xgi-org · maximelucas · Oct 24, 2024 · Oct 23, 2024 · Oct 23, 2024 · Oct 23, 2024
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
+# Generated while building documentation.
+doc/auto_examples
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css
@@ -55,10 +55,7 @@ html[data-theme="light"] table.data tbody tr:nth-child(even) {
     background-color: #ffffff; /* Lighter gray */
 }
 
-/* Fixed width for the navbar items */
-.bd-header ul.navbar-nav {
-    width: 475px;
-}
+
 /* Remove whitespace to the right of the xgi logo */
 .bd-header .navbar-header-items__start {
     width: 100px;

diff --git a/docs/source/assets/images/Filtering_2024_Fig1.png b/docs/source/assets/images/Filtering_2024_Fig1.png
diff --git a/docs/source/assets/images/Simpliciality_2023_Fig3.png b/docs/source/assets/images/Simpliciality_2023_Fig3.png
diff --git a/docs/source/assets/images/XGI_2023_Fig2.png b/docs/source/assets/images/XGI_2023_Fig2.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -14,6 +14,7 @@
 import os
 import sys
 from datetime import date, datetime
+from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
 
 import requests
 
@@ -87,6 +88,7 @@
     "sphinx.ext.viewcode",
     "sphinx_copybutton",
     "sphinx_design",
+    "sphinx_gallery.gen_gallery",
     "nbsphinx",
     "nbsphinx_link",
 ]
@@ -231,7 +233,7 @@
             "icon": "fab fa-twitter-square",  # Font Awesome icon
         },
     ],
-    "header_links_before_dropdown": 4,
+    "header_links_before_dropdown": 5,
     "switcher": {
         "json_url": (
             "https://xgi.readthedocs.io/en/latest/_static/version_switcher.json"
@@ -247,6 +249,7 @@
     "installing": [],
     "tutorial": [],
     "xgi-data": [],
+    "auto_examples/index": [],
     "gallery": [],
     "contribute": [],
     "user_guides": [],
@@ -261,6 +264,27 @@
 
 htmlhelp_basename = "XGIDoc"
 
+# -- Options for Sphinx Gallery ----------------------
+
+
+sphinx_gallery_conf = {
+    # path to your examples scripts
+    "examples_dirs": "../../examples",
+    "subsection_order": ExplicitOrder(
+        [
+            "../../examples/basic",
+            "../../examples/layouts",
+            "../../examples/stats",
+            "../../examples/advanced",
+        ]
+    ),
+    "within_subsection_order": "FileNameSortKey",
+    # path where to save gallery generated examples
+    "gallery_dirs": "auto_examples",
+    "plot_gallery": "True",
+    "image_scrapers": ("matplotlib",),
+}
+
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {

diff --git a/docs/source/gallery.rst b/docs/source/gallery.rst
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -15,9 +15,9 @@
    user_guides
    api_reference
    xgi-data
+   auto_examples/index
    contribute
    using-xgi
-   gallery
 
