Build docs with Sphinx

.github/workflows/documentation.yml

@@ -0,0 +1,39 @@
+# Based on https://github.com/actions/starter-workflows/blob/main/pages/static.yml
+name: documentation
+
+on:
+    push:
+        branches: [$default-branch]
+    workflow_dispatch:
+
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+jobs:
+    docs:
+        environment:
+            name: github-pages
+            url: ${{ steps.deployment.outputs.page_url }}
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python for Docs
+              uses: actions/setup-python@v5
+              with:
+                python-version: '3.x'
+            - name: Install sphinx
+              run: |
+                    python -m pip install --upgrade pip
+                    pip install sphinx sphinx-rtd-theme
+            - name: Build Docs
+              run: |
+                    sphinx-build docs docs/_build
+            - name: Upload artifact
+              uses: actions/upload-pages-artifact@v3
+              with:
+                path: './docs/_build'
+            - name: Deploy to GitHub Pages
+              id: deployment
+              uses: actions/deploy-pages@v4

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/conf.py

@@ -0,0 +1,43 @@
+# 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
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath('..'))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'mssm'
+copyright = '2024, Joshua Krause'
+author = 'Joshua Krause'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc']
+
+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_theme_options = {
+
+    # Toc options
+    'collapse_navigation': True,
+    'sticky_navigation': True,
+    'navigation_depth': 8
+}
+
+
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,28 @@
+.. mssm documentation master file, created by
+   sphinx-quickstart on Fri Sep 27 15:37:49 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+mssm documentation
+==================
+
+This is the documentation for the **exposed** API of ``mssm``. The source code for internal functions is available on `GitHub <https://github.com/JoKra1/mssm>`_ and can be
+consulted to understand their implementation. ``mssm`` is a toolbox to estimate Generalized Additive Mixed Models (GAMMs), Generalized Additive Mixed Models of Location Scale
+and Shape (GAMMLSS), and more general (mixed) smooth models in the sense defined by `Wood, Pya, & Säfken (2016) <https://doi.org/10.1080/01621459.2016.1180986>`_.
+mssm is an excellent choice for the modeling of multi-level time-series data, often estimating additive models with separate smooths for thousands of levels in a couple of minutes.
+
+Currently, ``mssm`` supports Gaussian (G)AMMs (:func:`mssm.src.python.exp_fam.Gaussian`), Gamma GAMMs (:func:`mssm.src.python.exp_fam.Gamma`), and Binomial GAMMs (:func:`mssm.src.python.exp_fam.Binomial`).
+For GAMMLSS models, Gaussian models (:func:`mssm.src.python.exp_fam.GAUMLSS`), Gamma models (:func:`mssm.src.python.exp_fam.GAMMALS`), and Multionimal models (:func:`mssm.src.python.exp_fam.MULNOMLSS`) are supported.
+
+If you are missing a family, don't worry - all you need to do is to implement the :func:`mssm.src.python.exp_fam.Family` template class for GAMM models and the :func:`mssm.src.python.exp_fam.GAMLSSFamily` template class for GAMMLSS models.
+To estimate the most general kind of smooth model, you only have to implement the :func:`mssm.src.python.exp_fam.GENSMOOTHFamily` template class.
+
+To get started with ``mssm`` the tutorial and visualization code available `here <https://github.com/JoKra1/mssm_tutorials>`_ might also be helpful.
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules

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/modules.rst

@@ -0,0 +1,7 @@
+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   mssm

docs/mssm.rst

@@ -0,0 +1,22 @@
+mssm package
+============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mssm.src
+
+Submodules
+----------
+
+mssm.models module
+------------------
+
+.. automodule:: mssm.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/mssm.src.python.rst

@@ -0,0 +1,53 @@
+mssm.src.python package
+=======================
+
+Submodules
+----------
+
+mssm.src.python.compare module
+------------------------------
+
+.. automodule:: mssm.src.python.compare
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mssm.src.python.constraints module
+----------------------------------
+
+.. automodule:: mssm.src.python.constraints
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mssm.src.python.exp\_fam module
+-------------------------------
+
+.. automodule:: mssm.src.python.exp_fam
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mssm.src.python.formula module
+------------------------------
+
+.. automodule:: mssm.src.python.formula
+   :members: Formula, VarType,lhs,reparam
+   :undoc-members:
+   :show-inheritance:
+
+mssm.src.python.terms module
+----------------------------
+
+.. automodule:: mssm.src.python.terms
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mssm.src.python.utils module
+----------------------------
+
+.. automodule:: mssm.src.python.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/mssm.src.rst

@@ -0,0 +1,10 @@
+mssm.src package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mssm.src.python

pyproject.toml

@@ -12,7 +12,7 @@ before-test = "ls"
 skip = ["pp*","cp313-musllinux*"]
 test-skip = "*-win32 *i686"
 test-requires = ["pytest", "pytest-cov", "mssmViz", "numdifftools"]
-test-command = "pytest {project}/tests -k-hard --cov={project}"
+test-command = 'pytest {project}/tests -k "not _hard" --cov={project}'
 
 [project]
 dependencies=["numpy >= 1.24.1",