Update dependency hypernetx to v2 #410

Fix typos in documenatation
Update (readthdocs) documentation scripts to use poetry
Remove unnecessary documentation Workflow
Update core dependencies to be more loosely constrained
Remove CI/CD scripts from Makefile
Remove CI/CD instructions from Readme
Update requirements.txt
Bump werkzeug from 3.0.2 to 3.0.3 by @dependabot in https://github.com/pnnl/HyperNetX/pull/153
Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in https://github.com/pnnl/HyperNetX/pull/152

New Contributors

@dependabot made their first contribution in https://github.com/pnnl/HyperNetX/pull/153

Full Changelog: pnnl/HyperNetX@v2.3.1...v2.3.2

`v2.3.1`: HNX v2.3.1

Compare Source

Hotfixes

Add decorator dependency
Update poetry.lock
Fix publish pypi workflow

Full Changelog: pnnl/HyperNetX@v2.3.0...v2.3.1

`v2.3.0`

Compare Source

Changed

Update Glossary with new terms and figure
Update Hypergraph docstrings
Refactor and add more tests
Update Visualization Tutorial
Change required Python version to ^3.10,<=3.12
Upgrade core dependencies
Update Tutorial 10, Hypergraph Modularity

Added

Add functionality to add and remove nodes, edges, and incidences on Hypergraph
Add Hypergraph arithmetic operations such as sum, difference, union, intersection
Add Hypergraph Arithmetic Operations tutorial
Add internal classes, IncidenceStore and PropertyStore, to support HypergraphView
Add new factory methods to support the creation of Hypergraph objects
Add support for Poetry to manage packaging, build, publishing, and environments

Removed

Remove EntitySet and replaced with HypergraphView
Remove setup.cfg and replaced with pyproject.toml

Fixed

Update usage of deprecated NetworkX methods

Changelog from 2.2.0 to 2.3.0

The following logs were generated using git log v2.2.0..HEAD --pretty=format:"- %s (%h, %an, %ad)"

