submit#

Cluster submission with the inspection gate.

dry_run and deploy are importable pieces (used by the deploy_pipeline notebook); main composes them into the CLI, which refuses to submit until a dry run has been produced and shown. The dry-run output is stored next to the SGE logs for the post-hoc record:

python -m openplaces.flow.submit --config recipe=US_footprint-cheer-2026 \
    admin_ids=US-NC-BS,US-NC-CE

Functions#

dry_run([snakefile, extra_args, verbose])

Produce, print, and store a Snakemake dry run (the inspection gate).

deploy([cores, snakefile, extra_args])

Run the workflow: on the cluster (profile) or locally (cores).

Module Contents#

openplaces.flow.submit.dry_run(config=None, targets=(), snakefile=None, extra_args=(), verbose=True) → tuple[int, str, pathlib.Path]#

Produce, print, and store a Snakemake dry run (the inspection gate).

Parameters:

  • config (dict or list of str, optional) – Workflow config (e.g. {'recipe': ..., 'admin_ids': [...]} or ['recipe=...', 'admin_ids=a,b']).

  • targets (tuple of str) – Optional Snakemake targets.

  • snakefile (str or Path, optional) – Defaults to <code_root>/workflow/Snakefile.

  • extra_args (tuple of str) – Additional snakemake arguments (e.g. ('--forcerun', 'rule')).

  • verbose (bool) – Print the dry-run output.

Returns:

The dry run’s exit code, its combined stdout+stderr, and the path it was stored at (under the logs directory, for the post-hoc record).

Return type:

(returncode, output, stored_path)

openplaces.flow.submit.deploy(profile=None, config=None, targets=(), cores=None, snakefile=None, extra_args=()) → int#

Run the workflow: on the cluster (profile) or locally (cores).

Streams Snakemake’s output to the console and returns its exit code. Callers are expected to have produced a dry run first (dry_run); the CLI (main) enforces that.

Parameters:

  • profile (str or Path, optional) – Snakemake profile directory (e.g. ‘workflow/profiles/scc’); resolved against the code root when relative. Mutually exclusive with local execution.

  • config – As in dry_run.

  • targets – As in dry_run.

  • snakefile – As in dry_run.

  • extra_args – As in dry_run.

  • cores (int, optional) – Local execution with this many cores (default 4) when no profile is given.