BALSAMIC
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chore: Update development versions & GitHub Actions
Description
As we need to bump black version due to security issues: https://github.com/Clinical-Genomics/BALSAMIC/pull/1420, I've also took the opportunity to update the dev requirements and update GitHub Action versions
Changed
- Development requirements versions
- GitHub Actions versions
Fixed (hopefully 🙏 )
- Links checker github action failing because of redirects (https://lychee.cli.rs/troubleshooting/redirects/)
Removed
- [Description]
Documentation
- [ ] N/A
- [ ] Updated Balsamic documentation to reflect the changes as needed for this PR.
- [Document Name]
Tests
Feature Tests
- [x] Test installation of a clean environment
- [x] Test pytest locally
- [x] Test GitHub actions locally
Pipeline Integrity Tests
-
Report deliver (generation of the
.hk
file)- [x] N/A
- [ ] Verified
-
TGA T/O Workflow
- [x] N/A
- [ ] Verified
-
TGA T/N Workflow
- [x] N/A
- [ ] Verified
-
UMI T/O Workflow
- [x] N/A
- [ ] Verified
-
UMI T/N Workflow
- [x] N/A
- [ ] Verified
-
WGS T/O Workflow
- [x] N/A
- [ ] Verified
-
WGS T/N Workflow
- [x] N/A
- [ ] Verified
-
QC Workflow
- [x] N/A
- [ ] Verified
-
PON Workflow
- [x] N/A
- [ ] Verified
Clinical Genomics Stockholm
Documentation
-
Atlas documentation
- [x] N/A
- [ ] Updated: [Link]
-
Web portal for Clinical Genomics
- [x] N/A
- [ ] Updated: [Link]
User Changes
- [x] N/A
- [ ] This PR affects the output files or results.
- [ ] User feedback is considered unnecessary because [Justification].
- [ ] Affected users have been included in the development process and given a chance to provide feedback.
Infrastructure Changes
-
Stored files in Housekeeper
- [x] N/A
- [ ] Updated: [Link]
-
CG (CLI and delivered/uploaded files)
- [x] N/A
- [ ] Updated: [Link]
-
Servers (configuration files on Hasta)
- [x] N/A
- [ ] Updated: [Link]
-
Scout interface
- [x] N/A
- [ ] Updated: [Link]
Checklist
[!IMPORTANT]
Ensure that all checkboxes below are ticked before merging.
For Developers
-
PR Description
- [x] Provided a comprehensive description of the PR.
- [x] Linked relevant user stories or issues to the PR.
-
Documentation
- [x] Verified and updated documentation if necessary.
-
Tests
- [x] Described and tested the functionality addressed in the PR.
- [x] Ensured integration of the new code with existing workflows.
- [x] Confirmed that meaningful unit tests were added for the changes introduced.
- [ ] Checked that the PR has successfully passed all relevant code smells and coverage checks.
-
Review
- [ ] Addressed and resolved all the feedback provided during the code review process.
- [ ] Obtained final approval from designated reviewers.
For Reviewers
-
Code
- [ ] Code implements the intended features or fixes the reported issue.
- [ ] Code follows the project's coding standards and style guide.
-
Documentation
- [ ] Pipeline changes are well-documented in the CHANGELOG and relevant documentation.
-
Tests
- [ ] The author provided a description of their manual testing, including consideration of edge cases and boundary conditions where applicable, with satisfactory results.
-
Review
- [ ] Confirmed that the developer has addressed all the comments during the code review.