updated glossary to remove duplicate terms and docstring to fix spelling (34f047a, Brenda Praggastis, Wed May 15 17:15:52 2024 -0700)
updated doc strings for s-connected components (d125c45, Brenda Praggastis, Wed May 15 17:07:33 2024 -0700)
updated the glossary, so it should be good now (771240e, Brenda Praggastis, Wed May 15 17:03:08 2024 -0700)
Pull request #179: Adding demo with attributes (7e253a0, Bonicillo, Mark A, Wed May 15 22:16:04 2024 +0000)
Pull request #178: Defaults2 (50d890d, Bonicillo, Mark A, Wed May 15 22:10:33 2024 +0000)
Merge branch 'develop' into defaults_backup (1e1c2a1, Brenda Praggastis, Wed May 15 15:04:05 2024 -0700)
Merge branch 'defaults_backup' into defaults_backup (001bc1e, Brenda Praggastis, Wed May 15 15:03:59 2024 -0700)
hypview added user defined props (19707ac, Brenda Praggastis, Wed May 15 13:56:51 2024 -0700)
adding two new tutorials under basic (773fa84, audun myers, Wed May 15 16:50:08 2024 -0400)
Pull request #177: Defaults backup (9516ca8, Bonicillo, Mark A, Wed May 15 20:46:04 2024 +0000)
Update tests (eedba46, Mark Bonicillo, Wed May 15 12:35:47 2024 -0700)
test (a2b8e3c, Brenda Praggastis, Wed May 15 13:18:53 2024 -0700)
created set_defaults (6f17867, Brenda Praggastis, Wed May 15 13:12:56 2024 -0700)
Merge branch 'defaults' of into defaults (145581e, Brenda Praggastis, Wed May 15 12:36:47 2024 -0700)
removed default_properties_df (0b2ccea, Brenda Praggastis, Wed May 15 12:36:32 2024 -0700)
Update tests (70e52f9, Mark Bonicillo, Wed May 15 12:35:47 2024 -0700)
Update Tutorial 2 - Visualization Methods.ipynb (a71c259, audun myers, Wed May 15 15:26:00 2024 -0400)
created self.defaults (793b715, Brenda Praggastis, Wed May 15 11:28:38 2024 -0700)
Pull request #176: Glossary (357d339, Bonicillo, Mark A, Wed May 15 18:24:33 2024 +0000)
Merge branch 'develop' into glossary (65cd70b, Mark Bonicillo, Wed May 15 11:21:26 2024 -0700)
Pull request #175: Fix tutorial imports (a98e917, Bonicillo, Mark A, Wed May 15 18:04:42 2024 +0000)
adding figure to glossary describing HNX structure (c5588ba, audun myers, Wed May 15 14:02:17 2024 -0400)
Fix tutorial imports (b248be0, Mark Bonicillo, Wed May 15 10:47:34 2024 -0700)
new glossary again (d2eb5b1, Brenda Praggastis, Wed May 15 10:52:55 2024 -0700)
new glossary (66ff679, Brenda Praggastis, Wed May 15 10:42:18 2024 -0700)
new glossary (e5d8972, Brenda Praggastis, Wed May 15 10:34:07 2024 -0700)
glossary and classes init updated (9d94a8b, Brenda Praggastis, Wed May 15 09:59:46 2024 -0700)
Pull request #172: Add, update docstrings in hypergraph (27ed0fb, Bonicillo, Mark A, Wed May 15 16:49:55 2024 +0000)
Merge remote-tracking branch 'develop' into update-hypergraph-docstrings (501247a, Mark Bonicillo, Mon May 13 15:44:03 2024 -0700)
Pull request #174: Add tests for union, intersection; update other tests (75153a2, Bonicillo, Mark A, Mon May 13 22:35:06 2024 +0000)
Add tests for union, intersection; update other tests (1bfe844, Mark Bonicillo, Mon May 13 15:20:48 2024 -0700)
Merge remote-tracking branch 'develop' into update-hypergraph-docstrings (5622b8e, Mark Bonicillo, Thu May 9 08:54:06 2024 -0700)
Pull request #173: Ndarray (55e7321, Bonicillo, Mark A, Thu May 9 06:59:23 2024 +0000)
Fix import error in ndarray factory method (54b6704, Mark Bonicillo, Wed May 8 16:59:28 2024 -0700)
Add ndarray test on constructor; fix docstrings (c515db1, Mark Bonicillo, Wed May 8 16:55:28 2024 -0700)
Fix malformed table (1594fc0, Mark Bonicillo, Wed May 8 16:11:49 2024 -0700)
Update LICENSE.rst to 2024 (4277fef, Mark Bonicillo, Wed May 8 15:50:34 2024 -0700)
Fix math syntax (1cdbc44, Mark Bonicillo, Wed May 8 15:40:21 2024 -0700)
Refactor matrix methods; update tests and docstrings (0104565, Mark Bonicillo, Wed May 8 14:29:11 2024 -0700)
Remove typing from Hypergraph constructor (4279ae4, Mark Bonicillo, Wed May 8 10:38:23 2024 -0700)
Update remove methods and its docstrings; updates tests (4185dda, Mark Bonicillo, Tue May 7 17:08:42 2024 -0700)
updated docstrings (01998e9, Brenda Praggastis, Mon May 6 17:02:09 2024 -0700)
add ndarray factory method (d65f52d, Brenda Praggastis, Mon May 6 16:27:17 2024 -0700)
Add, update docstrings in hypergraph (cf3a299, Mark Bonicillo, Mon May 6 11:55:29 2024 -0700)
Pull request #171: Update documentation (4e1a27e, Bonicillo, Mark A, Thu May 2 21:27:04 2024 +0000)
Update Python version references in docs; update docs Makefile (a58f0f5, Mark Bonicillo, Thu May 2 14:05:59 2024 -0700)
Update long description (29a42e0, Mark Bonicillo, Thu May 2 13:07:22 2024 -0700)
Fix Sphinx errors, warnings on docstrings (f33a152, Mark Bonicillo, Wed May 1 14:09:28 2024 -0700)
Remove references to non-existing modules; fix docstrings (e8a0ea0, Mark Bonicillo, Tue Apr 30 15:06:54 2024 -0700)
Remove helpers.py; remove unused imports (f26b58d, Mark Bonicillo, Mon Apr 29 16:24:59 2024 -0700)
