Add automatic inspection for what mne calls are made from actions for…

… documentation purposes

Makefile

@@ -15,10 +15,10 @@ test:
 update_docs:
 	rm -fr docs_updated
 	cp -fr docs docs_updated
-	python scripts/update_docs.py docs_updated
+	python -m scripts.update_docs docs_updated
 
 .PHONY: serve_docs
-serve_docs: update_docs
+serve_docs:
 	mkdocs serve
 
 .PHONY: cov

docs/about.md

@@ -9,7 +9,7 @@ Meggie focuses on:
 1. **Multi-Subject Management**: It makes it easy to work with many subjects' data at once.
 2. **Clear Analysis Steps**: It helps users go step by step from starting data to results.
 
-Compared to other tools like FieldTrip, MNE-Python, EEGLAB, Brainstorm, and mnelab, Meggie is unique because it's built with Python, it's easy for anyone to use, and it's designed for handling multiple subjects' data efficiently.
+Compared to other tools like FieldTrip, MNE-Python, EEGLAB, Brainstorm, and MNELAB, Meggie is unique because it's built with Python, it's easy for anyone to use, and it's designed for handling multiple subjects' data efficiently.
 
 ## Plugins
 

meggie/actions/epochs_delete/tests/test_epochs_delete.py

@@ -11,5 +11,4 @@ def test_epochs_delete(self):
             action_name="epochs_delete",
             handler=DeleteEpochs,
             data=data,
-            patch_paths=["meggie.actions.epochs_delete"],
         )

meggie/actions/epochs_delete_from_all/tests/test_epochs_delete_from_all.py

@@ -11,5 +11,4 @@ def test_epochs_delete_from_all(self):
             action_name="epochs_delete_from_all",
             handler=DeleteEpochsFromAll,
             data=data,
-            patch_paths=["meggie.actions.epochs_delete_from_all"],
         )

meggie/actions/epochs_info/tests/test_epochs_info.py

@@ -11,6 +11,5 @@ def test_epochs_info(self):
             action_name="epochs_info",
             handler=Info,
             data=data,
-            patch_paths=["meggie.actions.epochs_info"],
         )
         assert content

meggie/actions/epochs_plot/__init__.py

@@ -26,4 +26,5 @@ def run(self):
     @subject_action
     def handler(self, subject, params):
         epochs = subject.epochs.get(params["name"])
-        epochs.content.plot()
+        mne_epochs = epochs.content
+        mne_epochs.plot()

meggie/actions/epochs_plot/tests/test_epochs_plot.py

@@ -7,9 +7,4 @@ def test_epochs_plot(self):
 
         data = {"outputs": {"epochs": ["Epochs"]}}
 
-        self.run_action(
-            action_name="epochs_plot",
-            handler=PlotEpochs,
-            data=data,
-            patch_paths=["meggie.actions.epochs_plot"],
-        )
+        self.run_action(action_name="epochs_plot", handler=PlotEpochs, data=data)

meggie/actions/epochs_plot_image/__init__.py

@@ -28,7 +28,8 @@ def run(self):
     @subject_action
     def handler(self, subject, params):
         epochs = subject.epochs.get(params["name"])
-        figs = epochs.content.plot_image()
+        mne_epochs = epochs.content
+        figs = mne_epochs.plot_image()
         for fig in figs:
             ch_type = get_figure_title(fig)
             title = "{0}_{1}".format(params["name"], ch_type)

meggie/actions/epochs_plot_image/tests/test_epochs_plot_image.py

@@ -11,5 +11,4 @@ def test_epochs_plot_image(self):
             action_name="epochs_plot_image",
             handler=PlotEpochsImage,
             data=data,
-            patch_paths=["meggie.actions.epochs_plot_image"],
         )

meggie/actions/evoked_delete/tests/test_evoked_delete.py

@@ -11,5 +11,4 @@ def test_evoked_delete(self):
             action_name="evoked_delete",
             handler=DeleteEvoked,
             data=data,
-            patch_paths=["meggie.actions.evoked_delete"],
         )

meggie/actions/evoked_delete_from_all/tests/test_evoked_delete_from_all.py

@@ -11,5 +11,4 @@ def test_evoked_delete_from_all(self):
             action_name="evoked_delete_from_all",
             handler=DeleteEvokedFromAll,
             data=data,
-            patch_paths=["meggie.actions.evoked_delete_from_all"],
         )

