MAINT: Use VTK prerelease wheels in pre jobs (#11629)

Author: larsoner

Diff for: examples/preprocessing/locate_ieeg_micro.py

@@ -19,6 +19,7 @@
 import numpy as np
 import nibabel as nib
 import mne
+import mne_gui_addons
 
 # path to sample sEEG
 misc_path = mne.datasets.misc.data_path()
@@ -55,7 +56,7 @@
 # launch the viewer with only the CT (note, we won't be able to use
 # the MR in this case to help determine which brain area the contact is
 # in), and use the user interface to find the locations of the contacts
-gui = mne.gui.locate_ieeg(raw.info, head_ct_t, CT_orig)
+gui = mne_gui_addons.locate_ieeg(raw.info, head_ct_t, CT_orig)
 
 # we'll programmatically mark all the contacts on one electrode shaft
 for i, pos in enumerate([(-52.66, -40.84, -26.99), (-55.47, -38.03, -27.92),

Diff for: mne/tests/test_surface.py

@@ -164,22 +164,26 @@ def test_read_curv():
     assert np.logical_or(bin_curv == 0, bin_curv == 1).all()
 
 
-def test_decimate_surface_vtk():
+@pytest.mark.parametrize('n_tri', (4, 3, 2))
+def test_decimate_surface_vtk(n_tri):
     """Test triangular surface decimation."""
     pytest.importorskip('pyvista')
     points = np.array([[-0.00686118, -0.10369860, 0.02615170],
                        [-0.00713948, -0.10370162, 0.02614874],
                        [-0.00686208, -0.10368247, 0.02588313],
                        [-0.00713987, -0.10368724, 0.02587745]])
     tris = np.array([[0, 1, 2], [1, 2, 3], [0, 3, 1], [1, 2, 0]])
-    for n_tri in [4, 3, 2]:  # quadric decimation creates even numbered output.
-        _, this_tris = decimate_surface(points, tris, n_tri)
-        assert len(this_tris) == n_tri if not n_tri % 2 else 2
+    _, this_tris = decimate_surface(points, tris, n_tri)
+    want = (n_tri, n_tri - 1)
+    if n_tri == 3:
+        want = want + (1,)
+    assert len(this_tris) in want
     with pytest.raises(ValueError, match='exceeds number of original'):
         decimate_surface(points, tris, len(tris) + 1)
     nirvana = 5
     tris = np.array([[0, 1, 2], [1, 2, 3], [0, 3, 1], [1, 2, nirvana]])
-    pytest.raises(ValueError, decimate_surface, points, tris, n_tri)
+    with pytest.raises(ValueError, match='undefined points'):
+        decimate_surface(points, tris, n_tri)
 
 
 @requires_freesurfer('mris_sphere')
@@ -238,7 +242,9 @@ def test_marching_cubes(dtype, value, smooth):
     # verts and faces are rather large so use checksum
     rtol = 1e-2 if smooth else 1e-9
     assert_allclose(verts.sum(axis=0), [14700, 14700, 14700], rtol=rtol)
-    assert_allclose(triangles.sum(axis=0), [363402, 360865, 350588])
+    tri_sum = triangles.sum(axis=0).tolist()
+    # old VTK (9.2.6), new VTK
+    assert tri_sum in [[363402, 360865, 350588], [364089, 359867, 350408]]
     # test fill holes
     data[24:27, 24:27, 24:27] = 0
     verts, triangles = _marching_cubes(data, level, smooth=smooth,

Diff for: requirements.txt

@@ -43,4 +43,3 @@ mne-qt-browser
 darkdetect
 qdarkstyle
 threadpoolctl
-mne-gui-addons

Diff for: requirements_doc.txt

@@ -1,18 +1,19 @@
 # requirements for building docs
 sphinx!=4.1.0,<6
-https://github.com/numpy/numpydoc/archive/main.zip
+git+https://github.com/numpy/numpydoc.git@main
 pydata_sphinx_theme==0.13.1
-https://github.com/sphinx-gallery/sphinx-gallery/archive/master.zip
+git+https://github.com/sphinx-gallery/sphinx-gallery@master
 sphinxcontrib-bibtex>=2.5
 memory_profiler
 neo
 seaborn!=0.11.2
 sphinx_copybutton
 sphinx-design
 sphinxcontrib-youtube
-https://github.com/mne-tools/mne-bids/archive/main.zip
+git+https://github.com/mne-tools/mne-bids@main
 pyxdf
-https://github.com/mne-tools/mne-connectivity/archive/main.zip
+git+https://github.com/mne-tools/mne-connectivity.git@main
+git+https://github.com/mne-tools/mne-gui-addons.git@main
 pygments>=2.13
 pytest
 graphviz

Diff for: tools/azure_dependencies.sh

@@ -18,7 +18,7 @@ elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" scipy statsmodels pandas scikit-learn dipy matplotlib
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://test.pypi.org/simple" openmeeg
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps vtk
+	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://wheels.vtk.org" vtk
 	python -m pip install --progress-bar off git+https://github.com/pyvista/pyvista
 	python -m pip install --progress-bar off git+https://github.com/pyvista/pyvistaqt
 	python -m pip install --progress-bar off --upgrade --pre imageio-ffmpeg xlrd mffpy python-picard patsy pillow

Diff for: tools/github_actions_dependencies.sh

@@ -29,7 +29,7 @@ else
 	pip install $STD_ARGS --pre git+https://github.com/nilearn/nilearn
 	pip install $STD_ARGS --pre --only-binary ":all:" -i "https://test.pypi.org/simple" openmeeg
 	echo "VTK"
-	pip install $STD_ARGS --pre --only-binary ":all:" vtk
+	pip install $STD_ARGS --pre --only-binary ":all:" -i "https://wheels.vtk.org" vtk
 	python -c "import vtk"
 	echo "PyVista"
 	pip install --progress-bar off git+https://github.com/pyvista/pyvista

Diff for: tutorials/clinical/10_ieeg_localize.py

@@ -26,7 +26,6 @@
 use this module in your analysis to support the addition of new projects to
 MNE.
 """
-
 # Authors: Alex Rockhill <aprockhill@mailbox.org>
 #          Eric Larson <larson.eric.d@gmail.com>
 #