delta/python-packages/networkx.git/doc/reference/algorithms, branch main github.com: networkx/networkx.git Fix module docstring format for ismags reference article. (#6611) 2023-04-03T19:44:39+00:00 Ross Barnowski rossbar@berkeley.edu 2023-04-03T19:44:39+00:00 020eaf626d6252f71a75751f63c57cbcc3d55573 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. 
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.
 add simple cycle enumerator for undirected class (#6461) 2023-03-28T20:18:28+00:00 Kelly Boothby boothby@dwavesys.com 2023-03-28T20:18:28+00:00 e49d8db79eef19294acedae7425e8022a97a4891 * 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> 
* 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>
 DOC: Minor formatting fixups to get rid of doc build warnings. (#6363) 2023-01-13T20:45:23+00:00 Ross Barnowski rossbar@berkeley.edu 2023-01-13T20:45:23+00:00 150daea06aeb7acd88d09fdf946a6210e97476a8 Minor formatting fixups to get rid of doc build warnings. 
Minor formatting fixups to get rid of doc build warnings.
 Laplace centrality for issue 4973 (#5399) 2023-01-09T19:14:34+00:00 Gabor Berei 42115089+gaborberei@users.noreply.github.com 2023-01-09T19:14:34+00:00 498bdfa33dd2869c3aae2ca87ec97223fdc0a2db * 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> 
* 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>
 Preliminary VF2++ Implementation (#5788) 2022-09-06T22:04:39+00:00 Konstantinos Petridis petridkon@gmail.com 2022-09-06T22:04:39+00:00 bffcd74649fb95a57fb834846eb3c7d9693c55b8 * Preliminary implementation of the candidate node pair ordering of VF2++ * Removed unused lines of code * Added todos * Added demo and pseudocode for VF2++ * Pointed out a problem with the pseudocode * Initialisation of the VF2++ basis structure * Initialise the GraphMatcher * Remove useless changes * Check labels for the node ordering + demo * Code to verify the ordering * Implement the ISO feasibility check * Implement the IND feasibility * Create State class * Fixed Dan's code for the ordering * Preliminary form of the node ordering * Add visualisation * Use list comprehension for the Ti computation * Remove function * Create Unit Tests * Add labels check + update unit tests * Add pre-computation of G-labels * Remove todo * First implementation of the candidate selection * Initial version of candidate selection * Remove unnecessary files * Merge candidate selection cases into one * Create a function to incrementally update Ti and Ti_out * Unit Test for the Ti updating * Implement the Ti/Ti_out restoring * Finish the restoring of Ti and create unit test * Update test file names * Uncommented test section * Replace redundant loop with for-any * Create unit test for candidate selection using the same label for all nodes * Create unit test for candidate selection using different labels for the nodes * Update feasibility tests without the use of the state class * Create more unit tests for the feasibility checking * Provide explanation for the unit tests * First successful test of the complete ISO VF2++ algorithm (except from the buggy ordering) * Fix bug: when popping a node to climb up the DFS tree we need the previous node ordering (containing the node that we just popped) * Create a separate file for the VF2++ ISO algorithm * Delete file * Remove redundant iteration and memory use * Demo for different labels * Add benchmark for the incremental Ti updating * Remove unnecessary class * Fix bug with the ordering WOOOHOOOOO * Unit tests for the node ordering * Add unit tests for the VF2++ ISO * Fix ordering * Probablly fix logic error in ordering * Reformatted with black * Test precommit * Test precommit * Test pre commit * Testing pre commit * Update networkx/algorithms/isomorphism/tests/VF2++/test_vf2pp.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Add unit tests for vf2++ * Added vf2++ unit test * Added precheck for VF2++ * Add unit tests for the precheck * Updated the benchmarking * Updated the benchmark * Apply hooks * Add documentation for the ordering * Add documentation for the candidate selection * Added documentation for the feasibility * Added documentation for vf2++ * Separate functions for ISO feasibility * Refine unit tests * Apply hooks * Force reformat all files * Remove redundant return statements from VF2__ * Apply hooks * Apply hooks * Format * Minor changes * Add unit tests * Adjusted benchmark * Fix benchmark * Isort * Isort benchmark * Apply optimization in the candidate selection * Track matched node with pointer * Adjust benchmark * Restructure in VF2 function * Make VF2++ EXTREMELY PRETTY * Removed sorting in feasibility rules * Get rid of visited set, check mapping instead * Update networkx/algorithms/isomorphism/tests/VF2++/test_vf2pp.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Made color assignement deterministic in VF2++ unit tests * Add keyword argument in unit tests * Hoepfully fix pipeline errors * Add vf2++ unit tests for multigraphs * Add Unit tests for Feasibility * Add unit tests for feasibility on multi graphs * Finalize feasibility tests for multigraph settings * Update documentation * Remove list comprehension and boost performance * Add unit tests for both graphs and multi graphs, using same labels * Isort * Optimized precheck * Replace loop with any * Optimize multigraph chceck * Transfer except statement * Check order consistency * Cache degrees and labels from the beginning * Delete benchmark to create new * Fix precheck bug * Adjust unit tests * Add benchmark for perofmance comparison between VF2 and VF2++ * Fix Ti computing tests * Hopefully fix isort * Add benchmark for the candidate selection methods * Rename modules: lower case, remove + * Refactor VF2++ arguments * Adjust VF2++ to work with multiple node labels * Add unit tests for multiple labels * Adjust for different number of labels per node * Finish arguments of VF2++ * Add user functions * Exported the two vf2++ functions * Added underscore prefix to private functions and fixed tests * Update networkx/algorithms/isomorphism/vf2pp.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/isomorphism/demo.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Update networkx/algorithms/isomorphism/vf2pp.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Apply suggested changes * Refactor rst files * Rm unnecessary toctree from isomorphism page. * Autodoc vf2pp module + public functions. * Rm dedicated vf2pp reference article. * Rm extra vf2pp listing from autosummaries. * Add summary of three functions to module docstring. * Make sure docstrings match their functions. * Refactor everything * Format code * Add unit test * Inline process level function in node ordering * Perform intersection first rather than last * Update networkx/algorithms/isomorphism/vf2pp_helpers/candidates.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Replace return statement with multiple operations and make it more readable * Update networkx/algorithms/isomorphism/vf2pp_helpers/feasibility.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Fix multigraph bug in update_Tinout * Abstract the argmax function * Add unit test for first case of candidate selection * Create unit test for all candidate selection cases * Remove re-definition of namedtuple parameters * Update doc/reference/algorithms/isomorphism.rst Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update networkx/algorithms/__init__.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Delete benchmark file * Add demo file * Create util file containing the helper functions, common across all unit tests * Fix CI/CD * Make unit tests for Ti updating specific * Remove util functions from vf2pp tests * Remove utils functions from multivf2pp tests * Remove utils functions from candidate tests * Remove utils functions from ordering checks * Remove utils functions from Ti tests * Add example in docstring * Remove unused utils functions * Separate initialization of vf2pp * Inline functions and add new abstract function for pushing to stack * Inline push to stack * Add commentsa * Separate precheck functions * Replace method with existing networkx function * Include label initialization inside parameter initializer function * Rename Tiout to Titilde * Update networkx/algorithms/isomorphism/tests/vf2pp/test_Ti_computing.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Use canonical setitem for dictionary insertions * Update networkx/algorithms/isomorphism/tests/vf2pp/test_precheck.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Remove variable assignement * Merge unit tests of vf2pp for graphs and multigraphs into the same file * Update networkx/algorithms/isomorphism/vf2pp.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update networkx/algorithms/isomorphism/vf2pp.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Update networkx/algorithms/isomorphism/vf2pp.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Change variable name * Update networkx/algorithms/isomorphism/vf2pp.py Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> * Re-write ordering unit tests * Rename vf2pp solver * Update networkx/algorithms/isomorphism/vf2pp_helpers/feasibility.py Co-authored-by: Dan Schult <dschult@colgate.edu> * Replace abstractified argmax function with two loops for readability * Apply final changes * Fix mistake * Update ref guide to reflect new fn names. * Update docstrings * Fix line length in module docstring * Copy updated parameter section to all 3 public fns. * Add Yields section to all_isomorphisms fn. Co-authored-by: Ross Barnowski <rossbar@berkeley.edu> Co-authored-by: Dan Schult <dschult@colgate.edu> 
* Preliminary implementation of the candidate node pair ordering of VF2++

