Bring up to date with fMRIPrep 24.1.1

.circleci/get_data.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python3
 """Download test data."""
+
 import sys
 
 from aslprep.tests.utils import download_test_data
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     data_dir = sys.argv[1]
     dset = sys.argv[2]
     download_test_data(dset, data_dir)

.codespellrc

@@ -3,4 +3,4 @@ skip = .git,*.pdf,*.svg,*.html,dataset_description.json
 # te - TE
 # Weill - name
 # reson - Reson. abbreviation in citation
-ignore-words-list = te,weill,reson
+ignore-words-list = te,weill,reson,ND

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Lint code
+name: Contribution checks
 
 on:
   push:
@@ -12,26 +12,27 @@ defaults:
   run:
     shell: bash
 
-jobs:
-  stable:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.10']
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
+jobs:
+  style:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        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-pyproject flake8-unused-arguments \
-          flake8-use-fstring pep8-naming
-      - name: Check aslprep
-        run: python -m flake8 aslprep
+      - run: pipx run ruff check .
+      - run: pipx run ruff format --diff .
+
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.maint/update_authors.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Update and sort the creators list of the zenodo record."""
+
 import json
 import sys
 from pathlib import Path
@@ -36,30 +37,30 @@ def read_md_table(md_text):
     keys = None
     retval = []
     for line in md_text.splitlines():
-        if line.strip().startswith("| --- |"):
-            keys = (k.replace("*", "").strip() for k in prev.split("|"))
+        if line.strip().startswith('| --- |'):
+            keys = (k.replace('*', '').strip() for k in prev.split('|'))
             keys = [k.lower() for k in keys if k]
             continue
         elif not keys:
             prev = line
             continue
 
-        if not line or not line.strip().startswith("|"):
+        if not line or not line.strip().startswith('|'):
             break
 
-        values = [v.strip() or None for v in line.split("|")][1:-1]
-        retval.append({k: v for k, v in zip(keys, values) if v})
+        values = [v.strip() or None for v in line.split('|')][1:-1]
+        retval.append({k: v for k, v in zip(keys, values, strict=False) if v})
 
     return retval
 
 
 def sort_contributors(entries, git_lines, exclude=None, last=None):
     """Return a list of author dictionaries, ordered by contribution."""
     last = last or []
-    sorted_authors = sorted(entries, key=lambda i: i["name"])
+    sorted_authors = sorted(entries, key=lambda i: i['name'])
 
-    first_last = [" ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors]
-    first_last_excl = [" ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []]
+    first_last = [' '.join(val['name'].split(',')[::-1]).strip() for val in sorted_authors]
+    first_last_excl = [' '.join(val['name'].split(',')[::-1]).strip() for val in exclude or []]
 
     unmatched = []
     author_matches = []
@@ -77,15 +78,15 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
         if val not in author_matches:
             author_matches.append(val)
 
-    names = {" ".join(val["name"].split(",")[::-1]).strip() for val in author_matches}
+    names = {' '.join(val['name'].split(',')[::-1]).strip() for val in author_matches}
     for missing_name in first_last:
         if missing_name not in names:
             missing = sorted_authors[first_last.index(missing_name)]
             author_matches.append(missing)
 
     position_matches = []
     for i, item in enumerate(author_matches):
-        pos = item.pop("position", None)
+        pos = item.pop('position', None)
         if pos is not None:
             position_matches.append((i, int(pos)))
 
@@ -97,7 +98,7 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
     return author_matches, unmatched
 
 
-def get_git_lines(fname="line-contributors.txt"):
+def get_git_lines(fname='line-contributors.txt'):
     """Run git-line-summary."""
     import shutil
     import subprocess as sp
@@ -106,31 +107,32 @@ def get_git_lines(fname="line-contributors.txt"):
 
     lines = []
     if contrib_file.exists():
-        print("WARNING: Reusing existing line-contributors.txt file.", file=sys.stderr)
+        print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr)
         lines = contrib_file.read_text().splitlines()
 
-    git_line_summary_path = shutil.which("git-line-summary")
+    git_line_summary_path = shutil.which('git-line-summary')
     if not lines and git_line_summary_path:
-        print("Running git-line-summary on repo")
+        print('Running git-line-summary on repo')
         lines = sp.check_output([git_line_summary_path]).decode().splitlines()
-        lines = [l for l in lines if "Not Committed Yet" not in l]
-        contrib_file.write_text("\n".join(lines))
+        lines = [line for line in lines if 'Not Committed Yet' not in line]
+        contrib_file.write_text('\n'.join(lines))
 
     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. """
-            * (git_line_summary_path is None)
+                * (git_line_summary_path is None)
+            )
         )
-    return [" ".join(line.strip().split()[1:-1]) for line in lines if "%" in line]
+    return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
 
 
 def _namelast(inlist):
     retval = []
     for i in inlist:
-        i["name"] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
+        i['name'] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
         retval.append(i)
     return retval
 
@@ -142,13 +144,13 @@ def cli():
 
