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* codespell: pre-commit, config, typos fixed (#6662)Yaroslav Halchenko2023-05-0312-27/+27
| | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Adding GitHub Links next to Dheeraj's name in the contributors list (#6670)Dheeraj Ravindranath2023-04-281-1/+1
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* 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>
* Update release process (#6622)Jarrod Millman2023-04-051-7/+4
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* Bump release versionJarrod Millman2023-04-041-0/+2
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* Designate 3.1 releasenetworkx-3.1Jarrod Millman2023-04-043-16/+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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* Fix typos (#6620)Harri Nieminen2023-04-043-8/+8
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* Resolve NXEP4 with justification for not implementing it. (#6617)Ross Barnowski2023-04-041-7/+26
| | | | | | | | | | | | | | | | * Resolve NXEP4 with justification for not implementing it. * Update doc/developer/nxeps/nxep-0004.rst Co-authored-by: Dan Schult <dschult@colgate.edu> * Update nxep-0004.rst The title is long and makes the table of contents look sloppy. I think the shorter name is clear and given the text it shouldn't cause confusion. @rossbar Feel free to remove this commit, if you prefer. --------- Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com> Co-authored-by: Dan Schult <dschult@colgate.edu>
* Fix module docstring format for ismags reference article. (#6611)Ross Barnowski2023-04-031-4/+0
| | | | | | | Improperly formatted Notes/References sections was causing a sphinx parsing error which led to a very poorly formatted html page. Fixing the numpydoc formatting for the module docstring + minor munging of the heading levels was sufficient to fix this.
* Minor docs/test maintenance (#6614)Ross Barnowski2023-04-032-1/+1
| | | | | | | * doc: fix docstring heading, eliminate sphinx error. * doc: change extension of included file to prevent duplicate labels. * tst: add warnings filter for deprecated forest_str.
* Update team galleries (#6569)Jarrod Millman2023-03-292-73/+201
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* add simple cycle enumerator for undirected class (#6461)Kelly Boothby2023-03-291-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * add simple cycle enumerator for undirected class * Implemented Gupta & Suzumura and refactored Johnson in a common form and unified their call-site. Now, users can enumerate simple cycles of directed or undireced graphs, with bounded or unbounded length, all from the same `simple_cycles` function. I abandoned the stretch goal of enumerating chordless cycles, as they are not gracefully handled by the algorithms of Johnson nor Gupta & Suzumura. * updated tests for simple_cycles to include undirected graphs * * fixed documentation issues, elaborated on algorithm details * restricted to nontrivial components * removed specialized DFS to pick edges from undirected components lemma: if G is a biconnected graph with at least 3 nodes and e is an edge in G, then e belongs to a cycle * added tests for undirected and bounded cases for simple_cycles * added handling for digons in multigraphs * * Improved support for multigraphs * Split chordless_cycles out from simple_cycles because the case analysis got so tricky * Added enhanced cycle-testing framework to tests for simple_cycles * Added tests for multigraphs * Needs more documentation * * Documented simple_cycles * Caught incorrectly-handled case of parallel self-loops * removed chordless option from simple_cycles * typos/raises/leftovers in docs and error/corner tests * add a quick example to chordless_cycles * Add chordless_cycles to docs --------- Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Mridul Seth <git@mriduls.com>
* Deprecate shortest_path functions to have consistent return values in v3.3 ↵Dan Schult2023-03-282-0/+7
| | | | | | | (#6567) * Deprecate single_target..._length to channge to return a dict in v3.3 * deprecate shortest_path in case of all_pairs
* Add examples clarifying ambiguity of nbunch (#6513)Navya Agarwal2023-03-171-2/+34
| | | | | | * Add example clarifying nbunch to the glossary entry Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Add documentation building to contributor guide (#6437)Ross Barnowski2023-02-272-11/+18
| | | | | | | | | | | * Add documentation blding to contrib guide. * Move adding-examples section back under docs. * Add html-noplot option to build docs w/out gallery. * Add note about building docs without gallery. * Add blurbs about doc & gallery dependencies.
