STY: Lint and style check full repository

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
+# 2024-02-05 - [email protected] - STY: ruff --fix + 1 ignore [git-blame-ignore-rev]
+e7dc59fbc7df88dfabbff154f4cc3d24721b6b4f
 # 2024-01-16 - [email protected] - STY: ruff --fix --unsafe-fixes (with cleanup) [git-blame-ignore-rev]
 66734bd0164d1dae3cf299fa9d9d682c22eeda66
 # 2024-01-16 - [email protected] - STY: ruff format and ruff --fix [git-blame-ignore-rev]

.github/workflows/contrib.yml

@@ -26,8 +26,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - run: pipx run ruff fmriprep
-      - run: pipx run ruff format --diff fmriprep
+      - run: pipx run ruff .
+      - run: pipx run ruff format --diff .
 
   codespell:
     name: Check for spelling errors

fmriprep/cli/workflow.py

@@ -51,26 +51,26 @@
     fmriprep_dir = config.execution.fmriprep_dir
     version = config.environment.version
 
     retval['return_code'] = 1
     retval['workflow'] = None
 
     banner = [f'Running fMRIPrep version {version}']
     notice_path = data.load.readable('NOTICE')
     if notice_path.exists():
         banner[0] += '\n'
         banner += [f"License NOTICE {'#' * 50}"]
         banner += [f'fMRIPrep {version}']
         banner += notice_path.read_text().splitlines(keepends=False)[1:]
         banner += ['#' * len(banner[1])]
     build_log.log(25, f"\n{' ' * 9}".join(banner))
 
     # warn if older results exist: check for dataset_description.json in output folder
     msg = check_pipeline_version('fMRIPrep', version, fmriprep_dir / 'dataset_description.json')
     if msg is not None:
         build_log.warning(msg)
 
     # Please note this is the input folder's dataset_description.json
     dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
     if dset_desc_path.exists():
         from hashlib import sha256
 
@@ -84,7 +84,7 @@
 
     # Called with reports only
     if config.execution.reports_only:
         build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
         session_list = (
             config.execution.bids_filters.get('bold', {}).get('session')
             if config.execution.bids_filters
@@ -103,7 +103,7 @@
                 ', '.join(failed_reports),
             )
 
         retval['return_code'] = len(failed_reports)
         return retval
 
     # Build main workflow
@@ -116,14 +116,14 @@
     ]
 
     if config.execution.derivatives:
         init_msg += [f'Searching for derivatives: {config.execution.derivatives}.']
 
     if config.execution.fs_subjects_dir:
         init_msg += [f"Pre-run FreeSurfer's SUBJECTS_DIR: {config.execution.fs_subjects_dir}."]
 
     build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
 
     retval['workflow'] = init_fmriprep_wf()
 
     # Check for FS license after building the workflow
     if not check_valid_fs_license():
@@ -144,17 +144,17 @@
 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \
 (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html"""
             )
         retval['return_code'] = 126  # 126 == Command invoked cannot execute.
         return retval
 
     # Check workflow for missing commands
     missing = check_deps(retval['workflow'])
     if missing:
         build_log.critical(
             'Cannot run fMRIPrep. Missing dependencies:%s',
             '\n\t* '.join([''] + [f'{cmd} (Interface: {iface})' for iface, cmd in missing]),
         )
         retval['return_code'] = 127  # 127 == command not found.
         return retval
 
     config.to_filename(config_file)
@@ -162,7 +162,7 @@
         'fMRIPrep workflow graph with %d nodes built successfully.',
         len(retval['workflow']._get_all_nodes()),
     )
     retval['return_code'] = 0
     return retval
 
 
@@ -171,7 +171,7 @@
     from .. import config
 
     config.load(config_file)
     logs_path = config.execution.fmriprep_dir / 'logs'
     boilerplate = workflow.visit_desc()
     citation_files = {
         ext: logs_path / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
@@ -187,15 +187,15 @@
             except FileNotFoundError:
                 pass
 
     citation_files['md'].write_text(boilerplate)
 
     if not config.execution.md_only_boilerplate and citation_files['md'].exists():
         from subprocess import CalledProcessError, TimeoutExpired, check_call
 
         from .. import data
 
         bib_text = data.load.readable('boilerplate.bib').read_text()
         citation_files['bib'].write_text(
             bib_text.replace('fMRIPrep <version>', f'fMRIPrep {config.environment.version}')
         )
 
