aliby.pipeline.PipelineParameters

class PipelineParameters(general, tiler, baby, extraction, postprocessing, reporting)

Bases: ParametersABC

Parameters that host what is run and how. It takes a list of dictionaries, one for general in collection: pass dictionary for each step ——————– expt_id: int or str Experiment id (if integer) or local path (if string). directory: str Directory into which results are dumped. Default is “../data”

Provides default parameters for the entire pipeline. This downloads the logfiles and sets the default timepoints and extraction parameters from there.

Methods

from_yaml(source)	Returns instance from a yaml filename or stdin
to_dict([iterable])	Recursive function to return a nested dictionary of the attributes of the class instance.
to_yaml([path])	Returns a yaml stream of the attributes of the class instance.
update(name, new_value)	Update values recursively if name is a dictionary, replace data where existing found or add if not.

default
from_dict
load_logs

Defines parameters as attributes

Methods

from_yaml(source)	Returns instance from a yaml filename or stdin
to_dict([iterable])	Recursive function to return a nested dictionary of the attributes of the class instance.
to_yaml([path])	Returns a yaml stream of the attributes of the class instance.
update(name, new_value)	Update values recursively if name is a dictionary, replace data where existing found or add if not.

default
from_dict
load_logs

__init__(general, tiler, baby, extraction, postprocessing, reporting)

Defines parameters as attributes

Methods

__init__(general, tiler, baby, extraction, ...)	Defines parameters as attributes
default([general, tiler, baby, extraction, ...])
from_dict(d)
from_yaml(source)	Returns instance from a yaml filename or stdin
load_logs()
to_dict([iterable])	Recursive function to return a nested dictionary of the attributes of the class instance.
to_yaml([path])	Returns a yaml stream of the attributes of the class instance.
update(name, new_value)	Update values recursively if name is a dictionary, replace data where existing found or add if not.

classmethod from_yaml(source)

Returns instance from a yaml filename or stdin

to_dict(iterable='null')

Recursive function to return a nested dictionary of the attributes of the class instance.

Return type

Dict

to_yaml(path=None)

Returns a yaml stream of the attributes of the class instance. If path is provided, the yaml stream is saved there.

Parameters

pathUnion[PosixPath, str]

Output path.

update(name, new_value)

Update values recursively if name is a dictionary, replace data where existing found or add if not. It warns against type changes.

If the existing structure under name is a dictionary, it looks for the first occurrence and modifies it accordingly.

If a leaf node that is to be changed is a collection, it adds the new elements.