docs: add tools for sphinx documentation

- add tools and documentation for sphinx to automatically generate documentation from code
- add other documentation (contributing/conduct files from basic template generated by poetry/cookiecutter)

python/.readthedocs.yml

@@ -0,0 +1,14 @@
+# Required
+version: 2
+
+# Image to use
+build:
+  image: testing
+
+# Configuration
+python:
+  version: 3.11
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

python/CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+<!--next-version-placeholder-->
+
+## v0.50.0 (18/01/2023)
+
+- First release of `bento-meta`!

python/CONDUCT.md

@@ -0,0 +1,43 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant homepage](http://contributor-covenant.org/version/1/4), version 1.4.

python/CONTRIBUTING.md

@@ -0,0 +1,71 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+## Types of Contributions
+
+### Report Bugs
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+You can never have enough documentation! Please feel free to contribute to any
+part of the documentation, such as the official docs, docstrings, or even
+on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `bento-meta` for local development.
+
+1. Download a copy of `bento-meta` locally.
+2. Install `bento-meta` using `poetry`:
+
+    ```console
+    $ poetry install
+    ```
+
+3. Use `git` (or similar) to create a branch for local development and make your changes:
+
+    ```console
+    $ git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+4. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests.
+
+5. Commit your changes and open a pull request.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include additional tests if appropriate.
+2. If the pull request adds functionality, the docs should be updated.
+3. The pull request should work for all currently supported operating systems and versions of Python.
+
+## Code of Conduct
+
+Please note that the `bento-meta` project is released with a
+Code of Conduct. By contributing to this project you agree to abide by its terms.

python/docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = bento-meta
+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)

python/docs/changelog.md

@@ -0,0 +1,2 @@
+```{include} ../CHANGELOG.md
+```

python/docs/conduct.md

@@ -0,0 +1,2 @@
+```{include} ../CONDUCT.md
+```

python/docs/conf.py

@@ -4,41 +4,40 @@
 # 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.
+# # -- Path setup --------------------------------------------------------------
 #
-import os
-import sys
-sys.path.insert(0, os.path.abspath('..'))
+# # 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 = 'bento_meta'
-copyright = '2020, FNLCR'
-author = 'Mark Jensen'
-
+project = u'bento-meta'
+copyright = u'2020, FNLCR'
+author = u'Mark Jensen, Mark Benson, Nelson Moore'
 
 # -- 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'
+    'myst_nb',
+    'autoapi.extension',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
 ]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+autoapi_dirs = ['../src']
 
 # 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 = []
-
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
 # -- Options for HTML output -------------------------------------------------
 

python/docs/contributing.md

@@ -0,0 +1,2 @@
+```{include} ../CONTRIBUTING.md
+```

python/docs/example.ipynb

@@ -0,0 +1,48 @@
+{
+    "cells": [
+        {
+            "attachments": {},
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "# Example usage\n",
+                "\n",
+                "To use `bento-meta` in a project:"
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": null,
+            "metadata": {},
+            "outputs": [],
+            "source": [
+                "# pip install bento_meta\n",
+                "\n",
+                "import bento_meta\n",
+                "\n",
+                "print(bento_meta.__version__)"
+            ]
+        }
+    ],
+    "metadata": {
+        "kernelspec": {
+            "display_name": "Python 3",
+            "language": "python",
+            "name": "python3"
+        },
+        "language_info": {
+            "codemirror_mode": {
+                "name": "ipython",
+                "version": 3
+            },
+            "file_extension": ".py",
+            "mimetype": "text/x-python",
+            "name": "python",
+            "nbconvert_exporter": "python",
+            "pygments_lexer": "ipython3",
+            "version": "3.8.5"
+        }
+    },
+    "nbformat": 4,
+    "nbformat_minor": 4
+}

python/docs/index.md

@@ -0,0 +1,13 @@
+```{include} ../README.md
+```
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+example.ipynb
+changelog.md
+contributing.md
+conduct.md
+autoapi/index
+```

python/docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=bento-meta
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.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%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

python/docs/requirements.txt

@@ -0,0 +1,3 @@
+myst-nb
+sphinx-autoapi
+sphinx-rtd-theme