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Workflow: sp run refreshes the code snapshot before the lock; re-clean erases exposure tombstones; missing run-dir undetected

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  • ¿Algo no está bien?
#958 0 comentarios 0 reacciones 0 asignados Ver en GitHub

Los mantenedores suelen responder en 1 día

@cailmdaley ya está trabajando en esto.

Desde el 10/10/2026.

  • #960 de @cailmdaley — abierto

Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
45/100
Tipo de issue
Error
Claridad
Bien especificado
Estado de actividad
Activo
Stack tecnológico
python, shell
Área
backend, devops

Línea de trabajo

Start by reading workflow/bin/sp around line 262 and the Snakemake lock behavior, then inspect workflow/scripts/clean_exposure.py around lines 58–80 and workflow/scripts/completeness.py around lines 405–406. Reproduce each reported failure and compare clean_exposure.py with the tombstone merge in clean_tile.py. Done means all three defects are fixed and covered by checks for repeated runs, repeated cleaning, and a missing run directory.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

Three workflow defects found while rewriting the workflow's comments (comment sweep, PR to follow). Each was confirmed against develop (f2ab8a56) by a second reader; none is fixed by the sweep, which changes no code.

1. sp run refreshes the campaign's code snapshot before Snakemake takes its lock — workflow/bin/sp:262. snapshot_code rsyncs the checkout into $STATE_DIR/code unconditionally, before either Snakemake invocation, including for sp run -n. A second sp run (or a dry run) against a live campaign therefore overwrites the code that its queued and running jobs re-read when they start, and only afterwards does Snakemake refuse on its lock. This defeats the snapshot's purpose (keeping mid-campaign edits away from running jobs). A fix probably belongs in bin/sp: take or test Snakemake's lock first, or snapshot into a fresh directory per launch.

2. Re-cleaning a reclaimed exposure erases its tombstone's stage records — workflow/scripts/clean_exposure.py:58–80. The record starts as {}, is filled only from the manifests currently on disk, and replaces the existing tombstone without reading it. On an exposure already reclaimed (its manifests gone) a second clean writes an empty record. clean_tile.py already merges into the prior tombstone; clean_exposure.py should do the same.

3. completeness.py cannot detect a missing run directory — workflow/scripts/completeness.py:405–406. With neither --run-dir nor SP_RUN, Path("") becomes ., so if not str(run_dir) never fires and the check runs against the current directory instead of raising its configuration error. Validate the raw setting before converting it to a Path.

Claude (Opus) and GPT-6.1 Sol on behalf of Cail.

Lenguaje dominante
Python
Estrellas
18
Forks
14
Merge medio
2 d 13 h
PR fusionados (30 d)
35

Preparar el entorno

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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