* NXEP 0 and NXEP 1 - change status to Accepted (#5343)Mridul Seth2023-02-222-2/+2
| | | | | * NXEP 1 - change status to Accepted * Move NXEP 0 to Accepted from Draft
* 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>
* Add project desc for visualization and ISMAGs (#6432)Dan Schult2023-02-181-2/+41
| | | | | * Add project desc for visualization and ISMAGs * Add section for expected time for each project
* Update developer requirements (#6429)Jarrod Millman2023-02-141-1/+1
| | | | | * Update developer requirements * Run linter
* Add Plausible Analytics to our docs (#6413)Mridul Seth2023-02-101-1/+7
| | | | | * Add Plausible Analytics to our docs * make prettier happy
* DOC: list pred method for MultiDiGraphs (#6409)Mridul Seth2023-02-031-1/+1
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* Add generate / write "network text" (formerly graph_str) (#5602)Jon Crall2023-01-303-0/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add graph_str Formatted Fix bug in choosing the source Fix test * Fixed issue in choosing source verticies for directed graphs * reasonable working state * Fixed logic issues Fix test, cleanup, formatting more tests, better comments, fix parent labels fix pypy issue Fix format * Fixes based on review * Cleaned up test names * Use open_file decor and remove graph_str * Remove useage of forest_str from doctest * Fix style * style * Update networkx/readwrite/text.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Fixed half sentense * Add max_depth * moved comment position * Describe max depth in algo description * Allow with_labels to be specified as a str * Update networkx/readwrite/text.py Co-authored-by: Mridul Seth <mail@mriduls.com> * Add network text autodoc stub * Add removal note for forest_str --------- Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Mridul Seth <mail@mriduls.com>
* DOC: Add banner for user survey annoucement (#6375)Mridul Seth2023-01-281-0/+1
| | | | | | | | | * DOC: Add banner for user survey annoucement * Add survey link in readme * update survey text * update wording on website
* DOC: Minor formatting fixups to get rid of doc build warnings. (#6363)Ross Barnowski2023-01-135-8/+8
| | | Minor formatting fixups to get rid of doc build warnings.
* Add nx-guide link in the tutorial (#6353)Paula Pérez Bianchi2023-01-121-0/+7
| | | | | | | | | | | | | * Add warning in community doc * fix unwanted change * Add nx-guides link in tutorial * Add Nx-guide reference in the tutorial * Capitalize X in section title. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Fix broken link nx guide (#6361)Paula Pérez Bianchi2023-01-121-1/+1
| | | | | | | | | * Add warning in community doc * fix unwanted change * fix broken link * change title to match notebook title
* 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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* Laplace centrality for issue 4973 (#5399)Gabor Berei2023-01-091-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * first commit, start testing * rename * formatting with black * formating example based on testing failure * deleting example from docstring * rewriting example based on eigenvector.py * rewrite docstring for other supplementary functions * formating with black * deleting custom scipy function * rewriting matrix manipulation * rewriting nbunch iteration based on review * rewriting dictionary update * update directed_laplacian_matrix_args params * rewriting docstring based on comments * update docstring * update docstring with Laplacian energy def * update docstring * bringing package imports into the function * adding laplacian.py to needs_numpy and needs_scipy tests * addig Laplacian centrality to centrality.rst * formatting with black * dictionary update fix * beatify docstring Co-authored-by: Dan Schult <dschult@colgate.edu> * beatify docstring Co-authored-by: Dan Schult <dschult@colgate.edu> * beatify docstring Co-authored-by: Dan Schult <dschult@colgate.edu> * beatify docstring Co-authored-by: Dan Schult <dschult@colgate.edu> * beautify with black * add ** to kwargs in function * add test file for local testing * black test file * black * replace nx.laplacian to direct import * adding pytest importskip and formating with black * adding laplacian centrality to the init file * changing import from direct to nx.laplacian * rewriting output for non-normalized option * rewriting tests using functions instead of class structure * mod with black * formating * formating * directed and undirected laplace and eigen values correction * black formating * adding asfptype for sparse eig solver and format with black * change from sparse solver to dense solver * change back A_2 eigval solver * format with black * black * change back to previous state * change back to previous state * new eigh func * fix eighvals func * adding laplacian matrix parameters * change alpha to None * change back alpha to 0.95 * adding nodeset and ful nodelist objects * adding nodeset and relevant error message * solving directed-undirected issue converting everything to sparse matrix * change line ending * untrack env files * isort test file * adding nodelist and noteset * black * change centrality calculation to nodeset instead of full nodelist * added comment * eigh_f func to one-liner * move eigh value calculation outside if condition * simplify row/column by advanced indexing * simplify row/column by advanced indexing for set diag * format with black * wrap doc_string to 88 chars and reword optional keywords. * handle nodelist and nodeset * remove casting as a csr_matrix * covert to dense since we have to for computing the spectrum anyway. * minor: ease readability * fix normalization * add tests for normalized and weight kwargs * fix black Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Gabor Berei <bereig@starschema.net>
