Merge branch 'master' into nordic

tsalo · web-flow · commit 0cf3dca4f004 · 2025-01-02T13:14:39.000-05:00
diff --git a/.circleci/ds005_partial_fasttrack_outputs.txt b/.circleci/ds005_partial_fasttrack_outputs.txt
@@ -14,11 +14,17 @@ sub-01/anat/sub-01_desc-ribbon_mask.json
 sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
 sub-01/anat/sub-01_hemi-L_desc-preproc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_desc-preproc_white.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_pial.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_white.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_desc-preproc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_desc-preproc_white.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_pial.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_white.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_partial_outputs.txt
@@ -25,6 +25,9 @@ sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
 sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 sub-01/anat/sub-01_hemi-L_pial.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_pial.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_white.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
@@ -34,6 +37,9 @@ sub-01/anat/sub-01_hemi-L_thickness.shape.gii
 sub-01/anat/sub-01_hemi-L_white.surf.gii
 sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 sub-01/anat/sub-01_hemi-R_pial.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_pial.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_white.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -34,7 +34,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
         dependencies: ['latest', 'pre']
         include:
           - os: ubuntu-latest
@@ -57,6 +57,8 @@ jobs:
         run: |
           sudo apt update
           sudo apt install -y --no-install-recommends graphviz
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v5
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -65,14 +67,32 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
+          uv tool install --with=tox-uv --with=tox-gh-actions tox
       - name: Show tox config
         run: tox c
       - name: Run tox
         run: tox -v --exit-and-dump-after 1200
       - uses: codecov/codecov-action@v5
         with:
-          file: coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
+
+  checks:
+    runs-on: "ubuntu-latest"
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ["style", "spellcheck"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v5
+      - name: Install tox
+        run: uv tool install tox --with=tox-uv
+      - name: Show tox config
+        run: tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: tox -e ${{ matrix.check }}
diff --git a/.maint/paper_author_list.py b/.maint/paper_author_list.py
@@ -38,7 +38,7 @@ def _aslist(inlist):
     aff_indexes = [
         ', '.join(
             [
-                '%d' % (affiliations.index(a) + 1)
+                str(affiliations.index(a) + 1)
                 for a in _aslist(author.get('affiliation', 'Unaffiliated'))
             ]
         )
@@ -52,7 +52,7 @@ def _aslist(inlist):
         file=sys.stderr,
     )
 
-    print('Authors (%d):' % len(author_matches))
+    print(f'Authors ({len(author_matches)}):')
     print(
         '{}.'.format(
             '; '.join(
diff --git a/.maint/update_authors.py b/.maint/update_authors.py
@@ -259,7 +259,7 @@ def _aslist(value):
     aff_indexes = [
         ', '.join(
             [
-                '%d' % (affiliations.index(a) + 1)
+                str(affiliations.index(a) + 1)
                 for a in _aslist(author.get('affiliation', 'Unaffiliated'))
             ]
         )
@@ -272,7 +272,7 @@ def _aslist(value):
             file=sys.stderr,
         )
 
-    print('Authors (%d):' % len(hits))
+    print(f'Authors ({len(hits)}):')
     print(
         '{}.'.format(
             '; '.join(
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,27 +1,36 @@
+24.1.2 (To be determined)
+=========================
+Bug fix release in the 24.1.x series.
+
+* FIX: Ensure fieldmap is resampled correctly in report (#3387)
+
+
 24.1.1 (October 10, 2024)
 =========================
 Bug fix release in the 24.1.x series.
 
 Precomputed functional derivatives were not being correctly detected,
 and a couple fixes for rare issues.
 
-  * FIX: Remove checks for unit zooms and symmetric rotations in template warp (#3376)
-  * FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
-  * FIX: Repair search for precomputed bold references (#3370)
-  * FIX: Repair search for precomputed transforms (#3369)
+* FIX: Remove checks for unit zooms and symmetric rotations in template warp (#3376)
+* FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
+* FIX: Repair search for precomputed bold references (#3370)
+* FIX: Repair search for precomputed transforms (#3369)
+
 
 24.1.0 (September 16, 2024)
 ===========================
 New feature release in the 24.1.x series.
 
 Handling of gradient echo fieldmaps is improved.
 
