Update base image and crane

[bio-boris]

Feature: Update python base image, crane image and python deps to reduce CVES. Specify linux as this repo cannot be uv installed on a mac.
Commits should be squashed for this small feature.

Hack to update uv lockfile on a mac

docker run --rm -v $(pwd):/app -w /app python:3.12.13-slim sh -c \
  "pip install uv -q && uv add 'cryptography>=46.0.5' 'python-multipart>=0.0.22' 'starlette>=0.49.3'"
  

Upgrading to starlette 0.5.0 breaks tests?? No , CI is just down.

[Copilot]

Pull request overview

This PR updates the Docker base images used for both the build and runtime stages to a specific Python 3.12 patch release, improving version pinning consistency for container builds.

Changes:

• Bump build-stage base image from python:3.12 to python:3.12.13.
• Bump runtime-stage base image from python:3.12 to python:3.12.13.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 53.34%. Comparing base (f948842) to head (f2acd6d).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #561   +/-   ##
=======================================
  Coverage   53.34%   53.34%           
=======================================
  Files          69       69           
  Lines        5931     5931           
=======================================
  Hits         3164     3164           
  Misses       2767     2767           

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 2 comments.

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