Merge pull request #493 from effigies/maint/modernize

fix: Adopt some more opinionated ruff rules, manual resolutions

Author: effigies

.circleci/version.py

@@ -2,4 +2,5 @@
 
 import sdcflows
 
-print(sdcflows.__version__, end='', file=open('/tmp/.docker-version.txt', 'w'))
+with open('/tmp/.docker-version.txt', 'w') as f:
+    f.write(sdcflows.__version__)

.git-blame-ignore-revs

@@ -1,3 +1,9 @@
+# Thu May 15 11:41:29 2025 -0400 - [email protected] - chore: Manual ruff fixes [ignore-rev]
+e5153dbc00b089144b9f4b415234b27c58b2388b
+# Thu May 15 11:11:38 2025 -0400 - [email protected] - run: ruff check --fix [ignore-rev]
+2bb216b0a12612e31713b34d8ab2ee98fa2cc703
+# Thu May 15 09:34:34 2025 -0400 - [email protected] - run: ruff check --fix [ignore-rev]
+dc3706038661984718da079e24a863842407a837
 # Thu May 15 09:29:29 2025 -0400 - [email protected] - run: ruff format [ignore-rev]
 d97ae316c0bdf71084a0732760ceed5221033fc2
 # Thu May 15 09:26:57 2025 -0400 - [email protected] - run: ruff check --fix [ignore-rev]

.maint/update_authors.py

@@ -130,10 +130,11 @@ def get_git_lines(fname='line-contributors.txt'):
     if not lines:
         raise RuntimeError(
             """\
-Could not find line-contributors from git repository.%s"""
-            % """ \
+Could not find line-contributors from git repository.{}""".format(
+                """ \
 git-line-summary not found, please install git-extras. """
-            * (cmd[0] is None)
+                * (cmd[0] is None)
+            )
         )
     return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
 
@@ -219,7 +220,7 @@ def zenodo(
         elif isinstance(creator['affiliation'], list):
             creator['affiliation'] = creator['affiliation'][0]
 
-    Path(zenodo_file).write_text('%s\n' % json.dumps(zenodo, indent=2, ensure_ascii=False))
+    Path(zenodo_file).write_text(f'{json.dumps(zenodo, indent=2, ensure_ascii=False)}\n')
 
 
 @cli.command()
@@ -266,10 +267,8 @@ def _aslist(value):
 
     aff_indexes = [
         ', '.join(
-            [
-                '%d' % (affiliations.index(a) + 1)
-                for a in _aslist(author.get('affiliation', 'Unaffiliated'))
-            ]
+            str(affiliations.index(a) + 1)
+            for a in _aslist(author.get('affiliation', 'Unaffiliated'))
         )
         for author in hits
     ]
@@ -280,15 +279,13 @@ def _aslist(value):
             file=sys.stderr,
         )
 
-    print('Authors (%d):' % len(hits))
-    print(
-        '%s.'
-        % '; '.join(['%s \\ :sup:`%s`\\ ' % (i['name'], idx) for i, idx in zip(hits, aff_indexes)])
-    )
+    print(f'Authors ({len(hits)}):')
+    print('; '.join([rf'{i["name"]} \ :sup:`{idx}`\ ' for i, idx in zip(hits, aff_indexes)]) + '.')
 
     print(
-        '\n\nAffiliations:\n%s'
-        % '\n'.join(['{0: >2}. {1}'.format(i + 1, a) for i, a in enumerate(affiliations)])
+        '\n\nAffiliations:\n{}'.format(
+            '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        )
     )
 
 

.pre-commit-config.yaml

@@ -12,12 +12,9 @@ repos:
       - id: end-of-file-fixer
       - id: fix-byte-order-marker
       - id: trailing-whitespace
-  # Enable when no significant PRs are in progress
-  # - repo: https://github.com/psf/black
-  #   rev: 23.1.0
-  #   hooks:
-  #     - id: black
-  # - repo: https://github.com/pycqa/isort
-  #   rev: 5.12.0
-  #   hooks:
-  #     - id: isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.5
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

docs/tools/apigen.py

@@ -27,7 +27,7 @@
 DEBUG = True
 
 
-class ApiDocWriter(object):
+class ApiDocWriter:
     """Class for automatic detection and parsing of API docs
     to Sphinx-parsable reST format"""
 
@@ -185,9 +185,8 @@ def _parse_module(self, uri):
             # nothing that we could handle here.
             return ([], [])
 
