API Documentation with Sphinx (#75)

* adding pydocstyle to pyproject.toml

* adding mesa_frames __init__ docstring

* adding mesa_frames/abstract __init__ docstring

* fixing mesa_frames/abstract/agents.py for ruff.pydocstyle

* fixing mesa_frames/abstract/mixin.py for ruff.pydocstyle

* fixing mesa_frames/abstract/space.py for ruff.pydocstyle

* adding __init__ to mesa_frames/concrete

* fixing arguments in __init__ of the module

* fixing mesa_frames/concrete/model.py for ruff.pydocstyle

* fixing mesa_frames/concrete/agents.py for ruff.pydocstyle

* fixing mesa_frames/concrete/pandas/agentset.py for ruff.pydocstyle

* adding __init__ to mesa_frames/concrete/pandas

* fixing mesa_frames/concrete/pandas/mixin.py for ruff.pydocstyle

* removing methods section (hard to mantain, and automatically generated by sphinx)

* removing properties (sphinx will generate that)

* moving parameters to __init__

* fixing mesa_frames/concrete/pandas/space.py

* adding __init__ to mesa_frames/concrete/polars

* removing docstring (sphinx will autogenerate from AgentSetDF)

* removing docstring (sphinx will autogenerate from GridDF)

* removing docstring (sphinx will autogenerate from DFMixin)

* deactivate D101 and D102 (too many errors due to inheritance)

* deactivating d105 (doesn't work well with inheritance)

* fixing mesa_frames/concrete/polars/agentset.py for ruff.pydocstyle

* fixing mesa_frames/concrete/polars/mixin.py for ruff.pydocstyle

* fixing mesa_frames/concrete/polars/space.py

* ignoring in tests, examples or docs

* test -> tests

* adding __init__ to type aliases

* removing commented test

* test fix

* adding sphinx dependencies

* quick starting sphinx

* updating dependencies for docs

* adding required dependencies

* configuring api documentation

* creating docs structure

* copying description from parent class for abstract classes

* renaming docs action to mkdocs

* changing requirements to mkdocs_requirements.txt

* moving mkdocs to docs/general

* unique gh action for deployment

* adding sphinx files to docs/api

* fix: checkout = false (checked out before)

* fix: unique gh pages actions

* fix: removed api from docs

* rename for clarity

* removed redundant/useless requirements

* moving to /reference for clarity (similar to polars)

* fix: update reqs

* adding section headers

* removing properties (automatically generated by sphinx)

* Revert "adding section headers"

This reverts commit fa1b20d.

* adding title

* adding description for backend specific classes (better for sphinx)

* run only 72-api-documentation-with-sphinx

* changing branch to main

.github/workflows/docs-gh-pages.yml

@@ -1,19 +1,38 @@
-name: Publish docs via GitHub Pages
+name: Build and Deploy Documentation
+
 on:
   push:
     branches:
       - main
 
 jobs:
-  build:
-    name: Deploy docs
+  build-and-deploy-docs:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout main
-        uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch all history for .git-restore-mtime to work correctly
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[docs]
+
+      - name: Build MkDocs site (general documentation)
+        run: mkdocs build --config-file mkdocs.yml --site-dir ./site
+
+      - name: Build Sphinx docs (api documentation)
+        run: |
+          sphinx-build -b html docs/api site/api
 
-      - name: Deploy docs
-        uses: mhausenblas/mkdocs-deploy-gh-pages@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          REQUIREMENTS: docs/requirements.txt
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site
+          force_orphan: true

docs/api/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     = source
+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/api/conf.py

