Use black to lint python files

Makefile

@@ -0,0 +1,8 @@
+.PHONY: format
+format:
+	black -t py39 meggie
+
+.PHONY: check
+check:
+	black --check -t py39 meggie
+	pylama meggie

dev-requirements.txt

@@ -0,0 +1,2 @@
+black
+pylama

meggie/actions/epochs_create/__init__.py

@@ -7,26 +7,29 @@
 from meggie.mainwindow.dynamic import Action
 from meggie.mainwindow.dynamic import subject_action
 
-from meggie.actions.epochs_create.dialogs.createEpochsFromEventsDialogMain import CreateEpochsFromEventsDialog
+from meggie.actions.epochs_create.dialogs.createEpochsFromEventsDialogMain import (
+    CreateEpochsFromEventsDialog,
+)
 from meggie.actions.epochs_create.controller.epoching import create_epochs_from_events
 
 
 class CreateEpochs(Action):
-    """ Shows a dialog for event selection and then creates epochs.
-    """
+    """Shows a dialog for event selection and then creates epochs."""
+
     def run(self):
         default_name = next_available_name(
-            self.experiment.active_subject.epochs.keys(), 'Epochs')
+            self.experiment.active_subject.epochs.keys(), "Epochs"
+        )
 
-        dialog = CreateEpochsFromEventsDialog(self.experiment, self.window, 
-                                              default_name, self.handler)
+        dialog = CreateEpochsFromEventsDialog(
+            self.experiment, self.window, default_name, self.handler
+        )
         dialog.show()
 
-
     @subject_action
     def handler(self, subject, params):
-        """
-        """
+        """ """
+
         @threaded
         def create():
             create_epochs_from_events(subject, params)

meggie/actions/epochs_create/controller/epoching.py

@@ -15,25 +15,24 @@
 
 
 def create_epochs_from_events(subject, params):
-    """ Creates epochs based on events.
-    """
+    """Creates epochs based on events."""
     raw = subject.get_raw()
 
     params = copy.deepcopy(params)
-    event_params = params['events']
-    reject_params = params['reject']
+    event_params = params["events"]
+    reject_params = params["reject"]
 
     # convert reject params from human readable units to standard units
     for key in reject_params:
         reject_params[key] /= get_scaling(key)
 
     # remove params that don't match with the channel types present in raw
-    if mne.pick_types(raw.info, meg='grad', eeg=False).size == 0:
-        reject_params.pop('grad', None)
-    if mne.pick_types(raw.info, meg='mag', eeg=False).size == 0:
-        reject_params.pop('mag', None)
+    if mne.pick_types(raw.info, meg="grad", eeg=False).size == 0:
+        reject_params.pop("grad", None)
+    if mne.pick_types(raw.info, meg="mag", eeg=False).size == 0:
+        reject_params.pop("mag", None)
     if mne.pick_types(raw.info, meg=False, eeg=True).size == 0:
-        reject_params.pop('eeg', None)
+        reject_params.pop("eeg", None)
 
     events = []
     category = {}
@@ -44,67 +43,79 @@ def create_epochs_from_events(subject, params):
     # so we just add placeholders as 1, 2, 3...
     if len(event_params) > 0:
         for idx, item in enumerate(event_params):
-            event_id = item['event_id']
-            mask = item['mask']
-            category_id = (
-                'id_' + str(event_id) + '_mask_' + str(mask))
+            event_id = item["event_id"]
+            mask = item["mask"]
+            category_id = "id_" + str(event_id) + "_mask_" + str(mask)
 
             new_events = find_events(raw, stim_channel, mask, event_id)
 
             if len(new_events) == 0:
-                logging.warning('No events found with setting ' +
-                                str(category_id))
+                logging.warning("No events found with setting " + str(category_id))
                 continue
 
             category[category_id] = idx + 1
             new_events[:, 2] = idx + 1
 
-            events.extend([[event[0] + int(round(raw.info['sfreq']*params['delay'])), 
-                            event[1], event[2]] 
-                           for event in new_events])
+            events.extend(
+                [
+                    [
+                        event[0] + int(round(raw.info["sfreq"] * params["delay"])),
+                        event[1],
+                        event[2],
+                    ]
+                    for event in new_events
+                ]
+            )
 
     if len(events) == 0:
         raise ValueError(
-            'No matching events found. Please check rejection limits and other parameters.')
+            "No matching events found. Please check rejection limits and other parameters."
+        )
 
