Autoformat with black and isort (#205)

* Add linting action. * Ignore external packages. * Run black and isort. * Consolidate tests. * Remove relative imports from tests.
PennLINC · Feb 14, 2023 · 649935b · 649935b
1 parent 3bdca40
commit 649935b
Show file tree

Hide file tree

Showing 44 changed files with 9,032 additions and 5,411 deletions.
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,37 @@
+name: Lint code
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  stable:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        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-unused-arguments flake8-use-fstring \
+          flake8-warnings pep8-naming
+      - name: Check aslprep
+        run: python -m flake8 aslprep
diff --git a/aslprep/__about__.py b/aslprep/__about__.py
@@ -2,15 +2,18 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Base module variables."""
 from ._version import get_versions
-__version__ = get_versions()['version']
+
+__version__ = get_versions()["version"]
 del get_versions
 
-__packagename__ = 'aslprep'
-__copyright__ = 'Copyright 2020, PENN LINC'
-__credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder'
-               'of the repository')
-__url__ = 'https://github.com/pennlinc/aslprep'
+__packagename__ = "aslprep"
+__copyright__ = "Copyright 2020, PENN LINC"
+__credits__ = (
+    "Contributors: please check the ``.zenodo.json`` file at the top-level folder"
+    "of the repository"
+)
+__url__ = "https://github.com/pennlinc/aslprep"
 
-DOWNLOAD_URL = (
-    'https://github.com/pennlinc/{name}/archive/{ver}.tar.gz'.format(
-        name=__packagename__, ver=__version__))
+DOWNLOAD_URL = "https://github.com/pennlinc/{name}/archive/{ver}.tar.gz".format(
+    name=__packagename__, ver=__version__
+)
diff --git a/aslprep/__init__.py b/aslprep/__init__.py
@@ -2,16 +2,11 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Top-module metadata."""
 
-from .__about__ import (
-    __copyright__,
-    __credits__,
-    __packagename__,
-    __version__,
-)
+from .__about__ import __copyright__, __credits__, __packagename__, __version__
 
 __all__ = [
-    '__copyright__',
-    '__credits__',
-    '__packagename__',
-    '__version__',
+    "__copyright__",
+    "__credits__",
+    "__packagename__",
+    "__version__",
 ]
diff --git a/aslprep/__main__.py b/aslprep/__main__.py
@@ -1,9 +1,11 @@
 from .cli.run import main
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import sys
+
     from . import __name__ as module
+
     # `python -m <module>` typically displays the command as __main__.py
-    if '__main__.py' in sys.argv[0]:
-        sys.argv[0] = '%s -m %s' % (sys.executable, module)
+    if "__main__.py" in sys.argv[0]:
+        sys.argv[0] = "%s -m %s" % (sys.executable, module)
     main()
diff --git a/aslprep/_warnings.py b/aslprep/_warnings.py
@@ -1,6 +1,6 @@
 """Manipulate Python warnings."""
-import warnings
 import logging
+import warnings
 
 _wlog = logging.getLogger("py.warnings")
 _wlog.addHandler(logging.NullHandler())
@@ -12,9 +12,7 @@ def _warn(message, category=None, stacklevel=1, source=None):
         category = type(category).__name__
         category = category.replace("type", "WARNING")
 
-    logging.getLogger("py.warnings").warning(
-        f"{category or 'WARNING'}: {message}"
-    )
+    logging.getLogger("py.warnings").warning(f"{category or 'WARNING'}: {message}")
 
 
 def _showwarning(message, category, filename, lineno, file=None, line=None):

diff --git a/aslprep/cli/aggregate_qc.py b/aslprep/cli/aggregate_qc.py
@@ -3,19 +3,20 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """aggregate qc of all the subjects"""
 import os
-import pandas as pd
 from pathlib import Path
 
+import pandas as pd
+
+
 def get_parser():
     """Build parser object"""
-    from argparse import ArgumentParser
-    from argparse import RawTextHelpFormatter
+    from argparse import ArgumentParser, RawTextHelpFormatter
 
     parser = ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
 
-    parser.add_argument('aslprep_dir', action='store', type=Path, help='aslprep output dir')
+    parser.add_argument("aslprep_dir", action="store", type=Path, help="aslprep output dir")
 