* Add dev release notes templateJarrod Millman2023-01-071-0/+44
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* Bump release versionJarrod Millman2023-01-071-0/+2
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* Fix docsJarrod Millman2023-01-071-2/+0
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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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* Create a Tikz latex drawing feature for networkx (#6238)Dan Schult2023-01-042-1/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Implemented conversion from networkx graph to latex graph. * Removed latex cache files uploaded by error. * Resolved placeholders file import issue. * Removed dependency to numpy * Updated test * Wrapped test for numpy dependency * Updated test name * format changes to nx_latex.py and friends. vertex -> node, vertices -> nodes PEP8 spacing and tabs pytest function instead of class (class not needed here -- no imports) Moved author info to CONTRIBUTORS.rst as our new standard converted list comprehension done for side-effects to for-loop. switch to f-strings from string-format calls update setup.py to remove conflicts * Remove numpy requirement for testing latex Also pep8 formatting * reorder imports in __init__ * Attempt to debug windows/appveyor adigraph error * try again * Remove types, run pre-commit * blackify * pyupgradify * inline latex placeholders and expected_tex. Check not multigraph. Add example Change variable name `file` to `latex_code` inline if/else for __init__ setup * Change tabs to spaces * pull apart Adigraph to simplify interface * remove class Adigraph completely in favor of functions * replace default layout to be circular. (matches adigraph and avoids using random seeds in tests * fix old version of isort result * update documentation and include with rst file. Update some tests * make docs more complete, checked and add tests * Cleanup extra file changes that aren't needed * Add TikZ version of to_latex as default * improve docs * Make the networkx latex interface via TikZ and not adigraph * fix rebase * Apply suggestions from code review Co-authored-by: Mridul Seth <mail@mriduls.com> * comment out print statements in tests * Turn off multigraph for latex * Remove tests of `line width` and edge label placement * add back line width style, fix placement of style on edges. * Set default layout to have radius 10 Co-authored-by: Mridul Seth <mail@mriduls.com> * fix docstring test * Minor docstring formatting nits. Co-authored-by: Luca Cappelletti <cappelletti.luca94@gmail.com> Co-authored-by: Mridul Seth <seth.mridul@gmail.com> Co-authored-by: Mridul Seth <git@mriduls.com> Co-authored-by: Mridul Seth <mail@mriduls.com> Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* fix warnings for make doctest (#6323)Dan Schult2023-01-041-1/+1
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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 Millman2022-12-153-27/+15
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* Add a contributor (#6256)Sultan Orazbayev2022-12-101-0/+1
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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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* plugin based backend infrastructure to use multiple computation backends (#6000)Mridul Seth2022-11-081-0/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Wrappers classes to dispatch to a backend * Rework the backend dispatching - Use __networkx_plugin__=name to find graph-like objects instead of subclassing - Add PluginInfo to smooth over differences in importlib.metadata across python versions - Add dispatch behavior override via environment variable to aid in testing plugins * Dispatch more algorithms and improve auto-test capabilities * Allow dispatcher decorator without a name - Name is taken from the decorated function - Raise error if backend doesn't implement a decorated function which is called - Check for duplicate names for dispatching algorithms * Make sphinx pick up backend docs * make black happy * Rename decorator to _dispatch as it's experimental * A few more dispatched functions * Make convert to and from methods for auto-testing - Rename `convert` to `convert_from_nx` - Add `convert_to_nx` function These will allow backends to return native objects when dispatching, but provide a mechanism to convert the result to the type expected by NetworkX tests for the auto-test plugin mechanism. * More dispatching * Include name with `convert_**_nx` methods * Remove known plugin names This check is not needed, as any plugin can register itself in the entry points section. The dispatching and auto-testing explicitly specify the plugin to use, so there is no need to hardcode the options. These were originally included for security, but any malicious actor would simply use one of the valid names, so having a hardcoded list does not actually provide any meaningful security. * Add `dispatchname` to dispatchable functions Co-authored-by: Jim Kitchen <jim22k@gmail.com> Co-authored-by: Erik Welch <erik.n.welch@gmail.com>
* Remove deprecated `find_cores` (#6139)Ross Barnowski2022-10-311-1/+0
| | | Remove deprecated find_cores.
* Update deprecations after 3.0 dep sprint (#6031)Jarrod Millman2022-10-111-28/+0
| | | | | * Update deprecation todo list * Remove silenced warnings
* 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>
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