     # prepare parameters for pick_types
-    if params['mag'] and params['grad']:
+    if params["mag"] and params["grad"]:
         meg = True
-    elif params['mag']:
-        meg = 'mag'
-    elif params['grad']:
-        meg = 'grad'
+    elif params["mag"]:
+        meg = "mag"
+    elif params["grad"]:
+        meg = "grad"
     else:
         meg = False
 
-    eeg = params['eeg']
+    eeg = params["eeg"]
 
     # find all proper picks, dont exclude bads
     picks = mne.pick_types(raw.info, meg=meg, eeg=eeg, exclude=[])
 
     if len(picks) == 0:
-        raise ValueError('You should select at least one channel type')
-
-    mne_epochs = mne.Epochs(raw, np.array(events),
-                            category, params['tmin'], params['tmax'],
-                            baseline=(params['bstart'], params['bend']),
-                            picks=picks, reject=reject_params)
+        raise ValueError("You should select at least one channel type")
+
+    mne_epochs = mne.Epochs(
+        raw,
+        np.array(events),
+        category,
+        params["tmin"],
+        params["tmax"],
+        baseline=(params["bstart"], params["bend"]),
+        picks=picks,
+        reject=reject_params,
+    )
 
     if len(mne_epochs.get_data()) == 0:
-        raise ValueError('Could not find any data. Perhaps the ' +
-                         'rejection thresholds are too strict...')
+        raise ValueError(
+            "Could not find any data. Perhaps the "
+            + "rejection thresholds are too strict..."
+        )
 
     n_dropped = len(events) - len(mne_epochs.get_data())
 
     if n_dropped > 0:
-        logging.getLogger('ui_logger').info(str(n_dropped) + ' epochs dropped.')
+        logging.getLogger("ui_logger").info(str(n_dropped) + " epochs dropped.")
 
     epochs_directory = subject.epochs_directory
-    epochs = Epochs(params['collection_name'],
-                    epochs_directory,
-                    params,
-                    content=mne_epochs)
+    epochs = Epochs(
+        params["collection_name"], epochs_directory, params, content=mne_epochs
+    )
 
     epochs.save_content()
-    subject.add(epochs, 'epochs')
-
+    subject.add(epochs, "epochs")

meggie/actions/epochs_create/dialogs/createEpochsFromEventsDialogMain.py

@@ -9,7 +9,9 @@
 
 import numpy as np
 
-from meggie.actions.epochs_create.dialogs.createEpochsFromEventsDialogUi import Ui_CreateEpochsFromEventsDialog
+from meggie.actions.epochs_create.dialogs.createEpochsFromEventsDialogUi import (
+    Ui_CreateEpochsFromEventsDialog,
+)
 from meggie.actions.epochs_create.controller.epoching import create_epochs_from_events
 
 from meggie.utilities.widgets.batchingWidgetMain import BatchingWidget
@@ -21,8 +23,7 @@
 
 
 class CreateEpochsFromEventsDialog(QtWidgets.QDialog):
-    """Dialog responsible for collecting parameters for epoch creation.
-    """
+    """Dialog responsible for collecting parameters for epoch creation."""
 
     def __init__(self, experiment, parent, default_name, handler):
         QtWidgets.QDialog.__init__(self, parent)
@@ -39,7 +40,8 @@ def __init__(self, experiment, parent, default_name, handler):
             experiment_getter=self._experiment_getter,
             parent=self,
             container=self.ui.groupBoxBatching,
-            geometry=self.ui.batchingWidgetPlaceholder.geometry())
+            geometry=self.ui.batchingWidgetPlaceholder.geometry(),
+        )
         self.ui.gridLayoutBatching.addWidget(self.batching_widget, 0, 0, 1, 1)
 
         self.ui.lineEditCollectionName.setText(default_name)
@@ -54,10 +56,9 @@ def _update_events(self):
 
         for event in events:
             item = QtWidgets.QListWidgetItem(
-                '%s, %s' % (
-                    'ID ' + str(event['event_id']),
-                    'mask=' + str(event['mask'])
-                ))
+                "%s, %s"
+                % ("ID " + str(event["event_id"]), "mask=" + str(event["mask"]))
+            )
             self.ui.listWidgetEvents.addItem(item)
 
     def _collect_parameter_values(self):
@@ -71,29 +72,34 @@ def _collect_parameter_values(self):
         grad = self.ui.checkBoxGrad.isChecked()
         eeg = self.ui.checkBoxEeg.isChecked()
 
