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Copilot AI commented Jan 13, 2026

Upgrades Python base image from 3.13.1-alpine to 3.14.2-alpine to address 4 vulnerabilities in SQLite and musl (2 critical, 2 high severity).

Before submitting this PR, please make sure:

  • You have added a few sentences describing the PR here.
  • The code passes all CI tests without any errors or warnings.
  • You have added tests (when appropriate).
  • You have added an entry in any relevant CHANGELOGs (when appropriate).
  • If you have made any changes to the scripts/ or docker/ directories, please ensure any image versions have been incremented accordingly!
  • You have updated the README or other documentation to account for these changes (when appropriate).

Changes

  • docker/python-plotting/Dockerfile: Base image python:3.13.1-alpinepython:3.14.2-alpine
  • docker/python-plotting/package.json: Version bump 2.0.62.0.7
  • workflows/methylation/methylation-cohort.wdl: Container reference updated to 2.0.7

Security Impact

Fixes vulnerabilities:

  • SNYK-ALPINE321-SQLITE-12675067 (Critical, CVE score 264)
  • SNYK-ALPINE321-SQLITE-11191065 (Critical, CVE-2025-6965, CVE score 263)
  • SNYK-ALPINE321-SQLITE-9712340 (High, CVE score 161)
  • SNYK-ALPINE321-MUSL-8720634 (High, CVE-2025-26519, CVE score 139)
Original prompt

Pull Request: #285


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Co-authored-by: adthrasher <1165729+adthrasher@users.noreply.github.com>
Copilot AI changed the title [WIP] Add new steps to workflow for better efficiency fix(docker): upgrade python-plotting to 3.14.2-alpine for security patches Jan 13, 2026
Copilot AI requested a review from adthrasher January 13, 2026 15:10
@adthrasher adthrasher marked this pull request as ready for review January 13, 2026 15:17
@adthrasher adthrasher merged commit 36c1bc2 into snyk-fix-ea1cc9c84bf033ad26092e5ee131a5e3 Jan 13, 2026
20 checks passed
@adthrasher adthrasher deleted the copilot/add-new-workflow-steps branch January 13, 2026 15:18
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2 participants