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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/Dockerfile

We 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:

Issue Score
critical severity Integer Overflow or Wraparound
SNYK-ALPINE321-SQLITE-12675067
  264  
critical severity CVE-2025-6965
SNYK-ALPINE321-SQLITE-11191065
  263  
high severity Integer Overflow or Wraparound
SNYK-ALPINE321-SQLITE-9712340
  161  
high severity CVE-2025-26519
SNYK-ALPINE321-MUSL-8720634
  139  
high severity CVE-2025-26519
SNYK-ALPINE321-MUSL-8720634
  139  

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  • Check the changes in this PR to ensure they won't cause issues with your project.
  • Max score is 1000. Note that the real score may have changed since the PR was raised.
  • This PR was automatically created by Snyk using the credentials of a real user.

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🦉 Integer Overflow or Wraparound

@kevin-benton
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Merge Risk: High

This upgrade to Python 3.14 introduces a significant breaking change.

Highlights:

  • Breaking Change: Code using return, break, or continue to exit a finally block will now raise a SyntaxError. This is part of PEP 765 and will require code modification. [5, 6]
  • Other Changes: The release also officially supports free-threaded (no-GIL) Python, defers the evaluation of type annotations, and adds a new zstd compression module. [1, 2, 5]

Source: Python 3.14 Release Notes
Recommendation: Before merging, search your codebase for any return, break, or continue statements within finally blocks and refactor them.

Notice 🤖: This content was augmented using artificial intelligence. AI-generated content may contain errors and should be reviewed for accuracy before use.

@adthrasher adthrasher requested a review from Copilot January 12, 2026 20:44
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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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@adthrasher
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The corresponding package.json needs to have the version updated. All references to the image also need to be bumped to the new version.

…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)

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<summary>Original prompt</summary>

> Pull Request: #285
> 
> 


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Co-authored-by: adthrasher <1165729+adthrasher@users.noreply.github.com>
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4 participants