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

.pre-commit-config.yaml

@@ -10,3 +10,11 @@ repos:
     hooks:
     -   id: black
         files: ^src/|^tests/
+- repo: https://github.com/codespell-project/codespell
+  # Configuration for codespell is in .pre-commit-config.yaml
+  rev: v2.4.1
+  hooks:
+  -    id: codespell
+       additional_dependencies:
+       -    tomli  # for python_version < '3.11'
+       exclude: ^doc/releases/.*\.rst

pyproject.toml

@@ -65,3 +65,10 @@ omit = [
 
 [tool.black]
 line-length = 120
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,*.pdf,*.svg,data,./doc/releases'
+check-hidden = true
+# ignore-regex = ''
+ignore-words-list = 'compiletime'

resources/generate_cambridgeneurotech_libray.py

@@ -8,7 +8,7 @@
 The script have been modified by Smauel Garcia (samuel.garcia@cnrs.fr):
   * more pytonic
   * improve code readability
-  * not more channel_device_index the order is the conatct index
+  * not more channel_device_index the order is the contact index
   * simpler function for plotting.
 
 2021-04-02
@@ -72,7 +72,7 @@
 
 def convert_probe_shape(listCoord):
     '''
-    This is to convert reference point probe shape inputed in excel
+    This is to convert reference point probe shape inputted in excel
     as string 'x y x y x y that outline the shape of one shanck
     and can be converted to an array to draw the porbe
     '''
@@ -95,7 +95,7 @@ def get_contact_order(connector, probe_type):
     This will help to re-order the probe contact later on.
     """
 
-    # first part of the function to opne the proper connector based on connector name
+    # first part of the function to open the proper connector based on connector name
 
     # header [0,1] is used to create a mutliindex
     df = pd.read_excel(probe_map_file, sheet_name=connector, header=[0,1])
@@ -188,7 +188,7 @@ def generate_CN_multi_shank(probe_info):
 
 def create_CN_figure(probe_name, probe):
     """
-    Create custum figire for CN with custum colors + logo
+    Create custom figire for CN with custom colors + logo
     """
     fig, ax = plt.subplots()
     fig.set_size_inches(18.5, 10.5)

resources/generate_neuropixels_library.py

@@ -51,7 +51,7 @@ def generate_all_npx():
 
         probe = _make_npx_probe_from_description(pt_metadata, model_name, elec_ids, shank_ids)
 
-        # ploting
+        # plotting
         fig, axs = plt.subplots(ncols=2)
 
         ax = axs[0]

src/probeinterface/io.py

@@ -728,7 +728,7 @@ def read_csv(file: str | Path):
 
 def write_csv(file, probe):
     """
-    Write contact postions into a 2 or 3 columns csv file
+    Write contact positions into a 2 or 3 columns csv file
     """
 
     raise NotImplementedError

src/probeinterface/neuropixels_tools.py

@@ -67,7 +67,7 @@ def _load_np_probe_features():
     "NP2020": "2020",
     # Ultra
     "NP1100": "1100",  # Ultra probe - 1 bank
-    "NP1110": "1110",  # Ultra probe - 16 banks no handle beacuse
+    "NP1110": "1110",  # Ultra probe - 16 banks no handle because
     "NP1121": "1121",  # Ultra probe - beta configuration
     # Opto
     "NP1300": "1300",  # Opto probe
@@ -103,7 +103,7 @@ def get_probe_length(probe_part_number: str) -> int:
     Returns
     -------
     probe_length : int
-        Lenth of full probe (microns)
+        Length of full probe (microns)
     """
 
     probe_length = 10_000
@@ -1128,7 +1128,7 @@ def get_saved_channel_indices_from_openephys_settings(
                         if len(possible_custom_streams) > 1:
                             warnings.warn(
                                 f"More than one custom parameters associated to {stream_name} "
-                                f"found. Using fisrt one"
+                                f"found. Using first one"
                             )
                         custom_stream = possible_custom_streams[0]
                     else:

src/probeinterface/probe.py

@@ -1154,7 +1154,7 @@ def add_probe_to_zarr_group(self, group: "zarr.Group") -> None:
             data = probe_arr[field_name]
             group.create_dataset(name=field_name, data=data, dtype=dtype, chunks=False)
 
