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Merge pull request #94 from sandialabs/sphinx-doc-attempt
Sphinx doc attempt (merge after testing refactoring)
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‎.github/workflows/ci-build.yml

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pip install -e ".[sparse,test]"
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python -m pytest -n auto optimism --cov=optimism -Wignore
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# we can also add the flag -n auto for parallel testing
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- name: docs
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run: |
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pip install -e ".[docs,sparse,test]"
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cd docs
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sphinx-apidoc -o source/ ../optimism -P
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make html
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build/html # Adjust this if your output directory is different
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publish_branch: gh-pages # The branch to deploy to
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- name: codecov
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uses: codecov/codecov-action@v4
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with:

‎.gitignore

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.spack-env/
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*.npz
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*.vtk
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# docs stuff
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build/
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docs/source/modules.rst
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docs/source/optimism.*

‎README.md

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# OptimiSM: Computational solid mechanics made easy with Jax
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![Continuous integration](https://github.com/sandialabs/optimism/actions/workflows/ci-build.yml/badge.svg)
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[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://sandialabs.github.io/optimism/)
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://sandialabs.github.io/optimism/dev/)
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[![Coverage](https://codecov.io/gh/sandialabs/optimism/branch/main/graph/badge.svg)](https://codecov.io/gh/sandialabs/optimism)
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## What is OptimiSM?
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‎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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%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.https://www.sphinx-doc.org/
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exit /b 1
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)
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if "%1" == "" goto help
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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/source/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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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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project = 'optimism'
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copyright = '2024, Brandon Talamini, Mike Tupek'
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author = 'Brandon Talamini, Mike Tupek'
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release = '0.1.0'
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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'sphinx_copybutton',
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'sphinx.ext.autodoc',
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'sphinx.ext.autosummary',
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'sphinx.ext.coverage',
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'sphinx.ext.napoleon',
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'sphinx.ext.viewcode'
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]
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templates_path = ['_templates']
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exclude_patterns = []
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html_theme = 'sphinx_rtd_theme'
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_static_path = ['_static']
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# autodoc_default_options = {
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# 'members': True
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# }

‎docs/source/index.rst

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.. optimism documentation master file, created by
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sphinx-quickstart on Fri Oct 18 12:13:55 2024.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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optimism documentation
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======================
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Add your content using ``reStructuredText`` syntax. See the
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`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
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documentation for details.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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modules
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optimism
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Indices and Tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎setup.py

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'metis'],
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#tests_require=[], # could put chex and pytest here
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extras_require={'sparse': ['scikit-sparse'],
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'test': ['pytest', 'pytest-cov', 'pytest-xdist']},
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'test': ['pytest', 'pytest-cov', 'pytest-xdist'],
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'docs': ['sphinx', 'sphinx-copybutton', 'sphinx-rtd-theme', 'sphinxcontrib-bibtex', 'sphinxcontrib-napoleon']},
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python_requires='>=3.7',
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version='0.0.1',
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license='MIT',

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