-        f = open(filename, 'rt')
-        functions, classes = self._parse_lines(f)
-        f.close()
+        with open(filename) as f:
+            functions, classes = self._parse_lines(f)
         return functions, classes
 
     def _parse_module_with_import(self, uri):
@@ -217,14 +216,10 @@ def _parse_module_with_import(self, uri):
                 continue
             obj = mod.__dict__[obj_str]
             # Check if function / class defined in module
-            if not self.other_defines and not getmodule(obj) == mod:
+            if not self.other_defines and getmodule(obj) != mod:
                 continue
             # figure out if obj is a function or class
-            if (
-                hasattr(obj, 'func_name')
-                or isinstance(obj, BuiltinFunctionType)
-                or isinstance(obj, FunctionType)
-            ):
+            if hasattr(obj, 'func_name') or isinstance(obj, (BuiltinFunctionType, FunctionType)):
                 functions.append(obj_str)
             else:
                 try:
@@ -278,7 +273,7 @@ def generate_api_doc(self, uri):
 
         # Make a shorter version of the uri that omits the package name for
         # titles
-        uri_short = re.sub(r'^%s\.' % self.package_name, '', uri)
+        uri_short = re.sub(rf'^{self.package_name}\.', '', uri)
 
         head = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n'
         body = ''
@@ -345,20 +340,12 @@ def _survives_exclude(self, matchstr, match_type):
         elif match_type == 'package':
             patterns = self.package_skip_patterns
         else:
-            raise ValueError('Cannot interpret match type "%s"' % match_type)
+            raise ValueError(f'Cannot interpret match type "{match_type}"')
         # Match to URI without package name
         L = len(self.package_name)
         if matchstr[:L] == self.package_name:
             matchstr = matchstr[L:]
-        for pat in patterns:
-            try:
-                pat.search
-            except AttributeError:
-                pat = re.compile(pat)
-            if pat.search(matchstr):
-                return False
-
-        return True
+        return not any(re.search(pat, matchstr) for pat in patterns)
 
     def discover_modules(self):
         r"""Return module sequence discovered from ``self.package_name``
@@ -426,7 +413,7 @@ def write_modules_api(self, modules, outdir):
         written_modules = []
 
         for ulm, mods in module_by_ulm.items():
-            print('Generating docs for %s:' % ulm)
+            print(f'Generating docs for {ulm}:')
             document_head = []
             document_body = []
 
@@ -438,11 +425,8 @@ def write_modules_api(self, modules, outdir):
                 document_body.append(body)
 
             out_module = ulm + self.rst_extension
-            outfile = os.path.join(outdir, out_module)
-            fileobj = open(outfile, 'wt')
-
-            fileobj.writelines(document_head + document_body)
-            fileobj.close()
+            with open(os.path.join(outdir, out_module), 'w') as fileobj:
+                fileobj.writelines(document_head + document_body)
             written_modules.append(out_module)
 
         self.written_modules = written_modules
@@ -497,14 +481,13 @@ def write_index(self, outdir, froot='gen', relative_to=None):
             relpath = (outdir + os.path.sep).replace(relative_to + os.path.sep, '')
         else:
             relpath = outdir
-        idx = open(path, 'wt')
-        w = idx.write
-        w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
-
-        title = 'API Reference'
-        w(title + '\n')
-        w('=' * len(title) + '\n\n')
-        w('.. toctree::\n\n')
-        for f in self.written_modules:
-            w('   %s\n' % os.path.join(relpath, f))
-        idx.close()
+        with open(path, 'w') as idx:
+            w = idx.write
+            w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
+
+            title = 'API Reference'
+            w(title + '\n')
+            w('=' * len(title) + '\n\n')
+            w('.. toctree::\n\n')
+            for f in self.written_modules:
+                w(f'   {os.path.join(relpath, f)}\n')

docs/tools/buildmodref.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 """Script to auto-generate API docs."""
 