-        # Annotations as a group (special attibutes are stored as annotations)
+        # Annotations as a group (special attributes are stored as annotations)
         annotations_group = group.create_group("annotations")
         for key, value in self.annotations.items():
             annotations_group.attrs[key] = value

src/probeinterface/probegroup.py

@@ -226,7 +226,7 @@ def set_global_device_channel_indices(self, channels: np.array | list):
                 f"Wrong channels size {channels.size} for the number of channels {self.get_contact_count()}"
             )
 
-        # first reset previsous indices
+        # first reset previous indices
         for i, probe in enumerate(self.probes):
             n = probe.get_contact_count()
             probe.set_device_channel_indices([-1] * n)

src/probeinterface/utils.py

@@ -113,7 +113,7 @@ def generate_unique_ids(min: int, max: int, n: int, trials: int = 20) -> np.arra
     Parameters
     ----------
     min : int
-        Minimun value permitted for an identifier
+        Minimum value permitted for an identifier
     max : int
         Maximum value permitted for an identifier
     n : int

src/probeinterface/wiring.py

@@ -60,7 +60,7 @@
         31, 30
     ],
 
-    # from PDF documention of mini-amp-64 page 5
+    # from PDF documentation of mini-amp-64 page 5
     'cambridgeneurotech_mini-amp-64': [
         # connector J2 TOP
         41, 39, 38, 37, 35, 34, 33, 32, 29, 30, 28, 26, 25, 24, 22, 20,

tests/test_io/test_openephys.py

@@ -97,7 +97,7 @@ def test_NP1_subset():
     assert len(probe_lf.contact_positions) == 200
 
     # Not specifying the stream_name should raise an Exception, because both the ProbeA-AP and
-    # ProbeA-LFP have custome channel selections
+    # ProbeA-LFP have custom channel selections
     with pytest.raises(AssertionError):
         probe = read_openephys(data_path / "OE_Neuropix-PXI-subset" / "settings.xml")
 

tests/test_io/test_spikeglx.py

@@ -86,7 +86,7 @@ def test_NP2_4_shanks():
     assert np.all(probe.contact_shape_params == {"width": contact_width})
     assert np.all(probe.contact_shapes == contact_shape)
 
-    # This file does not save the channnels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
+    # This file does not save the channels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
     ypos = probe.contact_positions[:, 1]
     assert np.min(ypos) == pytest.approx(0)
 
@@ -109,7 +109,7 @@ def test_NP2_2013_all():
     assert np.all(probe.contact_shape_params == {"width": contact_width})
     assert np.all(probe.contact_shapes == contact_shape)
 
-    # This file does not save the channnels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
+    # This file does not save the channels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
     ypos = probe.contact_positions[:, 1]
     assert np.min(ypos) == pytest.approx(0)
 
@@ -132,7 +132,7 @@ def test_NP2_2013_subset():
     assert np.all(probe.contact_shape_params == {"width": contact_width})
     assert np.all(probe.contact_shapes == contact_shape)
 
-    # This file does not save the channnels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
+    # This file does not save the channels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
     ypos = probe.contact_positions[:, 1]
     assert np.min(ypos) == pytest.approx(0)
 
@@ -154,7 +154,7 @@ def test_NP2_4_shanks_with_different_electrodes_saved():
     assert np.all(probe.contact_shape_params == {"width": contact_width})
     assert np.all(probe.contact_shapes == contact_shape)
 
-    # This file does not save the channnels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
+    # This file does not save the channels from 0 as the one above (NP2_4_shanks_g0_t0.imec0.ap.meta)
     ypos = probe.contact_positions[:, 1]
     assert np.min(ypos) == pytest.approx(4080.0)
     assert np.max(ypos) == pytest.approx(4785.0)