* Removed unused lines of code

* Added todos

* Added demo and pseudocode for VF2++

* Pointed out a problem with the pseudocode

* Initialisation of the VF2++ basis structure

* Initialise the GraphMatcher

* Remove useless changes

* Check labels for the node ordering + demo

* Code to verify the ordering

* Implement the ISO feasibility check

* Implement the IND feasibility

* Create State class

* Fixed Dan's code for the ordering

* Preliminary form of the node ordering

* Add visualisation

* Use list comprehension for the Ti computation

* Remove function

* Create Unit Tests

* Add labels check + update unit tests

* Add pre-computation of G-labels

* Remove todo

* First implementation of the candidate selection

* Initial version of candidate selection

* Remove unnecessary files

* Merge candidate selection cases into one

* Create a function to incrementally update Ti and Ti_out

* Unit Test for the Ti updating

* Implement the Ti/Ti_out restoring

* Finish the restoring of Ti and create unit test

* Update test file names

* Uncommented test section

* Replace redundant loop with for-any

* Create unit test for candidate selection using the same label for all nodes

* Create unit test for candidate selection using different labels for the nodes

* Update feasibility tests without the use of the state class

* Create more unit tests for the feasibility checking

* Provide explanation for the unit tests

* First successful test of the complete ISO VF2++ algorithm (except from the buggy ordering)

* Fix bug: when popping a node to climb up the DFS tree we need the previous node ordering (containing the node that we just popped)

* Create a separate file for the VF2++ ISO algorithm

* Delete file

* Remove redundant iteration and memory use

* Demo for different labels

* Add benchmark for the incremental Ti updating

* Remove unnecessary class

* Fix bug with the ordering WOOOHOOOOO

* Unit tests for the node ordering

* Add unit tests for the VF2++ ISO

* Fix ordering

* Probablly fix logic error in ordering

* Reformatted with black

* Test precommit

* Test precommit

* Test pre commit

* Testing pre commit

* Update networkx/algorithms/isomorphism/tests/VF2++/test_vf2pp.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Add unit tests for vf2++

* Added vf2++ unit test

* Added precheck for VF2++

* Add unit tests for the precheck

* Updated the benchmarking

* Updated the benchmark

* Apply hooks

* Add documentation for the ordering

* Add documentation for the candidate selection

* Added documentation for the feasibility

* Added documentation for vf2++

* Separate functions for ISO feasibility

* Refine unit tests

* Apply hooks

* Force reformat all files

* Remove redundant return statements from VF2__

* Apply hooks

* Apply hooks

* Format

* Minor changes

* Add unit tests

* Adjusted benchmark

* Fix benchmark

* Isort

* Isort benchmark

* Apply optimization in the candidate selection

* Track matched node with pointer

* Adjust benchmark

* Restructure in VF2 function

* Make VF2++ EXTREMELY PRETTY

* Removed sorting in feasibility rules

* Get rid of visited set, check mapping instead

* Update networkx/algorithms/isomorphism/tests/VF2++/test_vf2pp.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Made color assignement deterministic in VF2++ unit tests

* Add keyword argument in unit tests

* Hoepfully fix pipeline errors

* Add vf2++ unit tests for multigraphs

* Add Unit tests for Feasibility

* Add unit tests for feasibility on multi graphs

* Finalize feasibility tests for multigraph settings

* Update documentation

* Remove list comprehension and boost performance

* Add unit tests for both graphs and multi graphs, using same labels

* Isort

* Optimized precheck

* Replace loop with any

* Optimize multigraph chceck

* Transfer except statement

* Check order consistency

* Cache degrees and labels from the beginning

* Delete benchmark to create new

* Fix precheck bug

* Adjust unit tests

* Add benchmark for perofmance comparison between VF2 and VF2++

* Fix Ti computing tests

* Hopefully fix isort

* Add benchmark for the candidate selection methods

* Rename modules: lower case, remove +

* Refactor VF2++ arguments

* Adjust VF2++ to work with multiple node labels

* Add unit tests for multiple labels

* Adjust for different number of labels per node

* Finish arguments of VF2++

* Add user functions

* Exported the two vf2++ functions

* Added underscore prefix to private functions and fixed tests

* Update networkx/algorithms/isomorphism/vf2pp.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Update networkx/algorithms/isomorphism/demo.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Update networkx/algorithms/isomorphism/vf2pp.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Apply suggested changes

* Refactor rst files

* Rm unnecessary toctree from isomorphism page.

* Autodoc vf2pp module + public functions.

* Rm dedicated vf2pp reference article.

* Rm extra vf2pp listing from autosummaries.

* Add summary of three functions to module docstring.

* Make sure docstrings match their functions.

* Refactor everything

* Format code

* Add unit test

* Inline process level function in node ordering

* Perform intersection first rather than last

* Update networkx/algorithms/isomorphism/vf2pp_helpers/candidates.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Replace return statement with multiple operations and make it more readable

* Update networkx/algorithms/isomorphism/vf2pp_helpers/feasibility.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Fix multigraph bug in update_Tinout

* Abstract the argmax function

* Add unit test for first case of candidate selection

* Create unit test for all candidate selection cases

* Remove re-definition of namedtuple parameters

* Update doc/reference/algorithms/isomorphism.rst

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Update networkx/algorithms/__init__.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Delete benchmark file

