Update usage of SpikeInterface; pin NeuroConv; pin SpikeInterface

environments/environment-Linux.yml

@@ -15,7 +15,10 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
+      # For stability, NeuroConv is pinned at a commit equivalent to main branch on 8/7/2024
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
+      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
+      - spikeinterface == 0.101.0
       - scikit-learn == 1.4.0  # Tutorial data generation
       - tqdm_publisher >= 0.0.1  # Progress bars
       - tzlocal >= 5.2  # Frontend timezone handling

environments/environment-MAC-apple-silicon.yml

@@ -23,7 +23,10 @@ dependencies:
       - flask_restx == 1.1.0
       # NOTE: the NeuroConv wheel on PyPI includes sonpy which is not compatible with arm64, so build and install
       # NeuroConv from GitHub, which will remove the sonpy dependency when building from Mac arm64
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
+      # For stability, NeuroConv is pinned at a commit equivalent to main branch on 8/7/2024
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@cb8687f6456dea51545144bb2e81a0ee4fe36c02#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
+      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
+      - spikeinterface == 0.101.0
       - scikit-learn == 1.4.0  # Tutorial data generation
       - tqdm_publisher >= 0.0.1  # Progress bars
       - tzlocal >= 5.2  # Frontend timezone handling

environments/environment-MAC-intel.yml

@@ -18,7 +18,10 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
+      # For stability, NeuroConv is pinned at a commit equivalent to main branch on 8/7/2024
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
+      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
+      - spikeinterface == 0.101.0
       - scikit-learn == 1.4.0  # Tutorial data generation
       - tqdm_publisher >= 0.0.1  # Progress bars
       - tzlocal >= 5.2  # Frontend timezone handling

environments/environment-Windows.yml

@@ -18,7 +18,10 @@ dependencies:
       - flask == 2.3.2
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
+      # For stability, NeuroConv is pinned at a commit equivalent to main branch on 8/7/2024
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
+      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
+      - spikeinterface == 0.101.0
       - scikit-learn == 1.4.0  # Tutorial data generation
       - tqdm_publisher >= 0.0.1  # Progress bars
       - tzlocal >= 5.2  # Frontend timezone handling

src/pyflask/manageNeuroconv/manage_neuroconv.py

@@ -1723,12 +1723,12 @@ def generate_test_data(output_path: str):
         io.write(lf_meta_content)
 
     # Make Phy folder
-    waveform_extractor = spikeinterface.extract_waveforms(
+    sorting_analyzer = spikeinterface.extract_waveforms(
         recording=artificial_ap_band_in_uV, sorting=spiking, mode="memory"
     )
 
     export_to_phy(
-        waveform_extractor=waveform_extractor, 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
     )