Merge pull request #33 from PlasmaFAIR/docs

Add sphinx docs

.readthedocs.yaml

@@ -0,0 +1,33 @@
+# .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-20.04
+  tools:
+    python: "3.12"
+
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

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:
+
+   sdf_xarray

docs/conf.py

@@ -0,0 +1,108 @@
+# 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 = 'sdf-xarray'
+copyright = '2024, Peter Hill, Joel Adams'
+author = 'Peter Hill, Joel Adams'
+
+# The full version, including alpha/beta/rc tags
+release = get_version("sdf_xarray")
+# 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",
+]
+
+autosummary_generate = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+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
+
+# Enable numbered references
+numfig = True
+
+autodoc_type_aliases = {
+    "ArrayLike": "numpy.typing.ArrayLike",
+}
+
+autodoc_default_options = {
+    'ignore-module-all': True
+}
+autodoc_typehints = "description"
+autodoc_class_signature = "mixed"
+
+# 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
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ["_static"]
+html_static_path = []
+
+html_theme_options = {
+    "repository_url": "https://github.com/PlasmaFAIR/sdf-xarray",
+    "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),
+    "xarray": ("https://docs.xarray.dev/en/latest", None),
+}

docs/generated/sdf_xarray.SDFBackendArray.rst

@@ -0,0 +1,38 @@
+sdf\_xarray.SDFBackendArray
+===========================
+
+.. currentmodule:: sdf_xarray
+
+.. autoclass:: SDFBackendArray
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SDFBackendArray.__init__
+      ~SDFBackendArray.get_array
+      ~SDFBackendArray.get_duck_array
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~SDFBackendArray.datastore
+      ~SDFBackendArray.dtype
+      ~SDFBackendArray.shape
+      ~SDFBackendArray.variable_name
+      ~SDFBackendArray.ndim
+      ~SDFBackendArray.size
+
+

docs/generated/sdf_xarray.SDFDataStore.rst

@@ -0,0 +1,42 @@
+sdf\_xarray.SDFDataStore
+========================
+
+.. currentmodule:: sdf_xarray
+
+.. autoclass:: SDFDataStore
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SDFDataStore.__init__
+      ~SDFDataStore.acquire_context
+      ~SDFDataStore.close
+      ~SDFDataStore.get_attrs
+      ~SDFDataStore.get_dimensions
+      ~SDFDataStore.get_encoding
+      ~SDFDataStore.get_variables
+      ~SDFDataStore.load
+      ~SDFDataStore.open
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~SDFDataStore.lock
+      ~SDFDataStore.drop_variables
+      ~SDFDataStore.keep_particles
+      ~SDFDataStore.ds
+
+

docs/generated/sdf_xarray.SDFEntrypoint.rst

@@ -0,0 +1,37 @@
+sdf\_xarray.SDFEntrypoint
+=========================
+
+.. currentmodule:: sdf_xarray
+
+.. autoclass:: SDFEntrypoint
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SDFEntrypoint.__init__
+      ~SDFEntrypoint.guess_can_open
+      ~SDFEntrypoint.open_dataset
+      ~SDFEntrypoint.open_datatree
+      ~SDFEntrypoint.open_groups_as_dict
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~SDFEntrypoint.description
+      ~SDFEntrypoint.open_dataset_parameters
+      ~SDFEntrypoint.url
+
+