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refactor: Migrate analysis models to pydantic v2 #1306

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merged 18 commits into from Nov 2, 2023
Merged

refactor: Migrate analysis models to pydantic v2 #1306

merged 18 commits into from Nov 2, 2023

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ivadym
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@ivadym ivadym commented Oct 31, 2023 •
edited

This PR:

Changed:

  • Migrate analysis models to pydantic v2
  • Split analysis model into config and params models

Review and tests:

  • Tests pass
    • WGS-TO case completed successfully
    • TGA-TO case completed successfully
    • QC case completed successfully
  • Code review
  • New code is executed and covered by tests, and test approve

@ivadym ivadym self-assigned this Oct 31, 2023
@ivadym ivadym requested a review from a team as a code owner October 31, 2023 15:49
@ivadym ivadym mentioned this pull request Oct 31, 2023
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@ivadym ivadym linked an issue Oct 31, 2023 that may be closed by this pull request
Migrating from Pydantic v1 to v2 #1202
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codecov bot commented Oct 31, 2023 •
edited

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Files Coverage Δ
BALSAMIC/commands/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/config/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/config/case.py 100.00% <100.00%> (+3.44%) ⬆️
BALSAMIC/commands/config/pon.py 100.00% <100.00%> (+4.87%) ⬆️
BALSAMIC/commands/init/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/options.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/status.py 100.00% <100.00%> (ø)
BALSAMIC/commands/run/analysis.py 100.00% <100.00%> (ø)
... and 24 more

📢 Thoughts on this report? Let us know!.

mathiasbio
mathiasbio approved these changes Nov 2, 2023
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I have read through the changes twice, and I think this is that one time in time and space where a PR with these many changes had not a single thing to improve! 🌟

Well done! :D

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sonarcloud bot commented Nov 2, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
1.3% 1.3% Duplication

@ivadym ivadym merged commit b084920 into develop Nov 2, 2023
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@ivadym ivadym deleted the migrate-analysis branch November 2, 2023 16:03
@ivadym ivadym mentioned this pull request Nov 6, 2023
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@mathiasbio mathiasbio mathiasbio approved these changes

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Migrating from Pydantic v1 to v2
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@ivadym @mathiasbio