v0.7.4

• Response to PyOpenSci review, fixing Issue #453 among other things #470 (@nwlandry).
• Fixed issues created from merging PR #380 #471 (@nwlandry).
• Added the capability to generate the complement of a hypergraph #380 (@acombretrenouard).
• Fixed the directionality of BiGG reactions (See Issue #458) #459 (@pietrotraversa, @nwlandry).
• Fixed Issue #461 #462 (@maximelucas).

v0.7.3

• Added the ashist() method to the stats module#452 (@nwlandry).
• Feature: return the node collections to allow a colorbar corresponding to node colors #441 (@maximelucas).
• Added tutorials: XGI in X minutes #415 (@thomasrobiglio).
• Fixed an empty edge error when loading BiGG data #447 (@nwlandry).
• Changed rho to an optional arg in the HPPM method #446 (@nwlandry).
• Added a cleanup() method to DiHypergraph and SimplicialComplex and added a connected argument to the Hypergraph method #440 (@nwlandry).
• Added encapsulation DAG functionality #444 (@tlarock).
• Refactored the multilayer drawing function to be more standard and added headers to convert module #434 (@nwlandry).
• Added the weights option to to_line_graph() function. #427 (@tlarock).
• Added the ability for users to access the optional arguments of NetworkX layout functions. #439 (@nwlandry).
• Fixed Issue #331 #438 (@maximelucas).
• Refactored the draw module #435 (@maximelucas).
• Feature: added the aspect keyword for drawing, addressing Issue #430 #432 (@maximelucas).

v0.7.2

• Listed the available statistics in the stats module #405 (@thomasrobiglio).
• Implemented functions from this article #400 (@maximelucas).
• Reorganized the convert module #423 (@nwlandry).
• Refactored the core data structures and removed the function.py file, moving the functions to other locations #412 (@nwlandry).
• Small documentation fixes #422 (@nwlandry).
• Added a webpage listing projects and papers that use XGI #416 (@nwlandry).
• Added an optinion so that only the text in the Jupyter Notebooks counts towards the line counts #417 (@nwlandry).
• Fixed the _color_arg_to_dict and _scalar_arg_to_dict functions so they are more consistent #402 (@nwlandry).
• Fixed the IDView.ids type #406 (@leotrs).

v0.7.1

• Fix: Converting from a SimplicialComplex to a Hypergraph now adds all of its faces to the hypergraph, not just the maximal faces. Added unit tests for converting between Hypergraph and SimplicialComplex classes #399 (@thomasrobiglio).
• Moved the list of contributors from the readthedocs, license, setup, etc. into a dedicated file so that when contributors join or leave, we only update a single file. Renamed CONTRIBUTING.md to HOW_TO_CONTRIBUTE.md. #401 (@nwlandry).
• Added the ability to convert from a simplex dict to a SimplicialComplex #397 (@thomasrobiglio).
• Updated index.rst to add the DiHypergraph class to the quick references #392 (@thomasrobiglio).
• Addressed Issue #393 by adding the ability for draw_hypergraph() to handle nodes with non-integer IDs and isolated nodes. #394 (@thomasrobiglio).
• Fixed the short description and landing page on PyPI so that it is more readable #391 (@nwlandry).

v0.7

• Added the functionality to load datasets from the BiGG database #384 (@nwlandry).
• Added the draw_dihypergraph() method to draw directed hypergraphs #387 (@thomasrobiglio).
• Changed "an hypergraph" to "a hypergraph" in the docstrings #386 (@acombretrenouard).
• Fixed mathematical expressions that were not represented properly in the docstrings part 2 #382 (@nwlandry).
• Fixed mathematical expressions that were not represented properly in the docstrings #381 (@nwlandry).
• Added the DiHypergraph class, directed view classes, and directed stats classes #372 (@nwlandry).
• Added Katz-centrality algorithm #370 (@acombretrenouard).
• Added the draw_multilayer() drawing function #369 (@thomasrobiglio).
• Fixed members() and memberships() methods so that views are read-only #371 (@nwlandry).
• Added shortest path algorithms #368 (@acombretrenouard).

v0.6

• Added new drawing layouts (circular_layout, spiral_layout, and barycenter_kamada_kawai_layout) #360 (@thomasrobiglio).