@@ -213,11 +213,11 @@
             str(citation_files['html']),
         ]
 
         config.loggers.cli.info('Generating an HTML version of the citation boilerplate...')
         try:
-            check_call(cmd, timeout=10)  # noqa: S603
+            check_call(cmd, timeout=10)
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
             config.loggers.cli.warning('Could not generate CITATION.html file:\n%s', ' '.join(cmd))
 
         # Generate LaTex file resolving citations
         cmd = [
@@ -230,8 +230,8 @@
             '-o',
             str(citation_files['tex']),
         ]
         config.loggers.cli.info('Generating a LaTeX version of the citation boilerplate...')
         try:
-            check_call(cmd, timeout=10)  # noqa: S603
+            check_call(cmd, timeout=10)
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
             config.loggers.cli.warning('Could not generate CITATION.tex file:\n%s', ' '.join(cmd))

fmriprep/utils/bids.py

@@ -56,21 +56,21 @@
             patterns = _patterns
 
     derivs_cache = defaultdict(list, {})
     layout = BIDSLayout(derivatives_dir, config=['bids', 'derivatives'], validate=False)
     derivatives_dir = Path(derivatives_dir)
 
     # search for both boldrefs
     for k, q in spec['baseline'].items():
         query = {**q, **entities}
         item = layout.get(return_type='filename', **query)
         if not item:
             continue
         derivs_cache['%s_boldref' % k] = item[0] if len(item) == 1 else item
 
     for xfm, q in spec['transforms'].items():
         query = {**q, **entities}
         if xfm == 'boldref2fmap':
             query['to'] = fieldmap_id
         item = layout.get(return_type='filename', **q)
         if not item:
             continue
@@ -91,9 +91,9 @@
         '*_mixing.tsv',
         '*_timeseries.tsv',
     )
     ignore_file = Path(deriv_dir) / '.bidsignore'
 
     ignore_file.write_text('\n'.join(bids_ignore) + '\n')
 
 
 def write_derivative_description(bids_dir, deriv_dir):
@@ -228,14 +228,14 @@
         ignored_subs = all_subs.difference(selected_subs)
         if ignored_subs:
             for sub in ignored_subs:
                 validator_config_dict['ignoredFiles'].append('/sub-%s/**' % sub)
     with tempfile.NamedTemporaryFile(mode='w+', suffix='.json') as temp:
         temp.write(json.dumps(validator_config_dict))
         temp.flush()
         try:
-            subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])  # noqa: S603, S607
+            subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])  # noqa: S607
         except FileNotFoundError:
             print('bids-validator does not appear to be installed', file=sys.stderr)
 
 
 def check_pipeline_version(pipeline_name, cvers, data_desc):

pyproject.toml

@@ -176,6 +176,7 @@ extend-select = [
 extend-ignore = [
   "S311",  # We are not using random for cryptographic purposes
   "ISC001",
+  "S603",
 ]
 
 [tool.ruff.lint.flake8-quotes]
@@ -185,6 +186,7 @@ inline-quotes = "single"
 "*/test_*.py" = ["S101"]
 "fmriprep/utils/debug.py" = ["A002", "T100"]
 "docs/conf.py" = ["A001"]
+"docs/sphinxext/github_link.py" = ["BLE001"]
 
 [tool.ruff.format]
 quote-style = "single"

wrapper/pyproject.toml

@@ -63,10 +63,47 @@ universal = true
 # Developer tool configurations
 #
 
+# Disable black
 [tool.black]
+exclude = ".*"
+
+[tool.ruff]
 line-length = 99
-target-version = ['py39']
-skip-string-normalization = true
 
-[tool.isort]
-profile = 'black'
+[tool.ruff.lint]
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "YTT",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
+]
+extend-ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+]
+
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+"fmriprep/utils/debug.py" = ["A002", "T100"]
+"docs/conf.py" = ["A001"]
+
+[tool.ruff.format]
+quote-style = "single"

wrapper/src/fmriprep_docker/__main__.py

@@ -93,7 +93,7 @@ def _run(args, stdout=None, stderr=None):
 
 # De-fang Python 2's input - we don't eval user input
 try:
-    input = raw_input
+    input = raw_input  # noqa: A001
 except NameError:
     pass
 
@@ -116,7 +116,7 @@ def check_docker():
         if e.errno == ENOENT:
             return -1
         raise e
-    if ret.stderr.startswith(b"Cannot connect to the Docker daemon."):
+    if ret.stderr.startswith(b'Cannot connect to the Docker daemon.'):
         return 0
     return 1
 