-        collection_name = validate_name(
-            str(self.ui.lineEditCollectionName.text()))
+        collection_name = validate_name(str(self.ui.lineEditCollectionName.text()))
 
         reject = dict()
         if mag:
-            reject['mag'] = self.ui.doubleSpinBoxMagReject.value()
+            reject["mag"] = self.ui.doubleSpinBoxMagReject.value()
         if grad:
-            reject['grad'] = self.ui.doubleSpinBoxGradReject.value()
+            reject["grad"] = self.ui.doubleSpinBoxGradReject.value()
         if eeg:
-            reject['eeg'] = self.ui.doubleSpinBoxEEGReject.value()
-
-        params = {'mag': mag, 'grad': grad, 'eeg': eeg,
-                  'reject': reject,
-                  'tmin': tmin, 'tmax': tmax,
-                  'bstart': bstart, 'bend': bend,
-                  'delay': delay,
-                  'collection_name': collection_name,
-                  'events': self.events}
+            reject["eeg"] = self.ui.doubleSpinBoxEEGReject.value()
+
+        params = {
+            "mag": mag,
+            "grad": grad,
+            "eeg": eeg,
+            "reject": reject,
+            "tmin": tmin,
+            "tmax": tmax,
+            "bstart": bstart,
+            "bend": bend,
+            "delay": delay,
+            "collection_name": collection_name,
+            "events": self.events,
+        }
         return params
 
     def accept(self):
         if self.ui.listWidgetEvents.count() == 0:
-            message = 'Cannot create epochs from empty list.'
+            message = "Cannot create epochs from empty list."
             messagebox(self.parent, message)
             return
 
@@ -120,7 +126,7 @@ def acceptBatch(self):
         experiment = self.experiment
 
         if self.ui.listWidgetEvents.count() == 0:
-            message = 'Cannot create epochs from empty list.'
+            message = "Cannot create epochs from empty list."
             messagebox(self.parent, message)
             return
 
@@ -137,9 +143,8 @@ def acceptBatch(self):
                     self.handler(subject, params)
                     subject.release_memory()
                 except Exception as exc:
-                    self.batching_widget.failed_subjects.append((subject,
-                                                                 str(exc)))
-                    logging.getLogger('ui_logger').exception('')
+                    self.batching_widget.failed_subjects.append((subject, str(exc)))
+                    logging.getLogger("ui_logger").exception("")
 
         self.batching_widget.cleanup()
 
@@ -155,8 +160,9 @@ def on_pushButtonEdit_clicked(self, checked=None):
         if checked is None:
             return
 
-        self.bitDialog = BitSelectionDialog(self,
-                                            self.ui.spinBoxMask, self.ui.spinBoxEventID)
+        self.bitDialog = BitSelectionDialog(
+            self, self.ui.spinBoxMask, self.ui.spinBoxEventID
+        )
 
         self.bitDialog.show()
 
@@ -178,17 +184,18 @@ def on_pushButtonHelp_clicked(self, checked=None):
             "two digits can be 1 or 0, but anything else must be exactly as "
             "in the event id. Thus events with following id's would be allowed:"
             "\n\n0000010000010000 = 1040\n0000010000010001 = 1041\n"
-            "0000010000010010 = 1042\n0000010000010011 = 1043")
+            "0000010000010010 = 1042\n0000010000010011 = 1043"
+        )
 
-        messagebox(self.parent, help_message, 'Mask help')
+        messagebox(self.parent, help_message, "Mask help")
 
     def on_pushButtonAdd_clicked(self, checked=None):
         if checked is None:
             return
 
         event_params = {
-            'mask': self.ui.spinBoxMask.value(),
-            'event_id': self.ui.spinBoxEventID.value(),
+            "mask": self.ui.spinBoxMask.value(),
+            "event_id": self.ui.spinBoxEventID.value(),
         }
 
         if event_params not in self.events:
@@ -201,4 +208,3 @@ def on_pushButtonClear_clicked(self, checked=None):
 
         self.events = []
         self._update_events()
-