fix: correct rDock Job display name typo ("rRock" -> "rDock") - #18
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The run-rdock Job Definition's display name read "Run rRock docking". Correct it to "Run rDock docking". Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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im-rdkit-utilities==1.0.0 hard-pins im-data-manager-job-utilities==1.3.0, which conflicted with these Dockerfiles' older pins (1.1.1/1.0.1) and broke the build entirely (ResolutionImpossible) - not caught in #21 because the images weren't rebuilt locally at review time. Verified: mordred, moldb and oddt images now build and pass their jote suites end-to-end (mordred: 2/2, moldb's non-nextflow jobs, plus a direct check of updateChargeFlagInAtomBlock). prep's image build is separately blocked by an unrelated, pre-existing issue: its apt-get step pulls packages from bullseye-security that have since been pruned from the Debian mirror - confirmed this also fails identically on the pre-migration Dockerfile-prep, so it's not something this change introduced. Verified prep's pip resolution (the part this change actually touches) succeeds cleanly in isolation. Part of #18. Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
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Dockerfile-prep never ran apt-get update itself, relying on the package index baked into informaticsmatters/vs-rdkit-base:latest at base-image build time. Since bullseye-security periodically prunes superseded point-release .debs, that stale index eventually points at files that no longer exist, and the build starts failing with 404s - this is what was blocking jote for open3dalign, sucos, assemble_conformers, cluster_butina, enumerate, le_conformers, rdkit_dedup, rdkit_props, sa_score, screen and reactor after #21/#22. No version is pinned for openbabel here, so a fresh apt-get update resolves to whatever build is currently on the mirror instead (still 3.1.1, just a different point release). Verified: image builds; full im-virtual-screening/rdkit/xchem jote suite passes 32/32 (with NXF_VER=22.10.0 per docs/testing-jobs.md, for the nextflow-based jobs in the same suite). Part of #18. Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
This was referenced Aug 11, 2026
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* feat(18): drop the local utils.py The 35 modules that imported the local utils now take it from dm_job_utilities, which provides all of log, expand_path, read_delimiter, is_type and calc_geometric_mean. Importing the module rather than the names (`from dm_job_utilities import utils`) leaves every utils.x call site unchanged. This repo is the only consumer that actually reached the two functions #18 flags as blockers: - round_to_significant_number (5 uses, all in dmpk/pk_tmax_cmax_sim.py) is replaced by sigfig.round, as job-utilities' README directs. The local implementation leaned on builtin round() and so inherited its half-way behaviour: 2.675 rounded to 2.67 and 1.005 to 1.0, where sigfig gives 2.68 and 1.01. Over 12000 randomly generated PK-plausible values, none differ - simulated values do not land on exact decimal boundaries - so this is a correctness fix with no expected change to real output. Wrapped locally to pass warn=False, since sigfig warns when a value carries fewer significant figures than requested and the previous implementation was silent. - get_path_from_digest (used by assemble_conformers.py and prepare_enum_conf_lists.py) was deliberately dropped from job-utilities as obsolete, but the sharded directory layout it describes is still what one script writes and the other reads. It moves to digest_utils.py rather than being inlined into both. Every Dockerfile installing job-utilities is bumped to >= 1.4.0: dm_job_utilities.utils first appears in 1.3.0, so the images pinned at 1.0.1 and 1.1.1 would have failed at import. sigfig is added to Dockerfile-dmpk, which did not carry it. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * fix: repair the image builds broken by dropping utils.py Three separate faults, all mine, all in the Dockerfiles: - Five images COPY utils.py explicitly (fns, dmpk, plants, jaqpot, mordred); with the file gone the COPY could not resolve. Removed. The images that glob (COPY *.py) were unaffected, and that glob is also how digest_utils.py reaches vs-prep, which is where both its consumers run. - Changing the pins from == to >= left them unquoted, so /bin/sh read the > as a redirection: `pip install foo>=1.4.0` installed foo unpinned and wrote stdout to a file named "=1.4.0". Every spec containing >= or <= is now quoted. The builds that passed had been silently installing unpinned. - Dockerfile-rdock never needed bumping: prepare_rdock.py imports no utils at all, and the image is Python 2 (rdock:2013.1), where a modern job-utilities cannot install. Reverted to its original pin. Also bumps the remaining im-rdkit-utilities==1.0.0 pins to >= 1.1.2. That version pins job-utilities to ==1.3.0, so it conflicts with >= 1.4.0 - the same conflict rdkit-utilities 1.1.2 was released to fix. It only surfaced once the quoting was corrected. All nine images build locally, resolve dm_job_utilities.utils (and rdkit_utils where used) at the intended versions, and carry no stray redirect file. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
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What
The
run-rdockJob Definition indata-manager/im-virtual-screening.yamlhad atypo in its display name:
Why
The name is user-facing (shown in the Data Manager UI). "rRock" should be
"rDock", the name of the docking tool the Job runs.
Scope
Display-name only — no change to the command, image, variables, or tests.
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