Migrating to the PyData theme for the online docs

docs/source/api/recipes.rst

@@ -1,3 +1,5 @@
+.. _recipes:
+
 ##################
 Recipes
 ##################

docs/source/api/tutorials/focus.rst

@@ -1,5 +1,7 @@
+.. _focus_tutorials:
+
 ################
- Focus tutorials
+Focus tutorials
 ################
 
 
@@ -12,4 +14,9 @@
     focus_4
     focus_5
     focus_6
-    focus_7
+    focus_7
+
+.. seealso:: 
+
+   This is now too easy and you want to dive deeper into some features of XGI?
+   Go to the `In-depth Tutorials <in_depth.html>`_.

docs/source/api/tutorials/getting_started.rst

@@ -1,3 +1,5 @@
+.. _xgi_in_x_minutes:
+
 ###############
 Getting started
 ###############
@@ -7,4 +9,11 @@ Getting started
 
    getting_started_1
    getting_started_2
-   getting_started_3
+   getting_started_3
+
+
+
+.. seealso:: 
+
+   This is now too easy and you want to explore more of what XGI can do?
+   Go to the `Focus Tutorials <focus.html>`_.

docs/source/api/tutorials/in_depth.rst

@@ -1,3 +1,6 @@
+.. _indepth_tutorials:
+
+
 ##################
 In Depth tutorials
 ##################

docs/source/conf.py

@@ -20,8 +20,10 @@
 
 # -- Project information -----------------------------------------------------
 project = "XGI"
-copyright = "Copyright (C) 2021-2024 XGI Developers"
+copyright = "2021-2024 XGI Developers"
 release = "0.8.9"
+version = release
+today = "30-08-2024"
 
 # -- General configuration ---------------------------------------------------
 
@@ -130,7 +132,7 @@
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-# add_module_names = True
+add_module_names = False
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
@@ -154,17 +156,53 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "sphinx_rtd_theme"
+html_theme = "pydata_sphinx_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-# html_theme_options = {}
+html_theme_options = {
+    "navbar_end": [
+        "navbar-icon-links",
+    ],  # Place the social links at the end of the navbar
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://xgi.readthedocs.io/",
+            "icon": "fab fa-github-square",  # Font Awesome icon
+        },
+        {
+            "name": "Twitter",
+            "url": "https://twitter.com/xginets",
+            "icon": "fab fa-twitter-square",  # Font Awesome icon
+        },
+        {
+            "name": "Mastodon",
+            "url": "https://mathstodon.xyz/@xginets",
+            "icon": "fa-brands fa-mastodon",  # Font Awesome icon
+        },
+    ],
+}
+
+
+html_sidebars = {
+    "**": ["sidebar-nav-bs", "sidebar-ethical-ads"],
+    "index": [],
+    "installing": [],
+    "tutorial": [],
+    "xgi-data": [],
+    "gallery": [],
+    "contribute": [],
+    "user_guides": [],
+    "using-xgi": [],
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = ["_static"]
 # html_static_path = ["_static"]
 
+html_logo = "../../logo/logo.svg"
+
 html_show_sphinx = True
 
 htmlhelp_basename = "XGIDoc"

