Update to pathlib

Author: matthew-brett

findoutlie/outfind.py

@@ -1,8 +1,7 @@
 """ Module with routines for finding outliers
 """
 
-import os.path as op
-from glob import glob
+from pathlib import Path
 
 
 def detect_outliers(fname):
@@ -23,8 +22,7 @@ def find_outliers(data_directory):
         Dictionary with keys being filenames and values being lists of outliers
         for filename.
     """
-    image_fnames = glob(op.join(data_directory, '**', 'sub-*.nii.gz'),
-                        recursive=True)
+    image_fnames = Path(data_directory).glob('**/sub-*.nii.gz')
     outlier_dict = {}
     for fname in image_fnames:
         outliers = detect_outliers(fname)

scripts/find_outliers.py

@@ -5,14 +5,14 @@
     python3 scripts/find_outliers.py data
 """
 
-import os.path as op
+from pathlib import Path
 import sys
 
 from argparse import ArgumentParser, RawDescriptionHelpFormatter
 
 # Put the findoutlie directory on the Python path.
-PACKAGE_DIR = op.join(op.dirname(__file__), '..')
-sys.path.append(PACKAGE_DIR)
+PACKAGE_DIR = Path(__file__).parent / '..'
+sys.path.append(str(PACKAGE_DIR))
 
 from findoutlie import outfind
 

scripts/validate_data.py

@@ -5,7 +5,7 @@
     python3 scripts/validata_data.py data
 """
 
-import op as op
+from pathlib import Path
 import sys
 import hashlib