Remove EntitySet references; remove old AttrList (3646fb0, Mark Bonicillo, Mon Apr 29 16:03:19 2024 -0700)
Pull request #170: Upgrade Python to 3.10; upgrade core dependencies (c819ca2, Bonicillo, Mark A, Thu May 2 18:55:24 2024 +0000)
Upgrade Python to 3.10; upgrade core dependencies (bab41d5, Mark Bonicillo, Thu May 2 10:42:50 2024 -0700)
Pull request #169: Additems (be63722, Bonicillo, Mark A, Wed May 1 21:20:15 2024 +0000)
Minor cleanup (9222850, Mark Bonicillo, Wed May 1 14:16:35 2024 -0700)
added import for deepcopy (aa9fab3, Brenda Praggastis, Wed May 1 13:58:23 2024 -0700)
updated copy in PropertyStore to deep copy misc_properties (5687346, Brenda Praggastis, Wed May 1 13:36:19 2024 -0700)
updated construct from stores to return inplace or deep copy (116f41b, Brenda Praggastis, Wed May 1 13:35:03 2024 -0700)
restricting todataframe to only return on objects actually in the hypergraph (1f1921f, Brenda Praggastis, Wed May 1 13:32:47 2024 -0700)
Pull request #167: added items property to hyp_view and intersection and union to hypergraph (c519d05, Praggastis, Brenda, Tue Apr 30 20:05:49 2024 +0000)
Fix and refactor sum method; add tests (b178da6, Mark Bonicillo, Tue Apr 30 11:18:47 2024 -0700)
Merge branch 'develop', remote-tracking branch 'stash' into bpedits3 (787314d, Mark Bonicillo, Tue Apr 30 11:37:48 2024 -0700)
added items property to hyp_view and intersection and union to hypergraph (5bab9d7, Brenda Praggastis, Mon Apr 29 15:57:44 2024 -0700)
Pull request #165: Fix bugs, refactor methods in Hypergraph; add and update tests for Hypergraph (abd35cd, Bonicillo, Mark A, Mon Apr 29 20:47:19 2024 +0000)
Fix bug in get_cell_properties; update tests (65949c6, Mark Bonicillo, Wed Apr 24 13:58:13 2024 -0700)
Cleanup tests (d126e8b, Mark Bonicillo, Wed Apr 24 12:01:09 2024 -0700)
Pull request #166: Bpedits2 (6fd94ec, Praggastis, Brenda, Mon Apr 29 17:17:15 2024 +0000)
Run linter (b5dd816, Mark Bonicillo, Mon Apr 29 10:12:12 2024 -0700)
updates collapse to put user defined keys for equivalence classes first and allow for aggregations. (072770c, Brenda Praggastis, Fri Apr 26 18:42:56 2024 -0700)
replaced deep copy on to_dataframe since it wasn't copying misc properties (f825248, Brenda Praggastis, Fri Apr 26 18:41:55 2024 -0700)
fixes collapse so that chosen key will always be listed first (85cc730, Brenda Praggastis, Fri Apr 26 18:40:21 2024 -0700)
changed to_dataframe to only return a complete clone of dataframe - fixes misc properties not deep copying (783edd3, Brenda Praggastis, Fri Apr 26 18:39:19 2024 -0700)
Merge branch 'develop' into bpedits (293ee43, Brenda Praggastis, Fri Apr 26 14:19:57 2024 -0700)
note TODO and update on inplace (0cadce0, Brenda Praggastis, Fri Apr 26 14:12:44 2024 -0700)
Pull request #164: Fixing factory bug (db3576f, Myers, Audun D, Wed Apr 24 19:12:04 2024 +0000)
Revert "Adding init files to tests folder" (38bc621, Mark Bonicillo, Wed Apr 24 12:04:55 2024 -0700)
Linter (d76cd2a, Mark Bonicillo, Wed Apr 24 12:03:27 2024 -0700)
fixing edges and nodes methods in incicdence store (475f066, audun myers, Wed Apr 24 14:19:57 2024 -0400)
Adding init files to tests folder (068b248, audun myers, Wed Apr 24 11:31:00 2024 -0400)
Update factory.py (9348e3d, audun myers, Wed Apr 24 10:48:38 2024 -0400)
Pull request #163: Add eq method to Hypergraph; add tests for clone (62e9e2a, Bonicillo, Mark A, Tue Apr 23 22:29:59 2024 +0000)
Add eq method; add tests for clone (a6da1e3, Mark Bonicillo, Thu Apr 18 11:34:38 2024 -0700)
Pull request #162: Fix bug in components method; update tests (881c7ba, Bonicillo, Mark A, Tue Apr 23 21:51:29 2024 +0000)
Fix bug in components method; update tests (6c302f2, Mark Bonicillo, Tue Apr 23 14:43:57 2024 -0700)
Recovered changes to hypergraph.py (5909d07, Brenda Praggastis, Thu Apr 18 12:50:26 2024 -0700)
Pull request #161: Docs (a0813bc, Praggastis, Brenda, Thu Apr 18 18:41:11 2024 +0000)
Run linter (0852180, Mark Bonicillo, Thu Apr 18 11:37:15 2024 -0700)
refactored tests to be consistent with new core code (274d7ad, Brenda Praggastis, Wed Apr 17 18:55:56 2024 -0700)
updated modules to be consistent with new core code (14b8498, Brenda Praggastis, Wed Apr 17 18:55:38 2024 -0700)
updates to hypergraph and incidence store include doc string improvements and refactored collapse methods (3a53d74, Brenda Praggastis, Wed Apr 17 18:55:18 2024 -0700)
Merge branch 'develop' into docs (b9d801c, Brenda Praggastis, Wed Apr 17 11:26:23 2024 -0700)
updated hypergraph doc strings (fb1a3b9, Brenda Praggastis, Wed Apr 17 11:25:36 2024 -0700)
Pull request #160: removed inplace and changed remove to _remove for internal use (8adb1a7, Praggastis, Brenda, Wed Apr 17 18:20:28 2024 +0000)
Run linter (4270e44, Mark Bonicillo, Wed Apr 17 11:15:42 2024 -0700)
added ability to add a nested dictionary for nodes to edges (8a3244b, Brenda Praggastis, Tue Apr 16 21:11:09 2024 -0700)
