set up sphinx doc

.gitignore

@@ -6,4 +6,10 @@
 # exclude content of logfiles folders
 *.tsv
 *.mat
-check_my_code_report.txt
+check_my_code_report.txt
+
+# exclude content of files for virtual env (mostly for the doc)
+cpp_ptb
+
+# ignore file created by sphynx
+/docs/build

.readthedocs.yml

@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  builder: html
+  fail_on_warning: true
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

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 +1,139 @@
+# Setting up sphinx to create a matlab doc
+
+## Set up virtual environment
+
+```bash
+virtualenv -p python3 cpp_ptb
+source cpp_ptb/bin/activate
+
+pip install -r requirements.txt
+```
+
+## Quick start on the doc
+
+See the [sphinx doc](https://www.sphinx-doc.org/en/master/usage/quickstart.html)
+for more.
+
+This
+[blog post](https://medium.com/@richdayandnight/a-simple-tutorial-on-how-to-document-your-python-project-using-sphinx-and-rinohtype-177c22a15b5b)
+is also useful.
+
+```bash
+cd docs
+sphinx-quickstart # launch a basic interactive set up of sphinx
+```
+
+Answer the questions on prompt.
+
+## Setting up conf.py for matlab doc
+
+Following the documentation from
+[matlabdomain for sphinx](https://github.com/sphinx-contrib/matlabdomain).
+
+Specify the extensions you are using:
+
+```python
+extensions = [
+    'sphinxcontrib.matlab',
+    'sphinx.ext.autodoc']
+```
+
+`matlab_src_dir` in `docs/source/conf.py` should have the path (relative to `conf.py`)
+to the folder containing your matlab code:
+
+```python
+matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
+```
+
+## reStructured text markup
+
+reStructured text mark up
+[primer](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html).
+
+## "Templates"
+
+There are different ways you can document the help section of your matlab
+functions so it can be documented automatically by sphinx.
+
+```matlab
+function y = my_function(arg1, arg2)
+    %
+    % Describe what the function does here.
+    %
+    %  y = my_function_napoleon(arg1, arg2)
+    %
+    % :param arg1: The first input value
+    % :param arg2: The second input value
+    % :returns: The input value multiplied by two
+
+    y = arg1 + arg2
+```
+
+"Napoleon" way more similar to Numpy:
+
+```matlab
+function y = my_function_napoleon(arg1, arg2)
+    %
+    % Describe what the function does here.
+    %
+    %  y = my_function_napoleon(arg1, arg2)
+    %
+    % Parameters:
+    %    x: The first input value
+    %
+    %    y: The second input value
+    %
+    % Returns:
+    %    The input value multiplied by two
+
+    y = x * 2;
+```
+
+You then just need to insert this in your `.rst` file for the documentation to
+be done automatically.
+
+```rst
+
+.. automodule:: src .. <-- This is necessary for autodocumenting the rest
+
+.. autofunction:: my_function
+
+.. autofunction:: my_function_napoleon
+```
+
+## Build the documentation locally
+
+From the `docs` directory:
+
+```bash
+sphinx-build -b html source build
+```
+
+This will build an html version of the doc in the `build` folder.
+
+## Buid the documentation with Read the Docs
+
+Add a [`.readthedocs.yml`](../.readthedocs.yml) file in the root of your repo.
+
+See [HERE](https://docs.readthedocs.io/en/stable/config-file/v2.html) for
+details.
+
+You can then trigger the build of the doc by going to the [read the docs](https://readthedocs.org)
+website.
+
+You might need to be added as a maintainer of the doc.
+
+The doc can be built from any branch of a repo.
+
+<!-- TODO -->
+
+## Other matlab projects that use
+
+### Sphinx
+
+Some are listed
+[sphinx-contrib/matlabdomain#users](https://github.com/sphinx-contrib/matlabdomain#users)
+
+### Read the docs
+
+  - [qMRLab](https://github.com/qMRLab/qMRLab/wiki/Guideline:-Generating-Documentation)

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.http://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 +1,4 @@
+Sphinx
+sphinxcontrib-matlabdomain
+sphinxcontrib-napoleon
+sphinx_rtd_theme

docs/source/conf.py

@@ -0,0 +1,80 @@
+# 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
+sys.path.insert(0, os.path.abspath('../..'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'CPP_PTB'
+copyright = '2020, CPP_PTB developers'
+author = 'CPP_PTB developers'
+
+# The full version, including alpha/beta/rc tags
+release = 'v1.0.0'
+
+
+# -- 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 = [
+    'sphinxcontrib.matlab',
+    'sphinx.ext.autodoc']
+matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
+primary_domain = 'mat'
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+# -- 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_rtd_theme'
+
+# 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_logo = '_static/cpp_lab_logo.png'
+
+# html_theme_options = {
+#     'github_user': 'cpp-lln-lab',
+#     'github_repo': 'CPP_BIDS_SPM_pipeline',
+#     'github_button': True,
+#     'github_banner': True
+# }
+# html_theme_options = {
+#     'collapse_navigation': False,
+#     'display_version': False,
+#     'navigation_depth': 4,
+# }
+
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}