Merge pull request #4 from UMassCDS/sphinx

integrated sphinx autodocumentation into the code

Author: ginic

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 You should also add project tags for each release in Github, see [Managing releases in a repository](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository).
 
 ## [Unreleased]
-
+- Added example auto-built Sphinx documentation in the `docs` folder
 ## [1.0.0] - 2022-05-23
 ### Added
 - README and CHANGELOG

README.md

@@ -63,27 +63,37 @@ So what does each file in this repository do?
 ```
 .
 ├── cdstemplate     # The python package root - Any code you'd like to be able to import lives here
-│   ├── corpus_counter_script.py    # A script that takes a list of documents as input and outputs a CSV of word counts
-│   ├── __init__.py     # Indicates that this directory is a python package, you can put special import instructions here
-│   ├── word_count.py    # A module that has functions and classes to import
-│   └── utils.py    # A module that handles logging and other internals
+    ├── corpus_counter_script.py    # A script that takes a list of documents as input and outputs a CSV of word counts
+    ├── __init__.py     # Indicates that this directory is a python package, you can put special import instructions here
+    ├── word_count.py    # A module that has functions and classes to import
+    └── utils.py    # A module that handles logging and other internals
 ├── CHANGELOG.md    # Versioning information
 ├── dag_workflow.png    # An image that is linked to in this README
 ├── data    # Data files which may or may not be tracked in Git, but we reserve a folder for them so that users can all have the same relative paths
-│   ├── gutenberg     # Sample text input files, the raw inputs to our experiment pipeline.
-│   └── gutenberg_counts.csv     # The expected output file for our experiment. It's generated by `dvc repro` and is ignored by git.
+    ├── gutenberg     # Sample text input files, the raw inputs to our experiment pipeline.
+    └── gutenberg_counts.csv     # The expected output file for our experiment. It's generated by `dvc repro` and is ignored by git.
+├── docs     # Sphinx auto-documentation uses this folder to run its scripts and store documentation
+    ├── _build     # Contains the Sphinx doctree and html documentation source code
+        ├── doctrees     # A folder with doctree construction information
+        └── html   # A folder that contains the html code for all automatically created documentation
+    ├── _static     # A folder that can contain static code
+    ├── _templates    # A folder that can contain Sphinx templates
+    ├── conf.py    # A function that configures Sphinx according to user specifications  
+    ├── index.rst    # A directory that users can input new functions into for auto-documentation
+    ├── make.bat    # A function that runs auto-documentation
+    └── Makefile    # A function that creates html documentation based on functions in the index.rst file
 ├── dvc.lock    # Data Version Control uses this file to compare experiment versions. It's tracked in Git, but don't edit it manually.
 ├── dvc.yaml    # Create the Data Version Control pipeline stages here
 ├── notebooks
-│   └── word_count_prototype.ipynb    # A jupyter notebook that makes pretty plots
+    └── word_count_prototype.ipynb    # A jupyter notebook that makes pretty plots
 ├── pyproject.toml    # The setuptools build tools are installed, so you project can be installed
 ├── README.md     # You're reading it now!
 ├── setup.cfg   # Project metadata and dependencies are declared for proper installation
 └── tests
     └── test_word_count.py    # Unit and smoke tests for the word_count module
 ├── .dvc    # The configuration file for Data Version Control
 ├── .github
-|   └── workflows/python_package.yml    # Github Workflow file, configures running tests on Github every time a pull request to the main branch is made
+    └── workflows/python_package.yml    # Github Workflow file, configures running tests on Github every time a pull request to the main branch is made
 ├── .gitignore   # Lists files that should not be included in version control, created from Github's template .gitignore for Python.
 └── .dvcignore    # Lists files that Data Version Control should skip when checking for changes in stage dependencies.
 ```
@@ -97,6 +107,7 @@ The README, CHANGELOG and docstrings are just as important.
 - _README.md_ : Summarize the project's purpose and give installation instructions.
 - _CHANGELOG.md_ : Tell the user what has changed between versions and why, see [Keep A CHANGELOG](https://keepachangelog.com/en/1.0.0/)
 - docstrings: Appear directly in your code and give an overview of each function or object. They can be printed using `help(object)` from the python interpreter or used to automatically generate API documentation with a tool like [Sphinx](https://www.sphinx-doc.org/en/master/index.html). There are many different docstring formats. Your team can choose any they like, just be consistent. This template uses [reStructuredText style](https://peps.python.org/pep-0287/).
+- Sphinx  : Create html documentation for your functions based on the docstrings you write in the code. Use [Sphinx](https://www.sphinx-doc.org/en/master/index.html) to streamline the documentation process.
 
 Read [Real Python's Documenting Python Code: A Complete Guide](https://realpython.com/documenting-python-code/) for more ideas about effectively documenting code. The `.md` files are written using [Markdown](https://www.markdownguide.org/), a handy formatting language that is automatically rendered in Github.
 

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 +1,55 @@
+# 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 = 'testdoc'
+copyright = '2023, Luke Ruud'
+author = 'Luke Ruud'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- 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.napoleon"
+]
+
+# 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 = 'alabaster'
+
+# 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']

docs/index.rst

@@ -0,0 +1,24 @@
+.. testdoc documentation master file, created by
+   sphinx-quickstart on Mon Jul 24 13:17:26 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to testdoc's documentation!
+===================================
+
+
+.. automodule:: cdstemplate.word_count
+    :members:
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+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

setup.cfg

@@ -27,4 +27,5 @@ dev =
     black
     jupyter
     matplotlib
-    seaborn
+    seaborn
+    sphinx