added clone method to create a copy on which to make changes. (c18687d, Brenda Praggastis, Tue Apr 16 21:06:23 2024 -0700)
Pull request #159: Update tests add_* functionality (5227d27, Bonicillo, Mark A, Wed Apr 17 18:00:18 2024 +0000)
Fix bugs; refactor code; update tests (4a273c8, Mark Bonicillo, Wed Apr 17 10:37:05 2024 -0700)
Fix bug in PropertyStore; update add_edge tests (63e671d, Mark Bonicillo, Tue Apr 16 16:57:20 2024 -0700)
removed inplace and changed remove to _remove for internal use (c1a52cf, Brenda Praggastis, Tue Apr 16 13:47:42 2024 -0700)
Add tests for add_node and add_incidences (366f136, Mark Bonicillo, Tue Apr 16 14:11:55 2024 -0700)
Pull request #158: Update tests (f4c98ca, Bonicillo, Mark A, Tue Apr 16 00:08:16 2024 +0000)
Add test-core target (6fff636, Mark Bonicillo, Mon Apr 15 17:04:08 2024 -0700)
Update tests (1d6eba4, Mark Bonicillo, Mon Apr 15 11:02:12 2024 -0700)
Remove old notebooks (d3c6142, Mark Bonicillo, Thu Apr 11 11:19:52 2024 -0700)
Move tests to root-level (62f451d, Mark Bonicillo, Tue Apr 9 14:36:44 2024 -0700)
Pull request #157: Fix bugs in _add_item; add tests for add_edge (3a89c2c, Bonicillo, Mark A, Mon Apr 15 23:52:07 2024 +0000)
Fix bugs in _add_item; add tests for add_edge (857130a, Mark Bonicillo, Mon Apr 15 14:53:08 2024 -0700)
Pull request #156: Fix bug in Hypergraph.dual; update tests (d42a698, Bonicillo, Mark A, Fri Apr 12 15:27:05 2024 +0000)
Fix bug in Hypergraph.dual; update tests (111721c, Mark Bonicillo, Thu Apr 11 11:09:47 2024 -0700)
Pull request #155: updating index column naming for factory (7249e43, Myers, Audun D, Thu Apr 11 18:37:23 2024 +0000)
Fix formatting (3070166, Mark Bonicillo, Thu Apr 11 11:36:21 2024 -0700)
Fixed PR comments from mark (e9dc62d, audun myers, Thu Apr 11 14:24:19 2024 -0400)
updating index column naming for factory (20042b0, audun myers, Thu Apr 11 12:26:17 2024 -0400)
Pull request #154: difference_function fix (e6220d2, Praggastis, Brenda, Wed Apr 10 04:02:26 2024 +0000)
Add tests for difference method (307e062, Mark Bonicillo, Tue Apr 9 17:05:11 2024 -0700)
fixed difference of hypergraphs as it removed properties and shouldn't have (552ced6, Brenda Praggastis, Tue Apr 9 16:08:20 2024 -0700)
merged origin/develop into develop (890ca80, Brenda Praggastis, Tue Apr 9 15:10:16 2024 -0700)
Pull request #153: Infra update (370e671, Bonicillo, Mark A, Tue Apr 9 21:04:01 2024 +0000)
Move pytest config into pyproject (5012941, Mark Bonicillo, Tue Apr 9 13:39:12 2024 -0700)
Fix make targets (e51f4ca, Mark Bonicillo, Fri Apr 5 17:24:43 2024 -0700)
Add poetry (9591806, Mark Bonicillo, Mon Mar 25 11:19:36 2024 -0700)
Pull request #152: Updating factory to fix some nbugs and improve documentation (9d3d22a, Myers, Audun D, Tue Apr 9 20:50:31 2024 +0000)
Run linter (bcfe9d0, Mark Bonicillo, Tue Apr 9 13:44:41 2024 -0700)
Delete testing_factory.ipynb (15ebb13, audun myers, Tue Apr 9 16:14:46 2024 -0400)
Create testing_factory.ipynb (a1bd873, audun myers, Tue Apr 9 16:10:13 2024 -0400)
updating factory to fix bugs (f2fb670, audun myers, Tue Apr 9 16:00:43 2024 -0400)
Pull request #151: Hg functionality (4a848f7, Bonicillo, Mark A, Tue Apr 9 19:44:30 2024 +0000)
Cleanup tutorial 9 (d374d02, Mark Bonicillo, Tue Apr 9 12:11:20 2024 -0700)
Fix image link in tutorials 8 (ee33355, Mark Bonicillo, Tue Apr 9 12:04:59 2024 -0700)
Fix call to toplexes method in tutorial 1 (dd8ea58, Mark Bonicillo, Tue Apr 9 11:50:19 2024 -0700)
Update set and get methods on property store; fix bug (3311d58, Mark Bonicillo, Mon Apr 8 10:25:10 2024 -0700)
Run linter (9f23c13, Mark Bonicillo, Mon Apr 8 08:13:03 2024 -0700)
updated docs (4623ac7, Brenda Praggastis, Sun Apr 7 18:52:16 2024 -0700)
updated test_hypergraph so that toplexes test works (657b8ef, Brenda Praggastis, Sun Apr 7 18:51:54 2024 -0700)
hypergraph methods for add and remove and toplexes were updated , replaced keyword share_properties with inplace (9bd91f1, Brenda Praggastis, Sun Apr 7 18:51:27 2024 -0700)
added check for items not in incidence dataframe (efc0b64, Brenda Praggastis, Sun Apr 7 18:48:50 2024 -0700)
updated property_store so that _add_row can take multiple properties as kwargs. added copy to Property Store (0ceb77b, Brenda Praggastis, Sun Apr 7 18:45:27 2024 -0700)
Pull request #150: Tutorials no infra (3491c6c, Bonicillo, Mark A, Sat Apr 6 00:12:02 2024 +0000)
replaced Tutorial 10 with Francois's new version (4276532, Brenda Praggastis, Fri Apr 5 10:47:16 2024 -0700)
Update to_dataframe, add hypergraph_view tests (4916497, Mark Bonicillo, Fri Apr 5 16:52:24 2024 -0700)
removed files that don't belong in top level of tutorials (c863e84, Brenda Praggastis, Thu Apr 4 18:25:25 2024 -0700)
updated Tutorial 9 and corresponding module. (b7933eb, Brenda Praggastis, Thu Apr 4 18:21:44 2024 -0700)
