[RF] Use Black to reformat package

.github/workflows/lint.yml

@@ -3,10 +3,10 @@ name: Lint code
 on:
   push:
     branches:
-      - main_
+      - master
   pull_request:
     branches:
-      - main_
+      - master
 
 defaults:
   run:
@@ -30,8 +30,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install flake8 and related packages
         run: python -m pip install \
-          flake8 flake8-absolute-import flake8-black flake8-docstrings \
-          flake8-isort flake8-pyproject flake8-unused-arguments \
-          flake8-use-fstring pep8-naming
+          flake8 flake8-black \
+          flake8-isort flake8-pyproject
       - name: Check qsiprep
         run: python -m flake8 qsiprep

pyproject.toml

@@ -131,6 +131,7 @@ exclude = '''
     | _build
     | build
     | dist
+    | qsiprep/niworkflows
   )/
   | qsiprep/_version.py
 )
@@ -152,9 +153,10 @@ exclude = [
     "qsiprep/config.py",
     "qsiprep/data/",
     "qsiprep/tests/",
+    "qsiprep/niworkflows/",
     "qsiprep/utils/sentry.py",
 ]
-ignore = ["D107", "E203", "E402", "E722", "W503", "N803", "N806", "N815"]
+ignore = ["D107", "E203", "E402", "E722", "W503", "N803", "N806", "N815", "W605"]
 per-file-ignores = [
     "**/__init__.py : F401",
     "docs/conf.py : E265",

qsiprep/__about__.py

@@ -8,12 +8,14 @@
 except ImportError:
     __version__ = "0+unknown"
 
-__packagename__ = 'qsiprep'
-__copyright__ = 'Copyright 2019, Brain Behavior Laboratory, University of Pennsylvania'
-__credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder'
-               'of the repository')
-__url__ = 'https://github.com/pennlinc/qsiprep'
+__packagename__ = "qsiprep"
+__copyright__ = "Copyright 2019, Brain Behavior Laboratory, University of Pennsylvania"
+__credits__ = (
+    "Contributors: please check the ``.zenodo.json`` file at the top-level folder"
+    "of the repository"
+)
+__url__ = "https://github.com/pennlinc/qsiprep"
 
-DOWNLOAD_URL = (
-    'https://github.com/pennbbl/{name}/archive/{ver}.tar.gz'.format(
-        name=__packagename__, ver=__version__))
+DOWNLOAD_URL = "https://github.com/pennbbl/{name}/archive/{ver}.tar.gz".format(
+    name=__packagename__, ver=__version__
+)

qsiprep/__init__.py

@@ -11,9 +11,9 @@
 from .__about__ import __copyright__, __credits__, __packagename__, __version__  # noqa
 
 # cmp is not used by qsiprep, so ignore nipype-generated warnings
-warnings.simplefilter('ignore')
-warnings.filterwarnings('ignore', r'cmp not installed')
-warnings.filterwarnings('ignore', r'Enable tracemalloc')
-warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
-warnings.filterwarnings('ignore', category=ResourceWarning)
-warnings.filterwarnings('ignore', r'Using or importing the ABCs from')
+warnings.simplefilter("ignore")
+warnings.filterwarnings("ignore", r"cmp not installed")
+warnings.filterwarnings("ignore", r"Enable tracemalloc")
+warnings.filterwarnings("ignore", r"can't resolve package from __spec__ or __package__")
+warnings.filterwarnings("ignore", category=ResourceWarning)
+warnings.filterwarnings("ignore", r"Using or importing the ABCs from")

qsiprep/cli/convertODFs.py

@@ -13,92 +13,116 @@ def sink_mask_file(in_file, orig_file, out_dir):
     import os
 
     from nipype.utils.filemanip import copyfile, fname_presuffix
+
     os.makedirs(out_dir, exist_ok=True)
-    out_file = fname_presuffix(orig_file, suffix='_mask', newpath=out_dir)
+    out_file = fname_presuffix(orig_file, suffix="_mask", newpath=out_dir)
     copyfile(in_file, out_file, copy=True, use_hardlink=True)
     return out_file
 
 
 def fib_to_mif():
     """Convert fib to mif."""
     parser = ArgumentParser(
-        description='qsiprep: Convert DSI Studio fib file to MRtrix mif file.',
-        formatter_class=RawTextHelpFormatter)
+        description="qsiprep: Convert DSI Studio fib file to MRtrix mif file.",
+        formatter_class=RawTextHelpFormatter,
+    )
 
