Merge remote-tracking branch 'upstream/main' into gui

* upstream/main:
  FIX: close_connect (mne-tools#10388) [circle deploy]
  FIX: Bump deps (mne-tools#10376)
  [DOC] Small fixes [skip azure] [skip actions] (mne-tools#10381)
  FIX: coreg status bar (mne-tools#10368)

doc/Makefile

@@ -80,7 +80,7 @@ html-noplot:
 	@echo "Build finished. The HTML pages are in _build/html_stable."
 
 html_dev-front:
-	@PATTERN="\(plot_mne_dspm_source_localization.py\|plot_receptive_field.py\|plot_mne_inverse_label_connectivity.py\|plot_sensors_decoding.py\|plot_stats_cluster_spatio_temporal.py\|plot_20_visualize_evoked.py\)" make html_dev-pattern;
+	@PATTERN="\(30_mne_dspm_loreta.py\|50_decoding.py\|30_strf.py\|20_cluster_1samp_spatiotemporal.py\|20_visualize_evoked.py\)" make html_dev-pattern;
 
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml

doc/changes/latest.inc

@@ -114,7 +114,7 @@ Enhancements
 
 - :meth:`mne.preprocessing.ICA.plot_sources()` is now also supported by the ``qt`` backend (:gh:`10330` by `Martin Schulz`_)
 
-- Added :meth:`mne.viz.Brain.add_dipole` and :meth:`mne.viz.Brain.add_forward` to plot dipoles on a brain (:gh:`10373` by `Alex Rockhill`_)
+- Added :meth:`mne.viz.Brain.add_dipole` and :meth:`mne.viz.Brain.add_forward` to plot dipoles on a brain as well as :meth:`mne.viz.Brain.remove_dipole` and :meth:`mne.viz.Brain.remove_forward` (:gh:`10373` by `Alex Rockhill`_)
 