updated Tutorial 10 (8397e9c, Brenda Praggastis, Thu Apr 4 18:00:37 2024 -0700)
changed NList to AttrList to be consistent with previous version. (83dad8a, Brenda Praggastis, Thu Apr 4 14:22:59 2024 -0700)
Run linter (d03c651, Mark Bonicillo, Thu Apr 4 09:43:43 2024 -0700)
Tutorial 8 updates (9f70fea, Brenda Praggastis, Wed Apr 3 17:41:35 2024 -0700)
updated tutorials 5,6,7 (5ddb33b, Brenda Praggastis, Wed Apr 3 12:50:27 2024 -0700)
created to_dataframe method and removed property_view from property store (bd12e4d, Brenda Praggastis, Wed Apr 3 12:12:34 2024 -0700)
updated tutorial 2 (1a3d424, Brenda Praggastis, Wed Apr 3 11:44:33 2024 -0700)
updated vis (6421cdf, Brenda Praggastis, Wed Apr 3 11:21:27 2024 -0700)
update tutorials again (dbdfe71, Brenda Praggastis, Wed Apr 3 10:29:17 2024 -0700)
Remove setup.py (4ccbd11, Mark Bonicillo, Tue Apr 2 13:57:26 2024 -0700)
Run formatter (10a99f2, Mark Bonicillo, Tue Apr 2 12:01:46 2024 -0700)
Update tox.ini (10c259a, Mark Bonicillo, Tue Apr 2 11:41:08 2024 -0700)
Update ci.yml (46aed8d, Mark Bonicillo, Mon Apr 1 13:16:42 2024 -0700)
Fix github workflows (f655be4, Mark Bonicillo, Mon Apr 1 12:51:15 2024 -0700)
Cleanup required dependencies (a60bff3, Mark Bonicillo, Mon Apr 1 11:32:46 2024 -0700)
Update cz file (bad6401, Mark Bonicillo, Tue Mar 26 15:40:57 2024 -0700)
Update GH workflows (2eaa364, Mark Bonicillo, Tue Mar 26 15:36:23 2024 -0700)
Cleanup Makefile (d22d8a6, Mark Bonicillo, Mon Mar 25 23:51:17 2024 -0700)
testing new docs-deps (dd6436f, Mark Bonicillo, Mon Mar 25 22:46:23 2024 -0700)
testing (adb34e7, Mark Bonicillo, Mon Mar 25 22:26:24 2024 -0700)
Modify tox to integrate with poetry (7f6ee9d, Mark Bonicillo, Mon Mar 25 16:15:50 2024 -0700)
Add poetry (7703cf1, Mark Bonicillo, Mon Mar 25 11:19:36 2024 -0700)
Pull request #147: Hypergraph edit (638870a, Praggastis, Brenda, Mon Apr 1 21:59:00 2024 +0000)
removed old hypergraph code (1e1dbf7, Brenda Praggastis, Mon Apr 1 13:59:16 2024 -0700)
removed .github from .gitignore (3e1c8b6, Brenda Praggastis, Mon Apr 1 13:57:34 2024 -0700)
updated hypergraph from incidence matrix constructor (b9dbc0b, Brenda Praggastis, Fri Mar 29 18:08:47 2024 -0700)
Merge branch 'develop' into develop (d38b2ff, Brenda Praggastis, Wed Mar 27 12:40:53 2024 -0700)
removing notebooks not intended for sharing (126610b, Brenda Praggastis, Wed Mar 27 12:40:32 2024 -0700)
Pull request #145: Add HNX paper (d0a7e3d, Bonicillo, Mark A, Wed Mar 27 19:12:05 2024 +0000)
Add HNX paper (463d12f, Mark Bonicillo, Wed Mar 27 12:10:07 2024 -0700)
Pull request #144: Feature/hyp 367 (519c771, Bonicillo, Mark A, Wed Mar 27 18:54:43 2024 +0000)
Fix formatting (89c712b, Mark Bonicillo, Wed Mar 27 11:48:34 2024 -0700)
adding arithmetic for hypergraphs (29cfed8, Brenda Praggastis, Wed Mar 27 11:44:23 2024 -0700)
Bug fix: shouldn't require passing position for hyper-edges. (f93504f, Dustin Arendt, Tue Mar 26 14:51:52 2024 -0700)
Remove nwhy decorator reference (c180bd0, Mark Bonicillo, Mon Mar 25 09:24:08 2024 -0700)
Run linter; remove HNX_Paper (850ddd6, Mark Bonicillo, Mon Mar 25 09:18:30 2024 -0700)
updated hypergraph code class method constructors (f13a325, Brenda Praggastis, Fri Mar 22 14:36:00 2024 -0700)
Remove references to warn_nwhy deprecation decorator (f1c3e43, Mark Bonicillo, Fri Mar 22 11:43:24 2024 -0700)
Remove deprecated NetworkX functions (379bc19, Mark Bonicillo, Fri Mar 22 11:35:46 2024 -0700)
Remove unnecessary hypergraph test (3e70822, Mark Bonicillo, Fri Mar 22 11:11:56 2024 -0700)
Fix incidence_store bug; move, update, and fix incidence store tests; (c05c4b4, Mark Bonicillo, Fri Mar 22 11:09:03 2024 -0700)
Remove EntitySet and tests (598c69c, Mark Bonicillo, Fri Mar 22 09:37:24 2024 -0700)
add incidences reference to access _E HypergraphView (0373ac5, Brenda Praggastis, Thu Mar 21 17:58:39 2024 -0700)
removing hypergraph_outline to avoid versioning issues. new code is on hypergraph.py now (2d1f6db, Brenda Praggastis, Thu Mar 21 17:49:01 2024 -0700)
centrality tutorial 5 is ready to go (aaef8dc, Brenda Praggastis, Thu Mar 21 17:47:26 2024 -0700)
Updated the tutorials in basic 1,3,4 to work with new code.. (c1a80f0, Brenda Praggastis, Thu Mar 21 17:32:10 2024 -0700)
moved old hypergraph code into hypergraph_2.0 and set hypergraph to match hypergraph_outline. updated dogsAndcats for testing (b6c230d, Brenda Praggastis, Thu Mar 21 16:33:16 2024 -0700)
updated tests to work with new hypergraph code. commented out _by_setsystem tests until they can be upgraded (791cf89, Brenda Praggastis, Thu Mar 21 16:32:19 2024 -0700)
updated collapse in incidence to separate functions for equivalence classes and collapse identical elements. user can now specify keys when collapsing (06bd85d, Brenda Praggastis, Thu Mar 21 16:31:24 2024 -0700)
added is_empty to match old behavior (fc6b6a6, Brenda Praggastis, Thu Mar 21 16:30:11 2024 -0700)
