neuroconv update - WIP

environments/environment-Linux.yml

@@ -1,4 +1,4 @@
-name: nwb-guide
+name: nwb-guide-2
 channels:
   - conda-forge
   - defaults
@@ -16,10 +16,8 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
-      # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
-      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
-      - spikeinterface == 0.100.5
+      - neuroconv[full] == 0.6.6
+      - spikeinterface >= 0.101.2
       - 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

@@ -25,9 +25,9 @@ dependencies:
       # 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
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.6
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
-      - spikeinterface == 0.100.5
+      - spikeinterface >= 0.101.2
       - 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

@@ -19,10 +19,8 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
-      # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
-      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
-      - spikeinterface == 0.100.5
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.6
+      - spikeinterface >= 0.101.2
       - 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

@@ -19,10 +19,8 @@ dependencies:
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
       - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
-      # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
-      # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
-      - spikeinterface == 0.100.5
+      - neuroconv[dandi,compressors,ecephys,ophys,behavior,text] == 0.6.6
+      - spikeinterface >= 0.101.2
       - 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

@@ -1726,12 +1726,19 @@ def generate_test_data(output_path: str):
         io.write(lf_meta_content)
 
     # Make Phy folder
-    waveform_extractor = spikeinterface.extract_waveforms(
-        recording=artificial_ap_band_in_uV, sorting=spiking, mode="memory"
+    sorting_analyzer = spikeinterface.create_sorting_analyzer(
+        recording=artificial_ap_band_in_uV,
+        sorting=spiking,
     )
+    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")
 
     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,
     )