[pull] main from mne-tools:main

.github/workflows/tests.yml

@@ -50,7 +50,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 85
+    timeout-minutes: 90
     runs-on: ${{ matrix.os }}
     defaults:
       run:

doc/changes/dev/13371.bugfix.rst

@@ -0,0 +1 @@
+Fix the check in :func:`mne.make_forward_solution` that all MEG sensors are outside a spherical BEM model, by `Marijn van Vliet`_

doc/changes/dev/13376.bugfix.rst

@@ -0,0 +1 @@
+Ensure auto-computed plot scalings are always non-zero, by `Daniel McCloy`_.

mne/forward/_make_forward.py

@@ -553,9 +553,8 @@ def check_inside(x):
             else:
 
                 def check_inside(x):
-                    return (
-                        np.linalg.norm(x - bem["r0"], axis=1) < bem["layers"][-1]["rad"]
-                    )
+                    r0 = apply_trans(invert_transform(mri_head_t), bem["r0"])
+                    return np.linalg.norm(x - r0, axis=1) < bem["layers"][-1]["rad"]
 
         if "meg" in sensors:
             meg_loc = apply_trans(

mne/forward/tests/test_make_forward.py

@@ -574,6 +574,7 @@ def test_make_forward_solution_sphere(tmp_path, fname_src_small):
             1.0,
             rtol=1e-3,
         )
+
     # Number of layers in the sphere model doesn't matter for MEG
     # (as long as no sources are omitted due to distance)
     assert len(sphere["layers"]) == 4
@@ -592,6 +593,14 @@ def test_make_forward_solution_sphere(tmp_path, fname_src_small):
     with pytest.raises(RuntimeError, match="zero shells.*EEG"):
         make_forward_solution(fname_raw, fname_trans, src, sphere)
 
+    # Since the spherical model is defined in head space, the head->MRI transform should
+    # not matter for the check that MEG sensors are outside the sphere.
+    custom_trans = Transform("head", "mri")
+    custom_trans["trans"][0, 3] = 0.05  # move MEG sensors close to mesh
+    sphere = make_sphere_model()
+    fwd = make_forward_solution(fname_raw, custom_trans, src, sphere)
+    assert fwd["mri_head_t"]["trans"][0, 3] == -0.05
+
 
 @pytest.mark.slowtest
 @testing.requires_testing_data

mne/viz/tests/test_utils.py

@@ -129,6 +129,10 @@ def test_auto_scale():
     raw = read_raw_fif(raw_fname)
     epochs = Epochs(raw, read_events(ev_fname))
     rand_data = np.random.randn(10, 100)
+    # make a stim channel all zeros (gh 13376)
+    ix = raw.get_channel_types().index("stim")
+    raw.load_data()
+    raw._data[ix] = 0.0
 
     for inst in [raw, epochs]:
         scale_grad = 1e10
@@ -142,6 +146,8 @@ def test_auto_scale():
         scalings_new = _compute_scalings(scalings_def, inst)
         assert scale_grad == scalings_new["grad"]
         assert scalings_new["eeg"] != "auto"
+        # make sure an all-zero channel doesn't cause scaling=0 (gh 13376)
+        assert scalings_new["stim"] > 0
 
     with pytest.raises(ValueError, match="Must supply either Raw or Epochs"):
         _compute_scalings(scalings_def, rand_data)

mne/viz/utils.py

@@ -1423,6 +1423,8 @@ def _compute_scalings(scalings, inst, remove_dc=False, duration=10):
         this_data = this_data[np.isfinite(this_data)]
         if this_data.size:
             iqr = np.diff(np.percentile(this_data, [25, 75]))[0]
+            if iqr == 0:  # e.g. sparse stim channels, flat channels
+                iqr = 1.0
         else:
             iqr = 1.0
         scalings[key] = iqr

tools/github_actions_test.sh

@@ -21,14 +21,16 @@ if [[ ! -z "$CONDA_ENV" ]] && [[ "${RUNNER_OS}" != "Windows" ]] && [[ "${MNE_CI_
   INSTALL_PATH=$(python -c "import mne, pathlib; print(str(pathlib.Path(mne.__file__).parents[1]))")
   echo "Copying tests from ${PROJ_PATH}/mne-python/mne/ to ${INSTALL_PATH}/mne/"
   echo "::group::rsync mne"
-  rsync -a --partial --progress --prune-empty-dirs --exclude="*.pyc" --include="**/" --include="**/tests/*" --include="**/tests/data/**" --exclude="**" ${PROJ_PATH}/mne/ ${INSTALL_PATH}/mne/
+  set -x
+  rsync -a --partial --progress --prune-empty-dirs --exclude="*.pyc" --include="*/" --include="tests/**" --include="**/tests/**" --exclude="**" ${PROJ_PATH}/mne/ ${INSTALL_PATH}/mne/
   echo "::endgroup::"
   echo "::group::rsync doc"
   mkdir -p ${INSTALL_PATH}/doc/
-  rsync -a --partial --progress --prune-empty-dirs --include="**/" --include="**/api/*" --exclude="**" ${PROJ_PATH}/doc/ ${INSTALL_PATH}/doc/
+  rsync -a --partial --progress --prune-empty-dirs --include="api/" --include="api/*.rst" --exclude="*" ${PROJ_PATH}/doc/ ${INSTALL_PATH}/doc/
   test -f ${INSTALL_PATH}/doc/api/reading_raw_data.rst
   cd $INSTALL_PATH
   cp -av $PROJ_PATH/pyproject.toml .
+  set +x
   echo "::endgroup::"
 fi