diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml index 91e201373..98be52953 100644 --- a/environments/environment-Linux.yml +++ b/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 diff --git a/environments/environment-MAC-apple-silicon.yml b/environments/environment-MAC-apple-silicon.yml index 99eb52dcd..1b19124e0 100644 --- a/environments/environment-MAC-apple-silicon.yml +++ b/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 diff --git a/environments/environment-MAC-intel.yml b/environments/environment-MAC-intel.yml index 75d060825..68403db59 100644 --- a/environments/environment-MAC-intel.yml +++ b/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 diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml index e26b38e9a..b8570554c 100644 --- a/environments/environment-Windows.yml +++ b/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 diff --git a/src/pyflask/manageNeuroconv/manage_neuroconv.py b/src/pyflask/manageNeuroconv/manage_neuroconv.py index fd529f902..bad4f9c91 100644 --- a/src/pyflask/manageNeuroconv/manage_neuroconv.py +++ b/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 )