STY: Bump style dependencies, run isort on repo (#206)

* MAINT: Bump style dependencies

* MAINT: Add isort to style check

* MAINT: Add isort to style action check

* STY: Run `isort` on codebase

* MAINT: Add file to ignore large style changes when blaming

Author: mgxd

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# isort addition
+6f809fa9950654cbb7f755922c45dffbc88dc45d

.github/workflows/style.yml

@@ -25,8 +25,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install .[style]
+        pip install $(grep -e "black" -e "isort" setup.cfg | sed "s/ //g" | tr "\n" " ")
     - name: black code formatting check
       run: |
         black --check nibabies/

.pre-commit-config.yaml

@@ -10,3 +10,7 @@ repos:
     rev: 22.3.0
     hooks:
     -   id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+    - id: isort

nibabies/_warnings.py

@@ -1,6 +1,6 @@
 """Manipulate Python warnings."""
-import warnings
 import logging
+import warnings
 
 _wlog = logging.getLogger("py.warnings")
 _wlog.addHandler(logging.NullHandler())

nibabies/cli/parser.py

@@ -2,20 +2,20 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Parser."""
 import sys
+
 from .. import config
 
 
 def _build_parser():
     """Build parser object."""
+    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
     from functools import partial
     from pathlib import Path
-    from argparse import (
-        ArgumentParser,
-        ArgumentDefaultsHelpFormatter,
-    )
+
+    from niworkflows.utils.spaces import OutputReferencesAction, Reference
     from packaging.version import Version
+
     from .version import check_latest, is_flagged
-    from niworkflows.utils.spaces import Reference, OutputReferencesAction
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""
@@ -668,6 +668,7 @@ def parse_args(args=None, namespace=None):
     # Initialize --output-spaces if not defined
     if config.execution.output_spaces is None:
         from niworkflows.utils.spaces import Reference, SpatialReferences
+
         from ..utils.misc import cohort_by_months
 
         if config.workflow.age_months is None:

nibabies/cli/run.py

@@ -6,13 +6,14 @@
 
 def main():
     """Entry point."""
+    import gc
+    import sys
+    from multiprocessing import Manager, Process
     from os import EX_SOFTWARE
     from pathlib import Path
-    import sys
-    import gc
-    from multiprocessing import Process, Manager
+
+    from ..utils.bids import write_bidsignore, write_derivative_description
     from .parser import parse_args
-    from ..utils.bids import write_derivative_description, write_bidsignore
 
     parse_args()
 
@@ -133,17 +134,18 @@ def main():
             )
 
         if config.workflow.run_reconall:
-            from templateflow import api
             from niworkflows.utils.misc import _copy_any
+            from templateflow import api
 
             dseg_tsv = str(api.get("fsaverage", suffix="dseg", extension=[".tsv"]))
             _copy_any(dseg_tsv, str(config.execution.nibabies_dir / "desc-aseg_dseg.tsv"))
             _copy_any(dseg_tsv, str(config.execution.nibabies_dir / "desc-aparcaseg_dseg.tsv"))
         # errno = 0
     finally:
-        from ..reports.core import generate_reports
         from pkg_resources import resource_filename as pkgrf
 
+        from ..reports.core import generate_reports
+
         # Generate reports phase
         generate_reports(
             config.execution.participant_label,

nibabies/cli/version.py

@@ -2,9 +2,11 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Version CLI helpers."""
 
-from pathlib import Path
 from datetime import datetime
+from pathlib import Path
+
 import requests
+
 from .. import __version__
 
 RELEASE_EXPIRY_DAYS = 14
@@ -13,7 +15,7 @@
 
 def check_latest():
     """Determine whether this is the latest version."""
-    from packaging.version import Version, InvalidVersion
+    from packaging.version import InvalidVersion, Version
 
     latest = None
     date = None

nibabies/cli/workflow.py

@@ -12,10 +12,11 @@
 
 def build_workflow(config_file, retval):
     """Create the Nipype Workflow that supports the whole execution graph."""
-    from niworkflows.utils.bids import collect_participants, check_pipeline_version
+    from niworkflows.utils.bids import check_pipeline_version, collect_participants
     from niworkflows.utils.misc import check_valid_fs_license
-    from ..reports.core import generate_reports
+
     from .. import config
+    from ..reports.core import generate_reports
     from ..utils.misc import check_deps
     from ..workflows.base import init_nibabies_wf
 
@@ -134,9 +135,10 @@ def build_boilerplate(config_file, workflow):
     citation_files["md"].write_text(boilerplate)
 
     if not config.execution.md_only_boilerplate and citation_files["md"].exists():
-        from subprocess import check_call, CalledProcessError, TimeoutExpired
-        from pkg_resources import resource_filename as pkgrf
         from shutil import copyfile
+        from subprocess import CalledProcessError, TimeoutExpired, check_call
+
+        from pkg_resources import resource_filename as pkgrf
 
         # Generate HTML file resolving citations
         cmd = [

nibabies/config.py

@@ -86,12 +86,13 @@
     # Defer all custom import for after initializing the forkserver and
     # ignoring the most annoying warnings
     import random
-    from uuid import uuid4
+    from pathlib import Path
     from time import strftime
+    from uuid import uuid4
 
-    from pathlib import Path
     from nipype import __version__ as _nipype_ver
     from templateflow import __version__ as _tf_ver
+
     from . import __version__
 
 if not hasattr(sys, "_is_pytest_session"):
@@ -126,7 +127,9 @@
 if not _disable_et:
     # Just get so analytics track one hit
     from contextlib import suppress
-    from requests import get as _get_url, ConnectionError, ReadTimeout
+
+    from requests import ConnectionError, ReadTimeout
+    from requests import get as _get_url
 
     with suppress((ConnectionError, ReadTimeout)):
         _get_url("https://rig.mit.edu/et/projects/nipy/nipype", timeout=0.05)
@@ -215,7 +218,7 @@ def load(cls, settings, init=True, ignore=None):
     @classmethod
     def get(cls):
         """Return defined settings."""
-        from niworkflows.utils.spaces import SpatialReferences, Reference
+        from niworkflows.utils.spaces import Reference, SpatialReferences
 
         out = {}
         for k, v in cls.__dict__.items():
@@ -438,6 +441,7 @@ def init(cls):
 
         if cls._layout is None:
             import re
+
             from bids.layout import BIDSLayout, BIDSLayoutIndexer
 
             _db_path = cls.bids_database_dir or (cls.work_dir / cls.run_uuid / "bids_db")

nibabies/conftest.py

@@ -1,9 +1,9 @@
 """py.test configuration"""
 from pathlib import Path
 from tempfile import TemporaryDirectory
-from pkg_resources import resource_filename
 
 import pytest
+from pkg_resources import resource_filename
 
 FILES = (
     "functional.nii",