v0.5.8

• Formatted the codebase with ruff #346 (@leotrs).
• Improved the performance of flag_complex and random_flag_complex #355 (@maximelucas).
• Moved the IDDict class to utilities and removed unnecessary arguments in the IDView constructor #353 (@nwlandry).
• Up-versioned sphinx to v6.xxx and up-versioned sphinx-rtd-theme to >= 1.2 to be compatible with Sphinx v6.xxx. Updated the contribution guide and the GH, PyPI, and RTD landing pages #350 (@nwlandry).
• Fixed a bug in the double edge swap method #349 (@nwlandry)
• Updated the convert module methods to be able to return a hypergraph, addressing Issue #327. Now the conversion from a simplicial complex to a hypergraph only includes maximal faces #345 (@thomasrobiglio)
• Place a ceiling on IPython so that it is Python 3.8 compatible #344 (@nwlandry).
• Started fixing the cross references in the "See Also" section in the function/class docstrings #343 (@nwlandry).
• Feature: added complete_hypergraph #337 (@maximelucas).
• Updated the quickstart notebook #338 (@nwlandry).
• Added strict keyword to the maximal() method #332 (@nwlandry).
• Feature: added trivial hypergraph #335 (@maximelucas).

v0.5.7

• Changed the organization name to xgi-org and removed codecov from the test requirements file #334 (@nwlandry).
• Fix: improved the degree_counts documentation #329 (@maximelucas).
• Added the maximal() method to EdgeView, removed the maximal_simplices() method, and removed a bug from the duplicates() method #324 (@nwlandry).
• Fix: documented max_order in add_simplices_from() #328 (@maximelucas).
• Restructured folder for the generators and linalg modules #321 (@maximelucas).
• Added 3 clustering coefficient definitions to the algorithms module as well as to NodeStats #316 (@nwlandry).
• Added the ability to choose whether to output the index-to-ID mappings from to_bipartite_graph() method. Fixes #322 #323 (@leotrs).
• Added the ability to draw hypergraphs with hyperedges as convex hulls #320 (@thomasrobiglio).

v0.5.6

• Renamed convert_to_line_graph() to to_line_graph(), added an s parameter to the function, and added corresponding unit tests #318 (@nwlandry).
• Made the sparse warning in the adjacency_matrix() function more intelligible #315 (@nwlandry).
• Added a function for the normalized hypergraph laplacian #314 (@nwlandry).
• Added tests for draw functions #312 (@maximelucas).
• Updated the centrality functions so they more gracefully handle empty and disconnected hypergraphs #313 (@nwlandry).
• Added keep_isolates argument to the subhypergraph function #308 (@maximelucas).
• Fix: raise error for assortativity of empty hypergraph #307 (@maximelucas).
• Minor: renamed to from_max_simplices #306 (@maximelucas).

v0.5.5

• Refactored incidence_matrix() for ~4x speedup, made output consistent for empty matrices, added tests, and refactored multiorder_laplacian() so all internal variables are sparse if sparse=True. Fixes #301. #303 (@maximelucas).
• Renamed plotting functions, xgi_pylab module, and node/hyperedge/simplex plotting functions. All drawing functions now return axes. Added pca_transform() to rotate the node positions relative to the principal axes #300 (@nwlandry).
• Changed the Github actions to test all notebooks in the tutorial folder #299 (@nwlandry).
• Added the convert_to_line_graph() function and the vector_centrality() function, which uses it #290 (@goznalo-git).
• Fixed the quickstart notebook by updating the synchronization #294 (@nwlandry).
• Added more tests for the layout functions #296 (@maximelucas).
• Added basic tests for layout functions #293 (@maximelucas).
• Added tests for generators #291 (@maximelucas).
• Added the ability to specify sparsity in the matrix functions in the linalg module #284 (@nwlandry).
• Added the uniform_HSBM() and uniform_HPPM generative models #286 (@nwlandry).
• Up-versioned requirements to fix #287 and make compatible with NetworkX #288 (@nwlandry).
• Added code coverage with codecov and displayed coverage on main page #285 (@nwlandry).
• Fixed a bug in the add_edge() method #289 (@nwlandry).
• Added examples of sorting matrices by node/edge IDs to the documentation #282 (@nwlandry).
• Added the ability in draw() to plot any node positions by rescaling the plot area #279 (@maximelucas).