fix: pin numpy<2 in rdkit-base and dmpk images#19
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rdkit==2023.3.2 and matplotlib==3.7.1 both predate NumPy 2.0 and ship compiled extensions built against NumPy's 1.x C-API. With numpy left unpinned, a rebuild resolves the latest NumPy (currently 2.2.6) and those extensions fail at import with "AttributeError: _ARRAY_API not found" - hit by pk-tmax-cmax-sim (via matplotlib) and both descriptor-generator tests (via rdkit/mordred, inherited from vs-rdkit-base). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
This was referenced Jul 21, 2026
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Summary
Dockerfile-rdkit-base(rdkit==2023.3.2) andDockerfile-dmpk(matplotlib==3.7.1) both predate NumPy 2.0 (released June 2024) and ship compiled extensions built against NumPy's 1.x C-API.numpy, so a rebuild today silently resolves the latest NumPy (2.2.6) as a transitive dependency, breaking those older compiled extensions at import time withAttributeError: _ARRAY_API not found.pk-tmax-cmax-sim(via matplotlib) and bothdescriptor-generatortests inmanifest-im-mordred.yaml(via rdkit/mordred, which inherits fromvs-rdkit-base).numpy<2alongside the affected packages in both Dockerfiles.Found while running a full (non-dry-run)
jotepre-refactor health check across all job submodules insquonk2-jobs.Note:
informaticsmatters/vs-rdkit-baseis built and pushed to Docker Hub manually, outside CI (per the repo README), so this fix needs someone with push access to rebuild and republishvs-rdkit-base:latestafter merge — CI alone won't propagate it to jobs that buildFROMthat base image.Test plan
vs-rdkit-base,vs-dmpk:stable, andmordred:stablelocally with the pin in place — confirmednumpy==1.26.4resolves in both images.jote --manifest manifest-dmpk.yaml --allow-no-tests(real execution) —pk-tmax-cmax-sim/simple-executionnow passes.jote --manifest manifest-im-mordred.yaml --allow-no-tests(real execution) — bothdescriptor-generatortests (execution-2d,execution-3d) now pass.🤖 Generated with Claude Code