Major docs change.

JelfsMaterialsGroup · Oct 27, 2023 · 0af9a18 · 0af9a18
1 parent c2815c3
commit 0af9a18
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Showing 85 changed files with 282 additions and 937 deletions.
diff --git a/.github/workflows/publish_release.yml b/.github/workflows/publish_release.yml
@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: "pip"
       - run: pip install -e '.[dev]'
       - run: python -m build

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: "pip"
       - run: "pip install '.[dev]'"
       - run: ruff .
@@ -22,7 +22,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
       - run: mypy src
@@ -32,7 +32,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
       - run: black --check .
@@ -42,7 +42,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
       - run: pytest
diff --git a/README.rst b/README.rst
@@ -5,7 +5,7 @@
 :documentation: https://stko-docs.readthedocs.io
 :discord: https://discord.gg/zbCUzuxe2B
 
-.. figure:: docs/source/figures/stko.png
+.. figure:: docs/source/_static/stko.png
 
 .. image:: https://readthedocs.org/projects/stko-docs/badge/?version=latest
     :target: https://stko-docs.readthedocs.io/en/latest/?badge=latest

diff --git a/docs/Makefile b/docs/Makefile
@@ -1,10 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
+# You can set these variables from the command line.
+SPHINXOPTS    = -W --keep-going
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = stk
 SOURCEDIR     = source
 BUILDDIR      = build
 
@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/remake_modules.bash b/docs/remake_modules.bash
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/figures/stko.png → docs/source/_static/stko.png b/docs/source/figures/stko.png → docs/source/_static/stko.png
diff --git a/docs/source/_templates/class.rst b/docs/source/_templates/class.rst
@@ -0,0 +1,34 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {%- if not item.startswith('_') %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/source/_templates/module.rst b/docs/source/_templates/module.rst
@@ -0,0 +1,68 @@
+{{ 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:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: class.rst
+      :nosignatures:
+   {% 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: module.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/source/calculators.rst b/docs/source/calculators.rst
@@ -0,0 +1,20 @@
+Calculators
+===========
+
+.. toctree::
+  :maxdepth: 1
+
+  Calculator <_autosummary/stko.calculators.Calculator>
+
+  MMFFEnergy <_autosummary/stko.MMFFEnergy>
+  UFFEnergy <_autosummary/stko.UFFEnergy>
+  OpenBabelEnergy <_autosummary/stko.OpenBabelEnergy>
+  XTBEnergy <_autosummary/stko.XTBEnergy>
+  OrcaEnergy <_autosummary/stko.OrcaEnergy>
+  RmsdCalculator <_autosummary/stko.RmsdCalculator>
+  RmsdMappedCalculator <_autosummary/stko.RmsdMappedCalculator>
+  ShapeCalculator <_autosummary/stko.ShapeCalculator>
+  TorsionCalculator <_autosummary/stko.TorsionCalculator>
+  ConstructedMoleculeTorsionCalculator <_autosummary/stko.ConstructedMoleculeTorsionCalculator>
+  MatchedTorsionCalculator <_autosummary/stko.MatchedTorsionCalculator>
+  PlanarityCalculator <_autosummary/stko.PlanarityCalculator>