@@ -0,0 +1,77 @@
+import os
+
+# -- Path setup --------------------------------------------------------------
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here.
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path("..").resolve()))
+
+# -- Project information -----------------------------------------------------
+project = "mesa-frames"
+author = "Adam Amer"
+copyright = f"2023, {author}"
+
+# -- General configuration ---------------------------------------------------
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "numpydoc",
+    "sphinx_copybutton",
+    "sphinx_design",
+    "autodocsumm",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+html_show_sourcelink = False
+
+# -- Extension settings ------------------------------------------------------
+# intersphinx mapping
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "polars": ("https://pola-rs.github.io/polars/py-polars/html/", None),
+}
+
+# numpydoc settings
+numpydoc_show_class_members = False
+
+# Copybutton settings
+copybutton_prompt_text = r">>> |\.\.\. "
+copybutton_prompt_is_regexp = True
+
+# -- Custom configurations ---------------------------------------------------
+autoclass_content = "class"
+autodoc_member_order = "bysource"
+autodoc_default_options = {"special-members": True, "exclude-members": "__weakref__"}
+
+# -- GitHub link and user guide settings -------------------------------------
+github_root = "https://github.com/adamamer20/mesa-frames"
+web_root = "https://adamamer20.github.io/mesa-frames"
+
+html_theme_options = {
+    "external_links": [
+        {
+            "name": "User guide",
+            "url": f"{web_root}/user-guide/",
+        },
+    ],
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": github_root,
+            "icon": "fa-brands fa-github",
+        },
+    ],
+    "navbar_end": ["navbar-icon-links"],
+}

docs/api/index.rst

@@ -0,0 +1,27 @@
+mesa-frames API
+===============
+
+This page provides a high-level overview of all public mesa-frames objects, functions, and methods. All classes and functions exposed in the ``mesa_frames.*`` namespace are public.
+
+.. grid::
+
+    .. grid-item-card::
+
+        .. toctree::
+            :maxdepth: 2
+
+            reference/agents/index
+
+    .. grid-item-card::
+
+        .. toctree::
+           :maxdepth: 1
+
+           reference/model
+
+    .. grid-item-card::
+
+        .. toctree::
+            :maxdepth: 3
+
+            reference/space/index

docs/api/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/api/reference/agents/index.rst

@@ -0,0 +1,17 @@
+AgentSetDF
+==========
+
+.. currentmodule:: mesa_frames
+
+.. autoclass:: AgentSetPandas
+    :members:
+    :inherited-members:
+    :autosummary:
+    :autosummary-nosignatures:
+
+.. autoclass:: AgentSetPolars
+    :members:
+    :inherited-members:
+    :autosummary:
+    :autosummary-nosignatures:
+

docs/api/reference/model.rst

@@ -0,0 +1,10 @@
+ModelDF
+=======
+
+.. currentmodule:: mesa_frames
+
+.. autoclass:: ModelDF
+    :members:
+    :inherited-members:
+    :autosummary:
+    :autosummary-nosignatures:

docs/api/reference/space/grid/index.rst

@@ -0,0 +1,16 @@
+GridDF
+======
+
+.. currentmodule:: mesa_frames
+
+.. autoclass:: GridPandas
+    :members:
+    :inherited-members:
+    :autosummary:
+    :autosummary-nosignatures:
+
+.. autoclass:: GridPolars
+    :members:
+    :inherited-members:
+    :autosummary:
+    :autosummary-nosignatures:

docs/api/reference/space/index.rst

@@ -0,0 +1,8 @@
+Space
+=====
+This page provides a high-level overview of possible space objects for mesa-frames models.
+
+.. toctree::
+    :maxdepth: 2
+
+    grid/index

mesa_frames/abstract/agents.py

@@ -68,21 +68,7 @@ def __init__(self, model):
 
 
 class AgentContainer(CopyMixin):
-    """An abstract class for containing agents. Defines the common interface for AgentSetDF and AgentsDF.
-
-    Properties
-    ----------
-    model : ModelDF
-        Get the model associated with the AgentContainer.
-    random : Generator
-        Get the random number generator associated with the model.
-    agents : DataFrame | dict[str, DataFrame]
-        Get or set the agents in the AgentContainer.
-    active_agents : DataFrame | dict[str, DataFrame]
-        Get or set the active agents in the AgentContainer.
-    inactive_agents : DataFrame | dict[str, DataFrame]
-        Get the inactive agents in the AgentContainer.
-    """
+    """An abstract class for containing agents. Defines the common interface for AgentSetDF and AgentsDF."""
 