-    parser.add_argument('output_prefix', action='store', type=str, help='output prefix for group')
+    parser.add_argument("output_prefix", action="store", type=str, help="output prefix for group")
     return parser
 
 
@@ -25,21 +26,23 @@ def main():
     opts = get_parser().parse_args()
 
     allsubj_dir = os.path.abspath(opts.aslprep_dir)
-    outputfile  = os.getcwd() + '/' + str(opts.output_prefix) + '_allsubjects_qc.csv'
+    outputfile = os.getcwd() + "/" + str(opts.output_prefix) + "_allsubjects_qc.csv"
 
-    qclist=[]
+    qclist = []
     for r, d, f in os.walk(allsubj_dir):
         for filex in f:
             if filex.endswith("quality_control_cbf.csv"):
-                qclist.append(r+ '/'+ filex)
+                qclist.append(r + "/" + filex)
 
     datax = pd.read_csv(qclist[0])
-    for i in range(1,len(qclist)):
+    for i in range(1, len(qclist)):
         dy = pd.read_csv(qclist[i])
-        datax = pd.concat([datax,dy])
+        datax = pd.concat([datax, dy])
+
+    datax.to_csv(outputfile, index=None)
 
-    datax.to_csv(outputfile,index=None)
 
-if __name__ == '__main__':
-    raise RuntimeError("this should be run after running aslprep;\n"
-                       "it required installation of  aslprep")
+if __name__ == "__main__":
+    raise RuntimeError(
+        "this should be run after running aslprep;\n" "it required installation of  aslprep"
+    )
diff --git a/aslprep/cli/parser.py b/aslprep/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 packaging.version import Version
+
+    from ..niworkflows.utils.spaces import OutputReferencesAction, Reference
     from .version import check_latest, is_flagged
-    from ..niworkflows.utils.spaces import Reference, OutputReferencesAction
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""
@@ -38,18 +38,18 @@ def _min_one(value, parser):
         return value
 
     def _to_gb(value):
-        scale = {"G": 1, "T": 10 ** 3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
+        scale = {"G": 1, "T": 10**3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
         digits = "".join([c for c in value if c.isdigit()])
-        units = value[len(digits):] or "M"
+        units = value[len(digits) :] or "M"
         return int(digits) * scale[units[0]]
 
     def _drop_sub(value):
         return value[4:] if value.startswith("sub-") else value
 
     def _filter_pybids_none_any(dct):
         from ..pybids import layout
-        return {k: layout.Query.ANY if v == "*" else v
-                for k, v in dct.items()}
+
+        return {k: layout.Query.ANY if v == "*" else v for k, v in dct.items()}
 
     def _bids_filter(value):
         from json import loads
@@ -59,14 +59,10 @@ def _bids_filter(value):
 
     verstr = f"ASLPrep v{config.environment.version}"
     currentv = Version(config.environment.version)
-    is_release = not any(
-        (currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease)
-    )
+    is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
 