-    parser.add_argument('--fib',
-                        required=True,
-                        action='store',
-                        type=os.path.abspath,
-                        default='',
-                        help='DSI Studio fib file to convert')
-    parser.add_argument('--mif',
-                        type=os.path.abspath,
-                        required=False,
-                        action='store',
-                        default='',
-                        help='output path for a MRtrix mif file')
-    parser.add_argument('--ref_image',
-                        required=True,
-                        action='store',
-                        type=os.path.abspath,
-                        help='a NIfTI-1 format file with a valid q/sform.')
-    parser.add_argument('--subtract-iso',
-                        required=False,
-                        action='store_true',
-                        help='subtract ODF min so visualization looks similar in mrview')
+    parser.add_argument(
+        "--fib",
+        required=True,
+        action="store",
+        type=os.path.abspath,
+        default="",
+        help="DSI Studio fib file to convert",
+    )
+    parser.add_argument(
+        "--mif",
+        type=os.path.abspath,
+        required=False,
+        action="store",
+        default="",
+        help="output path for a MRtrix mif file",
+    )
+    parser.add_argument(
+        "--ref_image",
+        required=True,
+        action="store",
+        type=os.path.abspath,
+        help="a NIfTI-1 format file with a valid q/sform.",
+    )
+    parser.add_argument(
+        "--subtract-iso",
+        required=False,
+        action="store_true",
+        help="subtract ODF min so visualization looks similar in mrview",
+    )
     opts = parser.parse_args()
-    converter = FIBGZtoFOD(mif_file=opts.mif,
-                           fib_file=opts.fib,
-                           ref_image=opts.ref_image,
-                           subtract_iso=opts.subtract_iso)
+    converter = FIBGZtoFOD(
+        mif_file=opts.mif,
+        fib_file=opts.fib,
+        ref_image=opts.ref_image,
+        subtract_iso=opts.subtract_iso,
+    )
     converter.run()
 
 
 def mif_to_fib():
     """Convert mif to fib."""
     parser = ArgumentParser(
-        description='qsiprep: Convert MRtrix mif file to DSI Studio fib file',
-        formatter_class=RawTextHelpFormatter)
+        description="qsiprep: Convert MRtrix mif file to DSI Studio fib file",
+        formatter_class=RawTextHelpFormatter,
+    )
 
-    parser.add_argument('--mif',
-                        type=os.path.abspath,
-                        required=True,
-                        action='store',
-                        default='',
-                        help='MRtrix mif file to convert')
-    parser.add_argument('--fib',
-                        required=True,
-                        action='store',
-                        type=os.path.abspath,
-                        default='',
-                        help='the output path for the DSI Studio fib file')
-    parser.add_argument('--mask',
-                        required=False,
-                        action='store',
-                        type=os.path.abspath,
-                        help='a NIfTI-1 format mask file.')
-    parser.add_argument('--num_fibers',
-                        required=False,
-                        action='store',
-                        type=int,
-                        default=5,
-                        help='maximum number of fixels per voxel.')
-    parser.add_argument('--unit-odf',
-                        required=False,
-                        action='store_true',
-                        help='force ODFs to sum to 1.')
+    parser.add_argument(
+        "--mif",
+        type=os.path.abspath,
+        required=True,
+        action="store",
+        default="",
+        help="MRtrix mif file to convert",
+    )
+    parser.add_argument(
+        "--fib",
+        required=True,
+        action="store",
+        type=os.path.abspath,
+        default="",
+        help="the output path for the DSI Studio fib file",
+    )
+    parser.add_argument(
+        "--mask",
+        required=False,
+        action="store",
+        type=os.path.abspath,
+        help="a NIfTI-1 format mask file.",
+    )
+    parser.add_argument(
+        "--num_fibers",
+        required=False,
+        action="store",
+        type=int,
+        default=5,
+        help="maximum number of fixels per voxel.",
+    )
+    parser.add_argument(
+        "--unit-odf", required=False, action="store_true", help="force ODFs to sum to 1."
+    )
     opts = parser.parse_args()
     if opts.mask is not None:
-        converter = FODtoFIBGZ(mif_file=opts.mif,
-                               fib_file=opts.fib,
-                               num_fibers=opts.num_fibers,
-                               unit_odf=opts.unit_odf,
-                               mask_file=opts.mask)
+        converter = FODtoFIBGZ(
+            mif_file=opts.mif,
+            fib_file=opts.fib,
+            num_fibers=opts.num_fibers,
+            unit_odf=opts.unit_odf,
+            mask_file=opts.mask,
+        )
     else:
-        converter = FODtoFIBGZ(mif_file=opts.mif,
-                               fib_file=opts.fib,
-                               num_fibers=opts.num_fibers,
-                               unit_odf=opts.unit_odf)
+        converter = FODtoFIBGZ(
+            mif_file=opts.mif,
+            fib_file=opts.fib,
+            num_fibers=opts.num_fibers,
+            unit_odf=opts.unit_odf,
+        )
     converter.run()
 
 

qsiprep/cli/group_report.py

@@ -13,14 +13,16 @@
 def aggregate_reports():
     """Convert fib to mif."""
     parser = ArgumentParser(
-        description='qsiprep: Aggregate single subject reports into a group report.',
-        formatter_class=RawTextHelpFormatter)
+        description="qsiprep: Aggregate single subject reports into a group report.",
+        formatter_class=RawTextHelpFormatter,
+    )
 
-    parser.add_argument('qsiprep_derivatives_dir',
-                        type=Path,
-                        action='store',
-                        help='the root folder containing QSIPrep outputs (sub-XXXXX folders '
-                        'should be found at the top level in this folder).')
+    parser.add_argument(
+        "qsiprep_derivatives_dir",
+        type=Path,
+        action="store",
+        help="the root folder containing QSIPrep outputs (sub-XXXXX folders "
+        "should be found at the top level in this folder).",
+    )
     opts = parser.parse_args()
-    sys.exit(
-        generate_interactive_report_summary(opts.qsiprep_derivatives_dir))
+    sys.exit(generate_interactive_report_summary(opts.qsiprep_derivatives_dir))