Merge tag '1.13.3'

1.13.3 (May 09, 2025)

Patch release in the 1.13.x series.

This release resolves import errors introduced by excluding excess files in
the previous release. Only test modules were affected.

* ENH: Add PET info to nipreps.json (#942)

Author: effigies

.circleci/config.yml

@@ -120,27 +120,22 @@ jobs:
 
   get_data:
     docker:
-      - image: quay.io/condaforge/miniforge3:24.9.0-0
+      - image: quay.io/condaforge/miniforge3:latest
     working_directory: /tmp/data
     environment:
       - TEMPLATEFLOW_HOME: /tmp/templateflow
     steps:
-      - restore_cache:
-          keys:
-            - env-v0-{{ .Branch }}-
-            - env-v0-master-
-            - env-v0-
       - run:
-          name: Setup git-annex, DataLad & TemplateFlow
+          name: Add ~/.local/bin to path
+          command: |
+            echo export PATH=$HOME/.local/bin:$PATH >> $BASH_ENV
+      - run:
+          name: Setup git-annex and DataLad
           command: |
-            mamba install -y python=*=*cpython git-annex=*=alldep* unzip
-            python -m pip install --no-cache-dir -U datalad datalad-osf templateflow
+            mamba install -y git-annex=*=alldep* unzip uv
+            uv tool install --with=datalad-next --with=datalad-osf datalad
             git config --global user.name 'NiPreps Bot'
             git config --global user.email 'nipreps@gmail.com'
-      - save_cache:
-          key: env-v0-{{ .Branch }}-{{ .BuildNum }}
-          paths:
-            - /opt/conda
 
       - restore_cache:
           keys:

CHANGES.rst

@@ -1,14 +1,28 @@
+1.13.3 (May 09, 2025)
+=====================
+Patch release in the 1.13.x series.
+
+This release resolves import errors introduced by excluding excess files in
+the previous release. Only test modules were affected.
+
+* ENH: Add PET info to nipreps.json (#942)
+
+1.13.2 (May 08, 2025)
+=====================
+Patch release in the 1.13.x series.
+
+This release adjusts the build process to reduce the size of the installed package.
+
 1.13.1 (May 02, 2025)
 =====================
 Patch release in the 1.13.x series.
 
-This release adds the ``niworkflows.engine.splicer`` module, to facilitate sugery on wworkflows.
+This release adds the ``niworkflows.engine.splicer`` module, to facilitate sugery on workflows.
 
 * FIX: Allow passing arguments through tag decorator (#939)
 * ENH: Workflow splicer module (#938)
 * MNT: Bump astral-sh/setup-uv from 5 to 6 (#937)
 
-
 1.13.0 (March 20, 2025)
 =======================
 New feature release in the 1.13.x series.

niworkflows/conftest.py

@@ -34,11 +34,6 @@
 
 from . import load_resource
 
-try:
-    import importlib_resources
-except ImportError:
-    import importlib.resources as importlib_resources
-
 # disable ET
 os.environ['NO_ET'] = '1'
 
@@ -69,7 +64,6 @@ def _add_np(doctest_namespace):
     doctest_namespace['pd'] = pd
     doctest_namespace['os'] = os
     doctest_namespace['pytest'] = pytest
-    doctest_namespace['importlib_resources'] = importlib_resources
     doctest_namespace['find_resource_or_skip'] = find_resource_or_skip
     doctest_namespace['Path'] = Path
     doctest_namespace['datadir'] = data_dir

niworkflows/interfaces/tests/test_plotting.py

@@ -28,9 +28,15 @@
 
 from niworkflows import viz
 from niworkflows.interfaces.plotting import _get_tr
-from niworkflows.tests.data import load_test_data
 from niworkflows.utils.timeseries import _cifti_timeseries, _nifti_timeseries
 
+try:
+    from niworkflows.tests.data import load_test_data
+except ImportError:
+    import pytest
+
+    pytest.skip('niworkflows installed as wheel, data excluded', allow_module_level=True)
+
 
 def test_cifti_carpetplot():
     """Exercise extraction of timeseries from CIFTI2."""

niworkflows/tests/conftest.py

@@ -30,9 +30,16 @@
 from templateflow.api import get as get_template
 
 from niworkflows.testing import data_env_canary, test_data_env
-from niworkflows.tests.data import load_test_data
 
-datadir = load_test_data()
+
+@pytest.fixture
+def datadir():
+    try:
+        from niworkflows.tests.data import load_test_data
+    except ImportError:
+        pytest.skip('niworkflows installed as wheel, data excluded')
+
+    return load_test_data()
 
 
 def _run_interface_mock(objekt, runtime):

niworkflows/tests/test_confounds.py

@@ -31,7 +31,6 @@
 
 from ..interfaces.confounds import ExpandModel, SpikeRegressors
 from ..interfaces.plotting import CompCorVariancePlot, ConfoundsCorrelationPlot
-from .conftest import datadir
 
 
 def _smoke_test_report(report_interface, artifact_name):
@@ -43,7 +42,7 @@ def _smoke_test_report(report_interface, artifact_name):
     assert os.path.isfile(out_report), f'Report "{out_report}" does not exist'
 
 
-def _expand_test(model_formula):
+def _expand_test(model_formula, datadir):
     orig_data_file = os.path.join(datadir, 'confounds_test.tsv')
     exp_data_file = (
         pe.Node(
@@ -56,7 +55,7 @@ def _expand_test(model_formula):
     return pd.read_csv(exp_data_file, sep='\t')
 
 
-def _spikes_test(lags=None, mincontig=None, fmt='mask'):
+def _spikes_test(lags=None, mincontig=None, fmt='mask', *, datadir):
     orig_data_file = os.path.join(datadir, 'spikes_test.tsv')
     lags = lags or [0]
     spk_data_file = (
@@ -78,7 +77,7 @@ def _spikes_test(lags=None, mincontig=None, fmt='mask'):
     return pd.read_csv(spk_data_file, sep='\t')
 
 
-def test_expansion_variable_selection():
+def test_expansion_variable_selection(datadir):
     """Test model expansion: simple variable selection"""
     model_formula = 'a + b + c + d'
     expected_data = pd.DataFrame(
@@ -89,11 +88,11 @@ def test_expansion_variable_selection():
             'd': [9, 7, 5, 3, 1],
         }
     )
-    exp_data = _expand_test(model_formula)
+    exp_data = _expand_test(model_formula, datadir)
     pd.testing.assert_frame_equal(exp_data, expected_data)
 
 
-def test_expansion_derivatives_and_powers():
+def test_expansion_derivatives_and_powers(datadir):
     """Temporal derivatives and quadratics"""
     model_formula = '(dd1(a) + d1(b))^^2 + d1-2((c)^2) + d + others'
     # b_derivative1_power2 is dropped as an exact duplicate of b_derivative1
@@ -112,13 +111,13 @@ def test_expansion_derivatives_and_powers():
             'f': [np.nan, 6, 4, 2, 0],
         }
     )
-    exp_data = _expand_test(model_formula)
+    exp_data = _expand_test(model_formula, datadir)
     assert set(exp_data.columns) == set(expected_data.columns)
     for col in expected_data.columns:
         pd.testing.assert_series_equal(expected_data[col], exp_data[col], check_dtype=False)
 
 
-def test_expansion_na_robustness():
+def test_expansion_na_robustness(datadir):
     """NA robustness"""
     model_formula = '(dd1(f))^^2'
     expected_data = pd.DataFrame(
@@ -129,16 +128,16 @@ def test_expansion_na_robustness():
             'f_derivative1_power2': [np.nan, np.nan, 4, 4, 4],
         }
     )
-    exp_data = _expand_test(model_formula)
+    exp_data = _expand_test(model_formula, datadir)
     assert set(exp_data.columns) == set(expected_data.columns)
     for col in expected_data.columns:
         pd.testing.assert_series_equal(expected_data[col], exp_data[col], check_dtype=False)
 
