chore: add codespell support (config, workflow to detect/not fix) and make it fix some typos

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

TODO.md

@@ -25,7 +25,7 @@
   - [ ] global settings (e.g. color options, layout)
 - [x] unit list
     - [x] more columns to panel unit list
-    - [x] add settings to select colums
+    - [x] add settings to select columns
     - [x] add sparsity and channel id
     - [x] visible only when clicking on select column
     - [x] make x-axis scrollable

docs/source/views.rst

@@ -12,7 +12,7 @@ Controls
 ~~~~~~~~
 - **left click** : select single unit
 - **ctrl + left click** : add unit to selection
-- **mouse drag from within circle** : change channel visibilty and unit visibility on other views
+- **mouse drag from within circle** : change channel visibility and unit visibility on other views
 - **mouse drag from "diamond"** : change channel / unit radii size
 
 Screenshots

pyproject.toml

@@ -62,3 +62,10 @@ docs = [
     "sphinx>=5.0",
     "sphinx_rtd_theme",
 ]
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,pyproject.toml'
+check-hidden = true
+# ignore-regex = ''
+ignore-words-list = 'nd,gaus'

spikeinterface_gui/__init__.py

@@ -1,7 +1,7 @@
 """
 Some design notes:
   * controller is a layer between spikeinterface objects and every view
-  * every view can notify some signals to other view that are centralized bu the controller
+  * every view can notify some signals to other view that are centralized by the controller
   * views have settings
   * views have 2 implementations : qt (legacy) and panel (for the web)
     They need to implement the make_layout and the refresh for each backends (qt, panel).

spikeinterface_gui/backend_panel.py

@@ -207,7 +207,7 @@ def __init__(self, controller, layout_dict=None, user_settings=None):
         self.make_views(user_settings)
         self.create_main_layout()
 
-        # refresh all views wihtout notiying
+        # refresh all views without notiying
         self.controller.signal_handler.deactivate()
         self.controller.signal_handler.activate()
 
@@ -281,7 +281,7 @@ def create_main_layout(self):
 
         layout_zone = {}
         for zone, view_names in preset.items():
-            # keep only instanciated views
+            # keep only instantiated views
             view_names = [view_name for view_name in view_names if view_name in self.view_layouts.keys()]
 
             if len(view_names) == 0:

spikeinterface_gui/backend_qt.py

@@ -48,7 +48,7 @@ def notify_unit_color_changed(self):
         self.unit_color_changed.emit()
 
 
-# Used by controler to handle/callback signals
+# Used by controller to handle/callback signals
 class SignalHandler(QT.QObject):
     def __init__(self, controller, parent=None):
         QT.QObject.__init__(self, parent=parent)
@@ -165,13 +165,13 @@ def __init__(self, controller, parent=None, layout_dict=None, user_settings=None
         self.make_views(user_settings)
         self.create_main_layout()
 
-        # refresh all views wihtout notiying
+        # refresh all views without notiying
         self.controller.signal_handler.deactivate()
         for view in self.views.values():
             # refresh do not work because view are not yet visible at init
             view._refresh()
         self.controller.signal_handler.activate()
-        # TODO sam : all veiws are always refreshed at the moment so this is useless.
+        # TODO sam : all views are always refreshed at the moment so this is useless.
         # uncommen this when ViewBase.is_view_visible() work correctly
         # for view_name, dock in self.docks.items():
         #     dock.visibilityChanged.connect(self.views[view_name].refresh)

spikeinterface_gui/controller.py

@@ -66,7 +66,7 @@ def __init__(self, analyzer=None, backend="qt", parent=None, verbose=False, save
         self.main_settings = _default_main_settings.copy()
 
         self.num_channels = self.analyzer.get_num_channels()
-        # this now private and shoudl be acess using function
+        # this now private and should be access using function
         self._visible_unit_ids = [self.unit_ids[0]]
 
         # sparsity
@@ -552,7 +552,7 @@ def get_visible_unit_ids(self):
         return self._visible_unit_ids
 
     def get_visible_unit_indices(self):
-        """Get list of indicies of visible units"""
+        """Get list of indices of visible units"""
         unit_ids = list(self.unit_ids)
         visible_unit_indices = [unit_ids.index(u) for u in self._visible_unit_ids]
         return visible_unit_indices

spikeinterface_gui/ndscatterview.py

@@ -38,7 +38,7 @@ def __init__(self, controller=None, parent=None, backend="qt"):
         self.selected_comp = np.ones((ndim), dtype='bool')
         self.projection = self.get_one_random_projection()
 
-        #estimate limts
+        #estimate limits
         data = self.data
         if data.shape[0] > 1000:
             inds = np.random.choice(data.shape[0], 1000, replace=False)
@@ -280,7 +280,7 @@ def _qt_refresh(self, update_components=True, update_colors=True):
             self.update_selected_components()
 
         #ndscatter
-        # TODO sam: I have the feeling taht it is a bit slow
+        # TODO sam: I have the feeling that it is a bit slow
         self.scatter.clear()
 
         # scatter_x, scatter_y, spike_indices, selected_scatter_x, selected_scatter_y = self.get_plotting_data(concatenated=True)
@@ -297,7 +297,7 @@ def _qt_refresh(self, update_components=True, update_colors=True):
         self.scatter_select.setData(selected_scatter_x, selected_scatter_y)
 
 