     parser = ArgumentParser(
-        description="ASLPrep: ASL PREProcessing workflows v{}".format(
-            config.environment.version
-        ),
+        description="ASLPrep: ASL PREProcessing workflows v{}".format(config.environment.version),
         formatter_class=ArgumentDefaultsHelpFormatter,
     )
     PathExists = partial(_path_exists, parser=parser)
@@ -122,11 +118,11 @@ def _bids_filter(value):
     # Re-enable when option is actually implemented
     # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
     #                     help='select a specific run to be processed')
-    #g_bids.add_argument(
-       # "-t", "--task-id", action="store", help="select a specific task to be processed"
-   #)
+    # g_bids.add_argument(
+    # "-t", "--task-id", action="store", help="select a specific task to be processed"
+    # )
     g_bids.add_argument(
-       "--echo-idx",
+        "--echo-idx",
         action="store",
         type=int,
         help="select a specific echo to be processed in a multiecho series",
@@ -158,7 +154,7 @@ def _bids_filter(value):
         "--nthreads",
         "--n_cpus",
         "--n-cpus",
-        dest='nprocs',
+        dest="nprocs",
         action="store",
         type=PositiveInt,
         help="maximum number of threads across all processes",
@@ -181,8 +177,7 @@ def _bids_filter(value):
     g_perfm.add_argument(
         "--low-mem",
         action="store_true",
-        help="attempt to reduce memory usage (will increase disk usage "
-        "in working directory)",
+        help="attempt to reduce memory usage (will increase disk usage " "in working directory)",
     )
     g_perfm.add_argument(
         "--use-plugin",
@@ -192,9 +187,7 @@ def _bids_filter(value):
         type=IsFile,
         help="nipype plugin configuration file",
     )
-    g_perfm.add_argument(
-        "--anat-only", action="store_true", help="run anatomical workflows only"
-    )
+    g_perfm.add_argument("--anat-only", action="store_true", help="run anatomical workflows only")
     g_perfm.add_argument(
         "--boilerplate_only",
         action="store_true",
@@ -245,7 +238,7 @@ def _bids_filter(value):
 Non-standard spaces imply specific orientations and sampling grids. \
 Important to note, the ``res-*`` modifier does not define the resolution used for \
 the spatial normalization. To generate no ASL outputs, use this option without specifying \
-any spatial references."""
+any spatial references.""",
     )
 
     g_conf.add_argument(
@@ -279,7 +272,6 @@ def _bids_filter(value):
         default=None,
         help="Do not use boundary-based registration (no goodness-of-fit checks)",
     )
-
 
     g_conf.add_argument(
         "--m0_scale",
@@ -303,7 +295,7 @@ def _bids_filter(value):
         default=0,
         type=int,
         help="Number of initial volumes to ignore",
-        )
+    )
     g_conf.add_argument(
         "--smooth_kernel",
         action="store",
@@ -313,18 +305,18 @@ def _bids_filter(value):
     )
 
     g_conf.add_argument(
-         "--scorescrub",
-         action="store_true",
-         default=False,
-         help=" Sudipto algoritms for denoising CBF"
+        "--scorescrub",
+        action="store_true",
+        default=False,
+        help=" Sudipto algoritms for denoising CBF",
     )
 
     g_conf.add_argument(
-         "--basil",
-         action="store_true",
-         default=False,
-         help=" FSL's CBF computation with spatial regularization and \
-          partial volume correction"
+        "--basil",
+        action="store_true",
+        default=False,
+        help=" FSL's CBF computation with spatial regularization and \
+          partial volume correction",
     )
     # Confounds options
 
@@ -440,8 +432,7 @@ def _bids_filter(value):
         "--stop-on-first-crash",
         action="store_true",
         default=False,
-        help="Force stopping on first crash, even if a work directory"
-        " was specified.",
+        help="Force stopping on first crash, even if a work directory" " was specified.",
     )
     g_other.add_argument(
         "--notrack",
@@ -480,14 +471,16 @@ def _bids_filter(value):
 That means some severe flaw was found in it and we strongly
 discourage its usage."""
             % (config.environment.version, _reason),
-            file=sys.stderr,)
+            file=sys.stderr,
+        )
 
     return parser
 
 
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
+
     from ..niworkflows.utils.spaces import Reference, SpatialReferences
 
     parser = _build_parser()
@@ -556,9 +549,7 @@ def parse_args(args=None, namespace=None):
 
         build_log.info(f"Clearing previous aslprep working directory: {work_dir}")
         if not clean_directory(work_dir):
-            build_log.warning(
-                f"Could not clear all contents of working directory: {work_dir}"
-            )
+            build_log.warning(f"Could not clear all contents of working directory: {work_dir}")
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
@@ -584,9 +575,7 @@ def parse_args(args=None, namespace=None):
             "Making sure the input data is BIDS compliant (warnings can be ignored in most "
             "cases)."
         )
-        validate_input_dir(
-            config.environment.exec_env, opts.bids_dir, opts.participant_label
-        )
+        validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
     # Setup directories
     config.execution.log_dir = output_dir / "aslprep" / "logs"