Documentation

.github/workflows/ci.yaml

@@ -33,7 +33,16 @@ jobs:
           python -m black . --diff --check --verbose
           python -m isort . --diff --check-only --verbose
           python -m flake8 momentGW/ --verbose
-      - name: Run unit tests
+      #- name: Run unit tests
+      #  run: |
+      #    python -m pip install pytest pytest-cov
+      #    pytest --cov momentGW/
+      - name: Build documentation
         run: |
-          python -m pip install pytest pytest-cov
-          pytest --cov momentGW/
+          cd docs
+          make html
+      - name: Deploy documentation
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html

README.md

@@ -31,11 +31,11 @@ The `examples` directory contains more detailed usage examples.
 ### Publications
 
 The methods implemented in this package have been described in the following papers:
-- [*"A 'moment-conserving' reformulation of GW theory"*](https://doi.org/10.1063/5.0143291)
+- [A 'moment-conserving' reformulation of GW theory](https://doi.org/10.1063/5.0143291), *J. Chem. Phys.* 158, 124102 (2023).
 
 The data presented in the publications can be found in the `benchmark` directory.
 
 ### Contributing
 
 Contributions are welcome, and can be made by submitting a pull request to the `master` branch.
-The code uses [NumPy-style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html) and is formatted using [`black`](https://black.readthedocs.io/en/stable/), [`isort`](https://pycqa.github.io/isort/), [`ssort`](https://github.com/bwhmather/ssort), and [`flake8`](https://flake8.pycqa.org/en/latest/).
+The code uses [NumPy-style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html) and is formatted using [black](https://black.readthedocs.io/en/stable/), [isort](https://pycqa.github.io/isort/), [ssort](https://github.com/bwhmather/ssort), and [flake8](https://flake8.pycqa.org/en/latest/).

docs/Makefile

@@ -0,0 +1,21 @@
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+html:
+	sphinx-build -M html . _build
+
+postprocess:
+	# Post-processing generated files:
+	# If there is a line with a "Duplicate implicit target name" error, remove it:
+	for file in `find _build/html -name "*.html"`; do \
+		sed -i '/Duplicate implicit target name/d' $$file; \
+	done
+
+docs: html postprocess
+
+clean:
+	rm -rf _build autoapi
+
+.PHONY: html postprocess clean

docs/_templates/autoapi/base/base.rst

@@ -0,0 +1,7 @@
+.. {{ obj.type }}:: {{ obj.name }}
+
+	{% if summary %}
+
+	{{ obj.summary }}
+
+	{% endif %}

docs/_templates/autoapi/index.rst

@@ -0,0 +1,15 @@
+API Reference
+=============
+
+This page contains auto-generated API reference documentation [#f1]_.
+
+.. toctree::
+   :titlesonly:
+
+   {% for page in pages %}
+   {% if page.top_level_object and page.display %}
+   {{ page.include_path }}
+   {% endif %}
+   {% endfor %}
+
+.. [#f1] Created with `sphinx-autoapi <https://github.com/readthedocs/sphinx-autoapi>`_

