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Remove unused Python dependencies and move ruff to dev-requirements #6101

Description

@Yicong-Huang

Task Summary

amber/requirements.txt carries unused packages, and a dev tool in the wrong file:

Package Finding
Deprecated==1.2.14 Last import removed in #2847; nothing else needs it
protobuf==7.34.1 No google.protobuf import anywhere; betterproto 2.0 does not require it
pybase64==1.3.2 (operator-requirements.txt) Zero references in the entire git history
ruff==0.14.7 Lint tool in runtime requirements, so it lands in LICENSE-binary-python; belongs in dev-requirements.txt

Remove the three unused packages, move ruff to dev-requirements.txt (CI's Ruff lint step then runs after dev deps install), drop the matching LICENSE-binary-python entries, and add comments to the transitive pins (setuptools, python-dateutil, s3fs/aiobotocore, SQLAlchemy/pg8000, scikit-image) explaining why they stay.

Task Type

  • Refactor / Cleanup
  • DevOps / Deployment / CI
  • Testing / QA
  • Documentation
  • Performance
  • Other

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