NL-BioImaging / biomero / 28578636469

92%

Build Type

push

github

Committed by web-flow

Commit Message

Add Configurable Slurm Compatibility Features To BIOMERO (#30)

Final PR Summary
This PR upstreams a complete set of cluster-specific compatibility patches into core BIOMERO as backward-compatible, opt-in configuration options. All default behavior is unchanged unless explicitly enabled.

What moved into core BIOMERO
Feature	Config key / env var	Default
Shared config/env precedence helper	— (internal)	—
SACCT history window (absolute or relative)	sacct_start_time / BIOMERO_SACCT_START_TIME, sacct_days_ago / BIOMERO_SACCT_START_DAYS_AGO	unchanged
ZIP/UNZIP command (7z or 7za, or explicit override)	slurm_zip_cmd / BIOMERO_SLURM_ZIP_CMD	auto-detect
Env-file-based sbatch submission	env_file_submission / BIOMERO_ENV_FILE_SUBMISSION	off
Generated-script env-file sourcing	$OPTIONAL_ENV in job_template.sh	no-op
Generated-script GPU flag normalization (--nv)	inject_gpu_flag / BIOMERO_INJECT_GPU_FLAG	off
Fallback GPU Slurm resources (gpu_partition, gpu_gres)	GPU_PARTITION / BIOMERO_GPU_PARTITION, GPU_GRES / BIOMERO_GPU_GRES	off (per-workflow settings still take precedence)
Optional APPTAINER_BINDPATH export	slurm_data_bind_path	unset (not required)
Optional conversion job partition	slurm_conversion_partition	unset
Apptainer tmp/cache dir overrides	slurm_apptainer_tmpdir, slurm_apptainer_cachedir	unset
sbatch-based image pull/build	slurm_pull_command / BIOMERO_PULL_COMMAND	off
Script hardening (set -eo pipefail) and output verification	job_template.sh	shipped
[MODELS] section renamed to [WORKFLOWS]	config file	backward-compatible alias kept
slurm_default_partition fallback routing	slurm_default_partition / BIOMERO_DEFAULT_PARTITION	unset
Global sbatch parameters for all job types	sbatch_* keys in [SLURM] section	unset
What remains opt-in
env-file submission, GPU flag injection, shared GPU fallback defaults, sbatch-based image pulling, apptainer tmp/cache overrides, slurm_data_bind_path, slurm_conversion_partition, slurm_default_partition
What remains external-re... (continued)

Coverage Stats

301 of 332 new or added lines in 2 files covered. (90.66%)

103 existing lines in 1 file now uncovered.

4186 of 4564 relevant lines covered (91.72%)

0.92 hits per line