Merge branch 'main' of https://github.com/adamamer20/mesa-frames into…

… 65-sugarscape-instantaneous-growback-polars-with-loops

.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

.markdownlint.json

@@ -1,3 +1,4 @@
 {
-    "MD013": false
+    "MD013": false,
+    "MD046": false
 }

README.md

@@ -1,8 +1,8 @@
-# mesa-frames
+# mesa-frames 🚀
 
-mesa-frames is an extension of the [mesa](https://github.com/projectmesa/mesa) framework, designed for complex simulations with thousands of agents. By storing agents in a DataFrame, mesa-frames significantly enhances the performance and scalability of mesa, while maintaining a similar syntax. mesa-frames allows for the use of [vectorized functions](https://vegibit.com/what-is-a-vectorized-operation-in-pandas/) whenever simultaneous activation of agents is possible.
+mesa-frames is an extension of the [mesa](https://github.com/projectmesa/mesa) framework, designed for complex simulations with thousands of agents. By storing agents in a DataFrame, mesa-frames significantly enhances the performance and scalability of mesa, while maintaining a similar syntax. mesa-frames allows for the use of [vectorized functions](https://stackoverflow.com/a/1422198) which significantly speeds up operations whenever simultaneous activation of agents is possible.
 
-## Why DataFrames?
+## Why DataFrames? 📊
 
 DataFrames are optimized for simultaneous operations through [SIMD processing](https://en.wikipedia.org/wiki/Single_instruction,_multiple_data). At the moment, mesa-frames supports the use of two main libraries: pandas and Polars.
 
@@ -11,11 +11,11 @@ DataFrames are optimized for simultaneous operations through [SIMD processing](h
 
 The following is a performance graph showing execution time using mesa and mesa-frames for the [Boltzmann Wealth model](https://mesa.readthedocs.io/en/stable/tutorials/intro_tutorial.html).
 
-![Performance Graph](https://github.com/adamamer20/mesa_frames/blob/main/docs/images/readme_plot_0.png)
+![Performance Graph with Mesa](https://github.com/adamamer20/mesa_frames/blob/main/examples/boltzmann_wealth/boltzmann_with_mesa.png)
 
-![Performance Graph without Mesa](https://github.com/adamamer20/mesa_frames/blob/main/docs/images/readme_plot_1.png)
+![Performance Graph without Mesa](https://github.com/adamamer20/mesa_frames/blob/main/examples/boltzmann_wealth/boltzmann_no_mesa.png)
 
-(The script used to generate the graph can be found [here](https://github.com/adamamer20/mesa_frames/blob/main/docs/scripts/readme_plot.py), but if you want to additionally compare vs Mesa, you have to uncomment `mesa_implementation` and its label)
+(The script used to generate the graph can be found [here](https://github.com/adamamer20/mesa_frames/blob/main/examples/boltzmann_wealth/performance_plot.py), but if you want to additionally compare vs Mesa, you have to uncomment `mesa_implementation` and its label)
 
 ## Installation
 
@@ -45,10 +45,7 @@ conda activate myenv
 Then, to install mesa-frames itself:
 
 ```bash
-# For pandas backend
-pip install -e .[pandas]
-# Alternatively, for Polars backend
-pip install -e .[polars]
+pip install -e .
 ```
 
 ### Installing in a Python Virtual Environment
@@ -69,10 +66,7 @@ source myenv/bin/activate  # On Windows, use `myenv\Scripts\activate`
 Then, to install mesa-frames itself:
 
 ```bash
-# For pandas backend
-pip install -e .[pandas]
-# Alternatively, for Polars backend
-pip install -e .[polars]
+pip install -e .
 ```
 
 ## Usage
@@ -141,11 +135,11 @@ class MoneyModelDF(ModelDF):
             self.step()
 ```
 
-## What's Next?
+## What's Next? 🔮
 
 - Refine the API to make it more understandable for someone who is already familiar with the mesa package. The goal is to provide a seamless experience for users transitioning to or incorporating mesa-frames.
 - Adding support for default mesa functions to ensure that the standard mesa functionality is preserved.
-- Adding GPU functionality (cuDF and Rapids).
+- Adding GPU functionality (cuDF and Dask-cuDF).
 - Creating a decorator that will automatically vectorize an existing mesa model. This feature will allow users to easily tap into the performance enhancements that mesa-frames offers without significant code alterations.
 - Creating a unique class for AgentSet, independent of the backend implementation.
 

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

docs/general/development/index.md

@@ -0,0 +1,4 @@
+# Development Guidelines
+
+!!! warning
+    This page is in construction, check it again soon.