[MAINT] run tests on parallel threads

.github/workflows/test_with_free_threaded_python.yml

@@ -0,0 +1,62 @@
+---
+# Runs tests suite with free threaded python.
+#
+###
+name: test free threaded python
+
+on:
+    pull_request:
+    workflow_dispatch:
+    push:
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+env:
+    FORCE_COLOR: true
+
+jobs:
+
+    free_threaded:
+        name: 'Test with ${{ matrix.py }} on ${{ matrix.os }}'
+
+        runs-on: ${{ matrix.os }}
+
+        strategy:
+            fail-fast: false
+            matrix:
+                py: [3.14t]
+                os: [macos-latest, ubuntu-latest]
+                env: [free_threaded]
+
+        steps:
+        -   uses: actions/checkout@v6
+
+        -   name: Install the latest version of uv
+            uses: astral-sh/setup-uv@v7
+
+        -   name: Setup python
+            uses: actions/setup-python@v6
+            with:
+                python-version: ${{ matrix.py }}
+                allow-prereleases: true
+
+        -   name: Install dependencies
+            run: |
+                uv venv -p 3.14t
+                source .venv/bin/activate
+                uv pip install -e '.[test,dicomfs,dicom,viewers,indexed_gzip,spm,zstd]'
+                uv pip install pytest-run-parallel
+
+        -   name: Run test suite
+            # run on several threads
+            # this may take a bit longer with fewer threads
+            # but as some tests can be flaky,
+            # they will more systematically fail with more threads
+            id: test_free_threaded
+            run: |
+                source .venv/bin/activate
+                PYTEST_RUN_PARALLEL_VERBOSE=1
+                N_THREADS=16
+                pytest -ra --strict-config --strict-markers --showlocals --capture=no --parallel-threads $N_THREADS nibabel

.gitignore

@@ -82,3 +82,15 @@ for_testing/
 # Generated by setuptools_scm #
 ###############################
 _version.py
+
+# files generated by tests #
+############################
+another_image.nii
+another_image.npy
+image.hdr
+stream
+streamlines.trk
+test.dtseries.nii
+test.hdr
+test.img
+test.nii

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -422,6 +422,7 @@ def test_pixdim_checks(self):
             hdr['pixdim'][i] = -1
             assert self._dxer(hdr) == self._pixdim_message
 
+    @pytest.mark.thread_unsafe
     def test_nifti_qfac_checks(self):
         # Test qfac is 1 or -1 or 0
         hdr = self.header_class()
@@ -438,6 +439,7 @@ def test_nifti_qfac_checks(self):
         assert fhdr['pixdim'][0] == 1
         assert message == 'pixdim[0] (qfac) should be 1 (default) or 0 or -1; setting qfac to 1'
 
+    @pytest.mark.thread_unsafe
     def test_pixdim_log_checks(self):
         # pixdim can be zero or positive
         HC = self.header_class

nibabel/cifti2/tests/test_new_cifti2.py

@@ -287,6 +287,7 @@ def check_series_map(mapping):
     assert mapping.series_unit == 'SECOND'
 
 
+@pytest.mark.thread_unsafe
 def test_dtseries():
     series_map = create_series_map((0,))
     geometry_map = create_geometry_map((1,))
@@ -308,6 +309,7 @@ def test_dtseries():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_dscalar():
     scalar_map = create_scalar_map((0,))
     geometry_map = create_geometry_map((1,))
@@ -329,6 +331,7 @@ def test_dscalar():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_dlabel():
     label_map = create_label_map((0,))
     geometry_map = create_geometry_map((1,))
@@ -350,6 +353,7 @@ def test_dlabel():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_dconn():
     mapping = create_geometry_map((0, 1))
     matrix = ci.Cifti2Matrix()
@@ -370,6 +374,7 @@ def test_dconn():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_ptseries():
     series_map = create_series_map((0,))
     parcel_map = create_parcel_map((1,))
@@ -391,6 +396,7 @@ def test_ptseries():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_pscalar():
     scalar_map = create_scalar_map((0,))
     parcel_map = create_parcel_map((1,))
@@ -412,6 +418,7 @@ def test_pscalar():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_pdconn():
     geometry_map = create_geometry_map((0,))
     parcel_map = create_parcel_map((1,))
@@ -433,6 +440,7 @@ def test_pdconn():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_dpconn():
     parcel_map = create_parcel_map((0,))
     geometry_map = create_geometry_map((1,))
@@ -454,6 +462,7 @@ def test_dpconn():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_plabel():
     label_map = create_label_map((0,))
     parcel_map = create_parcel_map((1,))
@@ -474,6 +483,7 @@ def test_plabel():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_pconn():
     mapping = create_parcel_map((0, 1))
     matrix = ci.Cifti2Matrix()
@@ -494,6 +504,7 @@ def test_pconn():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_pconnseries():
     parcel_map = create_parcel_map((0, 1))
     series_map = create_series_map((2,))
@@ -517,6 +528,7 @@ def test_pconnseries():
         del img2
 
