Merge branch 'fix-random-hypergraph' of https://github.com/xgi-org/xgi …

…into fix-random-hypergraph

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
     - uses: actions/checkout@v4
 
@@ -112,7 +112,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
     - uses: actions/checkout@v4
 

README.md

@@ -1,7 +1,7 @@
 <img src='https://github.com/xgi-org/xgi/blob/main/logo/logo.svg' alt="XGI" width='50%'></img>
 
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![Supports Python versions 3.8 and above.](https://img.shields.io/badge/Python%20versions%20supported-3.8%2B-forest
+[![Supports Python versions 3.9 and above.](https://img.shields.io/badge/Python%20versions%20supported-3.9%2B-forest
 )](https://www.repostatus.org/#active)
 [![Test Status](https://github.com/xgi-org/xgi/workflows/test/badge.svg?branch=main)](https://github.com/xgi-org/xgi/actions?query=workflow%3A%22test%22)
 [![codecov](https://codecov.io/gh/xgi-org/xgi/branch/main/graph/badge.svg?token=BI6TX2WDSG)](https://codecov.io/gh/xgi-org/xgi)
@@ -42,7 +42,7 @@ Comple**X** **G**roup **I**nteractions (**XGI**) is a Python package for higher-
 * Draw higher-order networks in a variety of **visually striking ways** (See our [gallery](https://xgi.readthedocs.io/en/stable/gallery.html) for several examples.)
 
 ## Installation<a id="installation"></a>
-XGI runs on Python 3.8 or higher.
+XGI runs on Python 3.9 or higher.
 
 To install the latest version of XGI, run the following command:
 ```sh

docs/source/api/algorithms.rst

@@ -11,5 +11,6 @@ algorithms package
    ~xgi.algorithms.centrality
    ~xgi.algorithms.clustering
    ~xgi.algorithms.connected
+   ~xgi.algorithms.properties
    ~xgi.algorithms.shortest_path
-   ~xgi.algorithms.properties
+   ~xgi.algorithms.simpliciality

docs/source/api/algorithms/xgi.algorithms.simpliciality.rst

@@ -0,0 +1,14 @@
+xgi.algorithms.simpliciality
+============================
+
+.. currentmodule:: xgi.algorithms.simpliciality
+
+.. automodule:: xgi.algorithms.simpliciality
+
+   .. rubric:: Functions
+
+   .. autofunction:: edit_simpliciality
+   .. autofunction:: simplicial_edit_distance
+   .. autofunction:: face_edit_simpliciality
+   .. autofunction:: mean_face_edit_distance
+   .. autofunction:: simplicial_fraction

docs/source/api/stats/xgi.stats.nodestats.rst

@@ -15,4 +15,7 @@
    .. autofunction:: h_eigenvector_centrality
    .. autofunction:: local_clustering_coefficient
    .. autofunction:: node_edge_centrality
-   .. autofunction:: two_node_clustering_coefficient
+   .. autofunction:: two_node_clustering_coefficient
+   .. autofunction:: local_simplicial_fraction
+   .. autofunction:: local_edit_simpliciality
+   .. autofunction:: local_face_edit_simpliciality

docs/source/installing.rst

@@ -13,7 +13,7 @@ To install XGI, execute the following in the command line:
    pip install xgi
 
 
-XGI was developed and tested for Python 3.8-3.12 on Mac OS, Windows, and Ubuntu.
+XGI was developed and tested for Python 3.9-3.13 on Mac OS, Windows, and Ubuntu.
 
 Once installed, go directly to the `User Guides <user_guides.html>`_ to get started!
 

docs/source/using-xgi.rst

@@ -42,6 +42,11 @@ Leonie Neuhäuser, Michael Scholkemper, Francesco Tudisco, and Michael T. Schaub
 :bdg-link-primary-line:`Paper <https://doi.org/10.1126/sciadv.adh4053>`
 :bdg-link-primary-line:`Code <https://git.rwth-aachen.de/netsci/publication-2023-learning-the-effective-order-of-a-hypergraph-dynamical-system>`
 
+Yuanzhao Zhang, Per Sebastian Skardal, Federico Battiston, Giovanni Petri, and Maxime Lucas, "Deeper but smaller: Higher-order interactions increase linear stability but shrink basins", *Science Advances* **10**,eado8049 (2024).
+
+:bdg-link-primary-line:`Paper <https://doi.org/10.1126/sciadv.ado8049>`
+:bdg-link-primary-line:`Code <https://github.com/maximelucas/basins_and_triangles>`
+
 2023
 ----
 
@@ -103,10 +108,6 @@ Gonzalo Contreras-Aso, Cristian Pérez-Corral, and Miguel Romance, "Uplifting ed
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2310.20335>`
 :bdg-link-primary-line:`Code <https://github.com/LaComarca-Lab/non-uniform-hypergraphs>`
 
-Yuanzhao Zhang, Per Sebastian Skardal, Federico Battiston, Giovanni Petri, and Maxime Lucas, "Deeper but smaller: Higher-order interactions increase linear stability but shrink basins", arXiv:2309.16581 (2023).
-
-:bdg-link-primary-line:`Paper <https://arxiv.org/abs/2309.16581>`
-:bdg-link-primary-line:`Code <https://github.com/maximelucas/basins_and_triangles>`
 
 Theses
 ======

pyproject.toml

@@ -7,7 +7,7 @@ name = "xgi"
 dynamic = ["version"]
 description = "XGI is a Python package for higher-order networks."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {file = "LICENSE.md"}
 authors = [
     {name = "XGI Developers", email = "[email protected]"}
@@ -30,11 +30,11 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3 :: Only",
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Topic :: Scientific/Engineering :: Bio-Informatics",