Merge branch 'main' into pre-commit-ci-update-config

Author: rly

.github/workflows/example_data_cache.yml

@@ -17,6 +17,9 @@ jobs:
     # Requirement settings identified as 'ExampleDataCache / {os}'
     name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
     strategy:
       fail-fast: false
       matrix:
@@ -27,7 +30,10 @@ jobs:
 
       - name: Get ephy_testing_data current head hash
         id: ephys
-        run: echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
+        run: |
+          HASH=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)
+          if [ -z "$HASH" ]; then echo "Failed to fetch ephy_testing_data hash" && exit 1; fi
+          echo "HASH_EPHY_DATASET=$HASH" >> $GITHUB_OUTPUT
       - name: Get cached ephys example data - ${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
         uses: actions/cache@v4
         id: cache-ephys-datasets
@@ -36,7 +42,10 @@ jobs:
           key: ephys-datasets-v2-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
       - name: Get ophys_testing_data current head hash
         id: ophys
-        run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
+        run: |
+          HASH=$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)
+          if [ -z "$HASH" ]; then echo "Failed to fetch ophys_testing_data hash" && exit 1; fi
+          echo "HASH_OPHYS_DATASET=$HASH" >> $GITHUB_OUTPUT
       - name: Get cached ophys example data - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
         uses: actions/cache@v4
         id: cache-ophys-datasets
@@ -45,13 +54,16 @@ jobs:
           key: ophys-datasets-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
       - name: Get behavior_testing_data current head hash
         id: behavior
-        run: echo "::set-output name=HASH_BEHAVIOR_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)"
+        run: |
+          HASH=$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)
+          if [ -z "$HASH" ]; then echo "Failed to fetch behavior_testing_data hash" && exit 1; fi
+          echo "HASH_BEHAVIOR_DATASET=$HASH" >> $GITHUB_OUTPUT
       - name: Get cached behavior example data - ${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }}
         uses: actions/cache@v4
         id: cache-behavior-datasets
         with:
           path: ./behavior_testing_data
-          key: behavior-datasets-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_behavior_DATASET }}
+          key: behavior-datasets-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }}
 
       - if: steps.cache-ephys-datasets.outputs.cache-hit != 'true' || steps.cache-ophys-datasets.outputs.cache-hit != 'true' || steps.cache-behavior-datasets.outputs.cache-hit != 'true'
         name: Install and configure AWS CLI

.github/workflows/testing_pipelines.yml

@@ -73,7 +73,10 @@ jobs:
       # Load example data caches
       - name: Get ephy_testing_data current head hash
         id: ephys
-        run: echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
+        run: |
+          HASH=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)
+          if [ -z "$HASH" ]; then echo "Failed to fetch ephy_testing_data hash" && exit 1; fi
+          echo "HASH_EPHY_DATASET=$HASH" >> $GITHUB_OUTPUT
 
       - name: Cache ephys dataset - ${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
         uses: actions/cache@v4
@@ -84,7 +87,10 @@ jobs:
 
       - name: Get ophys_testing_data current head hash
         id: ophys
-        run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
+        run: |
+          HASH=$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)
+          if [ -z "$HASH" ]; then echo "Failed to fetch ophys_testing_data hash" && exit 1; fi
+          echo "HASH_OPHYS_DATASET=$HASH" >> $GITHUB_OUTPUT
 
       - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
         uses: actions/cache@v4
@@ -95,14 +101,17 @@ jobs:
 
       - name: Get behavior_testing_data current head hash
         id: behavior
-        run: echo "::set-output name=HASH_BEHAVIOR_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)"
+        run: |
+          HASH=$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)
+          if [ -z "$HASH" ]; then echo "Failed to fetch behavior_testing_data hash" && exit 1; fi
+          echo "HASH_BEHAVIOR_DATASET=$HASH" >> $GITHUB_OUTPUT
 
       - name: Cache behavior dataset - ${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }}
         uses: actions/cache@v4
         id: cache-behavior-datasets
         with:
           path: ./behavior_testing_data
-          key: behavior-datasets-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_behavior_DATASET }}
+          key: behavior-datasets-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }}
 
       # Run pipeline tests
       - if: matrix.os != 'ubuntu-latest'

src/pyflask/manageNeuroconv/manage_neuroconv.py

@@ -1813,12 +1813,15 @@ def generate_test_data(output_path: str):
     sorting_analyzer = spikeinterface.create_sorting_analyzer(
         sorting=sorting, recording=artificial_ap_band_in_uV, mode="memory", sparse=False
     )
-    sorting_analyzer.compute(["random_spikes", "waveforms", "templates", "noise_levels"])
-    sorting_analyzer.compute("spike_amplitudes")
-    sorting_analyzer.compute("principal_components", n_components=5, mode="by_channel_local")
+    sorting_analyzer.compute(["random_spikes", "waveforms", "templates"])
 
     spikeinterface.exporters.export_to_phy(
-        sorting_analyzer=sorting_analyzer, output_folder=phy_output_folder, remove_if_exists=True, copy_binary=False
+        sorting_analyzer=sorting_analyzer,
+        output_folder=phy_output_folder,
+        remove_if_exists=True,
+        copy_binary=False,
+        compute_pc_features=False,
+        compute_amplitudes=False,
     )