixed comment in bfs_layers * fixed comment in bfs_layers
* Fix Louvain_partitions by yielding a copy of the sets in the partition ↵Dan Schult2022-08-212-2/+16
| | | | | gh-5901 (#5902) Fix gh-5901 by yielding a copy of the sets in the partition
* Allow unsortable nodes in approximation.treewidth functions (#5921)Dan Schult2022-08-212-12/+18
| | | | | | | | | * Allow unsortable nodes in approximate treewidth functions * Apply suggestions from code review Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* signature change for `node_link` functions: for issue #5787 (#5899)Kevin Brown2022-08-214-44/+242
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * added tests for new signature - kept all the original tests. Tagged the tests to remove after signature change is complete. - leveraged a test from test_cyctoscape.py, checks for warnings. - made new versions of tests that use attrs in the signature. * Verified that the new tests fail. Good. * update signatures with keywords * added warning message * adapted code to use keywords * move test with recwarn fixture outside of class when recwarn was used in a method, got an error. work fine in a function. * add warning to node_link_graph() * update node_link_graph() to use keywords * use recwarn in test to dectect warnings * added deprecation notices to doc strings. Needs version number for when deprecation will happen * added example code from doc string to tests * gave default values to elements of attrs the example code passes a dict with only some of the keywords defined. So the defaults needed to be provided * fixed name conflict * brace in docstring * drop braces in doc string example * Changed namespace to nx in doc string examples * update the examples - show the results of the examples - add more examples of serialization with json * Update doc desc and notes - Add reference to Serialization in the method description. - add a note that the keywords chose for the attributes names must match if the two functions are to be used together * clean up wording * document the version numbers for deprecating deprecate the change in 2.8.6 remove the change in 3.1 * Add note, on using old and new keywords together * Add Deprecation Warning to conftest.py * Add a reminder to remove code & docs in 3.1
* Remove old Appveyor cruft (#5924)Jarrod Millman2022-08-213-8/+4
| | | | | * Remove old Appveyor cruft * Fix Windows issue
* Update precommit hooks (#5923)Jarrod Millman2022-08-2115-245/+263
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* Add to about_us.rst (#5919)Dan Schult2022-08-211-10/+11
| | | Update about_us.rst
* Update lattice.py (#5914)Tigran Khachatryan2022-08-211-1/+1
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* Allow classes to relabel nodes -- casting (#5903)Dan Schult2022-08-212-2/+12
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* Add cache reset for when G._node is changed (#5894)Dan Schult2022-08-212-0/+28
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* Update docs to include description of the `return_seen` kwarg (#5891)Sultan Orazbayev2022-08-211-2/+15
| | | | | | | | | * Update docs to include description of the `return_seen` kwarg Update docs to include description of the `return_seen` kwarg (previously not documented) * Run black on the file * Update unweighted.py
* Add warning to nx_agraph about layout nondeterminism. (#5832)Ross Barnowski2022-08-201-1/+15
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* DOC: Switch to enumerated list in quotient_graph docstring (#5837)Matthias Bussonnier2022-08-201-6/+5
| | | | | Just came across a weird thing when trying to render with papyri, and it looks like what was attempted here was a list enumeration, so converting to a enumerated list instead of a code/verbatim block
* Add random_spanning_tree to documentation (#5810)Matt Schwennesen2022-08-201-0/+1
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* Bump release versionJarrod Millman2022-07-182-1/+7
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* Designate 2.8.5 releasenetworkx-2.8.5Jarrod Millman2022-07-182-7/+1
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* Add 2.8.5 release notesJarrod Millman2022-07-182-0/+59
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* Deploy docs on v2.8 branchJarrod Millman2022-07-181-3/+3
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* CI: add explicit path while installing pygraphviz wheels on macOS in GHA (#5805)Mridul Seth2022-07-181-3/+11
| | | Fixes installation of pygraphviz on macOS-latest in github actions
* Run CI against v2.8 branchJarrod Millman2022-07-184-5/+17
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* make lazy_import private and remove its internal use (#5878)Dan Schult2022-07-184-12/+40
| | | | | * make lazy_import private and remove its internal use * add back the non-lazy imports of numpy to utils.misc
* Gallery example: Morse code alphabet as a prefix tree (#5867)Ross Barnowski2022-07-181-0/+96
| | | | | * Add Morse trie encoding example to gallery. * Clarify explanation.
* Point to the latest URL for the description. (#5852)Tomoya Nishide2022-07-181-1/+1
| | | | | | | | | | | | | | * Point to Python 3.x doc for the description. This is a nit patch though, use 3.x document url as Python 2.x has been deprecated a long time ago. * Update doc/reference/glossary.rst Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * period. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Move factory attributes to the class instead of instance. (#5850)Dan Schult2022-07-184-16/+0
| | | Move factory attributes to the class instead of instance. ?speedup?
* Update tests in base class and simple rename in convert.py (#5848)Dan Schult2022-07-183-14/+56
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* Attempt to reverse slowdown from hasattr needed for cached_property (#5836)Dan Schult2022-07-1811-37/+145
| | | | | | | | | | | | | | | | | * 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
* Fix #5817 (#5822)Matt Schwennesen2022-07-181-10/+4
| | | | | * Potential fix? * removed unneeded line
* Update distance parameter description. (#5819)Ross Barnowski2022-07-181-1/+3
| | | | | | | | | | | | | | | | | | * Update distance parameter description. Update the description of the parameter in the closeness_centrality function to note that by default, the edge distances (weights) are assumed to be 1, and that no input validation is performed. * Fix styling. * Update networkx/algorithms/centrality/closeness.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Make black happy. Co-authored-by: Dan Schult <dschult@colgate.edu>
* Temporary fix for failing tests w/ scipy1.9. (#5816)Ross Barnowski2022-07-181-1/+3
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* Fix pydot colon check node-to-str conversion (#5809)Shaked Brody2022-07-182-3/+16
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* Fix typo in bipartite closeness_centrality and thought-o in tests (#5800)Dan Schult2022-07-182-4/+4
| | | Fix #5620 with typo in bipartite closeness_centrality and thought-o in tests
* Updated astar docstring (#5797)Lior2022-07-181-0/+12
| | | The docstring now reflects on heuristic admissibility and heuristic value caching
* Compute `is_weakly_connected` lazily (#5795)Matus Valo2022-07-181-1/+1
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* Compute `is_strongly_connected` lazily (#5793)Matus Valo2022-07-181-1/+1
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* Add more comprehensive tests for pydot (#5792)Mridul Seth2022-07-182-5/+29
| | | | | | | * Add more comprehensive tests for pydot * remove the second element from frozenset for cleaner tests Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
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