Refactor set property (f5bc644, Mark Bonicillo, Thu Mar 21 12:36:01 2024 -0700)
Add properties_uids method (aa263c4, Mark Bonicillo, Thu Mar 21 11:30:27 2024 -0700)
updated much of outline - time to start testing (b0b6055, Brenda Praggastis, Wed Mar 20 17:53:51 2024 -0700)
added implementation for weighted incidence matrix and incidence dataframe (ec8c369, Brenda Praggastis, Wed Mar 20 13:54:20 2024 -0700)
debugging new outline code (ac9127a, Brenda Praggastis, Wed Mar 20 10:32:37 2024 -0700)
Update tests and docstrings; cleanup code (04bb9a7, Mark Bonicillo, Wed Mar 20 10:23:59 2024 -0700)
adding functionality for collapsing and incidence matrix (c34278e, Brenda Praggastis, Tue Mar 19 20:19:37 2024 -0700)
Merge branch 'develop' into feature/hyp-367 (36590d6, Brenda Praggastis, Mon Mar 18 18:07:00 2024 -0700)
Pull request #143: HYP-396 Add CFF citation (b67b38b, Bonicillo, Mark A, Tue Mar 19 00:00:20 2024 +0000)
Update docs, add helper method, update tests (3642fa8, Mark Bonicillo, Mon Mar 18 13:53:20 2024 -0700)
Remove old propertystore and test (a4cfa30, Mark Bonicillo, Mon Mar 18 13:20:33 2024 -0700)
updating hypergraph_outline methods to work with draw) (dad6085, Brenda Praggastis, Mon Mar 18 10:29:10 2024 -0700)
updated to get basic functionality on hypergraph_outline. please review (47d6899, Brenda Praggastis, Sun Mar 17 16:23:54 2024 -0700)
Update set_property; update docs, tests (5f0bad5, Mark Bonicillo, Fri Mar 15 16:56:04 2024 -0700)
Updated factory to be more simple and allow indices to be provided. (3b13dd6, audun myers, Fri Mar 15 16:19:59 2024 -0400)
updates for simplifying factory and propertystore (2d60e4d, Brenda Praggastis, Fri Mar 15 08:13:15 2024 -0700)
fixed typo (54e887a, Brenda Praggastis, Thu Mar 14 15:19:56 2024 -0700)
updating for default properties (0e19ba7, Brenda Praggastis, Thu Mar 14 12:53:48 2024 -0700)
pulled and merged new content (044dddb, Brenda Praggastis, Thu Mar 14 11:18:59 2024 -0700)
fixing syntax errors (cc230af, Brenda Praggastis, Wed Mar 13 12:00:06 2024 -0700)
fixed syntax errors in 3 files (c016f3f, Brenda Praggastis, Wed Mar 13 08:57:29 2024 -0700)
Refactor Index param (9ed8b54, Mark Bonicillo, Wed Mar 13 15:05:19 2024 -0700)
changed uid column to 'uid' for edges and nodes and fixed index for uid_cols bug. (07c83af, audun myers, Wed Mar 13 14:21:35 2024 -0400)
HYP-396 Add CFF citation; add cff workflow and badge (44e06fa, Mark Bonicillo, Wed Mar 13 09:23:22 2024 -0700)
Adding level input to factory (e80403e, audun myers, Wed Mar 13 11:44:42 2024 -0400)
Add index param to PropertyStore (f947720, Mark Bonicillo, Tue Mar 12 17:03:16 2024 -0700)
Update property store, tests, notebook (4a9752a, Mark Bonicillo, Fri Mar 8 13:29:55 2024 -0800)
added list factory method (c400777, audun myers, Thu Mar 7 16:13:56 2024 -0500)
Added dictionary factory method and more examples (b43ec9e, audun myers, Thu Mar 7 15:39:29 2024 -0500)
updated factory to follow hypergraph_outline structure (0b5cf2e, audun myers, Thu Mar 7 14:31:57 2024 -0500)
removing tutorial to avoid conflicts (eab01de, Brenda Praggastis, Thu Mar 7 09:20:40 2024 -0800)
working on notebook (c0ea4d7, Brenda Praggastis, Thu Mar 7 09:18:37 2024 -0800)
updated hypergraph outline to notes from meeting (3dd9616, Brenda Praggastis, Wed Mar 6 14:11:26 2024 -0800)
updates from meeting (a53b7af, Brenda Praggastis, Wed Mar 6 12:06:21 2024 -0800)
updates (7ed7414, Brenda Praggastis, Wed Mar 6 10:41:14 2024 -0800)
updates on outline (052f029, Brenda Praggastis, Wed Mar 6 10:39:43 2024 -0800)
Run linter (4eadb9a, Mark Bonicillo, Wed Mar 6 09:11:38 2024 -0800)
returns empty list for nieghbors if level =2 (3c56622, audun myers, Wed Mar 6 10:37:38 2024 -0500)
Updating factory to have single dataframe to property store function (fe07fa1, audun myers, Wed Mar 6 10:36:13 2024 -0500)
Run linter (80fe95e, Mark Bonicillo, Tue Mar 5 13:26:55 2024 -0800)
Fix drawing module (d84d526, Mark Bonicillo, Tue Mar 5 13:10:49 2024 -0800)
Remove paper-related doc (76ffef3, Mark Bonicillo, Tue Mar 5 12:58:56 2024 -0800)
added outline of hypergraph constructor in hypergraph_outline.py (8943b7d, Brenda Praggastis, Tue Mar 5 11:12:07 2024 -0800)
merged develop into branch (ede25b2, Brenda Praggastis, Tue Mar 5 10:29:54 2024 -0800)
updated hypergraph outline with suggestions for factory methods (559e695, Brenda Praggastis, Tue Mar 5 10:23:14 2024 -0800)
updated test data (e5442db, Brenda Praggastis, Mon Mar 4 14:24:09 2024 -0800)
found small error in factory (6382c4d, audun myers, Fri Mar 1 17:10:18 2024 -0500)
added multiple fixes discussed in HNX meeting for factory methods (32f93f3, audun myers, Fri Mar 1 17:00:30 2024 -0500)
Revert "Add hypergraph_view factory method" (e2858fe, Mark Bonicillo, Wed Feb 28 12:37:19 2024 -0800)
