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Trial: python-package-scanner in security workflow#157

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Trial: python-package-scanner in security workflow#157
nevoodoo wants to merge 7 commits intomainfrom
test/python-package-scanner

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@nevoodoo
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@nevoodoo nevoodoo commented Mar 30, 2026

Just trialing the package scanner to see if this would solve our visibility issues into vulnerable deps: https://github.com/populationgenomics/python-package-scanner?tab=readme-ov-file

Trial run of the new vulnerability scanner alongside pip-audit
to compare results and dependency chain tracing.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Enables PR comments from python-package-scanner. Push restricted
to main to avoid double runs.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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github-actions bot commented Mar 30, 2026

🐳 Docker Image Built

A new Docker image has been built for this PR:

Image: australia-southeast1-docker.pkg.dev/cpg-common/images-dev/cpg_flow:2feef8c857dcf65f906ac85a811c96d1c2aa99a6

Pull command:

docker pull australia-southeast1-docker.pkg.dev/cpg-common/images-dev/cpg_flow:2feef8c857dcf65f906ac85a811c96d1c2aa99a6

🔗 View in Google Cloud Console


This comment was automatically generated by the Docker workflow.

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github-actions bot commented Mar 30, 2026

Vulnerability Audit

Found 16 vulnerabilities in 14 packages

Package Version Vulnerability Fix Dependency Chain
azure-core 1.37.0 CVE-2026-21226 1.38.0 hail > azure-identity > azure-core
bokeh 3.4.3 CVE-2026-21883 3.8.2 hail > bokeh
cryptography 46.0.3 CVE-2026-34073 46.0.6 hail > azure-identity > cryptography
cryptography 46.0.3 CVE-2026-26007 46.0.5 hail > azure-identity > cryptography
filelock 3.20.2 CVE-2026-22701 3.20.3 pre-commit > virtualenv > filelock
jaraco-context 6.0.2 CVE-2026-23949 6.1.0 twine > keyring > jaraco-context (dev)
orjson 3.11.5 CVE-2025-67221 3.11.6 hail > orjson
pillow 12.1.0 CVE-2026-25990 12.1.1 hail > bokeh > pillow
pip 25.3 CVE-2026-1703 26.0 pip-audit > pip-api > pip (dev)
pyasn1 0.6.1 CVE-2026-23490 0.6.2 cpg-utils > google-auth > pyasn1-modules > pyasn1
pyasn1 0.6.1 CVE-2026-30922 0.6.3 cpg-utils > google-auth > pyasn1-modules > pyasn1
pygments 2.19.2 CVE-2026-4539 None mkdocs-material > pygments (no fix available, dev)
pyjwt 2.10.1 CVE-2026-32597 2.12.0 hail > azure-identity > msal > pyjwt
requests 2.32.5 CVE-2026-25645 2.33.0 cpg-utils > requests
urllib3 2.6.2 CVE-2026-21441 2.6.3 metamist > urllib3
virtualenv 20.35.4 CVE-2026-22702 20.36.1 pre-commit > virtualenv

Summary

  • 13 fixable via dependency upgrade
  • 3 in dev dependencies only (2 fixable, 1 no fix)

@populationgenomics populationgenomics deleted a comment from github-actions bot Mar 30, 2026
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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