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Merge pull request ebezzam#3 from ebezzam/feat/docs
Add documentation files.
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‎.readthedocs.yaml‎

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the version of Python and other tools you might need
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build:
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os: ubuntu-20.04
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tools:
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python: "3.9"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/source/conf.py
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# If using Sphinx, optionally build your docs in additional formats such as PDF
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# formats:
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# - pdf
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# Optionally declare the Python requirements required to build your docs
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python:
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install:
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- requirements: docs/requirements.txt

‎README.rst‎

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python-dev-tips, `Slides <https://docs.google.com/presentation/d/1BnezhwUy22DiF72wss8GU_YIMfhjortz-uILdIFGuoM/edit?usp=sharing>`__
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******************************************************************************************************************************************
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.. image:: https://readthedocs.org/projects/python-dev-tips/badge/?version=latest
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:target: http://python-dev-tips.readthedocs.io/en/latest/
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:alt: Documentation Status
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.. image:: https://github.com/ebezzam/python-dev-tips/actions/workflows/python.yml/badge.svg
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:target: https://github.com/ebezzam/python-dev-tips/blob/main/.github/workflows/python.yml
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:alt: Unit tests and formatting
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Tutorial first given at ENS Ulm (January 2023) on how to develop a Python package. There is a slight focus on scientific computing, but the general principles apply to any Python project.
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.. contents:: **Table of Contents**
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TODO
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====
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- change documentation links to main branch
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- joblib example in profile
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- github page
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- point out features in scripts: object-oriented, asserts, tqdm, type hints
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- matplotlib, pytest, black in dev install
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- example file with hydra
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- manifest file to not include file in package
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- GitHub actions for releasing to PyPi when changes to version
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- documentation (autodoc)
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- adding badges to README

‎docs/Makefile‎

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/make.bat‎

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎docs/requirements.txt‎

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sphinx==4.0.1
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sphinx_rtd_theme==0.4.3
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docutils==0.16 # >0.17 doesn't render bullets

‎docs/source/badges.rst‎

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Badges
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======
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Adding badges to your GitHub repository and documentation amounts to simply adding an image.
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For example, in a `reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`__ file:
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.. code:: rst
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.. image:: https://readthedocs.org/projects/python-dev-tips/badge/?version=latest
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:target: http://python-dev-tips.readthedocs.io/en/latest/
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:alt: Documentation Status
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which when rendered will make the following badge:
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.. image:: https://readthedocs.org/projects/python-dev-tips/badge/?version=latest
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:target: http://python-dev-tips.readthedocs.io/en/latest/
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:alt: Documentation Status
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You can also create `badges from GitHub Actions <https://docs.github.com/en/actions/monitoring-and-troubleshooting-workflows/adding-a-workflow-status-badge>`__.
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.. code:: rst
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.. image:: https://github.com/ebezzam/python-dev-tips/actions/workflows/python.yml/badge.svg
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:target: https://github.com/ebezzam/python-dev-tips/blob/main/.github/workflows/python.yml
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:alt: Unit tests and formatting
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.. image:: https://github.com/ebezzam/python-dev-tips/actions/workflows/python.yml/badge.svg
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:target: https://github.com/ebezzam/python-dev-tips/blob/main/.github/workflows/python.yml
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:alt: Unit tests and formatting
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Finally, you can use `Badgen <https://badgen.net/>`__ to create custom badges.
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‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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# import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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import datetime
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import sys
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from unittest import mock
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import os
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sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))
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MOCK_MODULES = ["matplotlib", "matplotlib.pyplot", "numpy"]
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for mod_name in MOCK_MODULES:
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sys.modules[mod_name] = mock.Mock()
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# -- Project information -----------------------------------------------------
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project = "pydevtips"
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copyright = f"{datetime.date.today().year}, Eric Bezzam"
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author = "Eric Bezzam"
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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"sphinx_rtd_theme",
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"sphinx.ext.intersphinx",
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"sphinx.ext.autosummary",
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"sphinx.ext.autodoc",
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"sphinx.ext.napoleon",
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]
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autodoc_default_options = {
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"members": True,
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}
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autodoc_typehints = "none" # for cleaner sphinx output, don't show type hints
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3/", None),
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"NumPy [latest]": ("https://docs.scipy.org/doc/numpy/", None),
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"matplotlib": ("http://matplotlib.sourceforge.net/", None),
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}
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intersphinx_disabled_domains = ["std"]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = "sphinx_rtd_theme"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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# html_static_path = ["_static"]