 |release_announcement|
 

diff --git a/docs/source/sg_execution_times.rst b/docs/source/sg_execution_times.rst
@@ -0,0 +1,67 @@
+
+:orphan:
+
+.. _sphx_glr_sg_execution_times:
+
+
+Computation times
+=================
+**00:00.327** total execution time for 11 files **from all galleries**:
+
+.. container::
+
+  .. raw:: html
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. list-table::
+   :header-rows: 1
+   :class: table table-striped sg-datatable
+
+   * - Example
+     - Time
+     - Mem (MB)
+   * - :ref:`sphx_glr_auto_examples_advanced_plot_colormaps_colorbars.py` (``../../examples/advanced/plot_colormaps_colorbars.py``)
+     - 00:00.047
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_stats_plot_color_stat.py` (``../../examples/stats/plot_color_stat.py``)
+     - 00:00.042
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_basic_plot_simple_hypergraph_multilayer.py` (``../../examples/basic/plot_simple_hypergraph_multilayer.py``)
+     - 00:00.035
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_basic_plot_simple_hypergraph.py` (``../../examples/basic/plot_simple_hypergraph.py``)
+     - 00:00.033
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_advanced_plot_labels.py` (``../../examples/advanced/plot_labels.py``)
+     - 00:00.030
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_basic_plot_simple_hypergraph_hull.py` (``../../examples/basic/plot_simple_hypergraph_hull.py``)
+     - 00:00.026
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_basic_plot_simple_simplicial_complex.py` (``../../examples/basic/plot_simple_simplicial_complex.py``)
+     - 00:00.025
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_basic_plot_simple_hypergraph_outline.py` (``../../examples/basic/plot_simple_hypergraph_outline.py``)
+     - 00:00.024
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_layouts_plot_barycenter_spring_layout.py` (``../../examples/layouts/plot_barycenter_spring_layout.py``)
+     - 00:00.023
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_layouts_plot_simple_graph.py` (``../../examples/layouts/plot_simple_graph.py``)
+     - 00:00.022
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_layouts_plot_spiral_layout.py` (``../../examples/layouts/plot_spiral_layout.py``)
+     - 00:00.021
+     - 0.0
diff --git a/examples/GALLERY_HEADER.txt b/examples/GALLERY_HEADER.txt
@@ -0,0 +1,4 @@
+Gallery
+==================
+
+Introductory examples to XGI.
diff --git a/examples/advanced/README.txt b/examples/advanced/README.txt
@@ -0,0 +1,2 @@
+Advanced
+--------
diff --git a/examples/advanced/plot_colormaps_colorbars.py b/examples/advanced/plot_colormaps_colorbars.py
@@ -0,0 +1,35 @@
+"""
+========================
+Colormaps and colorbars
+========================
+
+Set colormaps and show colorbars.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+
+fig, ax = plt.subplots(figsize=(6, 2.5))
+
+ax, collections = xgi.draw(
+    H,
+    pos=pos,
+    node_fc=H.nodes.degree,
+    edge_fc=H.edges.size,
+    edge_fc_cmap="viridis",
+    node_fc_cmap="mako_r",
+)
+
+node_col, _, edge_col = collections
+
+plt.colorbar(node_col, label="Node degree")
+plt.colorbar(edge_col, label="Edge size")
+
+plt.show()
diff --git a/examples/advanced/plot_labels.py b/examples/advanced/plot_labels.py
@@ -0,0 +1,20 @@
+"""
+=================
+Show labels
+=================
+
+Draw hypergraph with labels.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+xgi.draw(H, pos=pos, node_labels=True, node_size=15, hyperedge_labels=True)
+
+plt.show()
diff --git a/examples/basic/README.txt b/examples/basic/README.txt
@@ -0,0 +1,2 @@
+Basic
+-----
diff --git a/examples/basic/plot_simple_hypergraph.py b/examples/basic/plot_simple_hypergraph.py
@@ -0,0 +1,20 @@
+"""
+=================
+Simple hypergraph
+=================
+
+Draw simple hypergraph with manual layout.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+xgi.draw(H, pos=pos)
+
+plt.show()
diff --git a/examples/basic/plot_simple_hypergraph_hull.py b/examples/basic/plot_simple_hypergraph_hull.py
@@ -0,0 +1,20 @@
+"""
+===================================
+Simple hypergraph with convex hulls
+===================================
+
+Draw simple hypergraph with convex hulls and manual layout.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+xgi.draw(H, pos=pos, hull=True)
+
+plt.show()
diff --git a/examples/basic/plot_simple_hypergraph_multilayer.py b/examples/basic/plot_simple_hypergraph_multilayer.py
@@ -0,0 +1,20 @@
+"""
+===================================
+Simple hypergraph as multilayer
+===================================
+
+Draw simple hypergraph as multilayer
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+ax3 = plt.axes(projection="3d")  # requires a 3d axis
+xgi.draw_multilayer(H, ax=ax3)
+
+plt.show()
diff --git a/examples/basic/plot_simple_hypergraph_outline.py b/examples/basic/plot_simple_hypergraph_outline.py
@@ -0,0 +1,20 @@
+"""
+===================================
+Simple hypergraph with outline
+===================================
+
+Draw simple hypergraph with outline and manual layout.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+xgi.draw(H, pos=pos, hull=True, edge_fc="white")
+
+plt.show()
diff --git a/examples/basic/plot_simple_simplicial_complex.py b/examples/basic/plot_simple_simplicial_complex.py
@@ -0,0 +1,20 @@
+"""
+=========================
+Simple simplicial complex
+=========================
+
+Draw simple simplicial complex with manual layout.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.SimplicialComplex(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+xgi.draw(H, pos=pos)
+
+plt.show()
diff --git a/examples/layouts/README.txt b/examples/layouts/README.txt
@@ -0,0 +1,2 @@
+Layouts
+-------
diff --git a/examples/layouts/plot_barycenter_spring_layout.py b/examples/layouts/plot_barycenter_spring_layout.py
@@ -0,0 +1,20 @@
+"""
+=================
+Barycenter spring 
+=================
+
+Draw simple hypergraph with barycenter_spring layout.
+"""
+
+import matplotlib.pyplot as plt
+
+import xgi
+
+hyperedges = [[1, 2, 3], [3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]]
+H = xgi.Hypergraph(hyperedges)
+
+
+pos = xgi.barycenter_spring_layout(H, seed=1)
+xgi.draw(H, pos=pos)
+
+plt.show()