Documentation #36
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Documentation #36
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Introduces new documentation files including installation instructions, overview, and links to README and license. Updates Sphinx configuration to include sphinx-copybutton and reorganizes index.rst for improved navigation. The GitHub workflow now installs sphinx-copybutton. README updated with a link to the documentation site.
Added the sphinx-new-tab-link extension to the Sphinx build process and configuration. Updated overview.md with a detailed explanation of RFdiffusion2's capabilities and differences from the original RFdiffusion, and excluded overview.md from Sphinx build patterns.
Improved the README with clearer setup, installation, and inference instructions, and added troubleshooting tips. Expanded the documentation by adding new usage examples, configuration options, and ORI token explanations. Updated Sphinx configuration and index to include new documentation files, and adjusted workflow and dependencies to comment out unused Sphinx extensions. Enhanced installation guide with troubleshooting for Apptainer image issues and clarified instructions for both Apptainer and source installations.
Introduced conda environment YAMLs and pip requirements for CUDA 12.1 and 12.4 support in the 'envs' directory. Updated installation documentation to guide users on using these files and troubleshooting environment setup. Minor README correction for pipeline argument.
Replaces ori_tokens.md with a new ori_tokens.rst containing detailed instructions and images. Updates configuration_options.md with more guidance on custom configs. Adjusts Sphinx conf.py exclude patterns and comments, updates index.rst to use the new ORI tokens doc, and adds supporting images. Minor typo fix in overview.md and clarifying comments in example usage docs.
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Pull Request Overview
This PR makes documentation and configuration updates to the RFdiffusion2 project. The changes focus on adding new documentation content, fixing typos, cleaning up trailing whitespace in dependency files, and adjusting Sphinx documentation settings.
- Adds comprehensive ORI tokens documentation with usage examples and recommendations
- Fixes typos and improves clarity in existing documentation
- Updates Sphinx configuration to exclude certain files and comment out color settings
Reviewed Changes
Copilot reviewed 9 out of 14 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| envs/requirements_cuda121.txt | Removes trailing whitespace from submitit dependency line |
| envs/cuda124_env.yml | Removes trailing whitespace from pyrosetta dependency line |
| envs/cuda121_env.yml | Removes trailing whitespace from pyrosetta dependency line |
| doc/source/usage/run_inference_example.md | Adds HTML comment describing document purpose |
| doc/source/usage/other_pipeline_example.md | Adds HTML comment explaining example purpose |
| doc/source/usage/ori_tokens.rst | Adds new comprehensive documentation for ORI tokens with examples and placement recommendations |
| doc/source/usage/configuration_options.md | Adds content about configuration options and custom config file creation |
| doc/source/overview.md | Fixes typo ("only the" → "only be") and updates note about RFdiffusion2 vs RFdiffusion usage |
| doc/source/index.rst | Updates included documentation files, switches ori_tokens from .md to .rst |
| doc/source/conf.py | Adds files to exclude_patterns and comments out color-admonition-background settings |
| README.md | Changes "Setup" to "Set-up" for consistency and fixes broken documentation link |
| .github/workflows/documentation_workflow.yml | Comments out sphinx-new-tab-link from pip install dependencies |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Created a page detailing how to add an ORI token to input PDB files.