API Documentation with Sphinx

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

@@ -1,19 +1,39 @@
-name: Publish docs via GitHub Pages
+name: Build and Deploy Documentation
+
 on:
   push:
     branches:
-      - main
+      # - main
+      - 72-api-documentation-with-sphinx
 
 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/__init__.py

@@ -1,3 +1,47 @@
+"""
+mesa-frames: High-performance extension for the Mesa agent-based modeling framework.
+
+mesa-frames extends the Mesa framework to support complex simulations with thousands
+of agents by storing agents in DataFrames. This approach significantly enhances
+performance and scalability while maintaining a syntax similar to Mesa.
+
+Key Features:
+- Utilizes DataFrame storage for agents, enabling vectorized operations
+- Supports both pandas and Polars as backend libraries
+- Provides similar syntax to Mesa for ease of transition
+- Allows for vectorized functions when simultaneous activation of agents is possible
+- Implements SIMD processing for optimized simultaneous operations
+- Includes GridDF for efficient grid-based spatial modeling
+
+Main Components:
+- AgentSetPandas: Agent set implementation using pandas backend
+- AgentSetPolars: Agent set implementation using Polars backend
+- ModelDF: Base model class for mesa-frames
+- GridDF: Grid space implementation for spatial modeling
+
+Usage:
+To use mesa-frames, import the necessary components and subclass them as needed:
+
+    from mesa_frames import AgentSetPolars, ModelDF, GridDF
+
+    class MyAgent(AgentSetPolars):
+        # Define your agent logic here
+
+    class MyModel(ModelDF):
+        def __init__(self, width, height):
+            super().__init__()
+            self.grid = GridDF(width, height, self)
+            # Define your model logic here
+
+Note: mesa-frames is in early development. API and usage patterns may change.
+
+For more detailed information, refer to the full documentation and API reference.
+
+Developed by: Adam Amer
+License: MIT
+GitHub: https://github.com/adamamer20/mesa_frames
+"""
+
 from mesa_frames.concrete.agents import AgentsDF
 from mesa_frames.concrete.model import ModelDF
 from mesa_frames.concrete.pandas.agentset import AgentSetPandas

mesa_frames/abstract/__init__.py

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+"""
+mesa-frames abstract components.
+
+This package contains abstract base classes and mixins that define the core
+interfaces and shared functionality for the mesa-frames extension.
+
+Classes:
+    agents.py:
+        - AgentContainer: Abstract base class for agent containers.
+        - AgentSetDF: Abstract base class for agent sets using DataFrames.
+
+    mixin.py:
+        - CopyMixin: Mixin class providing fast copy functionality.
+        - DataFrameMixin: Mixin class defining the interface for DataFrame operations.
+
+    space.py:
+        - SpaceDF: Abstract base class for all space classes.
+        - DiscreteSpaceDF: Abstract base class for discrete space classes (Grids and Networks).
+        - GridDF: Abstract base class for grid classes.
+
+These abstract classes and mixins provide the foundation for the concrete
+implementations in mesa-frames, ensuring consistent interfaces and shared
+functionality across different backend implementations (e.g., pandas, Polars).
+
+Usage:
+    These classes are not meant to be instantiated directly. Instead, they
+    should be inherited by concrete implementations in the mesa-frames package.
+
+    For example:
+
+    from mesa_frames.abstract import AgentSetDF, DataFrameMixin
+
+    class ConcreteAgentSet(AgentSetDF):
+        # Implement abstract methods here
+        ...
+
+Note:
+    The abstract classes use Python's ABC (Abstract Base Class) module to define
+    abstract methods that must be implemented by concrete subclasses.
+
+For more detailed information on each class, refer to their individual docstrings.
+"""