adds initial sphinx documentation

.gitignore

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

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 +1,72 @@
+# 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"
+release = "0.0.1"
+
+
+# -- 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

notebooks/pymc_demos.ipynb → docs/notebooks/pymc_demos.ipynb

@@ -62,7 +62,7 @@
             "outputs": [],
             "source": [
                 "sc_data_path = (\n",
-                "    pathlib.Path.cwd().parents[0] / \"causalpy\" / \"data\" / \"synthetic_control.csv\"\n",
+                "    pathlib.Path.cwd().parents[1] / \"causalpy\" / \"data\" / \"synthetic_control.csv\"\n",
                 ")\n",
                 "df = pd.read_csv(sc_data_path)\n",
                 "treatment_time = 70"
@@ -360,7 +360,7 @@
                 "\n",
                 "if export_images:\n",
                 "    plt.savefig(\n",
-                "        pathlib.Path.cwd().parents[0] / \"img\" / \"synthetic_control_pymc.svg\",\n",
+                "        pathlib.Path.cwd().parents[1] / \"img\" / \"synthetic_control_pymc.svg\",\n",
                 "        bbox_inches=\"tight\",\n",
                 "        format=\"svg\",\n",
                 "    )"
@@ -379,7 +379,7 @@
             "metadata": {},
             "outputs": [],
             "source": [
-                "its_data_path = pathlib.Path.cwd().parents[0] / \"causalpy\" / \"data\" / \"its.csv\"\n",
+                "its_data_path = pathlib.Path.cwd().parents[1] / \"causalpy\" / \"data\" / \"its.csv\"\n",
                 "df = pd.read_csv(its_data_path, parse_dates=[\"date\"])\n",
                 "df.set_index(\"date\", inplace=True)\n",
                 "treatment_time = pd.to_datetime(\"2017-01-01\")"
@@ -676,7 +676,7 @@
                 "\n",
                 "if export_images:\n",
                 "    plt.savefig(\n",
-                "        pathlib.Path.cwd().parents[0] / \"img\" / \"interrupted_time_series_pymc.svg\",\n",
+                "        pathlib.Path.cwd().parents[1] / \"img\" / \"interrupted_time_series_pymc.svg\",\n",
                 "        bbox_inches=\"tight\",\n",
                 "        format=\"svg\",\n",
                 "    )"
@@ -695,7 +695,7 @@
             "metadata": {},
             "outputs": [],
             "source": [
-                "did_data_path = pathlib.Path.cwd().parents[0] / \"causalpy\" / \"data\" / \"did.csv\"\n",
+                "did_data_path = pathlib.Path.cwd().parents[1] / \"causalpy\" / \"data\" / \"did.csv\"\n",
                 "\n",
                 "df = pd.read_csv(did_data_path)"
             ]
@@ -989,7 +989,7 @@
                 "\n",
                 "if export_images:\n",
                 "    plt.savefig(\n",
-                "        pathlib.Path.cwd().parents[0] / \"img\" / \"difference_in_differences_pymc.svg\",\n",
+                "        pathlib.Path.cwd().parents[1] / \"img\" / \"difference_in_differences_pymc.svg\",\n",
                 "        bbox_inches=\"tight\",\n",
                 "        format=\"svg\",\n",
                 "    )"
@@ -1009,7 +1009,7 @@
             "outputs": [],
             "source": [
                 "rd_data_path = (\n",
-                "    pathlib.Path.cwd().parents[0] / \"causalpy\" / \"data\" / \"regression_discontinuity.csv\"\n",
+                "    pathlib.Path.cwd().parents[1] / \"causalpy\" / \"data\" / \"regression_discontinuity.csv\"\n",
                 ")\n",
                 "df = pd.read_csv(rd_data_path)"
             ]
@@ -1304,7 +1304,7 @@
                 "\n",
                 "if export_images:\n",
                 "    plt.savefig(\n",
-                "        pathlib.Path.cwd().parents[0] / \"img\" / \"regression_discontinuity_pymc.svg\",\n",
+                "        pathlib.Path.cwd().parents[1] / \"img\" / \"regression_discontinuity_pymc.svg\",\n",
                 "        bbox_inches=\"tight\",\n",
                 "        format=\"svg\",\n",
                 "    )"
@@ -1323,7 +1323,7 @@
             "metadata": {},
             "outputs": [],
             "source": [
-                "rd_data_path = pathlib.Path.cwd().parents[0] / \"causalpy\" / \"data\" / \"drinking.csv\"\n",
+                "rd_data_path = pathlib.Path.cwd().parents[1] / \"causalpy\" / \"data\" / \"drinking.csv\"\n",
                 "df = (\n",
                 "    pd.read_csv(rd_data_path)[[\"agecell\", \"all\", \"mva\", \"suicide\"]]\n",
                 "    .rename(columns={\"agecell\": \"age\"})\n",