 Bugs
 ~~~~

doc/conf.py

@@ -6,14 +6,14 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from datetime import datetime, timezone
+import faulthandler
 import gc
 import os
 import subprocess
 import sys
 import time
 import warnings
-from datetime import datetime, timezone
-import faulthandler
 
 import numpy as np
 import matplotlib
@@ -732,6 +732,7 @@ def append_attr_meth_examples(app, what, name, obj, options, lines):
              size=xxl),
     ],
     # \u00AD is an optional hyphen (not rendered unless needed)
+    # If these are changed, the Makefile should be updated, too
     'carousel': [
         dict(title='Source Estimation',
              text='Distributed, sparse, mixed-norm, beam\u00ADformers, dipole fitting, and more.',  # noqa E501

mne/gui/_coreg.py

@@ -2,6 +2,7 @@
 from functools import partial
 import os
 import os.path as op
+import platform
 from pathlib import Path
 import time
 import queue
@@ -178,7 +179,6 @@ def _get_default(var, val):
         self._mri_fids_modified = False
         self._mri_scale_modified = False
         self._accept_close_event = True
-        self._auto_cleanup = True
         self._fid_colors = tuple(
             DEFAULTS['coreg'][f'{key}_color'] for key in
             ('lpa', 'nasion', 'rpa'))
@@ -230,9 +230,9 @@ def _get_default(var, val):
         # setup the window
         self._renderer = _get_renderer(
             size=self._defaults["size"], bgcolor=self._defaults["bgcolor"])
-        self._renderer._window_close_connect(self._close_callback)
+        self._renderer._window_close_connect(self._clean)
+        self._renderer._window_close_connect(self._close_callback, after=False)
         self._renderer.set_interaction(interaction)
-        self._renderer._status_bar_initialize()
 
         # coregistration model setup
         self._immediate_redraw = (self._renderer._kind != 'qt')
@@ -728,7 +728,9 @@ def _redraw(self, verbose=None):
                 draw_map[key]()
             self._redraws_pending.clear()
             self._renderer._update()
-            self._renderer._process_events()  # necessary for MacOS?
+            # necessary for MacOS
+            if platform.system() == 'Darwin':
+                self._renderer._process_events()
 
     def _on_mouse_move(self, vtk_picker, event):
         if self._mouse_no_mvt:
@@ -1707,18 +1709,17 @@ def _configure_dock(self):
         self._renderer._dock_add_stretch()
 
     def _configure_status_bar(self):
+        self._renderer._status_bar_initialize()
         self._widgets['status_message'] = self._renderer._status_bar_add_label(
             "", stretch=1
         )
         self._forward_widget_command(
             'status_message', 'hide', value=None, input_value=False
         )
 
-    def _set_automatic_cleanup(self, state):
-        """Enable/Disable automatic cleanup (for testing purposes only)."""
-        self._auto_cleanup = state
-
     def _clean(self):
+        if not self._accept_close_event:
+            return
         self._renderer = None
         self._widgets.clear()
         self._actors.clear()
@@ -1789,7 +1790,4 @@ def _close_callback(self):
                 modal=not MNE_3D_BACKEND_TESTING,
             )
             self._widgets["close_dialog"].show()
-
-        if self._accept_close_event and self._auto_cleanup:
-            self._clean()
         return self._accept_close_event

mne/gui/tests/test_coreg_gui.py

@@ -223,8 +223,9 @@ def test_coreg_gui_pyvista(tmp_path, renderer_interactive_pyvistaqt):
     assert not coreg._trans_modified
     assert op.isfile(tmp_trans)
 
+    # first, disable auto cleanup
+    coreg._renderer._window_close_disconnect(after=True)
     # test _close_callback()
-    coreg._set_automatic_cleanup(False)
     coreg.close()
     coreg._widgets['close_dialog'].trigger('Discard')  # do not save
     coreg._clean()  # finally, cleanup internal structures

mne/gui/tests/test_gui_api.py

@@ -334,7 +334,15 @@ def _check_widget_trigger(widget, mock, before, after, call_count=True,
     # --- END: dialog ---
 
     renderer.show()
+
+    renderer._window_close_connect(lambda: mock('first'), after=False)
+    renderer._window_close_connect(lambda: mock('last'))
+    old_call_count = mock.call_count
     renderer.close()
+    if renderer._kind == 'qt':
+        assert mock.call_count == old_call_count + 2
+        assert mock.call_args_list[-1].args == ('last',)
+        assert mock.call_args_list[-2].args == ('first',)
 
 
 def test_gui_api_qt(renderer_interactive_pyvistaqt):

mne/utils/misc.py

@@ -326,6 +326,14 @@ def _file_like(obj):
     return all(callable(getattr(obj, name, None)) for name in ('read', 'seek'))
 
 
+def _fullname(obj):