‎docs/source/documentation.rst‎

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Documentation
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=============
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We will be using `Sphinx <https://www.sphinx-doc.org/en/master/>`__ to generate documentation from
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docstrings that are written within code. Docstrings are long-form
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comments beneath class and functions declaration that typically describe:
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- What the function or class does.
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- Its inputs and their data types.
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- Its outputs and their data types.
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For example:
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.. code:: Python
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def add(a, b):
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"""
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Add two integers.
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Parameters
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----------
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a : int
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First integer.
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b : int
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Second integer.
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Returns
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-------
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result : int
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Sum of inputs.
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"""
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assert isinstance(a, int)
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assert isinstance(b, int)
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return a + b
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Which will be rendered as :func:`pydevtips.utils.add`.
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Initial setup
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-------------
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So you've diligently written your docstrings (or used GitHub Copilot!), and you
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want to generate your documentation.
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Here are some recommended steps to get started with Sphinx:
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#. Create a lightweight virtual environment for building the documentation. This can save a lot of time when building and publishing documentation remotely, as we'll show with `ReadTheDocs <https://readthedocs.org/>`__.
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.. code:: bash
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# create new environment, press enter to accept
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conda create -n docs_env python=3.9
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# activate environment
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conda activate docs_env
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# install requirements stored in `docs`
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# (may differ from our file depending on your needs)
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(docs_env) cd docs
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(docs_env) pip install -r requirements.txt
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#. Inside your virtual environment, run ``sphinx-quickstart`` to creates a lot of the boilerplate configurations. This will guide you through a set of questions, such as your project details. We recommend creating separate ``source`` and ``build`` directories.
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#. Build the documentation, e.g. with ``make html``.
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#. Open ``docs/build/html/index.html`` in a browser to see your initial documentation!
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Editing your documentation
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--------------------------
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The ``index.rst`` file will serve as the "homepage" for your documentation (built into ``index.html``).
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Typically, people have the same content as their README. Before you copy-and-paste
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the contents (!), you can directly insert the contents with the following line.
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.. code:: rst
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.. include:: ../../README.rst
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.. note::
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`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`__
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is the default plaintext markup language used by Sphinx. At this point, you may be thinking:
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*"But my README is a Markdown file (.md)..."*. While there are `tools <https://www.sphinx-doc.org/en/master/usage/markdown.html>`__
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to make Sphinx compatible with Markdown, I think you will save yourself more headaches to simply
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switch to reStructuredText. There are also `online tools <https://cloudconvert.com/md-to-rst>`__
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to help you with that.
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Adding new pages to your documentation amount to:
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#. Creating new RST files.
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#. Including them in your ``index.rst`` file.
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#. Rebuilding the documentation, e.g. with ``make html``.
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You may also need to edit the ``conf.py`` file to use different features.
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Check out our `index.rst <https://raw.githubusercontent.com/ebezzam/python-dev-tips/feat/docs/docs/source/index.rst>`__
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and `conf.py <https://github.com/ebezzam/python-dev-tips/blob/feat/docs/docs/source/conf.py>`__
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files for example configurations.
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You can do a clean build of your documentation with the following commands:
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.. code:: bash
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make clean
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make html
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Pro-tips
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--------
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* Changing to the ReadTheDocs theme inside `conf.py <https://github.com/ebezzam/python-dev-tips/blob/ec6b15c6718b96e2c1a00496d2cf7005755d006c/docs/source/conf.py#L75>`__.
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* `Intersphinx <https://docs.readthedocs.io/en/stable/guides/intersphinx.html>`__ for linking to other documentations.
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In the ``conf.py`` file: `add <https://github.com/ebezzam/python-dev-tips/blob/ec6b15c6718b96e2c1a00496d2cf7005755d006c/docs/source/conf.py#L43>`__
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the Sphinx extension, and `link <https://github.com/ebezzam/python-dev-tips/blob/ec6b15c6718b96e2c1a00496d2cf7005755d006c/docs/source/conf.py#L54>`__
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to the other documentation. Inside your documentation you can link to the other library, e.g.
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for data types:
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.. code:: Python
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...
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"""
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Parameters
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----------
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filter : :py:class:`~numpy.ndarray`
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"""
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...
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which renders as in :func:`pydevtips.fftconvolve.RFFTConvolve.__init__`
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with a clickable link to NumPy's documentation.
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* `Mock modules <https://github.com/ebezzam/python-dev-tips/blob/ec6b15c6718b96e2c1a00496d2cf7005755d006c/docs/source/conf.py#L24>`__ to keep your documentation virtual environment light.
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* `Add the path <https://github.com/ebezzam/python-dev-tips/blob/feat/docs/docs/source/conf.py#L22>`__
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to your package, so that it doesn't have to be installed (again keeping your documentation environment light!).
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* `Automate year <https://github.com/ebezzam/python-dev-tips/blob/ec6b15c6718b96e2c1a00496d2cf7005755d006c/docs/source/conf.py#L32>`__.
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Publishing
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----------
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With a set of HTML files, there are many ways to publish your documentation online.
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We present one approach through `ReadTheDocs <https://readthedocs.org/>`__ (RTD), which is
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free and very popular among Python developers. Another popular free options is through
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`GitHub Pages <https://pages.github.com/>`__. I prefer RTD to not have the GitHub username or
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organization in the documentation URL.
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To publish on RTD:
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#. Make an account: https://readthedocs.org/accounts/signup/
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#. Import a project from the `dashboard <https://readthedocs.org/dashboard/>`__. There are two ways to do this: (1) linking your GitHub account and selecting one of your **public** repositories, or (2) importing the project manually. When linking to GitHub, the documentation is re-built whenever there are changes to the selected branch.
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#. Check your project page for the build status.
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You can (optionally) define a `.readthedocs.yaml <https://github.com/ebezzam/python-dev-tips/blob/feat/docs/.readthedocs.yaml>`__
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file to ensure a build environment as close as possible to your local machine.

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