docs/_templates/autoapi/python/attribute.rst

@@ -0,0 +1 @@
+{% extends "python/data.rst" %}

docs/_templates/autoapi/python/class.rst

@@ -0,0 +1,60 @@
+{% if obj.display %}
+.. py:{{ obj.type }}:: {{ obj.short_name }}{% if obj.args %}({{ obj.args }}){% endif %}
+
+{% for (args, return_annotation) in obj.overloads %}
+      {{ " " * (obj.type | length) }}   {{ obj.short_name }}{% if args %}({{ args }}){% endif %}
+
+{% endfor %}
+
+
+   {% if obj.bases %}
+   {% if "show-inheritance" in autoapi_options %}
+   Bases: {% for base in obj.bases %}{{ base|link_objs }}{% if not loop.last %}, {% endif %}{% endfor %}
+   {% endif %}
+
+
+   {% if "show-inheritance-diagram" in autoapi_options and obj.bases != ["object"] %}
+   .. autoapi-inheritance-diagram:: {{ obj.obj["full_name"] }}
+      :parts: 1
+      {% if "private-members" in autoapi_options %}
+      :private-bases:
+      {% endif %}
+
+   {% endif %}
+   {% endif %}
+   {% if obj.docstring %}
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_classes = obj.classes|selectattr("display")|list %}
+   {% else %}
+   {% set visible_classes = obj.classes|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for klass in visible_classes %}
+   {{ klass.render()|indent(3) }}
+   {% endfor %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_properties = obj.properties|selectattr("display")|list %}
+   {% else %}
+   {% set visible_properties = obj.properties|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for property in visible_properties %}
+   {{ property.render()|indent(3) }}
+   {% endfor %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_attributes = obj.attributes|selectattr("display")|list %}
+   {% else %}
+   {% set visible_attributes = obj.attributes|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for attribute in visible_attributes %}
+   {{ attribute.render()|indent(3) }}
+   {% endfor %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_methods = obj.methods|selectattr("display")|list %}
+   {% else %}
+   {% set visible_methods = obj.methods|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for method in visible_methods %}
+   {{ method.render()|indent(3) }}
+   {% endfor %}
+{% endif %}

docs/_templates/autoapi/python/data.rst

@@ -0,0 +1,37 @@
+{% if obj.display %}
+.. py:{{ obj.type }}:: {{ obj.name }}
+   {%- if obj.annotation is not none %}
+
+   :type: {%- if obj.annotation %} {{ obj.annotation }}{%- endif %}
+
+   {%- endif %}
+
+   {%- if obj.value is not none %}
+
+   :value: {% if obj.value is string and obj.value.splitlines()|count > 1 -%}
+                Multiline-String
+
+    .. raw:: html
+
+        <details><summary>Show Value</summary>
+
+    .. code-block:: python
+
+        """{{ obj.value|indent(width=8,blank=true) }}"""
+
+    .. raw:: html
+
+        </details>
+
+            {%- else -%}
+              {%- if obj.value is string -%}
+                {{ "%r" % obj.value|string|truncate(100) }}
+              {%- else -%}
+                {{ obj.value|string|truncate(100) }}
+              {%- endif -%}
+            {%- endif %}
+   {%- endif %}
+
+
+   {{ obj.docstring|indent(3) }}
+{% endif %}

docs/_templates/autoapi/python/exception.rst

@@ -0,0 +1 @@
+{% extends "python/class.rst" %}

docs/_templates/autoapi/python/function.rst

@@ -0,0 +1,15 @@
+{% if obj.display %}
+.. py:function:: {{ obj.short_name }}({{ obj.args }}){% if obj.return_annotation is not none %} -> {{ obj.return_annotation }}{% endif %}
+
+{% for (args, return_annotation) in obj.overloads %}
+                 {{ obj.short_name }}({{ args }}){% if return_annotation is not none %} -> {{ return_annotation }}{% endif %}
+
+{% endfor %}
+   {% for property in obj.properties %}
+   :{{ property }}:
+   {% endfor %}
+
+   {% if obj.docstring %}
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+{% endif %}

docs/_templates/autoapi/python/method.rst

@@ -0,0 +1,19 @@
+{%- if obj.display %}
+.. py:method:: {{ obj.short_name }}({{ obj.args }}){% if obj.return_annotation is not none %} -> {{ obj.return_annotation }}{% endif %}
+
+{% for (args, return_annotation) in obj.overloads %}
+               {{ obj.short_name }}({{ args }}){% if return_annotation is not none %} -> {{ return_annotation }}{% endif %}
+
+{% endfor %}
+   {% if obj.properties %}
+   {% for property in obj.properties %}
+   :{{ property }}:
+   {% endfor %}
+
+   {% else %}
+
+   {% endif %}
+   {% if obj.docstring %}
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+{% endif %}

