micom.workflows.core

Makes it easier to run analyses on several samples in parallel.

Module Contents

Functions

save_results(results, path)	Save growth results to a file.
load_results(path)	Load growth results from a file.
workflow(func, args[, threads, description, progress])	Run analyses for several samples in parallel.

Attributes

GrowthResults

micom.workflows.core.GrowthResults

micom.workflows.core.save_results(results, path)

Save growth results to a file.

This will write all tables as CSV into a single ZIP file.

Parameters:

• results (GrowthResults) – The results as returned from grow.

• path (str) – A filepath for the generated file. Should end in .zip.

micom.workflows.core.load_results(path)

Load growth results from a file.

Parameters:

path (str) – Path to saved GrowthResults.

Returns:

The saved GrowthResults.

Return type:

GrowthResults

micom.workflows.core.workflow(func, args, threads=4, description=None, progress=True)

Run analyses for several samples in parallel.

This will analyze several samples in parallel. Includes a workaround for optlang memory leak.

Parameters:

• func (function) – A function that takes a single argument (can be any object) and that performs your analysis for a single sample.

• args (array-like object) – An array-like object (list, tuple, numpy array, pandas Series, etc.) that contains the arguments for each sample.

• threads (positive int) – How many samples to analyze in parallel at once.

• description (str) – The dewscription shown in front of the progress bar.

• progress (bool) – Whether to show a progress bar.