con/mechababs

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Automate BABs at scale and collect orchestration provenance

Stars: 1
Forks: 4
Open beginner issues: 0
Indexed issues: 73
Avg merge: 15h 39m
Merged PRs (30d): 24

Dominant language: Python
License: MIT
Last GitHub push: Sep 4, 2026
Latest indexed: Sep 15, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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73 open issues indexed

automate figuring out resources necessary for the job Open

automation

con/mechababs#3 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds002685 Failure report Open

dataset pipeline:fmriprep pipeline:mriqc

con/mechababs#5 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
avoid abs paths anywhere or bindmount them inside Open

automation provenance

con/mechababs#6 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Recording finished-job state — how is "done" stored? Open

automation fuzzy/slop

con/mechababs#13 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds000113 (StudyForrest) — session-level `babs init` fails on a structurally mixed dataset Open

babs-upstream upstream-NOT-FILED

con/mechababs#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
duct SIGINT during babs init / deploy loop doesn't abort cleanly Open

automation duct

con/mechababs#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Re-integrate con/duct resource monitoring after babs working-branch rebuild Open

babs-upstream duct provenance

con/mechababs#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Drop or hold the `resampling` fmriprep stage? Open

blocked decision pipeline:fmriprep

con/mechababs#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Scale-out to one full dataset (a different kind of shakeout) Open

automation pipeline:fmriprep

con/mechababs#18 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handling ~1k-subject datasets (subdataset-per-subject) Open

decision

con/mechababs#19 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Defacing / skull-strip verification gate Open

automation fmriprepDerivatives

con/mechababs#22 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Automate defacing / skull-strip verification Open

automation fmriprepDerivatives

con/mechababs#23 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Pipeline-as-unit for BABS (exploratory) Open

fuzzy/slop generalize

con/mechababs#27 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Composable config inputs for `babs init` (exploratory) Open

automation fuzzy/slop generalize

con/mechababs#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Make templateflow + FS-license bind-mounts portable (re-executable provenance) Open

automation pipeline:fmriprep provenance

con/mechababs#29 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
SLURM allocation is the throughput bottleneck — get more on Discovery Open

automation

con/mechababs#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
con-duct plot each job after mechababs finishes Open

automation duct

con/mechababs#35 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
BIDS-validate derivatives in finalize (deno validator, provenance-tracked) Open

automation

con/mechababs#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fetch the container once, not per-study Open

automation generalize performance

con/mechababs#37 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Meta-issue: upstream babs dependencies (part of M2) Open

babs-upstream epic

con/mechababs#38 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Epic: upstream babs dependencies (M4) Open

babs-upstream epic

con/mechababs#39 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds002785: minimal babs init fails — PermissionError stat-ing embedded FreeSurfer derivatives (likely transient) Open

dataset pipeline:fmriprep

con/mechababs#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds006623: annex content not retrievable — never mirrored to s3-PUBLIC (only copy on internal OpenNeuro remote) Open

dataset upstream

con/mechababs#43 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds004078: ~60 BOLD runs in one subject-level job exceeds walltime (no sessions to split on) Open

dataset pipeline:fmriprep

con/mechababs#44 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds006688 superseded by ds007116 — swap the stale ID in the curated list + re-run Open

dataset upstream

con/mechababs#45 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`babs merge` as a dependent (`afterany`) compute job + post-merge hook Open

babs-upstream upstream-NOT-FILED

con/mechababs#46 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Don't depend on a babs fork for real data processing Open

babs-upstream provenance

con/mechababs#47 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds004146: MP2RAGE-only (no _T1w) — use UNIT1_denoised as the fmriprep anatomical Open

dataset decision pipeline:fmriprep

con/mechababs#48 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds001499: s3-PUBLIC content fails git-annex hash verification (ses-16 T1w) — blocks mriqc for sub-CSI2/CSI3 Open

dataset upstream

con/mechababs#49 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Duct-wrap each iterate step Open

automation duct

con/mechababs#53 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Build the june-1 FAIL.txt report generator into the mechababs CLI Open

automation

con/mechababs#59 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
iterate decide(): merge / failure-handling policy refinements (defer to real-data) Open

automation decision

con/mechababs#66 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add-dataset: populate n_subjects / n_sessions from OpenNeuroStudies metadata Open

automation

con/mechababs#68 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Run babs e2e rootless (podman + --userns), retire the worktree-contamination guards Open

babs-upstream upstream-NOT-FILED

con/mechababs#70 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Data-license model for campaign + derivative outputs (inherit vs assert) Open

decision provenance

con/mechababs#75 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Derivatives can't leave the cluster that made them (STAMPED-D): per-derivative RIA with a machine-local URL Open

automation provenance

con/mechababs#79 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fs-license is bound twice in the generated invocation; the YAML comment is stale Open

automation pipeline:fmriprep

con/mechababs#80 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ds005747 / ds004044 MRIQC: OOM-killed at synthstrip even at 24G on a hard-enforcing cluster Open

automation dataset pipeline:mriqc

con/mechababs#83 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Publishing design: how a produced derivative becomes a published one Open

automation decision generalize provenance

con/mechababs#84 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Cluster YAMLs hardcode an allocation-assigned, expiring workspace path Open

automation generalize

con/mechababs#85 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Do a sweep over openneuro priority datasets Open

con/mechababs#86 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Meetup with Felix, Chris & Joe Open

con/mechababs#87 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fmriprep outputs: invitation for feedback Open

decision pipeline:fmriprep

con/mechababs#88 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Write a .bidsignore for the campaign Open

automation

con/mechababs#89 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Chained stage: run our selection to trim upstream-only wasted jobs Open

automation

con/mechababs#92 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Auto-generate docs/reference.md from the CLI + config schema Open

automation generalize

con/mechababs#96 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Config composition leaks: cluster/runtime settings land on the pipeline axis Open

automation decision fuzzy/slop generalize

con/mechababs#97 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add docs-drift guard to CI Open

con/mechababs#103 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Downstream fmriprep stages regenerate three anat outputs that `--derivatives` should reuse (upstream smriprep) Open

blocked pipeline:fmriprep upstream

con/mechababs#107 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
e2e: the documented campaign cleanup fails partway and leaves the campaign broken Open

automation

con/mechababs#109 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026

con/mechababs

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