Merge remote-tracking branch 'PlasmaFAIR/docs'

.gitignore

@@ -223,3 +223,6 @@ cython_debug/
 
 # Setuptools_scm generated version file
 src/**/_version.py
+
+# Generated API docs
+docs/generated

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

docs/Makefile

@@ -0,0 +1,20 @@
+# 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
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

docs/_templates/custom-class-template.rst

@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   {% 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 %}

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 %}

docs/api.rst

@@ -0,0 +1,10 @@
+===============
+ API Reference
+===============
+
+.. autosummary::
+   :toctree: generated
+   :template: custom-module-template.rst
+   :recursive:
+
+   fusiondls

docs/conf.py

@@ -0,0 +1,93 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+from importlib.metadata import version as get_version
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "fusiondls"
+copyright = "2024, Cyd Cowley, Mike Kryjak"
+author = "Cyd Cowley, Mike Kryjak"
+
+# The full version, including alpha/beta/rc tags
+release = get_version(project)
+# Major.minor version
+version = ".".join(release.split(".")[:2])
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx_autodoc_typehints",
+    "myst_nb",
+]
+
+autosummary_generate = True
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# Numpy-doc config
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_attr_annotations = True
+napoleon_preprocess_types = True
+
+# The default role for text marked up `like this`
+default_role = "any"
+
+# Tell sphinx what the primary language being documented is.
+primary_domain = "py"
+
+# Tell sphinx what the pygments highlight language should be.
+highlight_language = "python"
+
+# Include "todo" directives in output
+todo_include_todos = True
+
+# Don't execute notebook examples
+nb_execution_mode = "off"
+
+# Parse LaTeX in notebooks
+myst_enable_extensions = [
+    "amsmath",
+    "dollarmath",
+]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_book_theme"
+
+html_static_path = ["_static"]
+
+html_theme_options = {
+    "repository_url": "https://github.com/cydcowley/DLS-model",
+    "repository_branch": "main",
+    "path_to_docs": "docs",
+    "use_edit_page_button": True,
+    "use_repository_button": True,
+    "use_issues_button": True,
+    "home_page_in_toc": False,
+}
+
+pygments_style = "sphinx"
+
+# -- Options for intersphinx extension ---------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#configuration
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+}