 
-def test_spikes():
+def test_spikes(datadir):
     """Test outlier flagging"""
     outliers = [1, 1, 0, 0, 1]
-    spk_data = _spikes_test()
+    spk_data = _spikes_test(datadir=datadir)
     assert np.all(np.isclose(outliers, spk_data['motion_outlier']))
 
     outliers_spikes = pd.DataFrame(
@@ -148,30 +147,30 @@ def test_spikes():
             'motion_outlier02': [0, 0, 0, 0, 1],
         }
     )
-    spk_data = _spikes_test(fmt='spikes')
+    spk_data = _spikes_test(fmt='spikes', datadir=datadir)
     assert set(spk_data.columns) == set(outliers_spikes.columns)
     for col in outliers_spikes.columns:
         assert np.all(np.isclose(outliers_spikes[col], spk_data[col]))
 
     lags = [0, 1]
     outliers_lags = [1, 1, 1, 0, 1]
-    spk_data = _spikes_test(lags=lags)
+    spk_data = _spikes_test(lags=lags, datadir=datadir)
     assert np.all(np.isclose(outliers_lags, spk_data['motion_outlier']))
 
     mincontig = 2
     outliers_mc = [1, 1, 1, 1, 1]
-    spk_data = _spikes_test(lags=lags, mincontig=mincontig)
+    spk_data = _spikes_test(lags=lags, mincontig=mincontig, datadir=datadir)
     assert np.all(np.isclose(outliers_mc, spk_data['motion_outlier']))
 
 
-def test_CompCorVariancePlot():
+def test_CompCorVariancePlot(datadir):
     """CompCor variance report test"""
     metadata_file = os.path.join(datadir, 'confounds_metadata_test.tsv')
     cc_rpt = CompCorVariancePlot(metadata_files=[metadata_file], metadata_sources=['aCompCor'])
     _smoke_test_report(cc_rpt, 'compcor_variance.svg')
 
 
-def test_ConfoundsCorrelationPlot():
+def test_ConfoundsCorrelationPlot(datadir):
     """confounds correlation report test"""
     confounds_file = os.path.join(datadir, 'confounds_test.tsv')
     cc_rpt = ConfoundsCorrelationPlot(
@@ -182,7 +181,7 @@ def test_ConfoundsCorrelationPlot():
     _smoke_test_report(cc_rpt, 'confounds_correlation.svg')
 
 
-def test_ConfoundsCorrelationPlotColumns():
+def test_ConfoundsCorrelationPlotColumns(datadir):
     """confounds correlation report test"""
     confounds_file = os.path.join(datadir, 'confounds_test.tsv')
     cc_rpt = ConfoundsCorrelationPlot(

niworkflows/tests/test_registration.py

@@ -39,7 +39,7 @@
     SpatialNormalizationRPT,
 )
 from ..testing import has_freesurfer, has_fsl
-from .conftest import _run_interface_mock, datadir
+from .conftest import _run_interface_mock
 
 
 def _smoke_test_report(report_interface, artifact_name):
@@ -61,7 +61,7 @@ def test_FLIRTRPT(reference, moving):
 
 
 @pytest.mark.skipif(not has_freesurfer, reason='No FreeSurfer')
-def test_MRICoregRPT(monkeypatch, reference, moving, nthreads):
+def test_MRICoregRPT(monkeypatch, reference, moving, nthreads, datadir):
     """the MRICoreg report capable test"""
 
     def _agg(objekt, runtime):
@@ -120,7 +120,7 @@ def test_FLIRTRPT_w_BBR(reference, reference_mask, moving):
 
 
 @pytest.mark.skipif(not has_freesurfer, reason='No FreeSurfer')
-def test_BBRegisterRPT(monkeypatch, moving):
+def test_BBRegisterRPT(monkeypatch, moving, datadir):
     """the BBRegister report capable test"""
 
     def _agg(objekt, runtime):
@@ -145,7 +145,7 @@ def _agg(objekt, runtime):
     _smoke_test_report(bbregister_rpt, 'testBBRegister.svg')
 