     _copy_only_reference: list[str] = [
         "_model",
@@ -741,19 +727,6 @@ def pos(self) -> DataFrame | dict[str, DataFrame]:
 class AgentSetDF(AgentContainer, DataFrameMixin):
     """The AgentSetDF class is a container for agents of the same type.
 
-    Properties
-    ----------
-    active_agents(self) -> DataFrame
-        Get the active agents in the AgentSetDF.
-    agents(self) -> DataFrame
-        Get or set the agents in the AgentSetDF.
-    inactive_agents(self) -> DataFrame
-        Get the inactive agents in the AgentSetDF.
-    model(self) -> ModelDF
-        Get the model associated with the AgentSetDF.
-    random(self) -> Generator
-        Get the random number generator associated with the model.
-
     Parameters
     ----------
     model : ModelDF

mesa_frames/concrete/agents.py

@@ -67,22 +67,7 @@ def step(self):
 
 
 class AgentsDF(AgentContainer):
-    """A collection of AgentSetDFs. All agents of the model are stored here.
-
-    Properties
-    ----------
-    active_agents(self) -> dict[AgentSetDF, pd.DataFrame]
-        Get the active agents in the AgentsDF.
-    agents(self) -> dict[AgentSetDF, pd.DataFrame]
-        Get or set the agents in the AgentsDF.
-    inactive_agents(self) -> dict[AgentSetDF, pd.DataFrame]
-        Get the inactive agents in the AgentsDF.
-    model(self) -> ModelDF
-        Get the model associated with the AgentsDF.
-    random(self) -> np.random.Generator
-        Get the random number generator associated with the model.
-
-    """
+    """A collection of AgentSetDFs. All agents of the model are stored here."""
 
     _agentsets: list[AgentSetDF]
     _ids: pl.Series

mesa_frames/concrete/model.py

@@ -59,12 +59,6 @@ class ModelDF:
     It includes the basic attributes and methods necessary for initializing and
     running a simulation model.
 
-    Properties
-    ----------
-    agents : AgentsDF
-        An AgentSet containing all agents in the model, generated from the _agents attribute.
-    agent_types : list of type
-        A list of different agent types present in the model.
     """
 
     random: np.random.Generator

mesa_frames/concrete/pandas/agentset.py

@@ -62,12 +62,16 @@ def step(self):
 from mesa_frames.concrete.pandas.mixin import PandasMixin
 from mesa_frames.concrete.polars.agentset import AgentSetPolars
 from mesa_frames.types_ import AgentPandasMask, PandasIdsLike
+from mesa_frames.utils import copydoc
 
 if TYPE_CHECKING:
     from mesa_frames.concrete.model import ModelDF
 
 
-class AgentSetPandas(AgentSetDF, PandasMixin):  # noqa : D101
+@copydoc(AgentSetDF)
+class AgentSetPandas(AgentSetDF, PandasMixin):
+    """pandas-based implementation of AgentSetDF."""
+
     _agents: pd.DataFrame
     _mask: pd.Series
     _copy_with_method: dict[str, tuple[str, list[str]]] = {

mesa_frames/concrete/pandas/mixin.py

@@ -50,6 +50,8 @@ def _some_private_method(self):
 
 
 class PandasMixin(DataFrameMixin):
+    """pandas-based implementation of DataFrame operations."""
+
     def _df_add(
         self,
         df: pd.DataFrame,

mesa_frames/concrete/pandas/space.py

@@ -61,9 +61,13 @@ def step(self):
 
 from mesa_frames.abstract.space import GridDF
 from mesa_frames.concrete.pandas.mixin import PandasMixin
+from mesa_frames.utils import copydoc
 
 
+@copydoc(GridDF)
 class GridPandas(GridDF, PandasMixin):
+    """pandas-based implementation of GridDF."""
+
     _agents: pd.DataFrame
     _copy_with_method: dict[str, tuple[str, list[str]]] = {
         "_agents": ("copy", ["deep"]),