Merge pull request #568 from ghutchis/sphinx-breathe-docs

New docs using Sphinx + Breathe
OpenChemistry · May 20, 2021 · df0135f · df0135f
2 parents 3ce2ab6 + 818f0e1
commit df0135f
Show file tree

Hide file tree

Showing 205 changed files with 4,800 additions and 844 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+docs/build
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
@@ -7,6 +7,9 @@ set(doxygen_output_dir "${CMAKE_CURRENT_BINARY_DIR}")
 configure_file("${CMAKE_CURRENT_SOURCE_DIR}/doxyfile.in"
   "${CMAKE_CURRENT_BINARY_DIR}/doxyfile")
 
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in"
+  "${CMAKE_CURRENT_SOURCE_DIR}/conf.py")
+
 add_custom_target(documentation
   COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_CURRENT_BINARY_DIR}/html
   COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/doxyfile)
diff --git a/docs/_images/400px/benzene-mo.png b/docs/_images/400px/benzene-mo.png
diff --git a/docs/_images/400px/bondcentric.png b/docs/_images/400px/bondcentric.png
diff --git a/docs/_images/400px/c180.png b/docs/_images/400px/c180.png
diff --git a/docs/_images/400px/covid-spike.png b/docs/_images/400px/covid-spike.png
diff --git a/docs/_images/400px/ferrocene.png b/docs/_images/400px/ferrocene.png
diff --git a/docs/_images/400px/geoffclark3.png b/docs/_images/400px/geoffclark3.png
diff --git a/docs/_images/400px/gromacs-2.8M.png b/docs/_images/400px/gromacs-2.8M.png
diff --git a/docs/_images/400px/phenol-qtaim.png b/docs/_images/400px/phenol-qtaim.png
diff --git a/docs/_images/400px/qtaim.png b/docs/_images/400px/qtaim.png
diff --git a/docs/_images/400px/zeolite.png b/docs/_images/400px/zeolite.png
diff --git a/docs/_images/OpenChemistry.png b/docs/_images/OpenChemistry.png
diff --git a/docs/_images/avogadro2.png b/docs/_images/avogadro2.png
diff --git a/docs/_images/benzene-mo.png b/docs/_images/benzene-mo.png
diff --git a/docs/_images/bondcentric.png b/docs/_images/bondcentric.png
diff --git a/docs/_images/c180.png b/docs/_images/c180.png
diff --git a/docs/_images/covid-spike.png b/docs/_images/covid-spike.png
diff --git a/docs/_images/ferrocene.png b/docs/_images/ferrocene.png
diff --git a/docs/_images/geoffclark3.png b/docs/_images/geoffclark3.png
diff --git a/docs/_images/gromacs-2.8M.png b/docs/_images/gromacs-2.8M.png
diff --git a/docs/_images/phenol-qtaim.png b/docs/_images/phenol-qtaim.png
diff --git a/docs/_images/qtaim.png b/docs/_images/qtaim.png
diff --git a/docs/_images/zeolite.png b/docs/_images/zeolite.png
diff --git a/docs/_templates/footer.html b/docs/_templates/footer.html
@@ -0,0 +1,19 @@
+<footer class="container-fluid footer-copy">
+
+    <div class="container">
+
+      <div class="row">
+        <div class="col-md-10 py-2">
+          <p>
+            {{ copyright }} The website content uses the <a href="https://github.com/openchemistry/avogadrolibs/blob/master/LICENSE">BSD License</a> and is covered by the <a href="https://github.com/openchemistry/avogadrolibs/blob/master/CODE_OF_CONDUCT.md">Avogadro Code of Conduct</a>.
