Merge pull request #1061 from int-brain-lab/develop

Release 3.4.2

Author: oliche

.github/workflows/ibllib_ci.yml

@@ -35,12 +35,12 @@ jobs:
     - name: Install deps
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest flake8-docstrings
+        python -m pip install flake8 ruff flake8-docstrings
         pip install -r requirements.txt
         pip install -e .
-    - name: Flake8
+    - name: Flake8 & ruff
       run: |
-        python -m flake8
+        python -m ruff check .
         python -m flake8 --select D --ignore E ibllib/qc/camera.py ibllib/qc/task_metrics.py
     - name: Brainbox tests
       run: |

CHANGELOG.md

@@ -6,6 +6,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [3.4.2] 2025-11-24
+
+### Fixed
+- public method to create insertions in `ibllib.ephys.spikes`
+- 
+### Added
+- CI now uses ruff instead of flake8 to enforce linting
 
 ## [3.4.1] 2025-07-02
 
@@ -14,7 +21,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - SpikeSortingLoader takes into account revisions
 - There is a specific test for `spikeinterface` CI in our integration tests
 
-
 ## Release Note 3.4.0
 
 ### features

README.md

@@ -17,20 +17,17 @@ The library is currently 2 main modules:
 **Python Module**: Python 3.10 or higher, Python 3.12 recommended
 
 ## Installation, documentation and examples
-https://docs.internationalbrainlab.org
 
+Installation: https://docs.internationalbrainlab.org/02_installation.html
+Documentation and examples: https://docs.internationalbrainlab.org
 
 ## Contribution and development practices
-See https://int-brain-lab.github.io/iblenv/07_contribution.html
+See https://docs.internationalbrainlab.org/09_contribution.html
 
 We use Semantic Versioning.
 
 Before committing to your branch:
--   check formating `flake8`
+-   check formating `ruff check`
 -   run tests `python -m unittest discover`
 
 Pull request to `develop` or `main`.
-
-
-## Matlab Library
-The Matlab library has moved to its own repository here: https://github.com/int-brain-lab/ibllib-matlab/

brainbox/behavior/dlc.py

@@ -44,16 +44,20 @@ def insert_idx(array, values):
     return idx
 
 
+def valid_feature(x: str):
+    if x.endswith('_x') or x.endswith('_y') or x.endswith('_likelihood'):
+        return True
+    return False
+
+
 def likelihood_threshold(dlc, threshold=0.9):
-    """
-    Set dlc points with likelihood less than threshold to nan.
+    """Set dlc points with likelihood less than threshold to nan.
 
-    FIXME Add unit test.
     :param dlc: dlc pqt object
     :param threshold: likelihood threshold
     :return:
     """
-    features = np.unique(['_'.join(x.split('_')[:-1]) for x in dlc.keys()])
+    features = np.unique(['_'.join(x.split('_')[:-1]) for x in dlc.keys() if valid_feature(x)])
     for feat in features:
         nan_fill = dlc[f'{feat}_likelihood'] < threshold
         dlc.loc[nan_fill, (f'{feat}_x', f'{feat}_y')] = np.nan
@@ -268,7 +272,7 @@ def plot_trace_on_frame(frame, dlc_df, cam):
     # Threshold the dlc traces
     dlc_df = likelihood_threshold(dlc_df)
     # Features without tube
-    features = np.unique(['_'.join(x.split('_')[:-1]) for x in dlc_df.keys() if 'tube' not in x])
+    features = np.unique(['_'.join(x.split('_')[:-1]) for x in dlc_df.keys() if valid_feature(x) and 'tube' not in x])
     # Normalize the number of points across cameras
     dlc_df_norm = pd.DataFrame()
     for feat in features: