Merge pull request #466 from effigies/chore/baipp-upgrade

chore: Unpin build-and-inspect-python-package

Author: effigies

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
+# 2025-02-18 - markiewicz@stanford.edu - sty: ruff format [ignore-rev]
+78f2667f5801fa96cecbfd0aafcddc5723b1d096
 # 2024-07-19 - effigies@gmail.com - chore(ruff): ruff check --fix && ruff format [git-blame-ignore-rev]
 6333f4735f341e556113325c7bc9d0f2e284e418
 # 2024-03-07 - mathiasg@stanford.edu - STY: ruff format smriprep [git-blame-ignore-rev]

.github/workflows/build_test_deploy.yml

@@ -46,14 +46,15 @@ jobs:
         with:
           fetch-depth: 0
           persist-credentials: false
-      # Note that we cannot upgrade this past 2.9 until uv build resolves a bug
-      # or build-and-inspect-python-package lets us select build as a backend
+      # Note that we may need to revert to 2.9 if bugs are found in `uv build`,
+      # unless build-and-inspect-python-package lets us select build as a backend
       #
       # https://github.com/astral-sh/uv/issues/5450
       # or https://github.com/hynek/build-and-inspect-python-package/issues/155
       #
-      # When we do move on, we should leave a comment to fall back in case of future uv build bugs
-      - uses: hynek/build-and-inspect-python-package@v2.8
+      # If 2.9 is required, then we will need to pin to hatchling 1.26.x to avoid
+      # incompatibilities with twine and the package metadata emitted by hatchiling.
+      - uses: hynek/build-and-inspect-python-package@v2
         with:
           upload-name-suffix: -main
           attest-build-provenance-github: ${{ github.event_name != 'pull_request' }}

Makefile

@@ -18,6 +18,6 @@ docker:
 
 
 .git-blame-ignore-revs:
-	git log --grep "\[git-blame-ignore-rev\]" --pretty=format:"# %ad - %ae - %s%n%H" --date short \
+	git log --grep "ignore-rev\]" --pretty=format:"# %ad - %ae - %s%n%H" --date short \
 		> .git-blame-ignore-revs
 	echo >> .git-blame-ignore-revs

pyproject.toml

@@ -1,11 +1,5 @@
 [build-system]
-# Pin hatchling 1.26 to keep metadata 2.3
-# The hynek/build-and-inspect-python-package action is pinned at 2.8,
-# which in turn pins a twine that rejects 2.4.
-# Until uv build fixes a problem with its tar library, we're stuck here.
-# https://github.com/hynek/build-and-inspect-python-package/issues/155
-# https://github.com/astral-sh/uv/issues/5450
-requires = ["hatchling~=1.26.3", "hatch-vcs"]
+requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]

src/smriprep/interfaces/templateflow.py

@@ -205,8 +205,8 @@ def fetch_template_files(
     if specs.get('resolution') and not set(specs['resolution']) & set(available_resolutions):
         fallback_res = available_resolutions[0] if available_resolutions else None
         LOGGER.warning(
-            f"Template {name[0]} does not have resolution(s): {specs['resolution']}."
-            f"Falling back to resolution: {fallback_res}."
+            f'Template {name[0]} does not have resolution(s): {specs["resolution"]}.'
+            f'Falling back to resolution: {fallback_res}.'
         )
         specs['resolution'] = fallback_res
 

src/smriprep/utils/bids.py

@@ -143,7 +143,7 @@ def write_derivative_description(bids_dir, deriv_dir):
     if 'SMRIPREP_DOCKER_TAG' in os.environ:
         desc['GeneratedBy'][0]['Container'] = {
             'Type': 'docker',
-            'Tag': f"poldracklab/smriprep:{os.environ['SMRIPREP_DOCKER_TAG']}",
+            'Tag': f'poldracklab/smriprep:{os.environ["SMRIPREP_DOCKER_TAG"]}',
         }
     if 'SMRIPREP_SINGULARITY_URL' in os.environ:
         desc['GeneratedBy'][0]['Container'] = {

src/smriprep/workflows/anatomical.py

@@ -773,7 +773,7 @@ def init_anat_fit_wf(
         LOGGER.info('ANAT Stage 1: Adding template workflow')
         ants_ver = ANTsInfo.version() or '(version unknown)'
         desc += f"""\
- {"Each" if num_t1w > 1 else "The"} T1w image was corrected for intensity
+ {'Each' if num_t1w > 1 else 'The'} T1w image was corrected for intensity
 non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs {ants_ver}
 [@ants, RRID:SCR_004757]"""
         desc += '.\n' if num_t1w > 1 else ', and used as T1w-reference throughout the workflow.\n'

src/smriprep/workflows/outputs.py

@@ -1325,7 +1325,7 @@ def _combine_cohort(in_template):
         template = in_template.split(':')[0]
         if 'cohort-' not in in_template:
             return template
-        return f"{template}+{in_template.split('cohort-')[-1].split(':')[0]}"
+        return f'{template}+{in_template.split("cohort-")[-1].split(":")[0]}'
     return [_combine_cohort(v) for v in in_template]
 
 

src/smriprep/workflows/surfaces.py

@@ -1684,7 +1684,7 @@ def _get_surfaces(subjects_dir: str, subject_id: str, surfaces: list[str]) -> tu
 
     surf_dir = Path(subjects_dir) / subject_id / 'surf'
     all_surfs = {
-        surface: sorted(str(fn) for fn in surf_dir.glob(f"[lr]h.{surface.replace('_', '.')}"))
+        surface: sorted(str(fn) for fn in surf_dir.glob(f'[lr]h.{surface.replace("_", ".")}'))
         for surface in expanded_surfaces
     }