+          </p>
+        </div>
+        <br />
+        <div class="col-md-2 py-2">
+          <a class="btn btn-primary" href="https://opencollective.com/open-chemistry">Donate</a>
+        </div>
+      </div>
+
+    </div>
+
+  </footer>
diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html
@@ -0,0 +1,115 @@
+{%- extends "basic/layout.html" %}
+{%- import "static/webpack-macros.html" as _webpack with context %}
+
+{# prev/next buttons #}
+{% macro prev_next(prev, next, prev_title='', next_title='') %}
+ {%- if prev %}
+    <a class='left-prev' id="prev-link" href="{{ prev.link|e }}" title="{{ _('previous page')}}">{{ prev_title or prev.title }}</a>
+ {%- endif %}
+ {%- if next %}
+    <a class='right-next' id="next-link" href="{{ next.link|e }}" title="{{ _('next page')}}">{{ next_title or next.title }}</a>
+ {%- endif %}
+{% endmacro %}
+
+{%- block css %}
+    {{ _webpack.head_pre_bootstrap() }}
+    {{ _webpack.head_pre_icons() }}
+    {% block fonts %}
+      {{ _webpack.head_pre_fonts() }}
+    {% endblock %}
+    {{- css() }}
+    {{ _webpack.head_js_preload() }}
+{%- endblock %}
+
+{%- block extrahead %}
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="docsearch:language" content="en" />
+    {% for favicon in theme_favicons %}
+      {% if favicon.href[:4] == 'http'%}
+      <link rel="{{ favicon.rel }}" sizes="{{ favicon.sizes }}" href="{{ favicon.href }}">
+      {% else %}
+      <link rel="{{ favicon.rel }}" sizes="{{ favicon.sizes }}" href="{{ pathto('_static/' + favicon.href, 1) }}">
+      {% endif %}
+    {% endfor %}
+{%- endblock %}
+
+{# Silence the sidebar's, relbar's #}
+{% block header %}{% endblock %}
+{% block relbar1 %}{% endblock %}
+{% block relbar2 %}{% endblock %}
+{% block sidebarsourcelink %}{% endblock %}
+
+{% block body_tag %}
+  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
+{%- endblock %}
+{%- block content %}
+    {# Added to support a banner with an alert #}
+    <div class="container-fluid" id="banner"></div>
+
+    {% block docs_navbar %}
+    <nav class="navbar navbar-light navbar-expand-lg bg-light fixed-top bd-navbar" id="navbar-main">
+      {%- include "docs-navbar.html" %}
+    </nav>
+    {% endblock %}
+
+    <div class="container-xl">
+      <div class="row">
+          {% block docs_sidebar %}
+            {% if sidebars %}
+            <!-- Only show if we have sidebars configured, else just a small margin  -->
+            <div class="col-12 col-md-3 bd-sidebar">
+                {%- for sidebartemplate in sidebars %}
+                {%- include sidebartemplate %}
+                {%- endfor %}
+            </div>
+            {% endif %}
+          {% endblock %}
+
+          {% block docs_toc %}
+          {% if sidebars %}
+          <div class="d-none d-xl-block col-xl-2 bd-toc">
+            {% if meta is defined and not (meta is not none and 'notoc' in meta) %}
+              {% for toc_item in theme_page_sidebar_items %}
+              <div class="toc-item">
+                {% include toc_item %}
+              </div>
+              {% endfor %}
+            {% endif %}
+          </div>
+          {% endif %}
+          {% endblock %}
+
+          {% block docs_main %}
+          {% if sidebars %}
+            {% set content_col_class = "col-md-9 col-xl-7" %}
+            {% else %}
+            {% set content_col_class = "col-md-12 ol-sm-12 col-lg-12 col-xl-12" %}
+          {% endif %}
+          <main class="col-12 {{ content_col_class }} py-md-5 pl-md-5 pr-md-4 bd-content" role="main">
+            {% block docs_body %}
+              <div>
+                {% block body %} {% endblock %}
+              </div>
+              {% endblock %}
+              {% if theme_show_prev_next and pagename != 'index' %}
+              <div class='prev-next-bottom'>
+                {{ prev_next(prev, next) }}
+              </div>
+              {% endif %}
+          </main>
+          {% endblock %}
+
+      </div>
+    </div>
+
+
+  {%- block scripts_end %}
+  {{ _webpack.body_post() }}
+  {{ generate_google_analytics_script(id=theme_google_analytics_id) }}
+  {%- endblock %}
+
+{%- endblock %}
+
+{%- block footer %}
+{%- include "footer.html" %}
+{%- endblock %}
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_array.rst b/docs/api/class/class_avogadro_1_1_core_1_1_array.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Array
+===========================
+
+.. doxygenclass:: Avogadro::Core::Array
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_array_set.rst b/docs/api/class/class_avogadro_1_1_core_1_1_array_set.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::ArraySet
+==============================
+
+.. doxygenclass:: Avogadro::Core::ArraySet
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_array_set_1_1_holder.rst b/docs/api/class/class_avogadro_1_1_core_1_1_array_set_1_1_holder.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::ArraySet::Holder
+======================================
+
+.. doxygenclass:: Avogadro::Core::ArraySet::Holder
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_array_set_1_1_place_holder.rst b/docs/api/class/class_avogadro_1_1_core_1_1_array_set_1_1_place_holder.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::ArraySet::PlaceHolder
+===========================================
+
