sdcflows 2.13.0__tar.gz → 2.13.2__tar.gz

sdcflows-2.13.2/.circleci/version.py

@@ -0,0 +1,5 @@
+"""Get sdcflows version."""
+
+import sdcflows
+
+print(sdcflows.__version__, end='', file=open('/tmp/.docker-version.txt', 'w'))

sdcflows-2.13.2/.git-blame-ignore-revs

@@ -0,0 +1,6 @@
+# Thu May 15 09:29:29 2025 -0400 - markiewicz@stanford.edu - run: ruff format [ignore-rev]
+d97ae316c0bdf71084a0732760ceed5221033fc2
+# Thu May 15 09:26:57 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
+cacd409cce71f2e530ad1bd1e8b79f397cab81d4
+# Thu May 15 09:22:00 2025 -0400 - markiewicz@stanford.edu - run: pre-commit run --all [ignore-rev]
+2b40bee0d6b2c88628760a8b1513851a439411e8

{sdcflows-2.13.0 → sdcflows-2.13.2}/.github/workflows/docs-build-update.yml

@@ -94,7 +94,7 @@ jobs:
     - name: Push "master" docs to gh-pages after a push to master (typically, a PR merge).
       if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'
       run: |
-        if [[ "${CURBRANCH}" != "master" -a "${CURBRANCH}" != "main" ]]; then
+        if [[ "${CURBRANCH}" != "master" && "${CURBRANCH}" != "main" ]]; then
             echo "$CURBRANCH is not the default development branch"
             exit 1
         fi

{sdcflows-2.13.0 → sdcflows-2.13.2}/.github/workflows/validate.yml

@@ -17,11 +17,12 @@ permissions:
   contents: read
 
 jobs:
-  flake8:
+  style:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - run: pipx run flake8-pyproject sdcflows/
+    - run: pipx run ruff check sdcflows/
+    - run: pipx run ruff format --diff sdcflows/
 
   # codespell:
   #   runs-on: ubuntu-latest

{sdcflows-2.13.0 → sdcflows-2.13.2}/.maint/update_authors.py

@@ -8,9 +8,11 @@
 # ]
 # ///
 """Update and sort the creators list of the zenodo record."""
+
+import json
 import sys
 from pathlib import Path
-import json
+
 import click
 from fuzzywuzzy import fuzz, process
 
@@ -43,21 +45,18 @@ 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]
+        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})
 
     return retval
@@ -66,21 +65,15 @@ def read_md_table(md_text):
 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 = []
     for ele in git_lines:
-        matches = process.extract(
-            ele, first_last, scorer=fuzz.token_sort_ratio, limit=2
-        )
+        matches = process.extract(ele, first_last, scorer=fuzz.token_sort_ratio, limit=2)
         # matches is a list [('First match', % Match), ('Second match', % Match)]
         if matches[0][1] > 80:
             val = sorted_authors[first_last.index(matches[0][0])]
@@ -93,7 +86,7 @@ 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)]
@@ -101,7 +94,7 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
 
     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)))
 
@@ -113,7 +106,7 @@ 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
@@ -122,17 +115,17 @@ 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()
 
-    cmd = [shutil.which("git-line-summary")]
+    cmd = [shutil.which('git-line-summary')]
     if cmd == [None]:
-        cmd = [shutil.which("git-summary"), "--line"]
+        cmd = [shutil.which('git-summary'), '--line']
     if not lines and cmd[0]:
-        print(f"Running {' '.join(cmd)!r} on repo")
+        print(f'Running {" ".join(cmd)!r} on repo')
         lines = sp.check_output(cmd).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(
@@ -142,15 +135,15 @@ Could not find line-contributors from git repository.%s"""
 git-line-summary not found, please install git-extras. """
             * (cmd[0] 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()
-        if not i["name"]:
-            i["name"] = i.get("handle", "<Unknown Name>")
+        i['name'] = (f'{i.pop("name", "")} {i.pop("lastname", "")}').strip()
+        if not i['name']:
+            i['name'] = i.get('handle', '<Unknown Name>')
         retval.append(i)
     return retval
 
@@ -162,12 +155,13 @@ 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("-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('-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'
+)
+@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,
@@ -188,65 +182,53 @@ def zenodo(
     )
 
     zen_contributors, miss_contributors = sort_contributors(
-        _namelast(read_md_table(Path(contributors).read_text())),
-        data,
-        exclude=former
+        _namelast(read_md_table(Path(contributors).read_text())), data, exclude=former
     )
 
     zen_pi = _namelast(reversed(read_md_table(Path(pi).read_text())))
 
-    zenodo["creators"] = zen_creators
-    zenodo["contributors"] = zen_contributors + [
-        pi for pi in zen_pi if pi not in zen_contributors
-    ]
-    creator_names = {
-        c["name"] for c in zenodo["creators"]
-        if c["name"] != "<Unknown Name>"
-    }
-
-    zenodo["contributors"] = [
-        c for c in zenodo["contributors"]
-        if c["name"] not in creator_names
-    ]
+    zenodo['creators'] = zen_creators
+    zenodo['contributors'] = zen_contributors + [pi for pi in zen_pi if pi not in zen_contributors]
+    creator_names = {c['name'] for c in zenodo['creators'] if c['name'] != '<Unknown Name>'}
+
+    zenodo['contributors'] = [c for c in zenodo['contributors'] if c['name'] not in creator_names]
 
