ENH: integrate VirSorter 2 actions#29
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misialq wants to merge 11 commits intobokulich-lab:mainfrom
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Pull Request Overview
This PR re-integrates VirSorter 2 actions into the q2-viromics plugin by updating dependencies, refactoring internal module references, and revising CI/CD workflows.
- Updated import paths to use the new module structure.
- Renamed the function from checkv_analysis to checkv_run for improved consistency.
- Revised CI workflows and added the VirSorter 2 dependency in the conda recipe.
Reviewed Changes
Copilot reviewed 84 out of 84 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| q2_viromics/checkv/tests/init.py | Added license header |
| q2_viromics/checkv/db.py | Updated import paths for utility and types modules |
| q2_viromics/checkv/analysis.py | Updated imports and renamed the function to checkv_run |
| q2_viromics/checkv/init.py | Added license header and updated export list (all) |
| q2_viromics/init.py | Updated copyright information |
| pyproject.toml | Minor update to the plugin description |
| conda-recipe/meta.yaml | Added the VirSorter 2 dependency |
| Makefile | Updated test target with parallel test execution |
| .github/workflows/upload-coverage.yaml | Changed workflow trigger from "Test" to "CI" |
| .github/workflows/ci.yaml | Refactored to use reusable workflows for CI/CD integration |
VinzentRisch
previously approved these changes
Jun 5, 2025
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VinzentRisch
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VinzentRisch
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Hey @misialq
LGTM! I ran the fetch action and everything works as expected.
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This PR brings back actions from q2-virsorter2 - it seems that all the conda dependencies are compatible.