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* codespell: pre-commit, config, typos fixed (#6662)Yaroslav Halchenko2023-05-031-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | * 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"
* Adding GitHub Links next to Dheeraj's name in the contributors list (#6670)Dheeraj Ravindranath2023-04-281-1/+1
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* Update release process (#6622)Jarrod Millman2023-04-051-7/+4
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* Fix typos (#6620)Harri Nieminen2023-04-042-7/+7
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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>
* 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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* Deprecate shortest_path functions to have consistent return values in v3.3 ↵Dan Schult2023-03-281-0/+4
| | | | | | | (#6567) * Deprecate single_target..._length to channge to return a dict in v3.3 * deprecate shortest_path in case of all_pairs
* 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
* 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
* Add generate / write "network text" (formerly graph_str) (#5602)Jon Crall2023-01-301-0/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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: Minor formatting fixups to get rid of doc build warnings. (#6363)Ross Barnowski2023-01-133-5/+5
| | | Minor formatting fixups to get rid of doc build warnings.
* 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
* Create a Tikz latex drawing feature for networkx (#6238)Dan Schult2023-01-041-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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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* Add a contributor (#6256)Sultan Orazbayev2022-12-101-0/+1
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* Update deprecations after 3.0 dep sprint (#6031)Jarrod Millman2022-10-111-28/+0
| | | | | * Update deprecation todo list * Remove silenced warnings
* Update mentored projects list (#5985)Ross Barnowski2022-09-151-26/+6
| | | | | | | * Add vf2pp to completed projects list. * Rm vf2pp from projects list. * Add link to Konstantinos' 2022 GSoC proposal.
* Bump nodelink args deprecation expiration to v3.2 (#5933)Ross Barnowski2022-08-171-4/+2
| | | | | * Bump deprecation expiration for nodelink params to v3.2. * Fixup warnings filter.
* signature change for `node_link` functions: for issue #5787 (#5899)Kevin Brown2022-08-111-0/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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
* Add to about_us.rst (#5919)Dan Schult2022-08-081-10/+11
| | | Update about_us.rst
* Remove OrderedGraphs (#5813)Jarrod Millman2022-07-121-2/+0
| | | | | | Removes the deprecated OrderedGraph classes. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Dan Schult <dschult@colgate.edu>
* Clean up from PR #5779 (#5841)Jarrod Millman2022-07-051-2/+0
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* Remove pyyaml dependency (#5763)Jarrod Millman2022-06-211-4/+0
| | | | | | | | * Remove pyyaml dependency * Make mypy happy. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
* 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 gdal dependency (#5766)Jarrod Millman2022-06-162-2/+1
| | | | | | | | * Remove gdal dependency * [skip ci] Rm mention of gdal from roadmap. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
* Remove deprecated k-nearest-neighbors (#5769)Juanita Gomez2022-06-161-1/+0
| | | Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
* Remove coverage and performance from quality (#5775)Jarrod Millman2022-06-161-1/+0
| | | | | | | | * Remove coverage and performance from quality * [skip ci] rm coverage and performance from refguide. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
* Remove gpickle (#5773)Jarrod Millman2022-06-161-1/+0
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* Replace node_classification subpackage with a module (#5774)Dan Schult2022-06-161-3/+0
| | | | | | | * Replace node_classification subpackage with a module * update node_classification doc reference * remove node_classification from setup.py
* Remove generate_unique_node (#5780)Jarrod Millman2022-06-161-1/+0
| | | | | | | | * Remove generate_unique_node * [skip ci] rm from refguide. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
* Make chordal_graph_cliques a generator (#5758)Juanita Gomez2022-06-161-1/+0
| | | | | Make chordal_graph_cliques a generator Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Remove _naive_greedy_modularity_communities (#5760)Juanita Gomez2022-06-161-1/+0
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* Remove deprecated numeric_mixing_matrix (#5777)Juanita Gomez2022-06-161-1/+0
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* Change PyDot PendingDeprecation to Deprecation (#5781)Dan Schult2022-06-161-1/+1
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* Remove deprecated simrank_similarity_numpy (#5783)Juanita Gomez2022-06-161-1/+0
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* 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 decorator random_state (#5770)Dan Schult2022-06-151-1/+0
| | | Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com>
* Remove deprecated decorator preserve_random_state (#5768)Dan Schult2022-06-151-1/+0
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* Remove to_numpy_matrix & from_numpy_matrix (#5746)Dilara Tekinoglu2022-06-151-1/+0
| | | | | Rm to_numpy_matrix and from_numpy_matrix and related tests Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu>
* Remove deprecated display_pygraphviz (#5754)Juanita Gomez2022-06-151-1/+0
| | | | | * Remove deprecated display_pygraphviz * Remove display pygraphviz from deprecations file
* Rm jit.py (#5751)Dilara Tekinoglu2022-06-151-1/+0
| | | Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu>
* Rm `to_numpy_recarray` (#5737)Ross Barnowski2022-06-151-1/+0
| | | | | | | * Rm reminder from 3.0 deprecations list. * Rm to_numpy_recarray filter warning from conftest. * Deprecate to_numpy_recarray.
* Add PendingDeprecation for pydot (#5721)Jarrod Millman2022-06-111-0/+1
| | | | | * Add PendingDeprecation for pydot * Link to tracking issue
* Add initial_graph parameter to scale_free_graph and deprecate create_using ↵Ross Barnowski2022-06-071-0/+5
| | | | | | | | | | | | | | | (#5697) * Add initial_graph and deprecate create_using for scale_free_graph. * Add test for initial_graph kwarg. * doc and warningsfilter. * Fix formatting. * Update doc/developer/deprecations.rst Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com>
* Update release processJarrod Millman2022-05-211-7/+4
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* Run black on docs (#5513)Jarrod Millman2022-04-091-30/+41
| | | | | | | * Run black on docs * Remove redundant dependencies * Format docs
* Fix min_weight_matching to convert edge weights without reciprocal (#5394)Dan Schult2022-04-011-0/+1
| | | | | | | * 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
* Deprecate `to_tuple` (#5430)Ross Barnowski2022-03-281-0/+1
| | | | | | | | | * Add _to_tuple private fn to node_link.py. * Deprecate utils.misc.to_tuple. * Add deprecation note. * Add release note.
* Deprecate dict to numpy helpers (#5427)Ross Barnowski2022-03-261-0/+1
| | | | | | | | | | | | | * Convert to private fns and add deprecated public wrappers. * Modify existing tests to use private fns. * Add test that dep warnings are raised. * Add dep note. * Add release note. * Add importorskip(numpy).
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