meggie/actions/evoked_group_average/tests/test_evoked_group_average.py

@@ -16,13 +16,12 @@ def test_evoked_group_average(self):
             action_name="evoked_group_average",
             handler=GroupAverage,
             data=data,
-            patch_paths=["meggie.actions.evoked_group_average"],
         )
         dialog = self.find_dialog(GroupSelectionDialog)
 
         dialog.ui.checkBoxGroup_0.setCheckState(QtCore.Qt.Checked)
         dialog.ui.spinBoxGroup_0.setValue(1)
         dialog.ui.checkBoxGroup_1.setCheckState(QtCore.Qt.Checked)
-        dialog.ui.spinBoxGroup_1.setValue(2)
+        dialog.ui.spinBoxGroup_1.setValue(1)
 
         dialog.accept()

meggie/actions/evoked_info/tests/test_evoked_info.py

@@ -11,6 +11,5 @@ def test_evoked_info(self):
             action_name="evoked_info",
             handler=Info,
             data=data,
-            patch_paths=["meggie.actions.evoked_info"],
         )
         assert content

meggie/actions/evoked_plot/controller/evoked.py

@@ -71,9 +71,9 @@ def plot_evoked_topo(subject, evoked, ch_type):
     """Plots evoked time courses arranged as a topography"""
     evokeds = []
     labels = []
-    for key, evok in sorted(evoked.content.items()):
+    for key, mne_evoked in sorted(evoked.content.items()):
 
-        info = evok.info
+        info = mne_evoked.info
         if ch_type == "eeg":
             dropped_names = [
                 ch_name
@@ -87,11 +87,12 @@ def plot_evoked_topo(subject, evoked, ch_type):
                 if ch_idx not in mne.pick_types(info, eeg=False, meg=True)
             ]
 
-        evok = evok.copy().drop_channels(dropped_names)
+        mne_evoked = mne_evoked.copy().drop_channels(dropped_names)
+
+        ensure_montage(subject, mne_evoked, ch_type)
 
-        ensure_montage(subject, evok, ch_type)
+        evokeds.append(mne_evoked)
 
-        evokeds.append(evok)
         labels.append(key)
 
     colors = color_cycle(len(evoked.content.keys()))

meggie/actions/evoked_plot/tests/test_evoked_plot_all_channels.py

@@ -12,7 +12,6 @@ def test_evoked_plot_all_channels(self):
             action_name="evoked_plot",
             handler=PlotEvoked,
             data=data,
-            patch_paths=["meggie.actions.evoked_plot"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/evoked_plot/tests/test_evoked_plot_channel_averages.py

@@ -12,7 +12,6 @@ def test_evoked_plot_channel_averages(self):
             action_name="evoked_plot",
             handler=PlotEvoked,
             data=data,
-            patch_paths=["meggie.actions.evoked_plot"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/evoked_plot_topomap/__init__.py

@@ -52,8 +52,8 @@ def handler(self, subject, params):
         radius = params["radius"]
         evoked = subject.evoked.get(name)
 
-        for key, evok in sorted(evoked.content.items()):
-            channels = get_channels_by_type(evok.info)
+        for key, mne_evoked in sorted(evoked.content.items()):
+            channels = get_channels_by_type(mne_evoked.info)
             for ch_type in channels.keys():
                 title_elems = [name, key, ch_type]
                 times = np.arange(tmin, tmax, step)
@@ -80,7 +80,7 @@ def handler(self, subject, params):
                 if ch_type in ["mag", "grad"]:
                     sphere = radius
 
-                fig = evok.plot_topomap(
+                fig = mne_evoked.plot_topomap(
                     times=times, ch_type=ch_type, axes=axes, sphere=sphere
                 )
                 set_figure_title(fig, "_".join(title_elems))

meggie/actions/evoked_save/tests/test_evoked_save_all_channels.py

@@ -12,7 +12,6 @@ def test_evoked_save_all_channels(self):
             action_name="evoked_save",
             handler=SaveEvoked,
             data=data,
-            patch_paths=["meggie.actions.evoked_save"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/evoked_save/tests/test_evoked_save_channel_averages.py

@@ -12,7 +12,6 @@ def test_evoked_save_channel_averages(self):
             action_name="evoked_save",
             handler=SaveEvoked,
             data=data,
-            patch_paths=["meggie.actions.evoked_save"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/raw_event_info/tests/test_raw_event_info.py

