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feat: add biopython 1.87 to scientific-slim runenv#66

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PaulNewling merged 1 commit intomainfrom
paulnewling/scientific-slim-add-biopython
May 4, 2026
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feat: add biopython 1.87 to scientific-slim runenv#66
PaulNewling merged 1 commit intomainfrom
paulnewling/scientific-slim-add-biopython

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@PaulNewling PaulNewling commented May 4, 2026

Summary

  • Adds biopython==1.87 to python-3.12.10-scientific-slim/config.json.
  • Updates the variant description to reflect the new dependency.
  • Adds a minor changeset for @platforma-open/milaboratories.runenv-python-3.12.10-scientific-slim.

Why

The sequence-properties block currently bundles biopython per-block via pip + requirements.txt. Promoting biopython into the shared scientific-slim runenv lets that block (and future ones) drop the per-block bundle and pull biopython from the shared environment instead.

biopython==1.87 matches the version already pinned in blocks/sequence-properties/software/uv.lock.

Notes

  • No version bump in package.json — changesets handle that on merge.
  • No checker/whitelists/python-3.12.10-scientific-slim/ added. Builder treats a missing whitelist as non-fatal (builder/src/build.ts:478-482); biopython 1.87 on cpython 3.12 has a small native footprint and is expected to import cleanly across all five platforms. If CI flags an import on some platform, the checker emits a snippet to copy in.
  • Block-side switch (sequence-properties → scientific-slim) is a follow-up PR after this publishes.

Lets sequence-properties (and similar blocks) drop per-block biopython
bundling and rely on the shared scientific-slim runenv.
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Code Review

This pull request adds biopython version 1.87 to the scientific-slim Python 3.12.10 run environment. The changes include updating the dependency list in config.json, the package description in package.json, and adding a changeset file to document the minor version update. I have no feedback to provide.

@PaulNewling PaulNewling marked this pull request as ready for review May 4, 2026 15:20
@PaulNewling PaulNewling merged commit 79c5b59 into main May 4, 2026
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2 participants