+    klass = obj.__class__
+    module = klass.__module__
+    if module == 'builtins':
+        return klass.__qualname__
+    return module + '.' + klass.__qualname__
+
+
 def _assert_no_instances(cls, when=''):
     __tracebackhide__ = True
     n = 0
@@ -350,14 +358,15 @@ def _assert_no_instances(cls, when=''):
                     if isinstance(r, (list, dict)):
                         rep = f'len={len(r)}'
                         r_ = gc.get_referrers(r)
-                        types = (x.__class__.__name__ for x in r_)
+                        types = (_fullname(x) for x in r_)
                         types = "/".join(sorted(set(
                             x for x in types if x is not None)))
                         rep += f', {len(r_)} referrers: {types}'
                         del r_
                     else:
                         rep = repr(r)[:100].replace('\n', ' ')
-                    ref.append(f'{r.__class__.__name__}: {rep}')
+                    name = _fullname(r)
+                    ref.append(f'{name}: {rep}')
                     count += 1
                 del r
             del rr

mne/viz/_brain/_brain.py

@@ -745,7 +745,7 @@ def _clean(self):
         for renderer in self._renderer._all_renderers:
             renderer.RemoveAllLights()
         # app_window cannot be set to None because it is used in __del__
-        for key in ('lighting', 'interactor'):
+        for key in ('lighting', 'interactor', '_RenderWindow'):
             setattr(self.plotter, key, None)
         # Qt LeaveEvent requires _Iren so we use _FakeIren instead of None
         # to resolve the ref to vtkGenericRenderWindowInteractor
@@ -2441,7 +2441,7 @@ def add_dipole(self, dipole, trans, colors='red', alpha=1, scales=None):
 
         Parameters
         ----------
-        dipole : instance of Dipole | instance of Forward
+        dipole : instance of Dipole
             Dipole object containing position, orientation and amplitude of
             one or more dipoles or in the forward solution.
         %(trans_not_none)s

mne/viz/backends/_abstract.py

@@ -844,7 +844,11 @@ def _window_initialize(self):
         self._interactor_fraction = None
 
     @abstractmethod
-    def _window_close_connect(self, func):
+    def _window_close_connect(self, func, *, after=True):
+        pass
+
+    @abstractmethod
+    def _window_close_disconnect(self, after=True):
         pass
 
     @abstractmethod

mne/viz/backends/_notebook.py

@@ -337,17 +337,17 @@ def _menu_add_button(self, menu_name, name, desc, func):
 
 class _IpyStatusBar(_AbstractStatusBar, _IpyLayout):
     def _status_bar_initialize(self, window=None):
-        self._status_bar = self._status_bar_layout = HBox()
+        self._status_bar = HBox()
         self._layout_initialize(None)
 
     def _status_bar_add_label(self, value, *, stretch=0):
         widget = Text(value=value, disabled=True)
-        self._layout_add_widget(self._status_bar_layout, widget)
+        self._layout_add_widget(self._status_bar, widget)
         return _IpyWidget(widget)
 
     def _status_bar_add_progress_bar(self, stretch=0):
         widget = IntProgress()
-        self._layout_add_widget(self._status_bar_layout, widget)
+        self._layout_add_widget(self._status_bar, widget)
         return _IpyWidget(widget)
 
     def _status_bar_update(self):
@@ -388,7 +388,10 @@ def __init__(self, brain, width, height, dpi):
 
 
 class _IpyWindow(_AbstractWindow):
-    def _window_close_connect(self, func):
+    def _window_close_connect(self, func, *, after=True):
+        pass
+
+    def _window_close_disconnect(self, after=True):
         pass
 
     def _window_get_dpi(self):

mne/viz/backends/_qt.py

@@ -485,20 +485,19 @@ class _QtStatusBar(_AbstractStatusBar, _QtLayout):
     def _status_bar_initialize(self, window=None):
         window = self._window if window is None else window
         self._status_bar = window.statusBar()
-        self._status_bar_layout = self._status_bar.layout()
 
     def _status_bar_add_label(self, value, *, stretch=0):
         widget = QLabel(value)
-        self._layout_add_widget(self._status_bar_layout, widget, stretch)
+        self._layout_add_widget(self._status_bar.layout(), widget, stretch)
         return _QtWidget(widget)
 
     def _status_bar_add_progress_bar(self, stretch=0):
         widget = QProgressBar()
-        self._layout_add_widget(self._status_bar_layout, widget, stretch)
+        self._layout_add_widget(self._status_bar.layout(), widget, stretch)
         return _QtWidget(widget)
 
     def _status_bar_update(self):
-        self._status_bar_layout.update()
+        self._status_bar.layout().update()
 
 
