nipoppy.config.pipeline

Pipeline configuration.

Module Contents

class nipoppy.config.pipeline.BasePipelineConfig(/, **data)

Bases: nipoppy.config.container.SchemaWithContainerConfig, abc.ABC

Base schema for processing/BIDS pipeline configuration.

Parameters:

data (Any)

CONTAINER_INFO: nipoppy.config.container.ContainerInfo

DESCRIPTION: str | None

NAME: str

STEPS: list[nipoppy.config.pipeline_step.ProcPipelineStepConfig | nipoppy.config.pipeline_step.BidsPipelineStepConfig]

VERSION: str

get_analysis_level(step_name=None)

Return the analysis level for the given step.

If step is None, return the analysis level for the first step.

Parameters:

step_name (Optional[str])

Return type:

str

get_descriptor_file(step_name=None)

Return the path to the descriptor file for the given step.

If step is None, return the descriptor file for the first step.

Parameters:

step_name (Optional[str])

Return type:

pathlib.Path | None

get_fpath_container()

Return the path to the pipeline’s container.

Return type:

pathlib.Path

get_invocation_file(step_name=None)

Return the path to the invocation file for the given step.

Is step is None, return the invocation file for the first step.

Parameters:

step_name (Optional[str])

Return type:

pathlib.Path | None

get_step_config(step_name=None)

Return the configuration for the given step.

If step_name is None, return the configuration for the first step.

Parameters:

step_name (Optional[str])

Return type:

nipoppy.config.pipeline_step.BasePipelineStepConfig

validate_after()

Validate the pipeline configuration after creation.

Specifically: - If STEPS has more than one item, make sure that each step has a unique name.

classmethod validate_before(data)

Validate the pipeline configuration before instantiation.

Specifically: - Apply substitutions for pipeline name/version in the config

Parameters:

data (Any)

Return type:

Any

class nipoppy.config.pipeline.BidsPipelineConfig(/, **data)

Bases: BasePipelineConfig

Schema for BIDS pipeline configuration.

Parameters:

data (Any)

model_config

get_update_doughnut(step_name=None)

Return the update doughnut flag for the given step.

If step is None, return the flag for the first step.

Parameters:

step_name (Optional[str])

Return type:

pathlib.Path | None

class nipoppy.config.pipeline.ProcPipelineConfig(/, **data)

Bases: BasePipelineConfig

Schema for processing pipeline configuration.

Parameters:

data (Any)

TRACKER_CONFIG_FILE: pathlib.Path | None

model_config

get_pybids_ignore_file(step_name=None)

Return the list of regex patterns to ignore when building the PyBIDS layout.

If step is None, return the patterns for the first step.

Parameters:

step_name (Optional[str])

Return type:

pathlib.Path | None