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@cpg-software-ci-bot cpg-software-ci-bot released this 13 May 23:22
· 278 commits to main since this release
v0.2.3
325e848

v0.2.3 (2025-05-13)

Bug Fixes

  • cohort_dataset: Correction to syntax (181068d)

Build System

  • uv.lock: Bumping cryptography and jinja2 (d8dc7ed)

There are vulnerabilities identified in cryptography==43.0.3 and jinja2==3.1.5 which are fixed by bumping them in our uv.lock file

Code Style

  • BamPath: Rename class attributes for cleaner code (cb05603)

  • pretty-format-json: Add json formatter to pre-commit hook (40e2e96)

Continuous Integration

  • Add delete-me branch to test functionality of cleanup (c4fd31d)

  • Addressing code scanning results of zizmor (caffb2c)

  • Change link to h2 (5141c4b)

  • cleanup-sonarqube: Add production env to get secret access (b13a484)

  • cleanup-sonarqube: Address security alerts in workflows (45684c4)

  • cleanup-sonarqube: Check the project exists before the delete (243d8b8)

  • cleanup-sonarqube: Fix curl command (ffc0c04)

You need an admin token in order to delete, the global token failed. Also the format was wrong for sending the token, it needed to be in the Authorization: Bearer header.

  • cleanup-sonarqube: Show delete error (c972477)

  • cleanup-sonarqube: Tested and working cleanup action (de93183)

Tested by merging into delete-me branch. All working now. See the successful action here: https://github.com/populationgenomics/cpg-flow/actions/runs/14895431016/job/41836900804.

  • sonarqube: Add main project link as well (c6003cd)

  • sonarqube: Change link labels (90b47a3)

  • sonarqube: Enable quality gate (a4901a2)

  • sonarqube: Fix the metricKeys in the sonarqube-fetch.sh script (b955ff5)

  • sonarqube: Format headers and fix link style (fca4096)

  • sonarqube: Rename headings to PR and main branch (37eb8e2)

  • sonarqube: Rm link from chain emoji (ffac0f7)

  • sonarqube: Use version on push to sonarqube when running on main (11961bc)

  • test: Add emoji to the quality gate status (bbc8814)

  • test: Add GH_BOT_TOKEN to env (77211c3)

  • test: Address security code scanning on workflows (324da98)

  • test: Another sonarqube link fix (1a4fd9f)

  • test: Change from ref_name to head_ref for branch key (b6b0783)

  • test: Confirm the existence of the coverage and execution reports (5f3ee5d)

  • test: Convert SONAR_HOST_URL to variable not secret (be6e6a7)

  • test: Correct to use github actions variable github.sha (0e98c17)

  • test: Debugging final url - add echos (a24e0ab)

  • test: Fix environment variable access (9012348)

  • test: Fix extracting sonarqube api values (32232c9)

  • test: Fix GH_BOT_TOKEN to GH_TOKEN for gh cli command (ebde25a)

  • test: Fix output url (06ddc49)

  • test: Fix template name (cf9bfe6)

  • test: Fix template path (190b6b7)

  • test: Load template.md properly (c4f8dff)

  • test: Move sonarqube logic to it's own script (77b036e)

  • test: Mv reports to root directory (d38730d)

  • test: New PR comment format (18ae743)

  • test: New sonarqube PR comment template (5a35a19)

  • test: Pass in sonarqube version (the github sha) (69fa6d8)

  • test: Remove --edit-last so you get a new post every workflow run (1a17efb)

  • test: Revert back to accessing secret directly (e242145)

  • test: Rm --create-if-none flag - not needed (247671f)

  • test: Rm cat of execution/coverage file and output result link (38b2172)

  • test: Rm unused badge data from test.yaml (bbd9957)

  • test: Sonarqube scan every pr and create it's own project (ff77fde)

This is the (slightly hacky) work around for being limited to the community version where we can't do separate scans on each PR. The solution is make a new sonarqube project for every project-pr- and remove that project on merge to main (where a scan on main will then be performed). A little gross, and the main downside is creating an unnecessary number of projects cluttering the ui and also increasing the required specs on our sonarqube instance.

  • test: Try to fix the summary link, add env section (09f6494)

  • test: Update sonarqube summary template (ef84798)

  • test: Update to show all and new code stats (bcf7d7d)

  • test: Use vars context (3a9b95a)

Documentation

  • .github/CODEOWNERS: Added software team to code owners (8d12f7a)

Refactoring

  • test,pre-commit: Use gh pr comment and rm extra code from PR (b5a2c1d)

Testing

  • Add test_resources for the resources.py file (2772a9e)

  • Add unit tests for graph.py (6928743)

  • Update test_resources MockJob (e6a9b17)

Detailed Changes: v0.2.2...v0.2.3

Assets 6
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