 class _QtPlayback(_AbstractPlayback):
@@ -544,29 +543,45 @@ def _window_initialize(self):
         self._window = self.figure.plotter.app_window
         self._window.setLocale(QLocale(QLocale.Language.English))
         self._window.signal_close.connect(self._window_clean)
-        self._window_close_callbacks = list()
+        self._window_before_close_callbacks = list()
+        self._window_after_close_callbacks = list()
 
         # patch closeEvent
         def closeEvent(event):
+            # functions to call before closing
             accept_close_event = True
-            for callback in self._window_close_callbacks:
+            for callback in self._window_before_close_callbacks:
                 ret = callback()
                 # check if one of the callbacks ignores the close event
                 if isinstance(ret, bool) and not ret:
                     accept_close_event = False
+
             if accept_close_event:
                 self._window.signal_close.emit()
                 event.accept()
             else:
                 event.ignore()
+
+            # functions to call after closing
+            for callback in self._window_after_close_callbacks:
+                callback()
         self._window.closeEvent = closeEvent
 
     def _window_clean(self):
         self.figure._plotter = None
         self._interactor = None
 
-    def _window_close_connect(self, func):
-        self._window_close_callbacks.append(func)
+    def _window_close_connect(self, func, *, after=True):
+        if after:
+            self._window_after_close_callbacks.append(func)
+        else:
+            self._window_before_close_callbacks.append(func)
+
+    def _window_close_disconnect(self, after=True):
+        if after:
+            self._window_after_close_callbacks.clear()
+        else:
+            self._window_before_close_callbacks.clear()
 
     def _window_get_dpi(self):
         return self._window.windowHandle().screen().logicalDotsPerInch()

tools/azure_dependencies.sh

@@ -12,9 +12,9 @@ elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" python-dateutil pytz joblib threadpoolctl six cycler kiwisolver pyparsing patsy
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps --extra-index-url https://www.riverbankcomputing.com/pypi/simple PyQt5 PyQt5-sip PyQt5-Qt5
 	# SciPy Windows build is missing from conda nightly builds, and statsmodels does not work
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" "numpy<1.23.dev0+730"
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps scipy statsmodels
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" pandas scikit-learn dipy
+	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy
+	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps scipy
+	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" pandas scikit-learn dipy statsmodels
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py Pillow matplotlib
 	python -m pip install --progress-bar off --upgrade --pre --only-binary "vtk" vtk
 	python -m pip install --progress-bar off https://github.com/pyvista/pyvista/zipball/main

tools/github_actions_dependencies.sh

@@ -19,7 +19,7 @@ else
 	echo "NumPy/SciPy/pandas etc."
 	# TODO: Currently missing dipy for 3.10 https://github.com/dipy/dipy/issues/2489
 	# TODO: Revert this and Azure once https://github.com/numpy/numpy/pull/21054 is merged and a new wheel is out
-	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" "numpy<1.23.dev0+730" scipy pandas "scikit-learn>=0.24.2" statsmodels
+	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy scipy pandas scikit-learn statsmodels
 	echo "H5py, pillow, matplotlib"
 	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py pillow matplotlib
 	# We don't install Numba here because it forces an old NumPy version

tutorials/clinical/10_ieeg_localize.py

@@ -189,7 +189,7 @@ def plot_overlay(image, compare, title, thresh=None):
 #    reg_affine, _ = mne.transforms.compute_volume_registration(
 #         CT_orig, T1, pipeline='rigids', zooms=dict(translation=5)))
 #
-# And instead we just hard-code the resulting 4x4 matrix:
+# Instead we just hard-code the resulting 4x4 matrix:
 
 reg_affine = np.array([
     [0.99270756, -0.03243313, 0.11610254, -133.094156],

tutorials/preprocessing/70_fnirs_processing.py

@@ -338,7 +338,7 @@
 mne.viz.plot_evoked_topo(epochs['Right'].average(picks='hbo'), color='r',
                          axes=axes, legend=False)
 
-# Tidy the legend.
+# Tidy the legend:
 leg_lines = [line for line in axes.lines if line.get_c() == 'b'][:1]
 leg_lines.append([line for line in axes.lines if line.get_c() == 'r'][0])
 fig.legend(leg_lines, ['Left', 'Right'], loc='lower right')