Add Sphinx documentation (#13)

.github/workflows/documentation.yml

@@ -0,0 +1,34 @@
+name: "Build Documentation"
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - '**.py'
+      - '.github/workflows/unit_test.yml'
+      - 'pyproject.toml'
+jobs:
+  documentation:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+        cache: 'pip' # caching pip dependencies
+    - name: Install Dependencies
+      run: |
+        sudo apt-get install -y pandoc
+        python -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install ".[dev,doc]"
+    - name: Build Documentation
+      run: |
+        cd docs
+        make html
+    - name: Upload Documentation
+      uses: actions/upload-artifact@v4
+      with:
+        name: docs
+        path: docs/_build/html

.gitignore

@@ -172,5 +172,5 @@ src/capymoa/jar/moa.jar
 condaenv.*.requirements.txt
 data
 notebooks/*.png
-
+docs/notebooks
 *tfevents*

README.md

@@ -76,10 +76,12 @@ Python wrapper for MOA to allow efficient use of existing algorithms with a more
 # Tutorial notebooks
 These notebooks show how to do things. Data is available in the ```/data/``` directory (some of which will need to be downloaded, see instrucitons there). 
 
-* **DEMO.ipynb**: Contains simple examples on how to execute classification and regression, using MOA objets to configure synthetic generators or classifiers/regressors. 
-* **Evaluation_and_Data_Reading.ipynb**: Many examples showing how to perform different evaluations for classification and regression using different methods (i.e. a loop or buildin functions). 
-* **Learners_API_Examples.ipynb**: Similar to the DEMO, but shows more capabilities of the evaluator and learner objects.
-* **Using_sklearn_pytorch.ipynb**: Shows how one can use the API to run sklearn algorithms (those that implement ```partial_fit```) and PyTorch models. 
+* [`00_getting_started.ipynb`](notebooks/00_getting_started.ipynb): Contains simple examples on how to execute classification and regression, using MOA objets to configure synthetic generators or classifiers/regressors. 
+* [`01_evaluation_and_data_reading.ipynb`](notebooks/01_evaluation_and_data_reading.ipynb): Many examples showing how to perform different evaluations for classification and regression using different methods (i.e. a loop or buildin functions). 
+* [`02_learners_api_examples.ipynb`](notebooks/02_learners_api_examples.ipynb): Shows more capabilities of the evaluator and learner objects.
+* [`03_using_sklearn_pytorch.ipynb`](notebooks/03_using_sklearn_pytorch.ipynb): Shows how one can use the API to run sklearn algorithms (those that implement ```partial_fit```) and PyTorch models.
+* [`04_drift_streams.ipynb`](notebooks/04_drift_streams.ipynb): Shows how to setup
+   simulated concept drifts in data streams.
 
 # Test notebooks
 These show how some parts of the library were developed and provide comparisons of different options on how to do things. 

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:
+	@python -m $(SPHINXBUILD) -M help "$(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
+	@python -m $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

@@ -0,0 +1,36 @@
+# Contributing to Docs
+There are three source of documentation in this repository:
+
+ 1. Auto-generated documentation from the source code using Autodoc. See this 
+    [link](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html) 
+    for more information.
+
+ 2. Juptyer notebooks in the `/notebooks` directory are converted to markdown 
+    files and included in the documentation with `nbsphinx`. See this 
+    [link](https://nbsphinx.readthedocs.io) for more information.
+
+    To add a notebook to the documentation, add the notebook to the 
+    `/notebooks` directory and add the filename to the `toctree` in
+    `index.rst`.
+
+ 3. Manually written documentation in the `/docs` directory.
+
+## Prerequisites
+Install the documentation dependencies by running the following command in the
+root directory of the repository:
+
+```bash
+pip install --editable ".[doc,dev]"
+```
+
+## Building the Documentation
+To build the documentation, run the following command in `/docs`:
+
+```sh
+make html
+```
+
+Or on Windows:
+```cmd
+make.bat html
+```

docs/conf.py

@@ -0,0 +1,38 @@
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+from pathlib import Path
+
+project = 'CapyMOA'
+copyright = '2024, Heitor Murilo Gomes, Anton Lee, Nuwan Gunasekara, Marco Heyden'
+author = 'Heitor Murilo Gomes, Anton Lee, Nuwan Gunasekara, Marco Heyden'
+release = '0.0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc', 'nbsphinx', 'sphinx.ext.mathjax']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ['_static']
+
+# Setup symbolic links for notebooks
+
+notebooks = Path("../notebooks")
+notebook_doc_source = Path("notebooks")
+if not notebook_doc_source.exists():
+    os.symlink(notebooks, notebook_doc_source)
+

docs/index.rst

@@ -0,0 +1,33 @@
+.. CapyMOA documentation master file, created by
+   sphinx-quickstart on Fri Feb 23 08:41:28 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to CapyMOA's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Tutorials:
+
+   notebooks/00_getting_started.ipynb
+   notebooks/01_evaluation_and_data_reading.ipynb
+   notebooks/02_learners_api_examples.ipynb
+   notebooks/03_using_sklearn_pytorch.ipynb
+   notebooks/04_drift_streams.ipynb
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Modules:
+
+   source/capymoa.datasets
+   source/capymoa.evaluation
+   source/capymoa.learner
+   source/capymoa.stream
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+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/source/capymoa.datasets.rst

@@ -0,0 +1,29 @@
+Datasets
+========================
+
+Submodules
+----------
+
+capymoa.datasets.datasets module
+--------------------------------
+
+.. automodule:: capymoa.datasets.datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+capymoa.datasets.downloader module
+----------------------------------
+
+.. automodule:: capymoa.datasets.downloader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: capymoa.datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/capymoa.evaluation.rst

@@ -0,0 +1,29 @@
+Evaluation
+==========================
+
+Submodules
+----------
+
+capymoa.evaluation.evaluation module
+------------------------------------
+
+.. automodule:: capymoa.evaluation.evaluation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+capymoa.evaluation.visualization module
+---------------------------------------
+
+.. automodule:: capymoa.evaluation.visualization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: capymoa.evaluation
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/capymoa.learner.classifier.rst

@@ -0,0 +1,45 @@
+capymoa.learner.classifier package
+==================================
+
+Submodules
+----------
+
+capymoa.learner.classifier.CPSSDS module
+----------------------------------------
+
+.. automodule:: capymoa.learner.classifier.CPSSDS
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+capymoa.learner.classifier.OSNN module
+--------------------------------------
+
+.. automodule:: capymoa.learner.classifier.OSNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+capymoa.learner.classifier.batch module
+---------------------------------------
+
+.. automodule:: capymoa.learner.classifier.batch
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+capymoa.learner.classifier.classifiers module
+---------------------------------------------
+
+.. automodule:: capymoa.learner.classifier.classifiers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: capymoa.learner.classifier
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/capymoa.learner.regressor.rst

@@ -0,0 +1,21 @@
+capymoa.learner.regressor package
+=================================
+
+Submodules
+----------
+
+capymoa.learner.regressor.regressors module
+-------------------------------------------
+
+.. automodule:: capymoa.learner.regressor.regressors
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: capymoa.learner.regressor
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/capymoa.learner.rst

@@ -0,0 +1,30 @@
+Learners
+=======================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   capymoa.learner.classifier
+   capymoa.learner.regressor
+
+Submodules
+----------
+
+capymoa.learner.learners module
+-------------------------------
+
+.. automodule:: capymoa.learner.learners
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: capymoa.learner
+   :members:
+   :undoc-members:
+   :show-inheritance: