hpc-maths · gouarin · Nov 13, 2023 · Nov 13, 2023 · Nov 13, 2023
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -5,4 +5,5 @@ channels:
 
 dependencies:
   - breathe
-  - sphinx_rtd_theme
+  - doxygen
+  - pydata-sphinx-theme
diff --git a/docs/source/_static/dark_logo.png b/docs/source/_static/dark_logo.png
diff --git a/docs/source/_static/light_logo.png b/docs/source/_static/light_logo.png
diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -0,0 +1,12 @@
+API
+===
+
+.. toctree::
+   :caption: API reference
+   :maxdepth: 1
+
+   algorithm
+   interval
+   box
+   cell
+   subset
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -16,8 +16,6 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-import sphinx_rtd_theme
-
 # -- Project information -----------------------------------------------------
 
 project = 'Samurai'
@@ -42,7 +40,6 @@
     'sphinx.ext.todo',
     'sphinx.ext.mathjax',
     'breathe',
-    'sphinx_rtd_theme',
 ]
 
 breathe_projects = { 'samurai': '../xml' }
@@ -72,7 +69,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -88,15 +85,31 @@
 # 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"
+
+html_theme_options = {
+   "logo": {
+      "image_light": "_static/light_logo.png",
+      "image_dark": "_static/dark_logo.png",
+   },
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/hpc-maths/samurai",
+            "icon": "fa-brands fa-square-github",
+            "type": "fontawesome",
+        },
+    ],
+    "primary_sidebar_end": ["sidebar-ethical-ads.html"],
+}
 
 # 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 = {
-    'collapse_navigation': False,
-}
+# html_theme_options = {
+#     'collapse_navigation': False,
+# }
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -113,9 +126,9 @@
 #
 # html_sidebars = {}
 
-html_css_files = [
-    'css/custom.css',
-]
+# html_css_files = [
+#     'css/custom.css',
+# ]
 
 # -- Options for HTMLHelp output ---------------------------------------------
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,9 +1,15 @@
-.. _topics-index:
-
 ========================
  |project| documentation
 ========================
 
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+
+   tutorial <tutorial/index>
+   reference <reference/index>
+   api <api/index>
+
 The main goal of |project| is to provide a new data structure based on intervals and algebra of sets to handle efficiently adaptive mesh refinement methods based on a cartesian grid. Such an approach has to be versatile enough to handle both AMR and multi-resolution methods.
 
 Most of the existing data structures used for such a purpose are based on the construction of a tree (quadtree in 2d or octree in 3d).
@@ -20,63 +26,4 @@ In order to improve the efficiency of the tree / space-filling curve, the propos
 
 SAMURAI: Structured Adaptive mesh and MUlti-Resolution based on Algebra of Intervals.
 
-
-.. toctree::
-   :caption: Tutorial
-   :maxdepth: 1
-
-   tutorial/interval
-   tutorial/field
-   tutorial/algorithm
-   tutorial/operator_on_subset
-   tutorial/graduation
-   tutorial/level_set
-   tutorial/1d_burgers_amr
-
-.. :doc:`tutorial/interval`
-
-.. :doc:`tutorial/algorithm`
-
-.. :doc:`tutorial/operator_on_subset`
-
-.. :doc:`tutorial/graduation`
-
-.. :doc:`tutorial/level_set`
-
-.. :doc:`tutorial/1d_burgers_amr`
-
-.. toctree::
-   :caption: Test cases
-   :maxdepth: 1
-
-   LBM/test_cases
-
-.. toctree::
-   :caption: Reference
-   :maxdepth: 2
-
-   reference/subset
-
-.. :doc:`reference/subset`
-
-.. toctree::
-   :caption: API reference
-   :maxdepth: 2
-
-   api/algorithm
-   api/interval
-   api/box
-   api/cell
-   api/subset
-
-.. :doc:`api/algorithm`
-
-.. :doc:`api/interval`
-
-.. :doc:`api/box`
-
-.. :doc:`api/cell`
-
-.. :doc:`api/subset`
-
 .. _p4est: http://www.p4est.org/
diff --git a/docs/source/logo/logo.png b/docs/source/logo/logo.png
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -0,0 +1,8 @@
+Reference manual
+================
+
+.. toctree::
+   :caption: Reference
+   :maxdepth: 1
+
+   Algebra of set <subset>
diff --git a/docs/source/tutorial/index.rst b/docs/source/tutorial/index.rst
@@ -0,0 +1,14 @@
+Tutorials
+=========
+
+.. toctree::
+   :caption: Tutorial
+   :maxdepth: 1
+
+   interval
+   field
+   algorithm
+   operator_on_subset
+   graduation
+   level_set
+   1d_burgers_amr