-        # TODO sam : kepp the old implementation in mind
+        # TODO sam : keep the old implementation in mind
         # for unit_index, unit_id in enumerate(self.controller.unit_ids):
         #     if not self.controller.get_unit_visibility(unit_id):
         #         continue
@@ -367,7 +367,7 @@ def _qt_on_lasso_finished(self, points, shift_held=False):
         vertices = np.array(points)
         self._lasso_vertices.append(vertices)
 
-        # inside lasso and visibles
+        # inside lasso and visible
         ind_visibles,   = np.nonzero(np.isin(self.random_spikes_indices, self.controller.get_indices_spike_visible()))
         projected = self.apply_dot(self.data[ind_visibles, :])
         inside = inside_poly(projected, vertices)
@@ -550,7 +550,7 @@ def _on_panel_selection_geometry(self, event):
             else:
                 self._lasso_vertices = [polygon]
 
-            # inside lasso and visibles
+            # inside lasso and visible
             ind_visibles, = np.nonzero(np.isin(self.random_spikes_indices, self.controller.get_indices_spike_visible()))
             inds = self.random_spikes_indices[ind_visibles[selected]]
             self.controller.set_indices_spike_selected(inds)

spikeinterface_gui/probeview.py

@@ -713,6 +713,6 @@ def circle_from_roi(roi):
 ### Controls
 - **left click** : select single unit
 - **ctrl + left click** : add unit to selection
-- **mouse drag from within circle** : change channel visibilty and unit visibility on other views
+- **mouse drag from within circle** : change channel visibility and unit visibility on other views
 - **mouse drag from "diamond"** : change channel / unit radii size
 """

spikeinterface_gui/spikelistview.py

@@ -224,7 +224,7 @@ def _qt_on_spike_selection_changed(self):
         visible_inds = self.controller.get_indices_spike_visible()
         row_selected,  = np.nonzero(np.isin(visible_inds, selected_inds))
 
-        if row_selected.size>100:#otherwise this is verry slow
+        if row_selected.size>100:#otherwise this is very slow
             row_selected = row_selected[:10]
 
         # change selection

spikeinterface_gui/tests/testingtools.py

@@ -44,7 +44,7 @@ def make_analyzer_folder(test_folder, case="small", unit_dtype="str"):
     job_kwargs = dict(n_jobs=-1, progress_bar=True, chunk_duration="1s")
 
     recordings = []
-    sortings = []
+    sorting = []
     probes = []
     for i in range(num_probe):
         recording, sorting = si.generate_ground_truth_recording(
@@ -75,7 +75,7 @@ def make_analyzer_folder(test_folder, case="small", unit_dtype="str"):
             recording = recording.set_probe(probe)
 
             recordings.append(recording)
-            sortings.append(sorting)
+            sorting.append(sorting)
             probes.append(probe.copy())
 
         if 'split' in case:
@@ -105,7 +105,7 @@ def make_analyzer_folder(test_folder, case="small", unit_dtype="str"):
             count += n
         recording = recording.set_probegroup(probegroup)
 
-        sorting = si.aggregate_units(sortings)
+        sorting = si.aggregate_units(sorting)
 
     sorting = sorting.rename_units(sorting.unit_ids.astype(unit_dtype))
 

spikeinterface_gui/utils_panel.py

@@ -234,7 +234,7 @@ def is_position_inside(self, x, y, skip_other_positions=None, skip_distance=5):
         """
         Check if the given position (x, y) is inside the circle.
         If skip_other_positions is provided, check if the position is close to any of them
-        usinf the skip_distance.
+        using the skip_distance.
         """
         # Check if position is inside the circle
         distance = np.sqrt((x - self.center[0]) ** 2 + (y - self.center[1]) ** 2)

spikeinterface_gui/utils_qt.py

@@ -38,7 +38,7 @@
 
 
 def add_stretch_to_qtoolbar(tb):
-    # add an expending widget + a seprator
+    # add an expending widget + a separator
     empty = QT.QWidget()
     empty.setSizePolicy(QT.QSizePolicy.Expanding, QT.QSizePolicy.Preferred)
     tb.addWidget(empty)

spikeinterface_gui/view_base.py

@@ -78,7 +78,7 @@ def notify_unit_color_changed(self):
     def on_settings_changed(self, *params):
         # what to do when one settings is changed
         # optionally views can implement custom method
-        # but the general case is to refesh
+        # but the general case is to refresh
         if self.backend == "qt" and hasattr(self, "_qt_on_settings_changed"):
             return self._qt_on_settings_changed()
         elif self.backend == "panel" and hasattr(self, "_panel_on_settings_changed"):
@@ -178,7 +178,7 @@ def get_unit_color(self, unit_id):
             html_color = matplotlib.colors.rgb2hex(color, keep_alpha=True)
             return html_color
 
-    # Default behavior for all views : this can be changed view by view for perfs reaons
+    # Default behavior for all views : this can be changed view by view for perfs reasons
     def on_spike_selection_changed(self):
         if not self.is_view_visible():
             return
@@ -252,7 +252,7 @@ def _qt_on_spike_selection_changed(self):
         pass
 
     def _qt_on_unit_visibility_changed(self):
-        # most veiw need a refresh
+        # most view need a refresh
         self.refresh()
 
     def _qt_on_channel_visibility_changed(self):
@@ -312,7 +312,7 @@ def _panel_on_spike_selection_changed(self):
         pass
 
     def _panel_on_unit_visibility_changed(self):
-        # most veiw need a refresh
+        # most view need a refresh
         self.refresh()
 
     def _panel_on_channel_visibility_changed(self):