From 187cf9400adaf410e93625d8eb1e553689198658 Mon Sep 17 00:00:00 2001 From: Paul Newling Date: Mon, 4 May 2026 08:17:16 -0700 Subject: [PATCH] feat: add biopython 1.87 to scientific-slim runenv Lets sequence-properties (and similar blocks) drop per-block biopython bundling and rely on the shared scientific-slim runenv. --- .changeset/scientific-slim-add-biopython.md | 5 +++++ python-3.12.10-scientific-slim/config.json | 3 ++- python-3.12.10-scientific-slim/package.json | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-) create mode 100644 .changeset/scientific-slim-add-biopython.md diff --git a/.changeset/scientific-slim-add-biopython.md b/.changeset/scientific-slim-add-biopython.md new file mode 100644 index 0000000..0857c20 --- /dev/null +++ b/.changeset/scientific-slim-add-biopython.md @@ -0,0 +1,5 @@ +--- +'@platforma-open/milaboratories.runenv-python-3.12.10-scientific-slim': minor +--- + +Add biopython 1.87 to the scientific-slim runenv. Enables blocks like sequence-properties to drop their per-block biopython bundling and rely on the shared runenv. diff --git a/python-3.12.10-scientific-slim/config.json b/python-3.12.10-scientific-slim/config.json index 601a9f6..b5f5c0c 100644 --- a/python-3.12.10-scientific-slim/config.json +++ b/python-3.12.10-scientific-slim/config.json @@ -4,7 +4,8 @@ "polars-lts-cpu==1.33.1", "numpy==2.2.6", "scipy==1.15.3", - "pyarrow==21.0.0" + "pyarrow==21.0.0", + "biopython==1.87" ], "skip": {}, "platformSpecific": {} diff --git a/python-3.12.10-scientific-slim/package.json b/python-3.12.10-scientific-slim/package.json index d9b85da..be6cda1 100644 --- a/python-3.12.10-scientific-slim/package.json +++ b/python-3.12.10-scientific-slim/package.json @@ -1,7 +1,7 @@ { "name": "@platforma-open/milaboratories.runenv-python-3.12.10-scientific-slim", "version": "1.0.1", - "description": "Python 3.12.10 run environment bundling polars-lts-cpu, numpy, scipy, and pyarrow for scientific/tabular workloads", + "description": "Python 3.12.10 run environment bundling polars-lts-cpu, numpy, scipy, pyarrow, and biopython for scientific/tabular workloads", "scripts": { "cleanup": "rm -rf ./pkg-*.tgz ./pydist ./dist/ ./build/", "reset": "pnpm run cleanup && rm -rf ./node_modules ./.turbo",