Update documentation page to provide package information

[sgosline]

As we're reworking the documentation page, it might be helpful to use some more python-native tools such as Sphynx to organize things and cover the package functionality. The build tools should be maintained on the github Readme but it'd be nice to have a formal structure for the docs. Also, it might be more managemeable than our current framework. Here is an example that David Degan built for another project: https://pnnl-compbio.github.io/bmdrc/#

[ymahlich]

link to the quick start guide: https://www.sphinx-doc.org/en/master/usage/quickstart.html
This is the guide that I followed for one of my other projects.

I think the goal should be to get this to compile on a local instance first and then figure out how we incorporate this into github actions / git hub hosted pages.

Also as a final side note, any additional documentation beyond source code docs that are autogenerated from docstrings need to be supplied some way. There are ways to do this using additional markdown files.

[ymahlich]

The conf.py that needs to be setup would look something like this:

# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

project = 'VaLPAS'
copyright = '2024, Yannick Mahlich, Logan Lewis, Jason McDermott'
author = 'Yannick Mahlich, Logan Lewis, Jason McDermott'
release = '0.1'

# -- Pathsetup ------
import os
import sys
sys.path.insert(0, os.path.abspath('../../src/'))
# sys.path.insert(0, os.path.abspath('../../src/valpas'))


# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

extensions = [
    'sphinx.ext.duration',
    'sphinx.ext.doctest',
    'sphinx.ext.napoleon',
    'sphinx.ext.autodoc',
    # 'sphinx.ext.viewcode',
    'sphinx.ext.autosummary',
    # 'autoapi.extension'
]
# autoapi_dirs = ['../../src']
# autosummary_generate = True
templates_path = ['_templates']
exclude_patterns = []



# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

html_theme = 'pydata_sphinx_theme'
html_static_path = ['_static']

# Automatically extract typehints when specified and place them in
# descriptions of the relevant function/method.
autodoc_typehints = "description"

# Don't show class signature with the class' name.
autodoc_class_signature = "separated"

importantly the path (sys.path.insert([...])) will have to be updated since coderdata follows a different root folder structure than what is generally considered the "python standard".

It is possible that there was some "automated" setup process that I do not remember that fills most of the conf.py file out dynamically based on some user input.