CHANGELOG.md

Changelog

v0.5.1

• draw() now correctly plots simplicial complexes with the max_order keyword #248 (@maximelucas).
• Changed the add_simplex method to be non recursive #247 (@maximelucas).
• Added tests for the SimplicialComplex class #245 (@maximelucas).
• Made all draw functions available from xgi #246 (@maximelucas).
• Added an indent to make hypergraph json files more readable #242 (@maximelucas).
• Improved the efficiency of the uid update function #239 (@nwlandry).
• Added the ability to display the node and hyperedge labels in draw() #234 (@mcontisc).
• Fixed the uid counter initialisation #225 (@maximelucas).
• Added the ability to pickle hypergraphs #229 (@nwlandry).
• Made random_hypergraph() and random_simplicialcomplex() faster #213 (@maximelucas).
• Fixed a bug in dynamical_assortativity() #230 (@nwlandry).
• Removed all random decorators #227 (@nwlandry).
• Modified unique_edge_sizes() so that the list of sizes is now sorted #226 (@nwlandry).
• Added the merge_duplicate_edges() function to merge multi-edges #210 (@nwlandry).
• Partial speed-up of draw function #211 (@iaciac).
• Added a simplicial synchronization function #212 (@Marconurisso).
• Sped up the add_simplices_from() method #223 (@maximelucas).
• Updated the add_simplices_from() method to match add_hyperedges_from() #220 (@maximelucas).

v0.5.0

• Fixed #214, added a powerset() function, added a subfaces() function, and added examples of these functions (#209).
• Refactored the NodeStats and EdgeStats classes to be more efficient (#209).
• Implemented set operations for NodeView and EdgeView (#208).
• Addressed #180 with density() and incidence_density() functions (#204 and #207).
• Added the << operator to "add" two hypergraphs together (#203).
• Improved the documentation (#202).
• Added Python 3.11 to the test suite (#201).
• Added an option to fill only some cliques with probabilities ps to xgi.flag_complex() (#200).
• Fixed Issue #198 (#199).
• Refactored load_xgi_data() to call dict_to_hypergraph() and fixed a bug in dict_to_hypergraph() (#193).
• Added num_edges_order() to get the number of edges of a given order and added an order parameter to the degree_counts() function (#192).
• Fixed #182 and #186 by adding a max_order argument to draw() and load_xgi_data() (#173) .
• Made draw() faster by refactoring _color_arg_to_dict() and _scalar_arg_to_dict() (#173).

Contributors: @leotrs, @maximelucas, and @nwlandry

v0.4.3

• Hypergraph.has_edge is now IDView.lookup, Hypergraph.duplicate_edges is now IDView.duplicates, and utilities.convert_labels_to_integer is now function.convert_labels_to_integer (#150).
• Added some unit tests for the convert module, the function module, and the classic generators module. Fixed for minor bugs encountered while writing tests and added documentation to Read The Docs for the drawing module. (#153)
• Fixed a bug in remove_node_from_edge() (#154).
• Implemented computation of moments for NodeStat and EdgeStat (#155).
• Implemented weak and strong node removal as per issue #167 (#156).
• Added a dynamics module and created a Kuramoto model synchronization function (#159).
• Added a cleanup method that removes artifacts specified by the user: multi-edges, singletons, isolates. It also can convert all labels to consecutive integers (#161).
• Modified the duplicates() method to not include the first instance of the node/edge in the list of duplicates (#161).
• Converted all instances of edges to sets from lists in response to issue #158 (#162).
• Added lambda function default arguments for $f$, $g$, $\varphi$, $\psi$ as defined by Tudisco and Higham. Default behavior is identical as before. Fixes #132 (#165).
• Added sum() as a stats method (#168).
• Added a benchmarking suite for the core hypergraph data structure using airspeed velocity (#170).
• Fixed issue #171 (#172)

Contributors: @nwlandry, @leotrs, and @saad1282

v0.4.2

• Keyword arguments are now consistent in the draw() function (#148).
• Notebooks are now formatted with black and the requirements have been updated to reflect this (#148).

Contributors: @nwlandry

v0.4.1

• Added the ability to color nodes and edges in xgi.draw() by value, iterable, or NodeStat/EdgeStat (#139, #142, and #143).
• Fixed the distortion of the node aspect ratio with different figure sizes in Issue #137.
• Moved the isolates() and singletons() method from the Hypergraph class to the NodeView and EdgeView classes respectively (#146).
• Fixed Hypergraph.copy() to not use the subhypergraph method (#145).
• filterby() now accepts NodeStat and EdgeStat objects instead of just strings (#144).
• Removed edit-mode install to run the Github Actions test suite (#136).
• Added unit tests (#147).

