revise.recon.context.PipelineContext

class revise.recon.context.PipelineContext(merged_config: 'Dict[str, Any]', raw_config: 'Dict[str, Any]', config_path: 'str', profile: 'Optional[str]', runtime: 'Dict[str, Any]', route_key: 'str', run_dir: 'Path', logger: 'logging.Logger', dry_run: 'bool' = False, legacy_config: 'Any' = None, legacy_runner: 'Any' = None, st_adata: 'Optional[AnnData]' = None, sc_ref_adata: 'Optional[AnnData]' = None, real_st_adata: 'Optional[AnnData]' = None, svc: 'Optional[SVC]' = None, stage_trace: 'List[str]' = <factory>, quality_metrics: 'Dict[str, Any]'=<factory>, artifacts: 'Dict[str, Any]'=<factory>, provenance: 'Dict[str, Any]'=<factory>)[source]

Bases: object

__init__(merged_config: ~typing.Dict[str, ~typing.Any], raw_config: ~typing.Dict[str, ~typing.Any], config_path: str, profile: str | None, runtime: ~typing.Dict[str, ~typing.Any], route_key: str, run_dir: ~pathlib.Path, logger: ~logging.Logger, dry_run: bool = False, legacy_config: ~typing.Any = None, legacy_runner: ~typing.Any = None, st_adata: <MagicMock id='135707052768080'> | None = None, sc_ref_adata: <MagicMock id='135707052768080'> | None = None, real_st_adata: <MagicMock id='135707052768080'> | None = None, svc: ~revise.svc.model.SVC | None = None, stage_trace: ~typing.List[str] = <factory>, quality_metrics: ~typing.Dict[str, ~typing.Any] = <factory>, artifacts: ~typing.Dict[str, ~typing.Any] = <factory>, provenance: ~typing.Dict[str, ~typing.Any] = <factory>) → None

Methods

__init__(merged_config, ~typing.Any], ...)

Attributes

`columns`
`dry_run`
`io`
`legacy_config`
`legacy_mode`
`legacy_runner`
`real_st_adata`
`route`
`sc_ref_adata`
`st_adata`
`svc`
`merged_config`
`raw_config`
`config_path`
`profile`
`runtime`
`route_key`
`run_dir`
`logger`
`stage_trace`
`quality_metrics`
`artifacts`
`provenance`

merged_config: Dict[str, Any]

raw_config: Dict[str, Any]

config_path: str

profile: str | None

runtime: Dict[str, Any]

route_key: str

run_dir: Path

logger: Logger

dry_run: bool = False

legacy_config: Any = None

legacy_runner: Any = None

st_adata: <MagicMock id='135707052768080'> | None = None

sc_ref_adata: <MagicMock id='135707052768080'> | None = None

real_st_adata: <MagicMock id='135707052768080'> | None = None

svc: SVC | None = None

stage_trace: List[str]

quality_metrics: Dict[str, Any]

artifacts: Dict[str, Any]

provenance: Dict[str, Any]

property io: Dict[str, Any]

property columns: Dict[str, Any]

property legacy_mode: bool

property route: Dict[str, Any]