+.. doxygenclass:: Avogadro::Core::ArraySet::PlaceHolder
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_atom.rst b/docs/api/class/class_avogadro_1_1_core_1_1_atom.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Atom
+==========================
+
+.. doxygenclass:: Avogadro::Core::Atom
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_atom_template.rst b/docs/api/class/class_avogadro_1_1_core_1_1_atom_template.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::AtomTemplate
+==================================
+
+.. doxygenclass:: Avogadro::Core::AtomTemplate
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_atom_typer.rst b/docs/api/class/class_avogadro_1_1_core_1_1_atom_typer.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::AtomTyper
+===============================
+
+.. doxygenclass:: Avogadro::Core::AtomTyper
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_avo_spglib.rst b/docs/api/class/class_avogadro_1_1_core_1_1_avo_spglib.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::AvoSpglib
+===============================
+
+.. doxygenclass:: Avogadro::Core::AvoSpglib
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_basis_set.rst b/docs/api/class/class_avogadro_1_1_core_1_1_basis_set.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::BasisSet
+==============================
+
+.. doxygenclass:: Avogadro::Core::BasisSet
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_bond.rst b/docs/api/class/class_avogadro_1_1_core_1_1_bond.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Bond
+==========================
+
+.. doxygenclass:: Avogadro::Core::Bond
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_bond_template.rst b/docs/api/class/class_avogadro_1_1_core_1_1_bond_template.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::BondTemplate
+==================================
+
+.. doxygenclass:: Avogadro::Core::BondTemplate
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_color3f.rst b/docs/api/class/class_avogadro_1_1_core_1_1_color3f.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Color3f
+=============================
+
+.. doxygenclass:: Avogadro::Core::Color3f
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_coordinate_block_generator.rst b/docs/api/class/class_avogadro_1_1_core_1_1_coordinate_block_generator.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::CoordinateBlockGenerator
+==============================================
+
+.. doxygenclass:: Avogadro::Core::CoordinateBlockGenerator
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_coordinate_set.rst b/docs/api/class/class_avogadro_1_1_core_1_1_coordinate_set.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::CoordinateSet
+===================================
+
+.. doxygenclass:: Avogadro::Core::CoordinateSet
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_crystal_tools.rst b/docs/api/class/class_avogadro_1_1_core_1_1_crystal_tools.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::CrystalTools
+==================================
+
+.. doxygenclass:: Avogadro::Core::CrystalTools
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_cube.rst b/docs/api/class/class_avogadro_1_1_core_1_1_cube.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Cube
+==========================
+
+.. doxygenclass:: Avogadro::Core::Cube
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_elements.rst b/docs/api/class/class_avogadro_1_1_core_1_1_elements.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Elements
+==============================
+
+.. doxygenclass:: Avogadro::Core::Elements
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_gaussian_set.rst b/docs/api/class/class_avogadro_1_1_core_1_1_gaussian_set.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::GaussianSet
+=================================
+
+.. doxygenclass:: Avogadro::Core::GaussianSet
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_gaussian_set_tools.rst b/docs/api/class/class_avogadro_1_1_core_1_1_gaussian_set_tools.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::GaussianSetTools
+======================================
+
+.. doxygenclass:: Avogadro::Core::GaussianSetTools
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_graph.rst b/docs/api/class/class_avogadro_1_1_core_1_1_graph.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Graph
+===========================
+
+.. doxygenclass:: Avogadro::Core::Graph
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_mesh.rst b/docs/api/class/class_avogadro_1_1_core_1_1_mesh.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Mesh
+==========================
+
+.. doxygenclass:: Avogadro::Core::Mesh
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_molecule.rst b/docs/api/class/class_avogadro_1_1_core_1_1_molecule.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Molecule
+==============================
+
+.. doxygenclass:: Avogadro::Core::Molecule
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_molecule_deserializer.rst b/docs/api/class/class_avogadro_1_1_core_1_1_molecule_deserializer.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::MoleculeDeserializer
+==========================================
+
+.. doxygenclass:: Avogadro::Core::MoleculeDeserializer
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_molecule_serializer.rst b/docs/api/class/class_avogadro_1_1_core_1_1_molecule_serializer.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::MoleculeSerializer
+========================================
+
+.. doxygenclass:: Avogadro::Core::MoleculeSerializer
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_mutex.rst b/docs/api/class/class_avogadro_1_1_core_1_1_mutex.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Mutex
+===========================
+
+.. doxygenclass:: Avogadro::Core::Mutex
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_name_atom_typer.rst b/docs/api/class/class_avogadro_1_1_core_1_1_name_atom_typer.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::NameAtomTyper
+===================================
+
+.. doxygenclass:: Avogadro::Core::NameAtomTyper
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_residue.rst b/docs/api/class/class_avogadro_1_1_core_1_1_residue.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Residue
+=============================
+
+.. doxygenclass:: Avogadro::Core::Residue
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_residue_data.rst b/docs/api/class/class_avogadro_1_1_core_1_1_residue_data.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::ResidueData
+=================================
+
+.. doxygenclass:: Avogadro::Core::ResidueData
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_ring_perceiver.rst b/docs/api/class/class_avogadro_1_1_core_1_1_ring_perceiver.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::RingPerceiver
+===================================
+
+.. doxygenclass:: Avogadro::Core::RingPerceiver
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_shared_mutex.rst b/docs/api/class/class_avogadro_1_1_core_1_1_shared_mutex.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::SharedMutex
+=================================
+
+.. doxygenclass:: Avogadro::Core::SharedMutex
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_slater_set.rst b/docs/api/class/class_avogadro_1_1_core_1_1_slater_set.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::SlaterSet
+===============================
+
+.. doxygenclass:: Avogadro::Core::SlaterSet
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_slater_set_tools.rst b/docs/api/class/class_avogadro_1_1_core_1_1_slater_set_tools.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::SlaterSetTools
+====================================
+
+.. doxygenclass:: Avogadro::Core::SlaterSetTools
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_space_groups.rst b/docs/api/class/class_avogadro_1_1_core_1_1_space_groups.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::SpaceGroups
+=================================
+
+.. doxygenclass:: Avogadro::Core::SpaceGroups
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_symbol_atom_typer.rst b/docs/api/class/class_avogadro_1_1_core_1_1_symbol_atom_typer.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::SymbolAtomTyper
+=====================================
+
+.. doxygenclass:: Avogadro::Core::SymbolAtomTyper
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_unit_cell.rst b/docs/api/class/class_avogadro_1_1_core_1_1_unit_cell.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::UnitCell
+==============================
+
+.. doxygenclass:: Avogadro::Core::UnitCell
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_variant.rst b/docs/api/class/class_avogadro_1_1_core_1_1_variant.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::Variant
+=============================
+
+.. doxygenclass:: Avogadro::Core::Variant
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1_variant_map.rst b/docs/api/class/class_avogadro_1_1_core_1_1_variant_map.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::VariantMap
+================================
+
+.. doxygenclass:: Avogadro::Core::VariantMap
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_core_1_1internal_1_1_array_ref_container.rst b/docs/api/class/class_avogadro_1_1_core_1_1internal_1_1_array_ref_container.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Core::internal::ArrayRefContainer
+=================================================
+
+.. doxygenclass:: Avogadro::Core::internal::ArrayRefContainer
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_io_1_1_cjson_format.rst b/docs/api/class/class_avogadro_1_1_io_1_1_cjson_format.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Io::CjsonFormat
+===============================
+
+.. doxygenclass:: Avogadro::Io::CjsonFormat
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_io_1_1_cml_format.rst b/docs/api/class/class_avogadro_1_1_io_1_1_cml_format.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Io::CmlFormat
+=============================
+
+.. doxygenclass:: Avogadro::Io::CmlFormat
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_io_1_1_dcd_format.rst b/docs/api/class/class_avogadro_1_1_io_1_1_dcd_format.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Io::DcdFormat
+=============================
+
+.. doxygenclass:: Avogadro::Io::DcdFormat
+   :members:
diff --git a/docs/api/class/class_avogadro_1_1_io_1_1_file_format.rst b/docs/api/class/class_avogadro_1_1_io_1_1_file_format.rst
@@ -0,0 +1,5 @@
+Class Avogadro::Io::FileFormat
+==============================
+
+.. doxygenclass:: Avogadro::Io::FileFormat
+   :members: