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* Designate 2.6.3 releasenetworkx-2.6.3v2.6Jarrod Millman2021-09-091-1/+1
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* Fix modularity functions (#5072)Jarrod Millman2021-09-097-274/+694
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * CI/MAINT: drop gdal tests (#5068) * Unpin gdal. * Try pinning to 3.3 * Pin setuptools instead. * remove gdal from workflows * modularity_max: provide labels to get_edge_data (#4965) * modularity_max: provide labels to get_edge_data * test greedy mod communities relabeled separately * Minor style changes + add note to test. Co-authored-by: Mathilde Leval <mleval@csod.com> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Improvements to greedy_modularity_community (#4996) * fix docstring importation at naive_greedy_modularity_communities * add resolution at docstring parameters at modularity_max.py * use weight arg instead of 'weight' key at greedy_modularity_communities() * separate test for non contiguous integers as node-labels * modularity_max: breaking the loop when given community size is reached (#4950) * modularity_max: allow input of desired number of communities * import warnings * format * format * improvements according to discussion * try to manually merge main + resolve conflicts * add test for n_communities parameter using circular ladder graph * style of test * greedy_modularity_communities with digraphs and multi(di)graphs (#5007) (#5007) * refactor N & m calculation @ greedy_modularity_communities() * add Newman 'Analysis of weighted networks' @ References * extend greedy_modularity_communities to DiGraph's * separate data structures init to a new function * remove unused 'merges' list * add @not_implemented_for('directed', 'multigraph') above naive_greedy_modularity_communities() * add tests for greed_modularity_communities() with directed & directed+weighted * use nx.all_neighbors() to access successors as well as predecessors at DiGraph's * extend greedy_modularity_communities() to MultiGraph's * extend greedy_modularity_communities() to MultiDiGraph's * refactor: remove encoder/decoder dicts (node-labels are already hashable) * b pulls data from in_degree isntead of out_degree * match the sequence of the return values with the docstring reference * test: modify existing Graphs instead of creating new ones * dq correction for multi-edges explanation & other minor edits * CNM -> Clauset-Newman-Moore & isinstance(G, (nx.MultiGraph, nx.MultiDiGraph)) -> G.is_MultiGraph() * amend @not_implemented_for decorator @ naive_greedy_modularity_communities() * Allow greedy_modularity_communities to use floating point weights or resolution (#5065) * revise mapped_queue to separate priority from element * update max_modularity to use new mapped_queue * change attribute names h, d to heap, position in MappedQueue * clean up initialization of data structures and handling of q0 * change i,j,k notation to u,v,w (no indexes since gh-5007) * Update networkx/utils/mapped_queue.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Mathilde Léval <9384853+mathilde-leval@users.noreply.github.com> Co-authored-by: Mathilde Leval <mleval@csod.com> Co-authored-by: Thanasis Mattas <thanasismatt@gmail.com> Co-authored-by: Martha Frysztacki <martha.frysztacki@kit.edu> Co-authored-by: Thanasis Mattas <atmattas@physics.auth.gr> Co-authored-by: Dan Schult <dschult@colgate.edu>
* Bump release versionJarrod Millman2021-09-081-1/+1
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* Designate 2.6.2 releasenetworkx-2.6.2Jarrod Millman2021-07-262-7/+1
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* Update release processJarrod Millman2021-07-261-6/+5
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* Remove default dependencies (#4967)Jarrod Millman2021-07-2310-38/+23
| | | | | * Remove default dependencies * Update release notes
* Bump release versionJarrod Millman2021-07-091-1/+1
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* Bump release versionJarrod Millman2021-07-082-1/+7
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* Designate 2.6.1 releasenetworkx-2.6.1Jarrod Millman2021-07-084-9/+2
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* Bump release versionJarrod Millman2021-07-082-1/+7
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* Update release processJarrod Millman2021-07-082-2/+4
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* Designate 2.6 releasenetworkx-2.6Jarrod Millman2021-07-081-1/+1
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* Finalize 2.6 release notes (#4958)Jarrod Millman2021-07-084-247/+736
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* Fix version pull down (#4954)Jarrod Millman2021-07-071-2/+1
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* Changes to rst files to make doctests pass (#4947)Dan Schult2021-07-0710-44/+35
| | | | | | | | | | | | | | | | | | | * rst double colons for example code * add nx. prefix to doctest function calls * Remove one line from 1->2 migration rst file the line shows code that works for 1.x *and* 2.x. But it no longer works for all v2.x code. Readers should just use the next line of code, so no reason to keep this in the file. * capture output from subplot and rename DiGraph as DG in introduction.rst * skip running the entire test suite as an example in old_release_log.rst * doctest of examples * remove changes to nexp files
* `descendants_at_distance` also for non-DiGraphs (#4952)Michael Dorner2021-07-071-2/+2
| | | | | | | | | | | * updated documentation on `descendants_at_distance` updated documentation only * Update networkx/algorithms/traversal/breadth_first_search.py Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Dan Schult <dschult@colgate.edu>
* Fix neighbor degree for directed graphs (#4948)Dan Schult2021-07-072-44/+57
| | | | | | | | | * Deprecate k_nearest_neighbors and fix parts of neighbor degree functions * Add tests for directed graphs fix errors in "degree" * tweak text and names * Remove comment lines of "obsolete code" at bottom of module
* fix typo for PR number of deprecation (#4949)Dan Schult2021-07-061-1/+1
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* Add matrix market to readwrite reference (#4934)Ross Barnowski2021-07-032-0/+101
| | | | | | | | | | | * Add matrix_market reference stub. * Add R/W examples to matrix_market stub. * Add matrix market to toctree. * Remove irrelevant factoid. * Re-name according to review suggestion.