docs/source/contribute.rst

@@ -0,0 +1,189 @@
+.. _contribute:
+
+****************
+Development
+****************
+
+
+Contribute
+==========
+
+If you want to contribute to this project, please make sure to read the
+`contributing guidelines <https://github.com/xgi-org/xgi/blob/main/HOW_TO_CONTRIBUTE.md>`_.
+We expect respectful and kind interactions by all contributors and users
+as laid out in our `code of conduct <https://github.com/xgi-org/xgi/blob/main/CODE_OF_CONDUCT.md>`_.
+
+The XGI community always welcomes contributions, no matter how small.
+We're happy to help troubleshoot XGI issues you run into,
+assist you if you would like to add functionality or fixes to the codebase,
+or answer any questions you may have.
+
+Some concrete ways that you can get involved:
+
+* **Get XGI updates** by following the XGI `Twitter <https://twitter.com/xginets>`_ account, signing up for our `mailing list <http://eepurl.com/igE6ez>`_, or starring this repository.
+* **Spread the word** when you use XGI by sharing with your colleagues and friends.
+* **Request a new feature or report a bug** by raising a `new issue <https://github.com/xgi-org/xgi/issues/new>`_.
+* **Create a Pull Request (PR)** to address an `open issue <https://github.com/xgi-org/xgi/issues>`_ or add a feature.
+* **Join our Zulip channel** to be a part of the `daily goings-on of XGI <https://xgi.zulipchat.com/join/7agfwo7dh7jo56ppnk5kc23r/>`_.
+
+
+Contributors
+============
+
+The XGI project has been helped by invaluable contributions from many members of the community. All listings are alphabetical.
+
+Core team
+---------
+
+.. raw:: html
+
+    <p>
+        <img src="https://github.com/acuschwarze.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/acuschwarze">@acuschwarze</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/alpatania.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/alpatania">@alpatania</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/iaciac.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/iaciac">@iaciac</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/leotrs.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/leotrs">@leotrs</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/lordgrilo.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/lordgrilo">@lordgrilo</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/maximelucas.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/maximelucas">@maximelucas</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/nwlandry.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/nwlandry">@nwlandry</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/tlarock.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/tlarock">@tlarock</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/thomasrobiglio.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/thomasrobiglio">@thomasrobiglio</a>
+    </p>
+
+
+Core team alumni
+----------------
+
+.. raw:: html
+
+    <p>
+        <img src="https://github.com/mcontisc.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/mcontisc">@mcontisc</a>
+    </p>
+
+Contributors
+------------
+
+.. raw:: html
+
+    <p>
+        <img src="https://github.com/acombretrenouard.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/acombretrenouard">@acombretrenouard</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/aleable.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/aleable">@aleable</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/arnaudon.png"
+                width="50" height="50" hspace="5"
+                style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/arnaudon">@arnaudon</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/colltoaction.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/colltoaction">@colltoaction</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/doabell.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/doabell">@doabell</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/goznalo-git.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/goznalo-git">@goznalo-git</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/marconurisso.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/marconurisso">@marconurisso</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/pgberlureau.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/pgberlureau">@pgberlureau</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/pietrotraversa.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/pietrotraversa">@pietrotraversa</a>
+    </p>
+
+    <p>
+        <img src="https://github.com/saad1282.png"
+            width="50" height="50" hspace="5"
+            style="border-radius: 50%; vertical-align: middle;"/>
+        <a href="https://github.com/saad1282">@saad1282</a>
+    </p>

docs/source/higher-order.rst

@@ -9,4 +9,19 @@ A *higher-order network* is formed by the collection of these higher-order inter
 Why higher-order interactions?
 ==============================
 
-Higher-order interactions can reveal more nuanced and sophisticated patterns of connection and can naturally encode different scales of interaction which are inaccessible to pairwise network representations. Higher-order networks can be helpful for describing social networks, ecological communities, co-authorship or citation networks, email, protein interactions, and many more examples. Higher-order networks can also exhibit rich dynamical behavior for simple models of contagion, synchronization, and opinion formation.
+Higher-order interactions can reveal more nuanced and sophisticated patterns of connection and can naturally encode different scales of interaction which are inaccessible to pairwise network representations. Higher-order networks can be helpful for describing social networks, ecological communities, co-authorship or citation networks, email, protein interactions, and many more examples. Higher-order networks can also exhibit rich dynamical behavior for simple models of contagion, synchronization, and opinion formation.
+
+
+Academic References
+===================
+
+* `The Why, How, and When of Representations for Complex Systems
+  <https://doi.org/10.1137/20M1355896>`_, Torres, L., Blevins, A.S., Bassett, D. and Eliassi-Rad, T., 2021. SIAM Review, 63(3), pp.435-485.
+
+* `Networks beyond pairwise interactions: Structure and dynamics
+  <https://doi.org/10.1016/j.physrep.2020.05.004>`_, Battiston, F., Cencetti, G., Iacopini, I., Latora, V., Lucas, M., Patania, A., Young, J.G. and Petri, G., 2020. Physics reports, 874, pp.1-92.
+
+* `What are higher-order networks? <https://arxiv.org/abs/2104.11329>`_, Bick, C., Gross, E., Harrington, H.A. and Schaub, M.T., 2023. SIAM Review, 65(3), pp.686-731.
+
+* `From networks to optimal higher-order models of complex systems
+  <https://www.nature.com/articles/s41567-019-0459-y>`_, Lambiotte, R., Rosvall, M. and Scholtes, I., 2019. Nature physics, 15(4), pp.313-320.