From 9888fb1e83251796c17dcb8aad973c43d10f4612 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Sat, 4 May 2024 12:13:08 -0500
Subject: [PATCH] Add autodoc

---
 docs/_config.yml                           | 13 ++++-
 docs/_templates/custom-class-template.rst  | 32 +++++++++++
 docs/_templates/custom-module-template.rst | 66 ++++++++++++++++++++++
 docs/_toc.yml                              |  3 +-
 docs/api.rst                               | 11 ++++
 5 files changed, 123 insertions(+), 2 deletions(-)
 create mode 100644 docs/_templates/custom-class-template.rst
 create mode 100644 docs/_templates/custom-module-template.rst
 create mode 100644 docs/api.rst

diff --git a/docs/_config.yml b/docs/_config.yml
index 6cff8b60..9b6f0348 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -11,4 +11,15 @@ repository:
 
 launch_buttons:
   notebook_interface          : jupyterlab
-  binderhub_url               : https://mybinder.org
\ No newline at end of file
+  binderhub_url               : https://mybinder.org
+
+sphinx:
+  extra_extensions:
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.napoleon'
+  - 'sphinx.ext.viewcode'
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.autosummary'
+  config:
+    autosummary_generate: True
+    templates_path: ['_templates']
\ No newline at end of file
diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst
new file mode 100644
index 00000000..16ebb2f3
--- /dev/null
+++ b/docs/_templates/custom-class-template.rst
@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
\ No newline at end of file
diff --git a/docs/_templates/custom-module-template.rst b/docs/_templates/custom-module-template.rst
new file mode 100644
index 00000000..74078355
--- /dev/null
+++ b/docs/_templates/custom-module-template.rst
@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
\ No newline at end of file
diff --git a/docs/_toc.yml b/docs/_toc.yml
index 208a1dec..b8d46617 100644
--- a/docs/_toc.yml
+++ b/docs/_toc.yml
@@ -9,4 +9,5 @@ chapters:
     - file: bulk_modulus_with_gpaw.ipynb
     - file: thermal_expansion_with_lammps.ipynb
     - file: free_energy_calculation.ipynb
-    - file: phasediagram.md
\ No newline at end of file
+    - file: phasediagram.md
+- file: api.rst
\ No newline at end of file
diff --git a/docs/api.rst b/docs/api.rst
new file mode 100644
index 00000000..042824ad
--- /dev/null
+++ b/docs/api.rst
@@ -0,0 +1,11 @@
+Interface
+=========
+
+Documentation of the classes and functions defined in the :code:`atomistics` package.
+
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   atomistics
\ No newline at end of file