remove scgpt components and workflows #1075
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Pull Request Overview
This pull request removes scGPT components and workflows from the codebase. The change appears to be a cleanup effort to deprecate and remove all scGPT-related functionality, which includes both integration and annotation workflows, along with their underlying components for tokenization, embedding generation, binning, and cell type annotation.
Key changes:
- Complete removal of scGPT integration and annotation workflows
- Deletion of all scGPT component modules (pad_tokenize, embedding, cross_check_genes, cell_type_annotation, binning)
- Removal of scGPT test resource generation scripts
- Addition of deprecation notice in CHANGELOG.md
Reviewed Changes
Copilot reviewed 27 out of 27 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| src/workflows/integration/scgpt_leiden/ | Removed complete integration workflow for scGPT with Leiden clustering |
| src/workflows/annotation/scgpt_annotation/ | Removed complete annotation workflow using scGPT models |
| src/scgpt/* | Removed all scGPT component modules and their implementations |
| resources_test_scripts/scgpt.sh | Removed test resource generation script for scGPT components |
| CHANGELOG.md | Added deprecation notice for scGPT functionality |
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DriesSchaumont
requested changes
Oct 3, 2025
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Changelog
... Describe your changes ...
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!