@@ -8,6 +8,5 @@ def test_raw_event_info(self):
         content = self.run_action(
             action_name="raw_event_info",
             handler=Info,
-            patch_paths=["meggie.actions.raw_event_info"],
         )
         assert content

meggie/actions/raw_measurement_info/tests/test_raw_measurement_info.py

@@ -8,6 +8,5 @@ def test_raw_measurement_info(self):
         content = self.run_action(
             action_name="raw_measurement_info",
             handler=Info,
-            patch_paths=["meggie.actions.raw_measurement_info"],
         )
         assert content

meggie/actions/raw_plot/tests/test_raw_plot.py

@@ -9,5 +9,4 @@ def test_raw_plot(self):
         self.run_action(
             action_name="raw_plot",
             handler=PlotRaw,
-            patch_paths=["meggie.actions.raw_plot"],
         )

meggie/actions/raw_plot_projections/tests/test_raw_plot_projections.py

@@ -8,5 +8,4 @@ def test_raw_plot_projections(self):
         self.run_action(
             action_name="raw_plot_projections",
             handler=PlotProjections,
-            patch_paths=["meggie.actions.raw_plot_projections"],
         )

meggie/actions/raw_resample/__init__.py

@@ -24,7 +24,8 @@ def handler(self, subject, params):
 
         @threaded
         def resample_fun():
-            subject.get_raw().resample(params["rate"])
+            raw = subject.get_raw()
+            raw.resample(params["rate"])
 
         resample_fun(do_meanwhile=self.window.update_ui)
         subject.save()

meggie/actions/spectrum_create/controller/spectrum.py

@@ -16,6 +16,7 @@
 @threaded
 def create_power_spectrum(subject, spectrum_name, intervals, fmin, fmax, nfft, overlap):
     """Creates a power spectrum item."""
+
     # get raw objects organized with average groups as keys
     ival_times, raw_block_groups = get_raw_blocks_from_intervals(subject, intervals)
 

meggie/actions/spectrum_delete/tests/test_spectrum_delete.py

@@ -11,5 +11,4 @@ def test_spectrum_delete(self):
             action_name="spectrum_delete",
             handler=DeleteSpectrum,
             data=data,
-            patch_paths=["meggie.actions.spectrum_delete"],
         )

meggie/actions/spectrum_delete_from_all/tests/test_spectrum_delete_from_all.py

@@ -11,5 +11,4 @@ def test_spectrum_delete_from_all(self):
             action_name="spectrum_delete_from_all",
             handler=DeleteSpectrumFromAll,
             data=data,
-            patch_paths=["meggie.actions.spectrum_delete_from_all"],
         )

meggie/actions/spectrum_group_average/tests/test_spectrum_group_average.py

@@ -16,13 +16,12 @@ def test_spectrum_group_average(self):
             action_name="spectrum_group_average",
             handler=GroupAverage,
             data=data,
-            patch_paths=["meggie.actions.spectrum_group_average"],
         )
         dialog = self.find_dialog(GroupSelectionDialog)
 
         dialog.ui.checkBoxGroup_0.setCheckState(QtCore.Qt.Checked)
         dialog.ui.spinBoxGroup_0.setValue(1)
         dialog.ui.checkBoxGroup_1.setCheckState(QtCore.Qt.Checked)
-        dialog.ui.spinBoxGroup_1.setValue(2)
+        dialog.ui.spinBoxGroup_1.setValue(1)
 
         dialog.accept()

meggie/actions/spectrum_info/tests/test_spectrum_info.py

@@ -11,6 +11,5 @@ def test_spectrum_info(self):
             action_name="spectrum_info",
             handler=Info,
             data=data,
-            patch_paths=["meggie.actions.spectrum_info"],
         )
         assert content

meggie/actions/spectrum_plot/tests/test_spectrum_plot_all_channels.py

@@ -12,7 +12,6 @@ def test_spectrum_plot_all_channels(self):
             action_name="spectrum_plot",
             handler=PlotSpectrum,
             data=data,
-            patch_paths=["meggie.actions.spectrum_plot"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/spectrum_plot/tests/test_spectrum_plot_channel_averages.py

@@ -12,7 +12,6 @@ def test_spectrum_plot_channel_averages(self):
             action_name="spectrum_plot",
             handler=PlotSpectrum,
             data=data,
-            patch_paths=["meggie.actions.spectrum_plot"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/spectrum_save/tests/test_spectrum_save_all_channels.py

@@ -12,7 +12,6 @@ def test_spectrum_save_all_channels(self):
             action_name="spectrum_save",
             handler=SaveSpectrum,
             data=data,
-            patch_paths=["meggie.actions.spectrum_save"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/spectrum_save/tests/test_spectrum_save_channels_averages.py

