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Repairs the :stable image, and moves the Jobs onto immutable tags.
⚠️ This release fixes a broken :stable
informaticsmatters/squonk2-fragmenstein:stable, which all five Job
Definitions pointed at, has segfaulted since 2025-11-10:
$ docker run --rm informaticsmatters/squonk2-fragmenstein:stable /code/merger.py --help
exit 139 # SIGSEGV
:stable was pushed 44 seconds after :1.1.1 — the two steps of
publish-stable. The first built :1.1.1 from the previous :stable base,
so it picked up Fragmenstein 0.13.36 and worked; the tag named after the
release did not contain the release. The second rebuilt the base with the
Fragmenstein 1.1.1 that requirements.txt asked for, whose rdkit_to_params
pyrosetta mock crashes.
The Data Manager treats stable as dynamic and re-pulls it, so installations
received the broken image.
What is in 1.2.0
Fragmenstein 1.1.3, which does not crash, and a base image the derived
build actually uses — Dockerfile-fragmenstein now takes a BASE_TAG build
argument that compose passes the tag it just built, so :1.2.0 and :stable
contain the same thing.
Debian 13, Python 3.12, Java 21, Nextflow 26.04.6. The Nextflow image was
on debian:11.11 — EOL, and carrying a snapshot.debian.org workaround for
mirrors that no longer serve it. The Fragmenstein base drops conda for
python:3.12.14-slim-trixie, taking the image from 2.27GB to 794MB.
| before | after | |
|---|---|---|
| python | 3.9.12 | 3.12.14 |
| fragmenstein | 0.13.36 | 1.1.3 |
| rdkit | 2023.09.1 | 2026.03.6 |
| numpy | — | 2.5.3 |
The workflows pass the Nextflow 25+ strict parser — addParams, env
outputs, bare optional, conditional publishDir, missing script: labels,
++ and top-level statements are all gone. They still run on 22.10.0.
Immutable tags throughout. The five Job Definitions move from floating
:stable at version: '1.0.0' to 1.2.0, and the Nextflow process
containers move with them — jote --image-tag does not rewrite those, so
leaving them floating would have meant the Jobs running 1.2.0 while their
processes ran something else. vs-prep also moves from :latest, which still
carries RDKit 2023.03.2, to :3.1.0.
Known issue
frag_merge_scoring.nf's scoring cost overwrites the running total instead of
adding to it, and emits no -COST- line. Behaviour is preserved here rather
than changed, because correcting it changes what is billed — see
InformaticsMatters/squonk2-jobs#72.