Fix messy notebook diffs. Merge branch 'main' into add-draw-bipartite

.github/workflows/check-urls.yml

@@ -0,0 +1,27 @@
+name: Check URLs
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: urls-checker
+      uses: urlstechie/urlchecker-action@master
+      with:
+        # A comma-separated list of file types to cover in the URL checks
+        file_types: .md,.py,.rst,ipynb
+
+        # Choose whether to include file with no URLs in the prints.
+        print_all: false
+
+        # The timeout seconds to provide to requests, defaults to 5 seconds
+        timeout: 5
+
+        # How many times to retry a failed request (each is logged, defaults to 1)
+        retry_count: 3
+
+        # choose if the force pass or not
+        force_pass : false

.github/workflows/publish_xgi.yml

@@ -0,0 +1,41 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload XGI to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools
+    - name: Build package
+      run: |
+        python setup.py sdist
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        skip-existing: true

CHANGELOG.md

@@ -1,5 +1,18 @@
 # Changelog
 
+## v0.8.2
+* Added an XGI-DATA page to ReadTheDocs with network statistics [#496](https://github.com/xgi-org/xgi/pull/496) (@nwlandry).
+* Added syntax highlighting in the tutorials [#497](https://github.com/xgi-org/xgi/pull/497) (@thomasrobiglio).
+* Changed the xgi-data index location to Github to support the move to Zenodo-hosted datasets [#494](https://github.com/xgi-org/xgi/pull/494) (@nwlandry)
+* Update the list of publications using XGI [#493](https://github.com/xgi-org/xgi/pull/493) (@nwlandry).
+
+## v0.8.1
+* Added the ability to draw a convex hull as an option in `draw_hyperedges` [#491](https://github.com/xgi-org/xgi/pull/491) (@maximelucas).
+* Fixed sphinx documentation errors [#487](https://github.com/xgi-org/xgi/pull/487) (@nwlandry).
+* Rewrote the `draw_multilayer` function [#486](https://github.com/xgi-org/xgi/pull/486) (@maximelucas).
+* Updated the "Projects Using XGI" page [#489](https://github.com/xgi-org/xgi/pull/489) (@nwlandry).
+* Added support for Python 3.12 [#488](https://github.com/xgi-org/xgi/pull/488) (@nwlandry).
+
 ## v0.8
 * Made `IDViews` respect edge insertion order in the `from_view` method [#482](https://github.com/xgi-org/xgi/pull/482) (@nwlandry).
 * Fixed issues in drawing functions [#476](https://github.com/xgi-org/xgi/pull/476) (@maximelucas).

README.md

@@ -66,7 +66,7 @@ To get started, take a look at the [tutorials](https://xgi.readthedocs.io/en/sta
 
 
 ## Corresponding Data
-A number of higher-order datasets are available in the [XGI-DATA repository](https://gitlab.com/complexgroupinteractions/xgi-data) and can be easily accessed with the `load_xgi_data()` function.
+A number of higher-order datasets are available in the [XGI-DATA repository](https://github.com/xgi-org/xgi-data) and can be easily accessed with the `load_xgi_data()` function.
 
 
 ## How to Contribute

docs/source/_static/custom.css

@@ -3,3 +3,31 @@
     margin-block-end: 0;
     padding-inline-start: 0.5em;
 }
+
+table {
+    font-family: Arial, Helvetica, sans-serif;
+    border-collapse: collapse;
+    width: 100%;
+}
+
+td, th {
+    border: 1px solid #ddd;
+    padding: 8px;
+}
+
+td a {
+    width: 100%;
+    display: block;
+}
+
+table tr:nth-child(even){background-color: #f2f2f2;}
+
+table tr:hover {background-color: #ddd;}
+
+th {
+    padding-top: 12px;
+    padding-bottom: 12px;
+    text-align: left;
+    background-color: #04AA6D;
+    color: white;
+}

docs/source/_static/table.js

@@ -0,0 +1,75 @@
+async function fetch_JSON_file(url) {
+    try {
+    const response = await fetch(url);
+
+    if (!response.ok) {
+       throw new Error(response);
+    }
+
+    const json_data = await response.json();
+    return json_data;
+    } catch (error) {
+    console.error('Error fetching JSON:', error);
+    }
+ }
+
+ function create_table(json_data) {
+    const body = document.body;
+    const section = document.getElementById("network-statistics")
+    const table = document.createElement('table');
+    const table_header = document.createElement('thead')
+    const table_body = document.createElement('tbody')
+
+    // Create header row
+    const header_row = document.createElement('tr');
+    const headers = ["Dataset", "|V|", "|E|", "|E<sub>unique</sub>|", "s<sub>max</sub>"]
+    const header_attrs = ["num-nodes", "num-edges", "num-unique-edges", "max-edge-size"]
+
+    for (const i in headers) {
+        const h = document.createElement('th');
+        h.innerHTML = headers[i];
+        header_row.appendChild(h)
+    }
+    table_header.appendChild(header_row)
+
+    // Create data rows
+    for (const key in json_data) {
+        const data_row = document.createElement('tr');
+
+        // dataset name
+        const td_name = document.createElement('td');
+        const url = json_data[key]["url"].split("/files")[0]
+        td_name.innerHTML = '<a href=' + url + '>' + key + '</a>';
+        data_row.appendChild(td_name);
+
+        for (const i in header_attrs){
+            const td = document.createElement('td');
+            const attr = header_attrs[i]
+            if (json_data[key][attr]) {
+                td.textContent = json_data[key][attr];
+            }
+            else {
+                td.textContent = "N/A"
+            }
+            data_row.appendChild(td);
+        }
+        table_body.appendChild(data_row);
+    }
+    table.appendChild(table_header)
+    table.appendChild(table_body)
+    console.log(table)
+    section.appendChild(table);
+ }
+
+ function display_table(){
+    url = 'https://raw.githubusercontent.com/xgi-org/xgi-data/main/index.json';
+    data = fetch_JSON_file(url)
+    .then(data => {
+       // Handle the JSON data
+       create_table(data);
+    })
+    .catch(error => {
+       // Handle errors
+       console.error('Error:', error);
+    });
+ }

