Work on fixing docstrings and splitting modules

aslprep/__init__.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Top-module metadata."""
+"""ASLPrep: A Robust Preprocessing Pipeline for ASL Data."""
 
 from aslprep.__about__ import __copyright__, __credits__, __packagename__, __version__
 

aslprep/__main__.py

@@ -1,3 +1,4 @@
+"""A way to run the ASLPrep CLI with a Python call."""
 from aslprep.cli.run import main
 
 if __name__ == "__main__":

aslprep/cli/__init__.py

@@ -0,0 +1 @@
+"""Command-line interfaces for ASLPrep."""

aslprep/cli/aggregate_qc.py

@@ -1,15 +1,15 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""aggregate qc of all the subjects"""
+"""Aggregate QC measures across all subjects in dataset."""
 import os
 from pathlib import Path
 
 import pandas as pd
 
 
 def get_parser():
-    """Build parser object"""
+    """Build parser object."""
     from argparse import ArgumentParser, RawTextHelpFormatter
 
     parser = ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
@@ -21,8 +21,7 @@ def get_parser():
 
 
 def main():
-    """Entry point"""
-
+    """Run the workflow."""
     opts = get_parser().parse_args()
 
     allsubj_dir = os.path.abspath(opts.aslprep_dir)

aslprep/cli/workflow.py

@@ -116,9 +116,7 @@ def build_boilerplate(config_file, workflow):
     config.load(config_file)
     logs_path = config.execution.output_dir / "aslprep" / "logs"
     boilerplate = workflow.visit_desc()
-    citation_files = {
-        ext: logs_path / ("CITATION.%s" % ext) for ext in ("bib", "tex", "md", "html")
-    }
+    citation_files = {ext: logs_path / f"CITATION.{ext}" for ext in ("bib", "tex", "md", "html")}
 
     if boilerplate:
         # To please git-annex users and also to guarantee consistency

aslprep/config.py

@@ -519,7 +519,7 @@ def init(cls):
 
 
 class seeds(_Config):
-    """Initialize the PRNG and track random seed assignments"""
+    """Initialize the PRNG and track random seed assignments."""
 
     master = None
     """Master seed used to generate all other tracked seeds"""
@@ -528,6 +528,7 @@ class seeds(_Config):
 
     @classmethod
     def init(cls):
+        """Initialize a seeds object."""
         cls.master = workflow.random_seed
         if cls.master is None:
             cls.master = random.randint(1, 65536)
@@ -538,7 +539,7 @@ def init(cls):
 
 
 def _set_ants_seed():
-    """Fix random seed for antsRegistration, antsAI, antsMotionCorr"""
+    """Fix random seed for antsRegistration, antsAI, antsMotionCorr."""
     val = random.randint(1, 65536)
     os.environ["ANTS_RANDOM_SEED"] = str(val)
     return val

aslprep/data/boilerplate.bib

@@ -178,7 +178,6 @@ @article{score_dolui
 	year = {2017},
 	keywords = {ADNI, Aged, Algorithms, Alzheimer Disease, Alzheimer's disease, arterial spin labeling, Artifacts, Brain, cerebral blood flow, Cerebrovascular Circulation, Female, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Angiography, Male, outlier rejection, Reproducibility of Results, Sensitivity and Specificity, Spin Labels},
 	pages = {1786--1797},
-	file = {Accepted Version:/Users/adebimpe/Zotero/storage/28WLPTXK/Dolui et al. - 2017 - Structural Correlation-based Outlier Rejection (SC.pdf:application/pdf;Accepted Version:/Users/adebimpe/Zotero/storage/QK82SC8R/Dolui et al. - 2017 - Structural Correlation-based Outlier Rejection (SC.pdf:application/pdf},
 }
 
 @misc{noauthor_ismrm_nodate,