-  * FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257)
-  * RF: Adapt to less T1w-centric smriprep (#3333)
-  * RF: Use acres over vendored data loader (#3323)
-  * DOC: Add benchmark page (#3312)
-  * MAINT: Move to tox to simplify test/CI setup (#3326)
-  * CI: Fix expected outputs for fieldmaps (#3321)
+* FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257)
+* RF: Adapt to less T1w-centric smriprep (#3333)
+* RF: Use acres over vendored data loader (#3323)
+* DOC: Add benchmark page (#3312)
+* MAINT: Move to tox to simplify test/CI setup (#3326)
+* CI: Fix expected outputs for fieldmaps (#3321)
+
 
 24.0.1 (July 16, 2024)
 ======================
diff --git a/Dockerfile b/Dockerfile
@@ -77,15 +77,6 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dAutomask" -or \
         -name "3dvolreg" \) -delete
 
-# Connectome Workbench 1.5.0
-FROM downloader AS workbench
-RUN mkdir /opt/workbench && \
-    curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
-    unzip workbench-linux64-v1.5.0.zip -d /opt && \
-    rm workbench-linux64-v1.5.0.zip && \
-    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
-    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
-
 # Micromamba
 FROM downloader AS micromamba
 
@@ -174,7 +165,6 @@ RUN apt-get update -qq \
 # Install files from stages
 COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
 COPY --from=afni /opt/afni-latest /opt/afni-latest
-COPY --from=workbench /opt/workbench /opt/workbench
 
 # Simulate SetUpFreeSurfer.sh
 ENV OS="Linux" \
@@ -198,10 +188,6 @@ ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
     AFNI_PLUGINPATH="/opt/afni-latest"
 
-# Workbench config
-ENV PATH="/opt/workbench/bin_linux64:$PATH" \
-    LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
-
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users fmriprep
 WORKDIR /home/fmriprep
diff --git a/env.yml b/env.yml
@@ -30,6 +30,8 @@ dependencies:
   - ants=2.5
   # Workflow dependencies: Convert3d
   - convert3d=1.4
+  # Workflow dependencies: Connectome Workbench
+  - connectome-workbench-cli=2.0
   # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
   - fsl-bet2=2111.8
   - fsl-flirt=2111.2
diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
@@ -105,9 +105,6 @@ def _to_gb(value):
         units = value[len(digits) :] or 'M'
         return int(digits) * scale[units[0]]
 
-    def _drop_sub(value):
-        return value[4:] if value.startswith('sub-') else value
-
     def _process_value(value):
         import bids
 
@@ -205,7 +202,7 @@ def _slice_time_ref(value, parser):
         '--participant_label',
         action='store',
         nargs='+',
-        type=_drop_sub,
+        type=lambda label: label.removeprefix('sub-'),
         help='A space delimited list of participant identifiers or a single '
         'identifier (the sub- prefix can be removed)',
     )
diff --git a/fmriprep/cli/tests/test_parser.py b/fmriprep/cli/tests/test_parser.py
@@ -82,9 +82,9 @@ def test_parser_valid(tmp_path, args):
         ('1000MB', 1),
         ('1T', 1000),
         ('1TB', 1000),
-        ('%dK' % 1e6, 1),
-        ('%dKB' % 1e6, 1),
-        ('%dB' % 1e9, 1),
+        ('1000000K', 1),
+        ('1000000KB', 1),
+        ('1000000000B', 1),
     ],
 )
 def test_memory_arg(tmp_path, argval, gb):
diff --git a/fmriprep/config.py b/fmriprep/config.py
@@ -149,11 +149,10 @@
     # Just get so analytics track one hit
     from contextlib import suppress
 
-    from requests import ConnectionError, ReadTimeout
-    from requests import get as _get_url
+    import requests
 
-    with suppress((ConnectionError, ReadTimeout)):
-        _get_url('https://rig.mit.edu/et/projects/nipy/nipype', timeout=0.05)
+    with suppress((requests.ConnectionError, requests.ReadTimeout)):
+        requests.get('https://rig.mit.edu/et/projects/nipy/nipype', timeout=0.05)
 
 # Execution environment
 _exec_env = os.name
diff --git a/fmriprep/conftest.py b/fmriprep/conftest.py
@@ -26,6 +26,11 @@ def copytree_or_skip(source, target):
         pytest.skip(f'Cannot copy {data_dir!r} into {target / data_dir.name}. Probably in a zip.')
 
 
+@pytest.fixture(scope='session', autouse=True)
+def _legacy_printoptions():
+    np.set_printoptions(legacy='1.21')
+
+
 @pytest.fixture(autouse=True)
 def _populate_namespace(doctest_namespace, tmp_path):
     doctest_namespace['copytree_or_skip'] = copytree_or_skip
diff --git a/fmriprep/interfaces/reports.py b/fmriprep/interfaces/reports.py
@@ -242,13 +242,13 @@ def _generate_segment(self):
         reg = {
             'FSL': [
                 'FSL <code>flirt</code> with boundary-based registration'
-                ' (BBR) metric - %d dof' % dof,
+                f' (BBR) metric - {dof} dof',
                 'FSL <code>flirt</code> rigid registration - 6 dof',
             ],
             'FreeSurfer': [
                 'FreeSurfer <code>bbregister</code> '
-                '(boundary-based registration, BBR) - %d dof' % dof,
-                'FreeSurfer <code>mri_coreg</code> - %d dof' % dof,
+                f'(boundary-based registration, BBR) - {dof} dof',
+                f'FreeSurfer <code>mri_coreg</code> - {dof} dof',
             ],
         }[self.inputs.registration][self.inputs.fallback]
 