docs/source/api/linalg/xgi.linalg.laplacian_matrix.rst

@@ -8,4 +8,5 @@ xgi.linalg.laplacian_matrix
    .. rubric:: Functions
 
    .. autofunction:: laplacian
+   .. autofunction:: multiorder_laplacian
    .. autofunction:: normalized_hypergraph_laplacian

docs/source/api/tutorials/XGI in 15 minutes.ipynb

@@ -28,7 +28,7 @@
    "source": [
     "## Uploading a dataset\n",
     "\n",
-    "In this tutorial we will construct a hypergraph describing real world data! With XGI we provide a companion data repository, [xgi-data](https://gitlab.com/complexgroupinteractions/xgi-data), with which you can easely load several datasets in standard format:"
+    "In this tutorial we will construct a hypergraph describing real world data! With XGI we provide a companion data repository, [xgi-data](https://github.com/xgi-org/xgi-data), with which you can easely load several datasets in standard format:"
    ]
   },
   {

docs/source/api/tutorials/case_study_zhang2022.ipynb

@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "417f4911",
    "metadata": {},
@@ -15,9 +14,9 @@
    "metadata": {},
    "source": [
     "Here, using XGI, we reproduce figures 1 and 2 of the paper  \n",
-    "\"Do higher-order interactions promote synchronization?\"  \n",
+    "\"Higher-order interactions shape collective dynamics differently in hypergraphs and simplicial complexes\"  \n",
     "Yuanzhao Zhang *, Maxime Lucas *, Federico Battiston  \n",
-    "[arXiv:2203.03060](https://doi.org/10.48550/arXiv.2203.03060)"
+    "[Nature Communications, 14(1), 2023, p.1605](https://doi.org/10.1038/s41467-023-37190-9)"
    ]
   },
   {
@@ -470,7 +469,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.10.6 ('venv': venv)",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -484,7 +483,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.18"
   },
   "toc": {
    "base_numbering": 1,

docs/source/api/tutorials/focus_tutorials.rst

@@ -12,5 +12,4 @@
     Tutorial 4 - Generative_Models
     Tutorial 5 - Plotting
     Tutorial 6 - Statistics
-    Tutorial 7 - Convex hulls hypergraph plotting
-    Tutorial 8 - Directed Hypergraphs
+    Tutorial 7 - Directed Hypergraphs

docs/source/conf.py

@@ -21,7 +21,7 @@
 # -- Project information -----------------------------------------------------
 project = "XGI"
 copyright = "Copyright (C) 2021-2023 XGI Developers"
-release = "0.8"
+release = "0.8.2"
 
 # -- General configuration ---------------------------------------------------
 
@@ -62,6 +62,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 html_css_files = ["custom.css"]
+html_js_files = ["table.js"]
 
 # If your documentation needs a minimal Sphinx version, state it here.
 needs_sphinx = "1.3"

docs/source/index.rst

@@ -10,6 +10,7 @@
    about
    contributors
    higher-order
+   xgi-data
    gallery
    using-xgi
 
@@ -106,7 +107,7 @@ XGI was developed and tested for Python 3.8-3.12 on Mac OS, Windows, and Ubuntu.
 Corresponding Data
 ==================
 
-A number of higher-order datasets are available in the `XGI-DATA repository <https://gitlab.com/complexgroupinteractions/xgi-data>`_ and can be easily accessed with the ``load_xgi_data()`` function.
+A number of higher-order datasets are available in the `XGI-DATA repository <https://github.com/xgi-org/xgi-data>`_ and can be easily accessed with the ``load_xgi_data()`` function.
 
 
 Contributing

docs/source/using-xgi.rst

@@ -12,20 +12,30 @@ Published work
 2023
 ----
 
+Gonzalo Contreras-Aso, Regino Criado, Guillermo Vera de Salas, and Jinling Yang, "Detecting communities in higher-order networks by using their derivative graphs", *Chaos, Solitons, and Fractals* **177**, 114200 (2023).
+
+:bdg-link-primary-line:`Paper <https://doi.org/10.1016/j.chaos.2023.114200>`
+:bdg-link-primary-line:`Code <https://github.com/LaComarca-Lab/HyperGraph-Communities>`
+
 Nicholas W. Landry and Juan Restrepo, "Opinion disparity in hypergraphs with community structure", *Physical Review E* **108**, 034311 (2023).
 