* Add demo file

* Create util file containing the helper functions, common across all unit tests

* Fix CI/CD

* Make unit tests for Ti updating specific

* Remove util functions from vf2pp tests

* Remove utils functions from multivf2pp tests

* Remove utils functions from candidate tests

* Remove utils functions from ordering checks

* Remove utils functions from Ti tests

* Add example in docstring

* Remove unused utils functions

* Separate initialization of vf2pp

* Inline functions and add new abstract function for pushing to stack

* Inline push to stack

* Add commentsa

* Separate precheck functions

* Replace method with existing networkx function

* Include label initialization inside parameter initializer function

* Rename Tiout to Titilde

* Update networkx/algorithms/isomorphism/tests/vf2pp/test_Ti_computing.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Use canonical setitem for dictionary insertions

* Update networkx/algorithms/isomorphism/tests/vf2pp/test_precheck.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Remove variable assignement

* Merge unit tests of vf2pp for graphs and multigraphs into the same file

* Update networkx/algorithms/isomorphism/vf2pp.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Update networkx/algorithms/isomorphism/vf2pp.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Update networkx/algorithms/isomorphism/vf2pp.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Change variable name

* Update networkx/algorithms/isomorphism/vf2pp.py

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>

* Re-write ordering unit tests

* Rename vf2pp solver

* Update networkx/algorithms/isomorphism/vf2pp_helpers/feasibility.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Replace abstractified argmax function with two loops for readability

* Apply final changes

* Fix mistake

* Update ref guide to reflect new fn names.

* Update docstrings
 * Fix line length in module docstring
 * Copy updated parameter section to all 3 public fns.
 * Add Yields section to all_isomorphisms fn.

Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
Co-authored-by: Dan Schult <dschult@colgate.edu>
 Add function bfs_layers to docs (#5932) 2022-08-17T07:22:08+00:00 Dan Schult dschult@colgate.edu 2022-08-17T07:22:08+00:00 09ded6ead5a9a3bb1d5b8349518fb5add6d10ca7 Add function bfs_layers to docs. fix two doc formatting typos 
Add function bfs_layers to docs. fix two doc formatting typos
 Replace LCA with naive implementations (#5883) 2022-08-13T23:59:11+00:00 Ross Barnowski rossbar@berkeley.edu 2022-08-13T23:59:11+00:00 19c1454d3dfa70a893ea67f2d78515658e8c08e5 * 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> 
* 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>
 Minor doc fixups (#5868) 2022-07-15T17:58:39+00:00 Ross Barnowski rossbar@berkeley.edu 2022-07-15T17:58:39+00:00 e79084b57e1553b5a1e3d80d940acc077ddb771a * 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. 
* 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.
 Corona Product (#5223) 2022-07-05T10:20:52+00:00 Ali Faraji 31096694+alifa98@users.noreply.github.com 2022-07-05T10:20:52+00:00 32c592325206c652c66ef58fdffbb8cc01278a15 * Corona product implemented. Todos: Docs Test for corona product * Corona Product Added and Works Correctly now. * document added. * corona product test added * corona product added to __all__ * add corona_product to operators.rst * precommit format fixed * Memory usage problem in the corona product improved * Update networkx/algorithms/operators/product.py Co-authored-by: Dan Schult <dschult@colgate.edu> * temp list replaced with generators * single qoutes problem in doc string * doc clean up Co-authored-by: Dan Schult <dschult@colgate.edu> * doc clean up Co-authored-by: Dan Schult <dschult@colgate.edu> * Update Tests `size()` is like the `number_of_edges()` method. Co-authored-by: Dan Schult <dschult@colgate.edu> Co-authored-by: Dan Schult <dschult@colgate.edu> 
* Corona product implemented.
Todos:
Docs
Test for corona product

* Corona Product Added and Works Correctly now.

* document added.

* corona product test added

* corona product added to __all__

* add corona_product to operators.rst

* precommit format fixed

* Memory usage problem in the corona product improved

* Update networkx/algorithms/operators/product.py

Co-authored-by: Dan Schult <dschult@colgate.edu>

* temp list replaced with generators

* single qoutes problem in doc string

* doc clean up

Co-authored-by: Dan Schult <dschult@colgate.edu>

* doc clean up

Co-authored-by: Dan Schult <dschult@colgate.edu>

* Update Tests

`size()` is like the `number_of_edges()` method.

Co-authored-by: Dan Schult <dschult@colgate.edu>

Co-authored-by: Dan Schult <dschult@colgate.edu>
 Implement directed edge swap (#5663) 2022-06-24T16:31:01+00:00 Ben Heil ben.jer.heil@gmail.com 2022-06-24T16:31:01+00:00 7d910e7184abd385c929f789b0c935ab143fc932 * 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> 
* 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>