     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 "affiliation" not in creator:
-            creator["affiliation"] = "Unknown affiliation"
-        elif 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)
-
-        if "affiliation" not in creator:
-            creator["affiliation"] = "Unknown affiliation"
-        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)
-    )
+    for creator in zenodo['creators']:
+        creator.pop('position', None)
+        creator.pop('handle', None)
+        if 'affiliation' not in creator:
+            creator['affiliation'] = 'Unknown affiliation'
+        elif 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)
+
+        if 'affiliation' not in creator:
+            creator['affiliation'] = 'Unknown affiliation'
+        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))
 
 
 @cli.command()
-@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")
-@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('-m', '--maintainers', type=click.Path(exists=True), default='.maint/MAINTAINERS.md')
+@click.option(
+    '-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')
 def publication(
     maintainers,
     contributors,
@@ -254,9 +236,8 @@ def publication(
     former_file,
 ):
     """Generate the list of authors and affiliations for papers."""
-    members = (
-        _namelast(read_md_table(Path(maintainers).read_text()))
-        + _namelast(read_md_table(Path(contributors).read_text()))
+    members = _namelast(read_md_table(Path(maintainers).read_text())) + _namelast(
+        read_md_table(Path(contributors).read_text())
     )
     former_names = _namelast(read_md_table(Path(former_file).read_text()))
 
@@ -267,11 +248,8 @@ def publication(
     )
 
     pi_hits = _namelast(reversed(read_md_table(Path(pi).read_text())))
-    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)):
@@ -281,16 +259,16 @@ def publication(
     # 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
@@ -298,30 +276,22 @@ def publication(
 
     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)
-            ]
-        )
+        '%s.'
+        % '; '.join(['%s \\ :sup:`%s`\\ ' % (i['name'], 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%s'
+        % '\n'.join(['{0: >2}. {1}'.format(i + 1, a) for i, a in enumerate(affiliations)])
     )
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     """ Install entry-point """
     cli()

{sdcflows-2.13.0 → sdcflows-2.13.2}/.pre-commit-config.yaml

@@ -1,10 +1,9 @@
 exclude: ".*/data/.*"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
-      - id: check-docstring-first
       - id: check-merge-conflict
       - id: check-json
       - id: check-toml

{sdcflows-2.13.0 → sdcflows-2.13.2}/CHANGES.rst

@@ -1,3 +1,21 @@
+2.13.2 (July 28, 2025)
+======================
+Patch release in the 2.13.x series.
+
+This includes a fix for cases where a scan contributes to multiple ``B0FieldIdentifier``\s.
+
+* [FIX] Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators (#497)
+
+
+2.13.1 (June 12, 2025)
+======================
+Patch release in the 2.13.x series.
+
+This includes a fix to ``init_fmap_preproc_wf`` node naming.
+
+* FIX: Use the sanitized id when naming through nipype (#495)
+
+
 2.13.0 (May 15, 2025)
 =====================
 Feature release in the 2.13.x series.

{sdcflows-2.13.0 → sdcflows-2.13.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sdcflows
-Version: 2.13.0
+Version: 2.13.2
 Summary: Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes.
 Project-URL: Documentation, https://www.nipreps.org/sdcflows
 Project-URL: Home, https://github.com/nipreps/sdcflows
@@ -35,14 +35,11 @@ Requires-Dist: templateflow>=23.1
 Requires-Dist: toml>=0.10
 Provides-Extra: all
 Requires-Dist: attrs>=20.1.0; extra == 'all'
-Requires-Dist: black; extra == 'all'
 Requires-Dist: coverage[toml]>=5.2.1; extra == 'all'
-Requires-Dist: flake8-pyproject; extra == 'all'
 Requires-Dist: furo; extra == 'all'
 Requires-Dist: importlib-resources; extra == 'all'
 Requires-Dist: ipykernel; extra == 'all'
 Requires-Dist: ipython; extra == 'all'
-Requires-Dist: isort; extra == 'all'
 Requires-Dist: nbsphinx; extra == 'all'
 Requires-Dist: pandoc; extra == 'all'
 Requires-Dist: pre-commit; extra == 'all'
@@ -53,14 +50,13 @@ Requires-Dist: pytest-cov>=2.11; extra == 'all'
 Requires-Dist: pytest-env; extra == 'all'
 Requires-Dist: pytest-xdist>=2.5; extra == 'all'
 Requires-Dist: pytest>=6; extra == 'all'
+Requires-Dist: ruff; extra == 'all'
 Requires-Dist: sphinx-argparse; extra == 'all'
 Requires-Dist: sphinx>=7.2.2; extra == 'all'
 Requires-Dist: sphinxcontrib-apidoc; extra == 'all'
 Provides-Extra: dev
-Requires-Dist: black; extra == 'dev'
-Requires-Dist: flake8-pyproject; extra == 'dev'
-Requires-Dist: isort; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
 Provides-Extra: doc
 Requires-Dist: attrs>=20.1.0; extra == 'doc'
 Requires-Dist: furo; extra == 'doc'