docs/_templates/autoapi/python/module.rst

@@ -0,0 +1,104 @@
+{% if not obj.display %}
+:orphan:
+
+{% endif %}
+:py:mod:`{{ obj.name }}`
+=========={{ "=" * obj.name|length }}
+
+.. py:module:: {{ obj.name }}
+
+{% if obj.docstring %}
+.. autoapi-nested-parse::
+
+   {{ obj.docstring|indent(3) }}
+
+{% endif %}
+
+{% block subpackages %}
+{% set visible_subpackages = obj.subpackages|selectattr("display")|list %}
+{% if visible_subpackages %}
+
+{% endif %}
+{% endblock %}
+{% block submodules %}
+{% set visible_submodules = obj.submodules|selectattr("display")|list %}
+{% if visible_submodules %}
+Submodules
+----------
+.. toctree::
+   :titlesonly:
+   :maxdepth: 1
+
+{% for submodule in visible_submodules %}
+   {{ submodule.short_name }}/index.rst
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% block content %}
+{% if obj.all is not none %}
+{% set visible_children = obj.children|selectattr("short_name", "in", obj.all)|list %}
+{% elif obj.type is equalto("package") %}
+{% set visible_children = obj.children|selectattr("display")|list %}
+{% else %}
+{% set visible_children = obj.children|selectattr("display")|rejectattr("imported")|list %}
+{% endif %}
+{% if visible_children %}
+{{ obj.type|title }} Contents
+{{ "-" * obj.type|length }}---------
+
+{% set visible_classes = visible_children|selectattr("type", "equalto", "class")|list %}
+{% set visible_functions = visible_children|selectattr("type", "equalto", "function")|list %}
+{% set visible_attributes = visible_children|selectattr("type", "equalto", "data")|list %}
+{% if "show-module-summary" in autoapi_options and (visible_classes or visible_functions) %}
+{% block classes scoped %}
+{% if visible_classes %}
+Classes
+~~~~~~~
+
+.. autoapisummary::
+
+{% for klass in visible_classes %}
+   {{ klass.id }}
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+
+{% block functions scoped %}
+{% if visible_functions %}
+Functions
+~~~~~~~~~
+
+.. autoapisummary::
+
+{% for function in visible_functions %}
+   {{ function.id }}
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+
+{% block attributes scoped %}
+{% if visible_attributes %}
+Attributes
+~~~~~~~~~~
+
+.. autoapisummary::
+
+{% for attribute in visible_attributes %}
+   {{ attribute.id }}
+{% endfor %}
+
+
+{% endif %}
+{% endblock %}
+{% endif %}
+{% for obj_item in visible_children %}
+{{ obj_item.render()|indent(0) }}
+{% endfor %}
+{% endif %}
+{% endblock %}

docs/_templates/autoapi/python/package.rst

@@ -0,0 +1 @@
+{% extends "python/module.rst" %}

docs/_templates/autoapi/python/property.rst

@@ -0,0 +1,15 @@
+{%- if obj.display %}
+.. py:property:: {{ obj.short_name }}
+   {% if obj.annotation %}
+   :type: {{ obj.annotation }}
+   {% endif %}
+   {% if obj.properties %}
+   {% for property in obj.properties %}
+   :{{ property }}:
+   {% endfor %}
+   {% endif %}
+
+   {% if obj.docstring %}
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+{% endif %}

docs/_templates/badges.html

@@ -0,0 +1,6 @@
+<div class="momentgw-badges">
+    <a class="github-button" href="https://github.com/{{theme_github_user}}/{{theme_github_repo}}" data-size="large"
+        data-show-count="true" aria-label="Star {{ theme_github_user }}/{{ theme_github_repo }} on GitHub">Star</a>
+</div>
+
+<script async defer src="https://buttons.github.io/buttons.js"></script>