@@ -12,7 +12,6 @@ def test_spectrum_save_channel_averages(self):
             action_name="spectrum_save",
             handler=SaveSpectrum,
             data=data,
-            patch_paths=["meggie.actions.spectrum_save"],
         )
         dialog = self.find_dialog(OutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/tfr_delete/tests/test_tfr_delete.py

@@ -11,5 +11,4 @@ def test_tfr_delete(self):
             action_name="tfr_delete",
             handler=DeleteTFR,
             data=data,
-            patch_paths=["meggie.actions.tfr_delete"],
         )

meggie/actions/tfr_delete_from_all/tests/test_tfr_delete_from_all.py

@@ -11,5 +11,4 @@ def test_tfr_delete_from_all(self):
             action_name="tfr_delete_from_all",
             handler=DeleteTFRFromAll,
             data=data,
-            patch_paths=["meggie.actions.tfr_delete_from_all"],
         )

meggie/actions/tfr_group_average/tests/test_tfr_group_average.py

@@ -16,13 +16,12 @@ def test_tfr_group_average(self):
             action_name="tfr_group_average",
             handler=GroupAverage,
             data=data,
-            patch_paths=["meggie.actions.tfr_group_average"],
         )
         dialog = self.find_dialog(GroupSelectionDialog)
 
         dialog.ui.checkBoxGroup_0.setCheckState(QtCore.Qt.Checked)
         dialog.ui.spinBoxGroup_0.setValue(1)
         dialog.ui.checkBoxGroup_1.setCheckState(QtCore.Qt.Checked)
-        dialog.ui.spinBoxGroup_1.setValue(2)
+        dialog.ui.spinBoxGroup_1.setValue(1)
 
         dialog.accept()

meggie/actions/tfr_info/tests/test_tfr_info.py

@@ -11,6 +11,5 @@ def test_tfr_info(self):
             action_name="tfr_info",
             handler=Info,
             data=data,
-            patch_paths=["meggie.actions.tfr_info"],
         )
         assert content

meggie/actions/tfr_plot/tests/test_tfr_plot_all_channels.py

@@ -12,7 +12,6 @@ def test_tfr_plot_all_channels(self):
             action_name="tfr_plot",
             handler=PlotTFR,
             data=data,
-            patch_paths=["meggie.actions.tfr_plot"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/tfr_plot/tests/test_tfr_plot_channel_averages.py

@@ -12,7 +12,6 @@ def test_tfr_plot_channel_averages(self):
             action_name="tfr_plot",
             handler=PlotTFR,
             data=data,
-            patch_paths=["meggie.actions.tfr_plot"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/tfr_plot_tse/tests/test_tfr_plot_tse_all_channels.py

@@ -12,7 +12,6 @@ def test_tfr_plot_tse_all_channels(self):
             action_name="tfr_plot_tse",
             handler=PlotTSE,
             data=data,
-            patch_paths=["meggie.actions.tfr_plot_tse"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/tfr_plot_tse/tests/test_tfr_plot_tse_channel_averages.py

@@ -12,7 +12,6 @@ def test_tfr_plot_tse_channel_averages(self):
             action_name="tfr_plot_tse",
             handler=PlotTSE,
             data=data,
-            patch_paths=["meggie.actions.tfr_plot_tse"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/tfr_save/tests/test_tfr_save_all_channels.py

@@ -12,7 +12,6 @@ def test_tfr_save_all_channels(self):
             action_name="tfr_save",
             handler=SaveTFR,
             data=data,
-            patch_paths=["meggie.actions.tfr_save"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/tfr_save/tests/test_tfr_save_channel_averages.py

@@ -12,7 +12,6 @@ def test_tfr_save_channel_averages(self):
             action_name="tfr_save",
             handler=SaveTFR,
             data=data,
-            patch_paths=["meggie.actions.tfr_save"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)

meggie/actions/tfr_save_tse/tests/test_tfr_save_tse_all_channels.py

@@ -12,7 +12,6 @@ def test_tfr_save_tse_all_channels(self):
             action_name="tfr_save_tse",
             handler=SaveTSE,
             data=data,
-            patch_paths=["meggie.actions.tfr_save_tse"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(False)

meggie/actions/tfr_save_tse/tests/test_tfr_save_tse_channel_averages.py

@@ -12,7 +12,6 @@ def test_tfr_save_tse_channel_averages(self):
             action_name="tfr_save_tse",
             handler=SaveTSE,
             data=data,
-            patch_paths=["meggie.actions.tfr_save_tse"],
         )
         dialog = self.find_dialog(TFROutputOptions)
         dialog.ui.radioButtonChannelAverages.setChecked(True)