biolm.protocols.runtime.backends package

Submodules

biolm.protocols.runtime.backends.local module

Local backend: run compiled pipeline and materialize results.

class biolm.protocols.runtime.backends.local.LocalRunResult(dataframe: ~pandas.core.frame.DataFrame, records: list[dict[str, typing.Any]], plan: ~biolm.protocols.runtime.spec.ExecutionPlan, pipeline: ~biolm.pipeline.data.DataPipeline | None = None, run_id: str | None = None, output_selections: list[biolm.protocols.outputs.OutputSelection] = <factory>, selected_records: list[dict[str, typing.Any]] = <factory>)

Bases: object

Result of a local protocol run.

dataframe: DataFrame

output_selections: list[biolm.protocols.outputs.OutputSelection]

pipeline: DataPipeline | None = None

plan: ExecutionPlan

records: list[dict[str, Any]]

run_id: str | None = None

selected_records: list[dict[str, Any]]

to_seqframe(*, molecule_type: str | None = None, path: str | Path | None = None)

Materialize results as a SeqFrame (requires seqframe extra).

biolm.protocols.runtime.backends.local.run_local(protocol: dict, inputs: dict[str, Any], *, output_dir: str | Path | None = None, verbose: bool = False, **pipeline_kwargs: Any) → LocalRunResult

Compile and execute a protocol locally via DataPipeline.

Module contents

Protocol runtime backends.