Sphinx docs

.gitignore

@@ -1,5 +1,9 @@
-*.egg-info
-*.DS_Store
 __pycache__
+_build
+.ipynb_checkpoints
 *_checkpoints
+*.DS_Store
+*.egg-info
+build/
 dist/
+docs/_build/

CONTRIBUTING.md

@@ -0,0 +1,69 @@
+# CONTRIBUTING
+
+This repository is under active development by a small number of contributors at the moment. Once the code and API has settled a bit we will open up and welcome contributions. But not yet.
+
+## Setup for local development
+
+1. Create a new environment using Python >=3.8, for example 3.10
+
+```
+conda create --name CausalPy python=3.10
+```
+
+2. Activate environment:
+
+```
+conda activate CausalPy
+```
+
+3. Install the package in editable mode
+
+```
+pip install -e .
+```
+
+4. Install development dependencies
+
+```
+pip install -r requirements-dev.txt
+pip install -r requirements-docs.txt
+```
+
+5. You may also need to run this to get pre-commit checks working
+
+```
+pre-commit install
+```
+
+6. Note: You may have to run the following command to make Jupyter Lab aware of the `CausalPy` environment.
+
+```
+python -m ipykernel install --user --name CausalPy
+```
+
+## Building the documentation locally
+
+Ensure the right packages (in `requirements-docs.txt`) are available in the environment. See the steps above.
+
+A local build of the docs is achieved by:
+
+```bash
+cd docs
+make html
+```
+
+Sometimes not all changes are recognised. In that case run:
+
+```bash
+make clean && make html
+```
+
+Docs are built in `docs/_build`, but these docs are _not_ committed to the GitHub repository due to `.gitignore`.
+
+## New releases [work in progress]
+
+1. Bump the release version in `causalpy/version.py`. This is automatically read by `setup.py` and `docs/config.py`.
+2. Update on pypi.org. In the root directory:
+  - `python setup.py sdist`
+  - update to pypi.org with `twine upload dist/*`
+3. _??? Do I have to do anything to update the docs on [`readthedocs`](https://readthedocs.org)???_

README.md

@@ -23,7 +23,16 @@ Another distinctive feature of this package is the ability to use different mode
 
 ## Installation
 
-[coming soon]
+To get the latest release:
+```bash
+pip install CausalPy
+```
+
+Alternatively, if you want the very latest version of the package you can install from GitHub:
+
+```bash
+pip install git+https://github.com/pymc-labs/CausalPy.git
+```
 
 ## Roadmap
 
@@ -113,57 +122,12 @@ Here are some general resources about causal inference:
 * Huntington-Klein, N. (2021). [The effect: An introduction to research design and causality](https://theeffectbook.net). Chapman and Hall/CRC.
 * Reichardt, C. S. (2019). Quasi-experimentation: A guide to design and analysis. Guilford Publications.
 
-## Contributions
-
-This repository is under active development by a small number of contributors at the moment. Once the code and API has settled a bit we will open up and welcome contributions. But not yet.
-
 ## License
 
 [Apache License 2.0](LICENSE)
 
 ---
 
-## Local development
-
-1. Create a new environment using Python >=3.8, for example 3.10
-
-```
-conda create --name CausalPy python=3.10
-```
-
-2. Activate environment:
-
-```
-conda activate CausalPy
-```
-
-3. Install the package in editable mode
-
-```
-pip install -e .
-```
-
-4. Install development dependencies
-
-```
-pip install -r requirements-dev.txt
-pip install -r requirements-docs.txt
-```
-
-5. You may also need to run this to get pre-commit checks working
-
-```
-pre-commit install
-```
-
-6. Note: You may have to run the following command to make Jupyter Lab aware of the `CausalPy` environment.
-
-```
-python -m ipykernel install --user --name CausalPy
-```
-
----
-
 ## Support
 
 <img src="img/pymc-labs-log.png" align="right" width="50%" />

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:
+	@$(SPHINXBUILD) -M help "$(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_plot_utils.rst

@@ -0,0 +1,9 @@
+:mod:`causalpy.plot_utils`
+==========================
+
+.. toctree::
+  :maxdepth: 1
+
+.. automodule:: causalpy.plot_utils
+   :members:
+   :undoc-members:

docs/api_pymc_experiments.rst

@@ -0,0 +1,9 @@
+:mod:`causalpy.pymc_experiments`
+================================
+
+.. toctree::
+  :maxdepth: 1
+
+.. automodule:: causalpy.pymc_experiments
+   :members:
+   :undoc-members:

docs/api_pymc_models.rst

@@ -0,0 +1,9 @@
+:mod:`causalpy.pymc_models`
+===========================
+
+.. toctree::
+  :maxdepth: 1
+
+.. automodule:: causalpy.pymc_models
+   :members:
+   :undoc-members:

docs/api_skl_experiments.rst

@@ -0,0 +1,9 @@
+:mod:`causalpy.skl_experiments`
+===============================
+
+.. toctree::
+  :maxdepth: 1
+
+.. automodule:: causalpy.skl_experiments
+   :members:
+   :undoc-members:

docs/api_skl_models.rst

@@ -0,0 +1,9 @@
+:mod:`causalpy.skl_models`
+==========================
+
+.. toctree::
+  :maxdepth: 1
+
+.. automodule:: causalpy.skl_models
+   :members:
+   :undoc-members:

docs/conf.py

@@ -0,0 +1,76 @@
+# 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
+
+
+# -- Path setup --------------------------------------------------------------
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../mypackage"))
+
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "CausalPy"
+copyright = "2022, Benjamin T. Vincent"
+author = "Benjamin T. Vincent"
+
+from causalpy.version import __version__
+
+release = __version__
+print(f"{release=}")
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.mathjax",
+    "sphinx.ext.autodoc",
+    "sphinx_autodoc_typehints",
+    "nbsphinx",
+    "myst_parser",
+]
+
+source_suffix = [".rst", ".md"]
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# MyST options for working with markdown files. Info about extensions here https://myst-parser.readthedocs.io/en/latest/syntax/optional.html?highlight=math#admonition-directives
+myst_enable_extensions = ["dollarmath", "amsmath", "colon_fence", "linkify"]
+
+# -- 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"]
+# TODO: version seems not to be displayed despite setting this to True
+html_theme_options = {
+    "display_version": True,
+}
+
+# -- Options for autodoc ----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#configuration
+
+# Automatically extract typehints when specified and place them in
+# descriptions of the relevant function/method.
+autodoc_typehints = "description"
+
+# Don't show class signature with the class' name.
+autodoc_class_signature = "separated"
+
+# Add "Edit on Github" link. Replaces "view page source" ----------------------
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "pymc-labs",  # Username
+    "github_repo": "CausalPy",  # Repo name
+    "github_version": "master",  # Version
+    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+}

docs/index.rst

@@ -0,0 +1,41 @@
+.. CausalPy documentation master file, created by
+   sphinx-quickstart on Mon Nov 14 18:28:13 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+CausalPy - Causal inference in quasi-experimental settings
+==========================================================
+
+A Python package focussing on causal inference in quasi-experimental settings. The package allows for sophisticated Bayesian model fitting methods to be used in addition to traditional OLS.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+Documentation outline
+=====================
+
+.. toctree::
+   :caption: Examples
+   :titlesonly:
+
+   notebooks/skl_demos.ipynb
+   notebooks/pymc_demos.ipynb
+
+.. toctree::
+   :caption: API Reference
+   :titlesonly:
+
+   api_skl_experiments
+   api_skl_models
+   api_pymc_experiments
+   api_pymc_models
+   api_plot_utils
+
+
+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