 
-def test_SpatialNormalizationRPT(monkeypatch, moving):
+def test_SpatialNormalizationRPT(monkeypatch, moving, datadir):
     """the SpatialNormalizationRPT report capable test"""
 
     def _agg(objekt, runtime):
@@ -164,7 +164,7 @@ def _agg(objekt, runtime):
     _smoke_test_report(ants_rpt, 'testSpatialNormalizationRPT.svg')
 
 
-def test_SpatialNormalizationRPT_masked(monkeypatch, moving, reference_mask):
+def test_SpatialNormalizationRPT_masked(monkeypatch, moving, reference_mask, datadir):
     """the SpatialNormalizationRPT report capable test with masking"""
 
     def _agg(objekt, runtime):
@@ -188,7 +188,7 @@ def _agg(objekt, runtime):
     _smoke_test_report(ants_rpt, 'testSpatialNormalizationRPT_masked.svg')
 
 
-def test_ANTSRegistrationRPT(monkeypatch, reference, moving):
+def test_ANTSRegistrationRPT(monkeypatch, reference, moving, datadir):
     """the SpatialNormalizationRPT report capable test"""
     from niworkflows import data
 

niworkflows/tests/test_segmentation.py

@@ -38,7 +38,7 @@
 )
 from ..interfaces.reportlets.segmentation import FASTRPT, ReconAllRPT
 from ..testing import has_freesurfer, has_fsl
-from .conftest import _run_interface_mock, datadir
+from .conftest import _run_interface_mock
 
 
 def _smoke_test_report(report_interface, artifact_name):
@@ -160,7 +160,7 @@ def test_SimpleShowMaskRPT():
     _smoke_test_report(msk_rpt, 'testSimpleMask.svg')
 
 
-def test_BrainExtractionRPT(monkeypatch, moving, nthreads):
+def test_BrainExtractionRPT(monkeypatch, moving, nthreads, datadir):
     """test antsBrainExtraction with reports"""
 
     def _agg(objekt, runtime):
@@ -201,7 +201,7 @@ def _agg(objekt, runtime):
 
 @pytest.mark.skipif(not has_fsl, reason='No FSL')
 @pytest.mark.parametrize('segments', [True, False])
-def test_FASTRPT(monkeypatch, segments, reference, reference_mask):
+def test_FASTRPT(monkeypatch, segments, reference, reference_mask, datadir):
     """test FAST with the two options for segments"""
     from nipype.interfaces.fsl.maths import ApplyMask
 

niworkflows/tests/test_viz.py

@@ -35,7 +35,6 @@
 from niworkflows.viz.plots import fMRIPlot
 
 from .. import viz
-from .conftest import datadir
 from .generate_data import _create_dtseries_cifti
 
 
@@ -135,7 +134,7 @@ def test_carpetplot(tr, sorting):
         ),
     ],
 )
-def test_fmriplot(input_files):
+def test_fmriplot(input_files, datadir):
     """Exercise the fMRIPlot class."""
     save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
     rng = np.random.default_rng(2010)
@@ -249,7 +248,7 @@ def test_plot_melodic_components(tmp_path):
     )
 
 
-def test_compcor_variance_plot(tmp_path):
+def test_compcor_variance_plot(tmp_path, datadir):
     """Test plotting CompCor variance"""
     out_dir = Path(os.getenv('SAVE_CIRCLE_ARTIFACTS', str(tmp_path)))
     out_file = str(out_dir / 'variance_plot_short.svg')

pyproject.toml

@@ -20,12 +20,12 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
 dependencies = [
     "acres",
     "attrs >=20.1",
-    "importlib_resources >= 5.7; python_version < '3.11'",
     "jinja2 >=3",
     "looseversion",
     "matplotlib >= 3.5",
@@ -98,6 +98,7 @@ exclude = [".git_archival.txt"]  # No longer needed in sdist
 packages = ["niworkflows"]
 exclude = [
     "niworkflows/data/tests/work",  # Large test data directory
+    "niworkflows/tests/data",  # Large test data directory
 ]
 
 ##  The following two sections configure setuptools_scm in the hatch way