Allow DataFramePropertyStore to accept regular or multiindex dfs; change properties to misc_properties (5cdb85c, Mark Bonicillo, Wed Feb 28 12:31:38 2024 -0800)
Finished adding all optional args to factory (747ca13, audun myers, Wed Feb 28 13:12:57 2024 -0500)
Add hypergraph_view factory method (d90b2c3, Mark Bonicillo, Wed Feb 28 08:30:02 2024 -0800)
Update property_store tests (b73e21f, Mark Bonicillo, Mon Feb 26 10:31:47 2024 -0800)
added all optional args for factory method (97ff5bd, audun myers, Mon Feb 26 12:06:41 2024 -0500)
small changes for better integration with hyp_view and existing code (4857324, Brenda Praggastis, Mon Feb 26 08:55:17 2024 -0800)
small modifications to integrate better with existing code and hyp_view (fd73f5b, Brenda Praggastis, Mon Feb 26 08:54:39 2024 -0800)
updates incorporating new property and incidence stores (15954cd, Brenda Praggastis, Mon Feb 26 08:53:55 2024 -0800)
updates (67b7edd, Brenda Praggastis, Fri Feb 23 15:51:08 2024 -0800)
updates (6a21358, Brenda Praggastis, Thu Feb 22 11:38:19 2024 -0800)
Update factory.py (1c2881b, audun myers, Fri Feb 23 16:45:17 2024 -0500)
Use MultiIndexDataframe for PropertyStore; update tests; add notebook (c9a94c6, Mark Bonicillo, Fri Feb 23 13:35:02 2024 -0800)
test nb and data (5e01079, Brenda Praggastis, Wed Feb 21 12:01:27 2024 -0800)
updates (ad7d792, Brenda Praggastis, Wed Feb 21 09:24:27 2024 -0800)
finished draft dataframe factory method. (c66e952, audun myers, Mon Feb 19 10:33:25 2024 -0500)
Implement DataFramePropertyStore; add tests (9a2e0f1, Mark Bonicillo, Fri Feb 16 01:03:21 2024 -0800)
updated attrlist (cf8ce22, Brenda Praggastis, Thu Feb 15 12:35:57 2024 -0800)
added methods (564abc1, Brenda Praggastis, Wed Feb 14 18:34:05 2024 -0800)
hiding files in gitignore (70b3eba, Brenda Praggastis, Wed Feb 14 17:25:41 2024 -0800)
slowly adding methods using proxies for incidence store and property store. (8f8f40d, Brenda Praggastis, Wed Feb 14 17:20:17 2024 -0800)
comments on incidence store (58d4c68, Brenda Praggastis, Wed Feb 14 11:30:18 2024 -0800)
updating view (d8c207e, Brenda Praggastis, Wed Feb 14 10:32:58 2024 -0800)
Added the contain_hyper_edges flag to extend hulls (rubber bands) around hyperedge positions. Useful for when the bipartite graph is passed in, e.g. with_additional_edges=H.bipartite() (73f9c2e, Dustin Arendt, Thu Feb 1 14:35:59 2024 -0800)
updated tutorial (d7af03f, Brenda Praggastis, Wed Feb 14 17:30:23 2024 -0800)
update paper folder (aa22bd5, Brenda Praggastis, Wed Oct 18 13:23:29 2023 -0700)
updated paper with orcid and doi ids (57e4075, Brenda Praggastis, Tue Oct 17 10:17:39 2023 -0700)
fixed bib error (ffd67a1, Brenda Praggastis, Mon Oct 16 12:45:46 2023 -0700)
rm pdf (c26dc10, Brenda Praggastis, Mon Oct 16 12:28:48 2023 -0700)
adding Github action (30a91d3, Brenda Praggastis, Mon Oct 16 12:22:23 2023 -0700)
adding paper for journal consideration (52e3cec, Brenda Praggastis, Mon Oct 16 12:14:22 2023 -0700)
Update factory (079cb3e, Mark Bonicillo, Wed Feb 14 12:46:11 2024 -0800)
Update property_store (32eec45, Mark Bonicillo, Wed Feb 14 06:43:48 2024 -0800)
updating tests to function correctly. (62f51a1, audun myers, Mon Feb 12 15:04:41 2024 -0500)
Coding incidence store and adding incidence store tests (3c09b18, audun myers, Mon Feb 12 12:25:43 2024 -0500)
Update property_store, tests; add factory stubs (9d89948, Mark Bonicillo, Tue Feb 6 15:53:49 2024 -0800)
updating descriptions on hypergraph and entityset methods (8045e3f, audun myers, Thu Jan 18 10:22:52 2024 -0500)
HYP-367 Add factory method stubs for PropertyStoreFactory; update tests; add methods to HarryPotter toy (1128fe2, Mark Bonicillo, Tue Jan 16 16:10:20 2024 -0800)
Adding comments at top of each method in hypergraph.py and entityset.py for where new methods will belong in stores. (1ec92ec, audun myers, Wed Jan 17 12:45:42 2024 -0500)
update incidence view and hypview (83a3723, Brenda Praggastis, Wed Jan 24 14:04:40 2024 -0800)
updated hypview and incidence store (13248dd, Brenda Praggastis, Wed Jan 24 13:59:25 2024 -0800)
Adding more detailed stubs (3bbee81, audun myers, Tue Jan 16 11:56:19 2024 -0500)
Continued stubbing out incidenceStore (23471bf, audun myers, Tue Jan 16 11:31:20 2024 -0500)
HYP-367 Add stubs for PropertyStore (6a0c087, Mark Bonicillo, Mon Jan 15 17:09:09 2024 -0800)
Merge pull request #147 from wlruys/networkx3-support-develop (f37c169, Mark Bonicillo, Mon Mar 4 11:02:31 2024 -0800)
Update usage of deprecated NetworkX adjacency matrix to graph conversion function. (18b04a4, dialecticDolt, Fri Feb 16 19:55:21 2024 -0600)
Pull request #142: Release/v2.2.0 (d31c24d, Bonicillo, Mark A, Fri Mar 1 23:21:35 2024 +0000)
Pull request #141: Release/v2.2.0 (706d842, Bonicillo, Mark A, Fri Mar 1 23:01:05 2024 +0000)
Pull request #138: Hotfix/joss paper (87be2bc, Bonicillo, Mark A, Wed Feb 14 23:54:01 2024 +0000)