 :bdg-link-primary-line:`Paper <https://doi.org/10.1103/PhysRevE.108.034311>`
-:bdg-link-primary-line:`Github <https://github.com/nwlandry/opinion-disparity-in-hypergraphs>`
+:bdg-link-primary-line:`Code <https://github.com/nwlandry/opinion-disparity-in-hypergraphs>`
+
+Timothy LaRock and Renaud Lambiotte, "Encapsulation Structure and Dynamics in Hypergraphs", *Journal of Physics: Complexity* **4**, 045007 (2023).
+
+:bdg-link-primary-line:`Paper <https://doi.org/10.1088/2632-072X/ad0b39>`
+:bdg-link-primary-line:`Code <https://github.com/tlarock/encapsulation-dynamics>`
 
 Nicolò Ruggieri, Martina Contisciani, Federico Battiston, and Caterina de Bacco, "Community detection in large hypergraphs", *Science Advances* **9**, eadg9159 (2023).
 
 :bdg-link-primary-line:`Paper <https://doi.org/10.1126/sciadv.adg9159>`
-:bdg-link-primary-line:`Github <https://github.com/nickruggeri/Hy-MMSBM>`
+:bdg-link-primary-line:`Code <https://github.com/nickruggeri/Hy-MMSBM>`
 
 Yuanzhao Zhang, Maxime Lucas, and Federico Battiston, "Higher-order interactions shape collective dynamics differently in hypergraphs and simplicial complexes", *Nature Communications* **14**, 1605 (2023).
 
 :bdg-link-primary-line:`Paper <http://doi.org/10.1038/s41467-023-37190-9>`
-:bdg-link-primary-line:`Github <https://github.com/maximelucas/HOI_shape_sync_differently>`
+:bdg-link-primary-line:`Code <https://github.com/maximelucas/HOI_shape_sync_differently>`
 
 
 Preprints
@@ -34,34 +44,38 @@ Preprints
 2023
 ----
 
+Gonzalo Contreras-Aso, Cristian Pérez-Corral, and Miguel Romance, "Uplifting edges in higher order networks: spectral centralities for non-uniform hypergraphs", arXiv:2310.20335 (2023).
+
+:bdg-link-primary-line:`Paper <https://arxiv.org/abs/2310.20335>`
+:bdg-link-primary-line:`Code <https://github.com/LaComarca-Lab/non-uniform-hypergraphs>`
+
 Iacopo Iacopini, Márton Karsai, and Alain Barrat, "The temporal dynamics of group interactions in higher-order social networks", arXiv:2306.09967 (2023).
 
 :bdg-link-primary-line:`Paper <https://arxiv.org/abs/2306.09967>`
 
 Nicholas W. Landry, Ilya Amburg, Mirah Shi, and Sinan Aksoy, "Filtering higher-order datasets", arXiv:2305.06910 (2023).
 
 :bdg-link-primary-line:`Paper <http://arxiv.org/abs/2305.06910>`
-:bdg-link-primary-line:`Github <https://github.com/nwlandry/filtering-higher-order-datasets>`
+:bdg-link-primary-line:`Code <https://github.com/nwlandry/filtering-higher-order-datasets>`
 
 Nicholas W. Landry, Jean-Gabriel Young, and Nicole Eikmeier, "The simpliciality of higher-order networks", arXiv:2308.13918 (2023).
 
 :bdg-link-primary-line:`Paper <https://doi.org/10.48550/arXiv.2308.13918>`
-:bdg-link-primary-line:`Github <https://github.com/nwlandry/the-simpliciality-of-higher-order-networks>`
-
-Timothy LaRock and Renaud Lambiotte, "Encapsulation Structure and Dynamics in Hypergraphs", arXiv:2307.04613 (2023).
-
-:bdg-link-primary-line:`Paper <https://arxiv.org/abs/2307.04613>`
-:bdg-link-primary-line:`Github <https://github.com/tlarock/encapsulation-dynamics>`
+:bdg-link-primary-line:`Code <https://github.com/nwlandry/the-simpliciality-of-higher-order-networks>`
 
 Yuanzhao Zhang, Per Sebastian Skardal, Federico Battiston, Giovanni Petri, 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:`Github <https://github.com/maximelucas/basins_and_triangles>`
+:bdg-link-primary-line:`Code <https://github.com/maximelucas/basins_and_triangles>`
 
 
 Theses
 ======
 
+Leonie Neuhäuser, "Modelling the effect of groups on network structure and dynamics", (2023).
+
+:bdg-link-primary-line:`Thesis <https://doi.org/10.18154/RWTH-2023-08686>`
+
 Thomas Robiglio, "Higher-order structures in face-to-face interaction networks", (2023).
 
 :bdg-link-primary-line:`Thesis <https://webthesis.biblio.polito.it/27942/>`