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Creating the external foundry documentation structure and first round of documentation for RFD3 (#143)
* Starting to put together the foundry and RFD3 external documentation Set up the foundation for Sphinx to be able to build the external docs, first draft of a ppi_design_tutorial has been completed. * Add RFdiffusion3 documentation and update toctree Added initial documentation for RFdiffusion3 under models/rfd3/docs/index.rst and linked it in the main docs toctree. Updated toctree maxdepth for better navigation and added a symlink for the rfd3 model documentation. * Update and expand RFdiffusion3 documentation Added introductory and reference documentation files, improved the index structure with general information and examples, and enhanced the PPI design tutorial with additional notes, figures, and clarifications. Also fixed a typo in a PDB filename. * Update RFD3 documentation and tutorial content Expanded the Sphinx static path to include RFD3 assets and made minor formatting and clarity improvements in the main and RFD3-specific documentation. The PPI design tutorial was revised for clarity, improved step-by-step instructions, and better separation of setup and execution steps. * Update RFD3 documentation and tutorials Added source_suffix to Sphinx conf.py for Markdown support. Updated index.rst to include new documentation sections. Expanded intro_inference_calculations.md with detailed instructions on inference input formats, job configuration, and output files. Improved input.md formatting for appendices and FAQs. Revised ppi_design_tutorial.md for clarity, added details on settings, and expanded explanations for hotspots and batch inference. * Update RFD3 docs: clarify input specs and file formats Expanded and clarified the documentation for RFdiffusion3 input specifications, including more detailed explanations of the 'contig' string, input file types, and example YAML/JSON formats. Improved the intro to inference calculations to better explain the structure and usage of settings files, and updated descriptions for job configuration and output files. Added a placeholder for configuration options documentation. * Update RFdiffusion3 input documentation and examples Expanded and clarified the documentation for RFdiffusion3 input specification, including detailed explanations of CLI arguments, InputSpecification fields, the InputSelection mini-language, contig string formatting, and advanced options such as partial diffusion and CIF parser arguments. Added more examples, debugging recommendations, and an updated FAQ. Also updated the output file naming explanation for clarity. Removed the obsolete configuration_options.md file. Note that images are still not being rendered correctly in many of the md files. Fix will be in future commit. * PPI tutorial and RFD3 docs update Created output files for PPI tutorial and listed their locations. Made edits to files to add labels to sections to remove sphinx warnings. * Delete docs/source/conf.py~ This is an auto-save file from emacs - it does not need to be in the repo. * Delete docs/source/index.rst~ This is an auto-saved copy of index.rst, it does not need to be in the repo * Adding missing images and fixing docs symlink * Fix grammatical error in RFdiffusion3 documentation Fixed typo, clarified enzyme design language. * Fix typos and enhance clarity in inference docs Corrected typos and improved clarity in the documentation regarding inference settings and file formats.
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‎.DS_Store‎

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‎.github/workflows/documentation.yml‎

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name: documentation
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: write
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jobs:
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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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- name: Install dependencies
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run: |
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pip install sphinx myst_parser furo sphinx-copybutton
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- name: Sphinx build
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run: |
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sphinx-build -M html docs/source/ docs/build/
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v3
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if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build/html
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force_orphan: true

‎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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project = 'foundry'
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copyright = '2025, Institute for Protein Design, University of Washington'
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author = 'Institute for Protein Design, University of Washington'
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release = '0.1.7'
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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 = ["myst_parser",
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"sphinx_copybutton"
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]
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templates_path = ['_templates']
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exclude_patterns = ["readme.md", "readmelink.md", "readme_link.rst"]
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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_theme = 'furo'
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html_static_path = ['_static', '../../models/rfd3/.assets']
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html_theme_options = {
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"sidebar_hide_name":False,
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#"announcement": "<em>THIS DOCUMENTATION IS CURRENTLY UNDER CONSTRUCTION</em>",
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"light_css_variables": {
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"color-brand-primary": "#F68A33", # Rosetta Teal
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"color-brand-content": "#37939B", # Rosetta Orange
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#"color-admonition-background": "#CCE8E8", # Rosetta light orange
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"font-stack": "Open Sans, sans-serif",
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"font-stack--headings": "Open Sans, sans-serif",
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"color-background-hover": "#DCE8E8ff",
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"color-announcement-background" : "#F68A33dd",
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"color-announcement-text": "#070707",
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"color-brand-visited": "#37939B",
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},
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"dark_css_variables": {
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"color-brand-primary": "#37939B", # Rosetta teal
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"color-brand-content": "#F68A33", # Rosetta orange
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#"color-admonition-background": "#20565B", # Rosetta light orange
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"font-stack": "Open Sans, sans-serif",
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"font-stack--headings": "Open Sans, sans-serif",
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"color-brand-visited": "#37939B",
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}
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}
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source_suffix = {
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".rst": "restructuredtext",
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".md": "markdown",
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}

‎docs/source/index.rst‎

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.. foundry documentation master file, created by
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sphinx-quickstart on Wed Dec 17 16:36:38 2025.
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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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Welcome to the official documentation for foundry
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=================================================
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`foundry <https://github.com/RosettaCommons/foundry/tree/production>`_ is a home for
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many of the machine learning models produced by `Rosetta Commons member labs <https://rosettacommons.org/about/labs/>`_.
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.. toctree::
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:maxdepth: 1
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:caption: General
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license_link.rst
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.. toctree::
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:maxdepth: 1
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:caption: Models
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models/rfd3/index

‎docs/source/license_link.rst‎

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LICENSE
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=======
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.. include:: ../../LICENSE.md
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:parser: myst_parser.sphinx_

‎docs/source/models/rfd3‎

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../../../models/rfd3/docs

‎docs/source/readme_link.rst‎

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README
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======
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.. include:: ../../README.md
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:parser: myst_parser.sphinx_

‎models/.DS_Store‎

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