Full Changelog:pnnl/HyperNetX@v2.2.0...v2.3

`v2.2.0`: HNX v2.2.0

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Improvements

Update drawing submodule
Reorganize tutorials
Update documentation, README
Update dependencies
Update CI/CD scripts, Makefile
Updated tests

Fixes

Fixes minor bugs in Hypergraph constructor and helper method

What's Changed

dependencies: change python-igraph to igraph by @szhorvat in https://github.com/pnnl/HyperNetX/pull/117

New Contributors

@szhorvat made their first contribution in https://github.com/pnnl/HyperNetX/pull/117

Full Changelog: pnnl/HyperNetX@v2.1.4...v2.2.0

`v2.1.4`: HNX v.2.1.4

Compare Source

Fixes

Addresses JOSS-paper related issues: #142, #143, #144, and #145.
Updates optional dependencies

Full Changelog: pnnl/HyperNetX@v2.1.3...v2.1.4

`v2.1.3`: HNX v2.1.3

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codecov · 2024-12-10T12:50:55Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.82%. Comparing base (cf8cf8e) to head (da88a14).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #410      +/-   ##
==========================================
- Coverage   97.77%   96.82%   -0.96%     
==========================================
  Files          38       38              
  Lines        3557     3557              
==========================================
- Hits         3478     3444      -34     
- Misses         79      113      +34

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Update dependency hypernetx to v2

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Update to HyperNetX 2 #411

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Update dependency hypernetx to v2 #410

Update dependency hypernetx to v2 #410

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Update dependency hypernetx to v2 #410

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Release Notes

v2.3.9

Hotfixes

v2.3.8

Hotfixes

v2.3.7

Hotfixes

v2.3.6

Hotfixes

v2.3.5: HNX v2.3.5

v2.3.4: HNX v2.3.4

Hotfixes

v2.3.3: HNX v2.3.3

What's New

What's Changed

Fixes

v2.3.2: HNX v2.3.2

What's Changed

New Contributors

v2.3.1: HNX v2.3.1

Hotfixes

v2.3.0

Changed

Added

Removed

Fixed

Changelog from 2.2.0 to 2.3.0

v2.2.0: HNX v2.2.0

Improvements

Fixes

What's Changed

New Contributors

v2.1.4: HNX v.2.1.4

Fixes

v2.1.3: HNX v2.1.3

Configuration

codecov bot commented Dec 10, 2024

Codecov Report

`v2.3.9`

`v2.3.8`

`v2.3.7`

`v2.3.6`

`v2.3.5`: HNX v2.3.5

`v2.3.4`: HNX v2.3.4

`v2.3.3`: HNX v2.3.3

`v2.3.2`: HNX v2.3.2

`v2.3.1`: HNX v2.3.1

`v2.3.0`

`v2.2.0`: HNX v2.2.0

`v2.1.4`: HNX v.2.1.4

`v2.1.3`: HNX v2.1.3