-from __future__ import division, print_function
-
 # stdlib imports
 import sys
 
@@ -16,7 +14,7 @@
 
 
 def abort(error):
-    print('*WARNING* API documentation not generated: %s' % error)
+    print(f'*WARNING* API documentation not generated: {error}')
     exit()
 
 
@@ -43,13 +41,13 @@ def writeapi(package, outdir, source_version, other_defines=True):
     docwriter = ApiDocWriter(package, rst_extension='.rst', other_defines=other_defines)
 
     docwriter.package_skip_patterns += [
-        r'\.%s$' % package,
+        rf'\.{package}$',
         r'.*test.*$',
         r'\.version.*$',
     ]
     docwriter.write_api_docs(outdir)
     docwriter.write_index(outdir, 'index', relative_to=outdir)
-    print('%d files written' % len(docwriter.written_modules))
+    print(f'{len(docwriter.written_modules)} files written')
 
 
 if __name__ == '__main__':

pyproject.toml

@@ -179,11 +179,15 @@ ignore = [
 line-length = 99
 
 [tool.ruff.lint]
-select = [
+extend-select = [
   "F",
   "E",
+  "C4",
   "W",
+  "B",
   "I",
+  "SIM",
+  "UP",
 ]
 ignore = [
   "E203",
@@ -198,6 +202,9 @@ inline-quotes = "single"
 [tool.ruff.lint.extend-per-file-ignores]
 "*/__init__.py" = ["F401"]
 "docs/conf.py" = ["E265"]
+"*/test_*.py" = [
+  "B018",  # Unassigned expressions are fine
+]
 
 [tool.ruff.format]
 quote-style = "single"

sdcflows/cli/main.py

@@ -25,7 +25,6 @@
 
 def main(argv=None):
     """Entry point for SDCFlows' CLI."""
-    import atexit
     import gc
     import os
     import sys
@@ -34,8 +33,6 @@ def main(argv=None):
     from sdcflows import config
     from sdcflows.cli.parser import parse_args
 
-    atexit.register(config.restore_env)
-
     # Run parser
     parse_args(argv)
 

sdcflows/cli/parser.py

@@ -22,7 +22,6 @@
 #
 """Standalone command line executable for estimation of fieldmaps."""
 
-import re
 from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
 from functools import partial
 from pathlib import Path
@@ -46,9 +45,7 @@ def _parse_participant_labels(value):
     ['s060']
 
     """
-    return sorted(
-        set(re.sub(r'^sub-', '', item.strip()) for item in re.split(r'\s+', f'{value}'.strip()))
-    )
+    return sorted({item.removeprefix('sub-') for item in value.split()})
 
 
 def _parser():
@@ -301,12 +298,10 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
+        suggested_path = bids_dir / 'derivatives' / f'sdcflows_{version.split("+")[0]}'
         parser.error(
             'The selected output folder is the same as the input BIDS folder. '
-            'Please modify the output path (suggestion: %s).'
-            % bids_dir
-            / 'derivatives'
-            / ('sdcflows_%s' % version.split('+')[0])
+            f'Please modify the output path (suggestion: {suggested_path}).'
         )
 
     if bids_dir in work_dir.parents:

sdcflows/config.py

@@ -124,6 +124,8 @@
     from importlib_metadata import version as get_version
 
 # Ignore annoying warnings
+import contextlib
+
 from sdcflows import __version__
 from sdcflows._warnings import logging
 
@@ -200,7 +202,7 @@
 _memory_gb = None
 try:
     if 'linux' in sys.platform:
-        with open('/proc/meminfo', 'r') as f_in:
+        with open('/proc/meminfo') as f_in:
             _meminfo_lines = f_in.readlines()
             _mem_total_line = [line for line in _meminfo_lines if 'MemTotal' in line][0]
             _mem_total = float(_mem_total_line.split()[1])
@@ -220,7 +222,7 @@
 class _Config:
     """An abstract class forbidding instantiation."""
 
-    _paths = tuple()
+    _paths = ()
 
     def __init__(self):
         """Avert instantiation."""
@@ -239,10 +241,8 @@ def load(cls, settings, init=True):
                 setattr(cls, k, v)
 
         if init:
-            try:
+            with contextlib.suppress(AttributeError):
                 cls.init()
-            except AttributeError:
-                pass
 
     @classmethod
     def get(cls):
@@ -647,13 +647,3 @@ def _process_initializer(config_file: Path):
 
     # Set the maximal number of threads per process
     os.environ['OMP_NUM_THREADS'] = f'{config.nipype.omp_nthreads}'
-
-
-def restore_env():
-    """Restore the original environment."""
-
-    for k in os.environ.keys():
-        del os.environ[k]
-
-    for k, v in environment._pre_sdcflows.items():
-        os.environ[k] = v