* split out deprecation. remove all changes to neighbor_degree (#4937)Dan Schult2021-07-014-15/+25
| | | fix k_nearest_neighbors defaults signature in deprecation
* fix trouble with init_cycle argument to two TSP functions (#4938)Dan Schult2021-06-302-10/+17
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* fix spelling in docstring of conftest.py (#4945)Dan Schult2021-06-301-1/+1
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* Fix numeric and degree assortativity coefficient calculation (#4928)Vitaliy Pozdnyakov2021-06-303-10/+38
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* Minor Improvements on Networkx/algorithms/community/quality.py (#4939)Dimitrios Papageorgiou2021-06-301-9/+11
| | | | | | | * Remove unused imports and fix minor docstring issues * inter_community parameter explanation * fix minor word nit
* Fixes #4275 - Add comment to parallel betweenness example (#4926)Alex Korbonits2021-06-281-1/+5
| | | | | | | * Add comment about single core CI/CD showing slower parallel output in example script. * less specific estimate of speedup Co-authored-by: Dan Schult <dschult@colgate.edu>
* move partition checking outside private _quotient_graph function (#4931)Dan Schult2021-06-281-3/+14
| | | | | * move partition checking outside private _quotient_graph function * fix typo
* Expand destringizer example in read_gml docstring (#4925)Randy2021-06-281-1/+13
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* Page number for Katz centrality reference (#4932)Chris McBride2021-06-261-1/+1
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* quotient_graph doc fix (#4930)Anthony Wilder Wohns2021-06-261-4/+3
| | | Remove reference to nonexistant `node_relation` parameter
* Add 3.0 migration guide (#4927)Jarrod Millman2021-06-252-0/+48
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* Bump release versionJarrod Millman2021-06-223-14/+8
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* Designate 2.6rc2 releasenetworkx-2.6rc2Jarrod Millman2021-06-223-9/+11
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* Update release process (#4866)Jarrod Millman2021-06-221-2/+2
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* Update read_gml docstring with destringizer ex (#4916)Randy2021-06-221-15/+16
| | | | | | | | | | | | | | | | | * Update read_gml docstring with destringizer ex Responding to issue 4877 by adding a simple destringizer example to the read_gml docstring. * Update doc strings The documentation stated that the code can read data types other than str without specifying a destringizer. While the code can write several other data types, a destringizer is required for any type other than str. The documentation is repeated in the file and was updated in all 5 places: the gml.py module docstring, as well as the read_gml, parse_gml, generate_gml, and write_gml docstrings. Co-authored-by: Randy Weaver <randyweaver@randys-mbp.attlocal.net>
* Deprecate numeric_mixing_matrix. (#4923)Ross Barnowski2021-06-224-0/+18
| | | | | * Deprecate numeric_mixing_matrix. * Add deprecation to release notes.