 
+@pytest.mark.thread_unsafe
 def test_pconnscalar():
     parcel_map = create_parcel_map((0, 1))
     scalar_map = create_scalar_map((2,))

nibabel/freesurfer/tests/test_io.py

@@ -144,6 +144,7 @@ def test_morph_data():
         assert np.array_equal(curv2, curv)
 
 
+@pytest.mark.thread_unsafe
 def test_write_morph_data():
     """Test write_morph_data edge cases"""
     values = np.arange(20, dtype='>f4')
@@ -211,6 +212,7 @@ def test_annot():
         assert names == names2
 
 
+@pytest.mark.thread_unsafe
 def test_read_write_annot():
     """Test generating .annot file and reading it back."""
     # This annot file will store a LUT for a mesh made of 10 vertices, with
@@ -244,6 +246,7 @@ def test_read_write_annot():
         assert names2 == names
 
 
+@pytest.mark.thread_unsafe
 def test_write_annot_fill_ctab():
     """Test the `fill_ctab` parameter to :func:`.write_annot`."""
     nvertices = 10
@@ -291,6 +294,7 @@ def test_write_annot_fill_ctab():
         assert names2 == names
 
 
+@pytest.mark.thread_unsafe
 def test_read_annot_old_format():
     """Test reading an old-style .annot file."""
 
@@ -353,6 +357,7 @@ def test_label():
     assert len(labels) == len(scalars)
 
 
+@pytest.mark.thread_unsafe
 def test_write_annot_maxstruct():
     """Test writing ANNOT files with repeated labels"""
     with InTemporaryDirectory():

nibabel/freesurfer/tests/test_mghformat.py

@@ -91,6 +91,7 @@ def test_read_mgh():
     assert_almost_equal(v[1, 2, 3, 1], 0.0018, 4)
 
 
+@pytest.mark.thread_unsafe
 def test_write_mgh():
     # write our data to a tmp file
     v = np.arange(120)
@@ -121,6 +122,7 @@ def test_write_mgh():
     assert_almost_equal(dat, v, 7)
 
 
+@pytest.mark.thread_unsafe
 def test_write_noaffine_mgh():
     # now just save the image without the vox2ras transform
     # and see if it uses the default values to save
@@ -188,6 +190,7 @@ def test_bad_dtype_mgh():
         bad_dtype_mgh()
 
 
+@pytest.mark.thread_unsafe
 def test_filename_exts():
     # Test acceptable filename extensions
     v = np.ones((7, 13, 3, 22), np.uint8)

nibabel/gifti/tests/test_gifti.py

@@ -562,6 +562,7 @@ def test_darray_dtype_coercion_failures():
         assert_array_equal(da_copy.data, da.data)
 
 
+@pytest.mark.thread_unsafe
 def test_gifti_file_close(recwarn):
     gii = load(get_test_data('gifti', 'ascii.gii'))
     with InTemporaryDirectory():

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -229,6 +229,7 @@ def test_load_metadata():
         assert img.version == '1.0'
 
 
+@pytest.mark.thread_unsafe
 def test_load_dataarray1():
     img1 = load(DATA_FILE1)
     # Round trip
@@ -247,6 +248,7 @@ def test_load_dataarray1():
         assert xform_codes.niistring[img.darrays[0].coordsys.xformspace] == 'NIFTI_XFORM_TALAIRACH'
 
 
+@pytest.mark.thread_unsafe
 def test_load_dataarray2():
     img2 = load(DATA_FILE2)
     # Round trip
@@ -257,6 +259,7 @@ def test_load_dataarray2():
         assert_array_almost_equal(img.darrays[0].data[:10], DATA_FILE2_darr1)
 
 
+@pytest.mark.thread_unsafe
 def test_load_dataarray3():
     img3 = load(DATA_FILE3)
     with InTemporaryDirectory():
@@ -266,6 +269,7 @@ def test_load_dataarray3():
         assert_array_almost_equal(img.darrays[0].data[30:50], DATA_FILE3_darr1)
 
