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[Snyk] Security upgrade python from 3.13.1-alpine to 3.14.2-alpine #285
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The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-ALPINE321-SQLITE-12675067 - https://snyk.io/vuln/SNYK-ALPINE321-SQLITE-11191065 - https://snyk.io/vuln/SNYK-ALPINE321-SQLITE-9712340 - https://snyk.io/vuln/SNYK-ALPINE321-MUSL-8720634 - https://snyk.io/vuln/SNYK-ALPINE321-MUSL-8720634
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This upgrade to Python 3.14 introduces a significant breaking change. Highlights:
Source: Python 3.14 Release Notes
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Pull request overview
This PR upgrades the Python base image in the plotting Dockerfile from version 3.13.1-alpine to 3.14.2-alpine to address critical and high severity security vulnerabilities in Alpine Linux dependencies (sqlite and musl).
Changes:
- Updates the Python Docker base image version to resolve 4 security vulnerabilities with severity scores ranging from 139 to 264
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The corresponding |
…tches (#287) 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: - [x] You have added a few sentences describing the PR here. - [x] The code passes all CI tests without any errors or warnings. - [x] You have added tests (when appropriate). - [x] You have added an entry in any relevant CHANGELOGs (when appropriate). - [x] If you have made any changes to the `scripts/` or `docker/` directories, please ensure any image versions have been incremented accordingly! - [x] 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-alpine` → `python:3.14.2-alpine` - `docker/python-plotting/package.json`: Version bump `2.0.6` → `2.0.7` - `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) <!-- START COPILOT CODING AGENT SUFFIX --> <!-- START COPILOT ORIGINAL PROMPT --> <details> <summary>Original prompt</summary> > Pull Request: #285 > > </details> <!-- START COPILOT CODING AGENT TIPS --> --- 💬 We'd love your input! Share your thoughts on Copilot coding agent in our [2 minute survey](https://gh.io/copilot-coding-agent-survey). --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: adthrasher <1165729+adthrasher@users.noreply.github.com>
Snyk has created this PR to fix 4 vulnerabilities in the dockerfile dependencies of this project.
Keeping your Docker base image up-to-date means you’ll benefit from security fixes in the latest version of your chosen image.
Snyk changed the following file(s):
docker/python-plotting/DockerfileWe recommend upgrading to
python:3.14.2-alpine, as this image has only 0 known vulnerabilities. To do this, merge this pull request, then verify your application still works as expected.Vulnerabilities that will be fixed with an upgrade:
SNYK-ALPINE321-SQLITE-12675067
SNYK-ALPINE321-SQLITE-11191065
SNYK-ALPINE321-SQLITE-9712340
SNYK-ALPINE321-MUSL-8720634
SNYK-ALPINE321-MUSL-8720634
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