* Fix assortativity coefficent calculation (#4851)Vitaliy Pozdnyakov2021-06-226-40/+173
| | | | | | | | Update calculation of assortativity coefficients and update tests to reflect new behavior. Introduces mapping kwarg to degree_mixing_matrix and remove 0-padded rows/cols from degree_mixing_matrix. Co-authored-by: Dan Schult <dschult@colgate.edu>
* Fix graph_class usage in to_undirected method (#4912)Tomohiro Endo2021-06-222-2/+49
| | | | | * fix error in the tests... now original code fails test Co-authored-by: Dan Schult <dschult@colgate.edu>
* Update docstrings for dfs and bfs edges and fix cross links (#4900)Ross Barnowski2021-06-213-34/+40
| | | | | | | | | | | * Fix edge_dfs link in dfs_edges docstring description. * Returns -> Yields in dfs_edges docstring. * Fix see also links and add References-style links. * Update links to dfs_edges f/ edge_dfs docstring. * Update bfs_edges docstring a la dfs_edges.
* Remove decorator dependency (#4739)Kelly Boothby2021-06-2119-282/+1258
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * added argmap decorator * removed most dependency on decorator * removed last reference to decorator? * Made the compilation of argmap-decorated functions lazy to reduce import time. * black * reworked try_finally to make cleanup cleaner * first pass at documentation; general cleanup * incorporated dschult's comments * rest formatted docstrings * added unit tests and fixed a few bugs that cropped up * Apply suggestions from code review Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Dan Schult <dschult@colgate.edu> * Exapnd docstrings for decorators.py * * refactored try_finally into a keyword-only argument * more tweaks to documentation re: @stefanv's comments * additional unit test for signature-clobbering decorators * spellcheck my txt and expand new test to help me grok it * rehash docstrings for sphinx * rewrite docs to provide some examples where argmap used without @argmap * doc tweak * last touches * documentation clarifications * run black * doc review * remove decorator module from github workflows and INSTALL.rst * add text to release_dev to describe highlights and improvements here Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Dan Schult <dschult@colgate.edu>
* Doc/fix 403 error drawing custom icons (#4906)Ross Barnowski2021-06-164-12/+23
| | | | | | | | | | | | * Add local copies of custom node icon pngs. * Update example to use local images. * Force FancyArrowPatch to respect tgt distances. min/max_target_distance kwargs are only supported by FancyArrowPatch. Force drawing with FAPs and add comment explaining how/why. * Add seed to layout for reproducibility.
* Update arrows default value in draw_networkx. (#4883)Ross Barnowski2021-06-162-2/+33
| | | | | | | * Update arrows default value in draw_networkx. * Add regression test for draw_networkx. * Parametrize regression tests to include nx.draw.
* Raise ValueError if None is added as a node. (#4892)Dan Schult2021-06-158-22/+55
| | | | | | | * Raise ValueError if None is added as a node. Removed some tests that checked that errors raised when None was a node. * update tutorial to make a stronger statement about None
* bugfix-for-issue-4353: modify default edge_id format (#4842)Berlin Cho2021-06-142-5/+158
| | | | Allow selection of an edge attribute to be the edge id when writing GraphML. Adds edge_id_from_attribute kwarg.
* Decode GraphML/yEd shape type (#4694)Attila Nagy2021-06-142-3/+45
| | | | Decode and preserve GraphML/yEd shape type and add tests for description and yworks GenericNode
* Fix conda instructions (#4884)Jarrod Millman2021-06-095-10/+19
| | | | | | | | | | | | | | | * Fix conda instructions * New idea * fix to have conda avoid -r in requirements.txt and avoid ~=2.12 which is pip specific * Hopefully fix macos pypy loading * try again without wheel? * Avoid dependencies on PyPy Co-authored-by: Dan Schult <dschult@colgate.edu>
* DOC: Fix links, use DOI links, wayback machine where required (#4868)Mridul Seth2021-06-0835-51/+50
| | | | | | | | | | | * Fix links, use DOI links, wayback machine where required * Add nx-guides to intersphinx mapping. * Replace external mpl link w/ intersphinx. * Update mpl intersphinx mapping. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Deserializing custom default properties graph ml (#4872)Jeroen Bergmans2021-06-072-2/+48
| | | | * Add test case for handling default node attributes from graphML * Add decode conversion to key defaults analogous to decode_data_elements
* spring_layout: ignore 'fixed' nodes not in the graph nodes (#4867)Danylo Ulianych2021-06-062-1/+4
| | | | | | | * spring_layout: ignore 'fixed' nodes not in the graph nodes * add api change to release notes Co-authored-by: Dan Schult <dschult@colgate.edu>
* Reformatted table to address issue #4852 (#4875)Salim BELHADDAD2021-06-061-11/+13
| | | The grid table was not properly formatted using reStructuredText Markup which is required by Sphinx.
* Fix docstring typo (#4871)Jarrod Millman2021-06-041-2/+2
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