Refresh README and bump artifact actions to Node 24 - #22
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Replace the legacy README with the published-paper version (badges, Docker, citation) and upgrade upload-artifact/download-artifact so the publish workflow no longer triggers Node 20 deprecation warnings. Co-authored-by: Cursor <cursoragent@cursor.com>
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Pull request overview
This PR refreshes the project’s top-level documentation to the published-paper README format and updates the artifact upload/download GitHub Actions versions in the trusted publish workflow to address the Node.js 20 deprecation warnings on hosted runners.
Changes:
- Replaces the legacy
README.mdwith a more structured, badge/citation-focused version including Docker usage and expanded usage sections. - Updates
actions/upload-artifactandactions/download-artifactmajor versions in the main publish workflow.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| README.md | Rewrites README content (badges, installation, quickstarts, supported models, arguments, citation). |
| .github/workflows/publish-main-branch-trusted.yml | Bumps artifact actions versions used for publishing/release steps. |
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| From source: | ||
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| 2. *(Optional)* For ESMC models (e.g. `biohub/ESMC-300M`), install Biohub's transformers fork: | ||
| ```sh | ||
| pip install git+https://github.com/Biohub/transformers.git@main | ||
| ``` | ||
| ```bash | ||
| git clone https://github.com/csi-greifflab/pepe-cli | ||
| cd pepe-cli | ||
| pip install . | ||
| ``` |
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Added an "Optional backends" subsection to the Installation section documenting the extra installs needed for ESMC (pip install git+https://github.com/Biohub/transformers.git@main) and METL (pip install git+https://github.com/gitter-lab/metl-pretrained.git). Committed in docs: add optional backend installation notes for ESMC and METL in README.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Summary
actions/upload-artifact@v4→@v6andactions/download-artifact@v4→@v7in the main publish workflow to resolve the Node.js 20 deprecation warning on GitHub-hosted runners.Test plan
build-and-publish-mainrun no longer shows the Node 20 deprecation warning for artifact actions.Made with Cursor