intialize documentation

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/README.md

@@ -0,0 +1,55 @@
+# Documentation
+
+We use [`Sphinx`](https://www.sphinx-doc.org/en/master/) and [`ReadtheDocs`](https://readthedocs.org/) to organize our [documentation page]().
+
+In addition, we utilize the following extensions to enhance the documentation :coffee:
+- `numpydoc`: We favor [numpy documentation style](https://numpydoc.readthedocs.io/en/latest/format.html) for API documentation.
+- `myst_parser`: We like to write documentation and guidelines in `markdown` format.
+
+## Build documentation
+
+The `sphinx` is already initialized in `docs` directory. In order to build the documentation, you will need additional packages listed in `docs/requirements.txt`.
+
+```bash
+pip install sphinx sphinx_rtd_theme myst-parser numpydoc
+cd docs
+make clean
+make html
+```
+
+Once the documentation building is done, open `docs/_build/html/index.html` to view.
+
+Use `make help` for other options.
+
+## User Guide
+
+User guidelines and tutorials are written in `.rst` or `.md` format.
+These files will be managed in `docs` directory.
+
+## API documentation
+
+The docstring for function or modules are automatically parsed using `sphinx`+`numpydoc`.
+Any inline function description, such as
+
+```py
+""" This is the form of a docstring.
+
+... description
+
+Attributes
+----------
+x : type
+    x description
+y : type
+    y description
+
+"""
+```
+
+will be parsed and displayed in API documentation. See `numpydoc` for more details.
+
+## ReadtheDocs
+
+`ReadtheDocs` runs `sphinx` internally and maintain the documentation website. We will always activate the `stable` and `latest` version, and few past-documentations will also be available for the support.
+
+@nmnaughton and @skim449 has access to the `ReadtheDocs` account.

docs/conf.py

@@ -0,0 +1,103 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list 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
+
+# import sphinx_rtd_theme
+
+sys.path.insert(0, os.path.abspath("../"))
+
+from miv.version import VERSION
+
+
+# -- Project information -----------------------------------------------------
+
+project = "Mind-in-Vitro MiV-OS"
+copyright = "2022, GazzolaLab"
+author = "Gazzola Lab"
+
+# The full version, including alpha/beta/rc tags
+release = VERSION
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx_autodoc_typehints",
+    #'sphinx.ext.napoleon',
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
+    "sphinx.ext.mathjax",
+    "numpydoc",
+    "myst_parser",
+]
+
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    "README.md",  # File reserved to explain how documentationing works.
+]
+
+autodoc_default_flags = [
+    "members",
+    "private-members",
+    "special-members",
+    "show-inheritance",
+]
+autosectionlabel_prefix_document = True
+
+source_parsers = {}
+source_suffix = [".rst", ".md"]
+
+master_doc = "index"
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+
+html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "repository_url": "https://github.com/GazzolaLab/MiV-OS",
+    "use_repository_button": True,
+}
+html_title = "MiV-OS"
+# html_logo = ""
+# pygments_style = "sphinx"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+html_css_files = ["css/*", "css/logo.css"]
+
+# -- Options for numpydoc ---------------------------------------------------
+numpydoc_show_class_members = False

docs/guide/tutorials.rst

@@ -0,0 +1,3 @@
+*****************
+Tutorial Examples
+*****************

docs/index.rst

@@ -0,0 +1,21 @@
+.. MiV-OS documentation master file, created by
+   sphinx-quickstart on Thu Mar 24 23:35:49 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to MiV-OS's documentation!
+================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   guide/tutorials
+
+
+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
+
+if "%1" == "" goto help
+
+%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
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,11 @@
+# File: docs/requirements.txt
+
+-r ../requirements.txt
+docutils
+myst-parser
+numpydoc
+readthedocs-sphinx-search==0.1.1
+sphinx==4.4.0
+sphinx-autodoc-typehints
+sphinx-book-theme
+sphinx_rtd_theme==1.0.0

setup.py

@@ -38,7 +38,20 @@
 ]
 
 # What packages are optional?
-EXTRAS = {"dev": ["black", "pre-commit", "pytest", "flake8"], "build": ["twine"]}
+EXTRAS = {
+    "dev": ["black", "pre-commit", "pytest", "flake8"],
+    "build": ["twine"],
+    "docs": [
+        "sphinx==4.4.0",
+        "sphinx_rtd_theme==1.0.0",
+        "sphinx-book-theme",
+        "readthedocs-sphinx-search==0.1.1",
+        "sphinx-autodoc-typehints",
+        "myst-parser",
+        "numpydoc",
+        "docutils",
+    ],
+}
 
 here = os.path.abspath(os.path.dirname(__file__))