Merge branch 'main' of github.com:SpikeInterface/probeinterface into update-get-probe

Author: alejoe91

.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

.github/workflows/full_tests.yml

@@ -1,4 +1,4 @@
-name: Test on Ubuntu
+name: Complete tests
 
 on:
   pull_request:
@@ -12,8 +12,13 @@ on:
 jobs:
   build-and-test:
 
-    runs-on: ubuntu-latest
-
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.14"]  # Lower and higher versions we support
+        os: [macos-latest, windows-latest, ubuntu-latest]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
@@ -26,9 +31,4 @@ jobs:
         pip install .[test]
     - name: Pytest
       run: |
-        pytest --cov=probeinterface --cov-report xml:./coverage.xml
-    - uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: true
-        file: ./coverage.xml
+        pytest -v

.github/workflows/full_tests_codecov.yml

@@ -0,0 +1,31 @@
+name: Test with Codecov
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 12 * * *"  # Daily at noon UTC
+
+
+jobs:
+  build-and-test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Pytest
+      run: |
+        pytest --cov=probeinterface --cov-report xml:./coverage.xml
+    - uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true
+        file: ./coverage.xml

.pre-commit-config.yaml

@@ -5,8 +5,16 @@ repos:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
--   repo: https://github.com/psf/black
+-   repo: https://github.com/psf/black-pre-commit-mirror
     rev: 25.9.0
     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

@@ -8,7 +8,7 @@ authors = [
 
 description = "Python package to handle probe layout, geometry and wiring to device."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
@@ -66,3 +66,10 @@ 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