diff --git a/fmriprep/reports/core.py b/fmriprep/reports/core.py
@@ -76,9 +76,12 @@ def generate_reports(
 
     if isinstance(subject_list, str):
         subject_list = [subject_list]
+    if isinstance(session_list, str):
+        session_list = [session_list]
 
     errors = []
     for subject_label in subject_list:
+        subject_label = subject_label.removeprefix('sub-')
         # The number of sessions is intentionally not based on session_list but
         # on the total number of sessions, because I want the final derivatives
         # folder to be the same whether sessions were run one at a time or all-together.
@@ -95,7 +98,7 @@ def generate_reports(
         else:
             # Beyond a threshold, we separate the anatomical report from the functional.
             bootstrap_file = data.load('reports-spec-anat.yml')
-            html_report = f'sub-{subject_label.lstrip("sub-")}_anat.html'
+            html_report = f'sub-{subject_label}_anat.html'
 
         report_error = run_reports(
             output_dir,
@@ -121,12 +124,11 @@ def generate_reports(
                     subject=subject_label, **filters
                 )
 
-            # Drop ses- prefixes
-            session_list = [ses[4:] if ses.startswith('ses-') else ses for ses in session_list]
+            session_list = [ses.removeprefix('ses-') for ses in session_list]
 
             for session_label in session_list:
                 bootstrap_file = data.load('reports-spec-func.yml')
-                html_report = f'sub-{subject_label.lstrip("sub-")}_ses-{session_label}_func.html'
+                html_report = f'sub-{subject_label}_ses-{session_label}_func.html'
 
                 report_error = run_reports(
                     output_dir,
diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
@@ -217,7 +217,7 @@ def validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True):
     # Limit validation only to data from requested participants
     if participant_label:
         all_subs = {s.name[4:] for s in bids_dir.glob('sub-*')}
-        selected_subs = {s[4:] if s.startswith('sub-') else s for s in participant_label}
+        selected_subs = {s.removeprefix('sub-') for s in participant_label}
         bad_labels = selected_subs.difference(all_subs)
         if bad_labels:
             error_msg = (
diff --git a/fmriprep/utils/telemetry.py b/fmriprep/utils/telemetry.py
@@ -116,7 +116,7 @@ def process_crashfile(crashfile):
                 scope.set_extra(k, strv[0])
             else:
                 for i, chunk in enumerate(strv):
-                    scope.set_extra('%s_%02d' % (k, i), chunk)
+                    scope.set_extra(f'{k}_{i:02d}', chunk)
 
         fingerprint = ''
         issue_title = f'{node_name}: {gist}'
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
diff --git a/fmriprep/workflows/bold/stc.py b/fmriprep/workflows/bold/stc.py
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/scripts/fetch_templates.py b/scripts/fetch_templates.py
diff --git a/tox.ini b/tox.ini

Original file line number	Diff line number	Diff line change
`@@ -38,7 +38,7 @@ def _aslist(inlist):`
`38`	`38`	`aff_indexes = [`
`39`	`39`	`', '.join(`
`40`	`40`	`[`
`41`		`- '%d' % (affiliations.index(a) + 1)`
	`41`	`+ str(affiliations.index(a) + 1)`
`42`	`42`	`for a in _aslist(author.get('affiliation', 'Unaffiliated'))`
`43`	`43`	`]`
`44`	`44`	`)`
`@@ -52,7 +52,7 @@ def _aslist(inlist):`
`52`	`52`	`file=sys.stderr,`
`53`	`53`	`)`
`54`	`54`
`55`		`- print('Authors (%d):' % len(author_matches))`
	`55`	`+ print(f'Authors ({len(author_matches)}):')`
`56`	`56`	`print(`
`57`	`57`	`'{}.'.format(`
`58`	`58`	`'; '.join(`
Original file line number	Diff line number	Diff line change
`@@ -259,7 +259,7 @@ def _aslist(value):`
`259`	`259`	`aff_indexes = [`
`260`	`260`	`', '.join(`
`261`	`261`	`[`
`262`		`- '%d' % (affiliations.index(a) + 1)`
	`262`	`+ str(affiliations.index(a) + 1)`
`263`	`263`	`for a in _aslist(author.get('affiliation', 'Unaffiliated'))`
`264`	`264`	`]`
`265`	`265`	`)`
`@@ -272,7 +272,7 @@ def _aslist(value):`
`272`	`272`	`file=sys.stderr,`
`273`	`273`	`)`
`274`	`274`
`275`		`- print('Authors (%d):' % len(hits))`
	`275`	`+ print(f'Authors ({len(hits)}):')`
`276`	`276`	`print(`
`277`	`277`	`'{}.'.format(`
`278`	`278`	`'; '.join(`