@@ -154,11 +154,11 @@ def _get_posargs(usage):
             line = targ.lstrip()
             if line.startswith('usage'):
                 continue
-            if line[0].isalnum() or line[0] == "{":
+            if line[0].isalnum() or line[0] == '{':
                 posargs.append(line)
-            elif line[0] == '[' and (line[1].isalnum() or line[1] == "{"):
+            elif line[0] == '[' and (line[1].isalnum() or line[1] == '{'):
                 posargs.append(line)
-        return " ".join(posargs)
+        return ' '.join(posargs)
 
     # Matches all flags with up to two nested square brackets
     # I'm sorry.
@@ -203,7 +203,7 @@ def _get_posargs(usage):
         'w',
     }
 
-    assert overlap == expected_overlap, "Clobbering options: {}".format(
+    assert overlap == expected_overlap, 'Clobbering options: {}'.format(
         ', '.join(overlap - expected_overlap)
     )
 
@@ -263,15 +263,15 @@ class ToDict(argparse.Action):
         def __call__(self, parser, namespace, values, option_string=None):
             d = {}
             for kv in values:
-                k, v = kv.split("=")
+                k, v = kv.split('=')
                 d[k] = os.path.abspath(v)
             setattr(namespace, self.dest, d)
 
     def _is_file(path, parser):
         """Ensure a given path exists and it is a file."""
         path = os.path.abspath(path)
         if not os.path.isfile(path):
-            raise parser.error("Path should point to a file (or symlink of file): <%s>." % path)
+            raise parser.error('Path should point to a file (or symlink of file): <%s>.' % path)
         return path
 
     parser = argparse.ArgumentParser(
@@ -288,7 +288,7 @@ def _is_file(path, parser):
     )
 
     parser.add_argument(
-        '-h', '--help', action='store_true', help="show this help message and exit"
+        '-h', '--help', action='store_true', help='show this help message and exit'
     )
     parser.add_argument(
         '--version', action='store_true', help="show program's version number and exit"
@@ -319,7 +319,7 @@ def _is_file(path, parser):
     )
     g_wrap.add_argument(
         '--output-spaces',
-        nargs="*",
+        nargs='*',
     )
 
     g_wrap.add_argument(
@@ -370,8 +370,8 @@ def _is_file(path, parser):
     )
     g_dev.add_argument(
         '--patch',
-        nargs="+",
-        metavar="PACKAGE=PATH",
+        nargs='+',
+        metavar='PACKAGE=PATH',
         action=ToDict,
         help='Sequence of PACKAGE=PATH specifications to patch a Python package into the '
         'container Python environment.',
@@ -431,7 +431,7 @@ def main():
         if opts.help:
             parser.print_help()
         if check == -1:
-            print("fmriprep: Could not find docker command... Is it installed?")
+            print('fmriprep: Could not find docker command... Is it installed?')
         else:
             print("fmriprep: Make sure you have permission to run 'docker'")
         return 1
@@ -477,7 +477,7 @@ def main():
                 return 0
 
     ret = subprocess.run(
-        ['docker', 'version', '--format', "{{.Server.Version}}"], stdout=subprocess.PIPE
+        ['docker', 'version', '--format', '{{.Server.Version}}'], stdout=subprocess.PIPE
     )
     docker_version = ret.stdout.decode('ascii').strip()
 
@@ -566,7 +566,7 @@ def main():
             if space.split(':')[0] not in (TF_TEMPLATES + NONSTANDARD_REFERENCES):
                 tpl = os.path.basename(space)
                 if not tpl.startswith('tpl-'):
-                    raise RuntimeError("Custom template %s requires a `tpl-` prefix" % tpl)
+                    raise RuntimeError('Custom template %s requires a `tpl-` prefix' % tpl)
                 target = '/home/fmriprep/.cache/templateflow/' + tpl
                 command.extend(['-v', ':'.join((os.path.abspath(space), target, 'ro'))])
                 spaces.append(tpl[4:])
@@ -599,10 +599,10 @@ def main():
         command.extend(main_args)
         command.extend(unknown_args)
 
-    print("RUNNING: " + ' '.join(command))
+    print('RUNNING: ' + ' '.join(command))
     ret = subprocess.run(command)
     if ret.returncode:
-        print("fMRIPrep: Please report errors to {}".format(__bugreports__))
+        print('fMRIPrep: Please report errors to {}'.format(__bugreports__))
     return ret.returncode