 
 @cli.command()
-@click.option("-z", "--zenodo-file", type=click.Path(exists=True), default=".zenodo.json")
-@click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
+@click.option('-z', '--zenodo-file', type=click.Path(exists=True), default='.zenodo.json')
+@click.option('-m', '--maintainers', type=click.Path(exists=True), default='.maint/MAINTAINERS.md')
 @click.option(
-    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+    '-c', '--contributors', type=click.Path(exists=True), default='.maint/CONTRIBUTORS.md'
 )
-@click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
-@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
+@click.option('--pi', type=click.Path(exists=True), default='.maint/PIs.md')
+@click.option('-f', '--former-file', type=click.Path(exists=True), default='.maint/FORMER.md')
 def zenodo(
     zenodo_file,
     maintainers,
@@ -175,45 +177,45 @@ def zenodo(
     zen_pi = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
+            key=lambda v: (int(v.get('position', -1)), v.get('lastname')),
         )
     )
 
-    zenodo["creators"] = zen_creators
-    zenodo["contributors"] = zen_contributors + zen_pi
+    zenodo['creators'] = zen_creators
+    zenodo['contributors'] = zen_contributors + zen_pi
 
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
     # Remove position
-    for creator in zenodo["creators"]:
-        creator.pop("position", None)
-        creator.pop("handle", None)
-        if isinstance(creator["affiliation"], list):
-            creator["affiliation"] = creator["affiliation"][0]
+    for creator in zenodo['creators']:
+        creator.pop('position', None)
+        creator.pop('handle', None)
+        if isinstance(creator['affiliation'], list):
+            creator['affiliation'] = creator['affiliation'][0]
 
-    for creator in zenodo["contributors"]:
-        creator.pop("handle", None)
-        creator["type"] = "Researcher"
-        creator.pop("position", None)
+    for creator in zenodo['contributors']:
+        creator.pop('handle', None)
+        creator['type'] = 'Researcher'
+        creator.pop('position', None)
 
-        if isinstance(creator["affiliation"], list):
-            creator["affiliation"] = creator["affiliation"][0]
+        if isinstance(creator['affiliation'], list):
+            creator['affiliation'] = creator['affiliation'][0]
 
-    Path(zenodo_file).write_text("%s\n" % json.dumps(zenodo, indent=2))
+    Path(zenodo_file).write_text(f'{json.dumps(zenodo, indent=2)}\n')
 
 
 @cli.command()
-@click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
+@click.option('-m', '--maintainers', type=click.Path(exists=True), default='.maint/MAINTAINERS.md')
 @click.option(
-    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+    '-c', '--contributors', type=click.Path(exists=True), default='.maint/CONTRIBUTORS.md'
 )
-@click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
-@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
+@click.option('--pi', type=click.Path(exists=True), default='.maint/PIs.md')
+@click.option('-f', '--former-file', type=click.Path(exists=True), default='.maint/FORMER.md')
 def publication(
     maintainers,
     contributors,
@@ -234,54 +236,61 @@ def publication(
     pi_hits = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
+            key=lambda v: (int(v.get('position', -1)), v.get('lastname')),
         )
     )
 
-    pi_names = [pi["name"] for pi in pi_hits]
-    hits = [hit for hit in hits if hit["name"] not in pi_names] + pi_hits
+    pi_names = [pi['name'] for pi in pi_hits]
+    hits = [hit for hit in hits if hit['name'] not in pi_names] + pi_hits
 
     def _aslist(value):
-        if isinstance(value, (list, tuple)):
+        if isinstance(value, list | tuple):
             return value
         return [value]
 
     # Remove position
     affiliations = []
     for item in hits:
-        item.pop("position", None)
-        for a in _aslist(item.get("affiliation", "Unaffiliated")):
+        item.pop('position', None)
+        for a in _aslist(item.get('affiliation', 'Unaffiliated')):
             if a not in affiliations:
                 affiliations.append(a)
 
     aff_indexes = [
-        ", ".join(
+        ', '.join(
             [
-                "%d" % (affiliations.index(a) + 1)
-                for a in _aslist(author.get("affiliation", "Unaffiliated"))
+                '%d' % (affiliations.index(a) + 1)
+                for a in _aslist(author.get('affiliation', 'Unaffiliated'))
             ]
         )
         for author in hits
     ]
 
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
-    print("Authors (%d):" % len(hits))
+    print('Authors (%d):' % len(hits))
     print(
-        "%s."
-        % "; ".join(["%s \\ :sup:`%s`\\ " % (i["name"], idx) for i, idx in zip(hits, aff_indexes)])
+        '{}.'.format(
+            '; '.join(
+                [
+                    rf'{i["name"]} \ :sup:`{idx}`\ '
+                    for i, idx in zip(hits, aff_indexes, strict=False)
+                ]
+            )
+        )
     )
 
     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)])
+        )
     )
 
 
-if __name__ == "__main__":
-    """Install entry-point"""
+if __name__ == '__main__':
+    """ Install entry-point """
     cli()

.pre-commit-config.yaml

@@ -1,16 +1,21 @@
+exclude: ".*/data/.*"
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 23.1.0
+      - id: trailing-whitespace
+        exclude: '.*\.svg'
+      - id: end-of-file-fixer
+        exclude: '.*\.svg'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
     hooks:
-    -   id: black
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+      - id: ruff
+        args: [ --select, ISC001, --fix ]

CHANGES.md

@@ -273,6 +273,6 @@ Bids validation
 
 ENH - Add  GE SCAN processing with deltam or cbf
 
-ENH - supressed freesurfer processing, FSL FLIRT with BBR for registration
+ENH - suppressed freesurfer processing, FSL FLIRT with BBR for registration
 
 ENH - basil and scorescrub as options, cbf computation is only default