 
+@pytest.mark.thread_unsafe
 def test_load_dataarray4():
     img4 = load(DATA_FILE4)
     # Round trip
@@ -285,6 +289,7 @@ def test_dataarray5():
     # Round trip tested below
 
 
+@pytest.mark.thread_unsafe
 def test_base64_written():
     with InTemporaryDirectory():
         with open(DATA_FILE5, 'rb') as fobj:
@@ -314,6 +319,7 @@ def test_base64_written():
         assert_array_almost_equal(darrays[1].data, DATA_FILE5_darr2)
 
 
+@pytest.mark.thread_unsafe
 def test_readwritedata():
     img = load(DATA_FILE2)
     with InTemporaryDirectory():
@@ -357,6 +363,7 @@ def test_load_getbyintent():
     assert da == []
 
 
+@pytest.mark.thread_unsafe
 def test_load_labeltable():
     img6 = load(DATA_FILE6)
     # Round trip
@@ -376,6 +383,7 @@ def test_load_labeltable():
         assert img.labeltable.labels[1].alpha == 1
 
 
+@pytest.mark.thread_unsafe
 def test_parse_dataarrays():
     fn = 'bad_daa.gii'
     img = gi.GiftiImage()
@@ -441,6 +449,7 @@ def test_parse_with_memmap_fallback():
     assert_array_almost_equal(img2.darrays[1].data, DATA_FILE7_darr2)
 
 
+@pytest.mark.thread_unsafe
 def test_external_file_failure_cases():
     # external file cannot be found
     with InTemporaryDirectory() as tmpdir:

nibabel/nicom/tests/test_csareader.py

@@ -64,6 +64,7 @@ def test_csa_len0():
     assert len(tags) == 44
 
 
+@pytest.mark.thread_unsafe
 def test_csa_nitem():
     # testing csa.read's ability to raise an error when n_items >= 200
     with pytest.raises(csa.CSAReadError):

nibabel/nicom/tests/test_dicomwrappers.py

@@ -522,6 +522,7 @@ class TestMultiFrameWrapper(TestCase):
         WRAPCLASS = didw.MultiframeWrapper
 
     @dicom_test
+    @pytest.mark.thread_unsafe
     def test_shape(self):
         # Check the shape algorithm
         fake_mf = deepcopy(self.MINIMAL_MF)

nibabel/streamlines/tests/test_streamlines.py

@@ -208,6 +208,7 @@ def test_load_complex_file(self):
                 with pytest.warns(Warning) if lazy_load else error_warnings():
                     assert_tractogram_equal(tfile.tractogram, tractogram)
 
+    @pytest.mark.thread_unsafe
     def test_save_tractogram_file(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
         trk_file = trk.TrkFile(tractogram)
@@ -232,6 +233,7 @@ def test_save_tractogram_file(self):
             tfile = nib.streamlines.load('dummy.trk', lazy_load=False)
             assert_tractogram_equal(tfile.tractogram, tractogram)
 
+    @pytest.mark.thread_unsafe
     def test_save_empty_file(self):
         tractogram = Tractogram(affine_to_rasmm=np.eye(4))
         for ext in FORMATS:
@@ -241,6 +243,7 @@ def test_save_empty_file(self):
                 tfile = nib.streamlines.load(filename, lazy_load=False)
                 assert_tractogram_equal(tfile.tractogram, tractogram)
 
+    @pytest.mark.thread_unsafe
     def test_save_simple_file(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
         for ext in FORMATS:
@@ -250,6 +253,7 @@ def test_save_simple_file(self):
                 tfile = nib.streamlines.load(filename, lazy_load=False)
                 assert_tractogram_equal(tfile.tractogram, tractogram)
 
+    @pytest.mark.thread_unsafe
     def test_save_complex_file(self):
         complex_tractogram = Tractogram(
             DATA['streamlines'],
@@ -286,6 +290,7 @@ def test_save_complex_file(self):
                 tfile = nib.streamlines.load(filename, lazy_load=False)
                 assert_tractogram_equal(tfile.tractogram, tractogram)
 
+    @pytest.mark.thread_unsafe
     def test_save_sliced_tractogram(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
         original_tractogram = tractogram.copy()
@@ -306,6 +311,7 @@ def test_save_unknown_format(self):
         with pytest.raises(ValueError):
             nib.streamlines.save(Tractogram(), '')
 
+    @pytest.mark.thread_unsafe
     def test_save_from_generator(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))