Contributors: @nwlandry, @leotrs, and @maximelucas

v0.4

• Added the stats package which implements NodeStat, EdgeStat and related functionality. This package now handles computation of edge size and degree (#120).
• Removed the EdgeSizeView and DegreeView classes (#120).
• Changed all imports to be relative in the xgi package (#121).
• Added an assortativity module (#122).
• Improved the performance of accessing edge members (#124).
• Added more operations for node and edge attributes besides "eq" (#125).
• Added a function to convert all node and edge labels to integers and store the old labels as properties (#127).
• • Renamed the egonet method to `edge_neighborhood (#129).
• Moved the neighbors method in the Hypergraph class to the IDView class so that node and edge neighbors are now supported (PR #129).
• Added a centrality module and added these methods to nodestats.py and edgestats.py (#130).
• Moved the load_xgi_data method to the readwrite module (#130).
• Added a generator for sunflower hypergraphs (#130).
• Added a Jupyter notebook as a quickstart guide (#131 and #134).
• Fixed a bug in the barycenter_spring_layout and weighted_barycenter_spring_layout methods to handle non-integer node IDs (#133).
• Added an isort configuration file so it no longer sorts the __init__.py files (#134).

Contributors: @leotrs, @nwlandry, and @iaciac

v0.3.1

• Refactored the subhypergraph methods
• Moved functions not related to the core Hypergraph data structure to functions.py
• Removed unnecessary duplicated functions (n_bunch_iter, get_edge_data, and has_node)
• Refactored the members() method as well as the NodeView and EdgeView classes for significant speedup.
• Github Actions now tests the docstrings and tutorial notebooks
• The add_edges_from method now supports different input formats.
• Fixed various bugs in the generative models module.
• A method for double edge swaps is now implemented.

Contributors: @leotrs and @nwlandry

v0.3

• Added the ability to convert to and from a NetworkX bipartite graph.
• Removed the shape property from Hypergraph and renamed the number_of_nodes() and number_of_edges() methods to the num_nodes and num_edges properties, respectively.
• Added random seed decorator as in NetworkX.
• Added a SimplicialComplex class.
• Added order and weighted arguments to the incidence_matrix and adjacency_matrix functions.
• Added an intersection_profile function.
• Added a laplacian function with argument order and a multiorder_laplacian function.
• Fix: Return an empty array rather than a 1x1 zero array when appropriate.
• Fix: Ensured that the incidence matrix is always has dimensions num_nodes x num_edges.
• Added 2 generators of random (maximal) simplicial complexes, and toy star-clique generator
• Extensively rewrote the documentation, updating the content and format on Read The Docs.
• Added an egonet function to get the edges neighboring a specified node.
• Added functions to visualize hypergraphs and simplicial complexes.
• Added the ability to get nodes and edges of given degrees/sizes respectively.
• Extended the members() function to be able to get different data types and to either get a single edge or all edges.
• Added the load_xgi_data function to load datasets from the xgi-data repository.
• Added two additional tutorials: a tutorial on visualizing higher-order networks and a case study replicating a recent paper.
• Changed the API of degree_histogram and added degree_counts based on #23.
• Refactored the IDDegreeView class and changed the API. Added the ability to specify order and the datatype.
• Added an abstract class IDDict to handle data validation.

Contributors: @iaciac, @leotrs, @lordgrilo, @maximelucas, @nwlandry, and @tlarock

v0.2

• H[attr] now accesses hypergraph attributes
• H.nodes[id] now accesses attributes, not bipartite neighbors
• Removed the__call__() functionality from H.nodes and H.edges
• H.nodes.memberships(id) and H.edges.members(id) now access the bipartite neighbors
• Created base classes for the Node/Edge Views and Degree/Edge Size Views to inherit from.
• Removed the NodeDataView and EdgeDataView.
• Updated the list of developers
• __getitem__() in the NodeView and EdgeView are now in a try-except block for greater efficiency.
• Removed the name attribute and fixed methods and tests to match.
• Fixed the erdos_renyi_hypergraph(), chung_lu_hypergraph(), and dcsbm_hypergraph() methods such that the number of nodes will always match the number the user specifies, even if the resulting hypergraph is disconnected.
• Changed the construction method from reading in a Pandas DataFrame to using the add_node_to_edge() method for a 2x speedup.
• Added some basic unit tests for the generative models.
• Added the dual keyword for the read_bipartite_edgelist() method.
• Added small functions to the Hypergraph class
• Added generator of random hypergraph
• Added functions for finding and removing isolates
• Refactored the has_edge() method in the Hypergraph class.

Contributors: @leotrs, @maximelucas, and @nwlandry