diff --git a/docs/source/parameters.rst b/docs/source/parameters.rst index 86e7649..5fe3e47 100644 --- a/docs/source/parameters.rst +++ b/docs/source/parameters.rst @@ -27,8 +27,8 @@ Job Dispatch Parameters .. code-block:: bash --job_dispatch_args " - --concatenate # Whether to concatenate recordings - --split-groups # Process different groups separately + --concatenate # Whether to concatenate recordings + --no-split-groups # Process different groups separately --debug # Run in DEBUG mode --debug-duration DURATION # Duration for debug mode (default: 30s) --input {aind,spikeglx,nwb,openephys} # Input data type diff --git a/environment/Dockerfile_base b/environment/Dockerfile_base index fcd70d5..f21a012 100644 --- a/environment/Dockerfile_base +++ b/environment/Dockerfile_base @@ -23,7 +23,7 @@ RUN apt-get update \ RUN apt-get install -y fonts-freefont-ttf RUN pip install --upgrade pip && \ - grep -E 'aind-data-schema|aind_metadata_upgrader|pyvips|wavpack-numcodecs|pynwb|hdmf-zarr' requirements.txt | xargs pip install + grep -E 'aind-data-schema|aind_metadata_upgrader|pyvips|wavpack-numcodecs|pynwb|hdmf-zarr|torch' requirements.txt | xargs pip install # Extract the spikeinterface version and install with extras RUN pip install --upgrade pip && \ diff --git a/environment/push_all.sh b/environment/push_all.sh index 962f980..e98df27 100644 --- a/environment/push_all.sh +++ b/environment/push_all.sh @@ -10,5 +10,4 @@ docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-pipeline-base docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-pipeline-nwb docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-spikesort-kilosort25 docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-spikesort-kilosort4 -docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-spikesort-spykingcircus2 -docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-unit-classifier \ No newline at end of file +docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-spikesort-spykingcircus2 \ No newline at end of file diff --git a/environment/requirements.txt b/environment/requirements.txt index 2f5aafe..e083a90 100644 --- a/environment/requirements.txt +++ b/environment/requirements.txt @@ -1,10 +1,10 @@ spikeinterface==0.102.1 pyvips==2.2.1 torch==2.6.0 -pynwb==2.8.3 +pynwb==2.8.2 hdbscan==0.8.40 neuroconv==0.6.7 wavpack-numcodecs==0.2.2 -hdmf-zarr==0.11.0 +hdmf-zarr==0.9.0 aind-data-schema==1.3.0 aind_metadata_upgrader==0.0.24 \ No newline at end of file diff --git a/pipeline/capsule_versions.env b/pipeline/capsule_versions.env index 8dd40b4..84270c7 100644 --- a/pipeline/capsule_versions.env +++ b/pipeline/capsule_versions.env @@ -1,5 +1,5 @@ -JOB_DISPATCH=18d3fa32828e18b7f871b2a86d0a93c88f0b081b -PREPROCESSING=9d57dfcd5f0e3e95191fb5d0ef6dac1c0c096a2a +JOB_DISPATCH=78d29b83f2878ef3980a49dcd0c20581bb79c37b +PREPROCESSING=fb9b1f65d31ea0371611f127077ede9e3ee5814f SPIKESORT_KS4=d463c618881f9d073ed51ca84f3474ee3eaee47a SPIKESORT_KS25=a29823ff57047f59fcdb9864010a6cbdc0d2c725 SPIKESORT_SC2=892b3bacabf5310255325ab6e0cdb7797b55cb32 @@ -9,5 +9,5 @@ VISUALIZATION=2f433c8058281461386bfba4c539993be0dc562b RESULTS_COLLECTOR=b54869aa4f09b22c03a1578270d42c1c4ba18afb NWB_SUBJECT=80091b8c61e649d001c1e53f0b0893ec3c94dfd7 NWB_ECEPHYS=c6dc3ac0fe2a811330d33c4803d43389c542d904 -NWB_UNITS=15a78df6c393fac5976fdff9ff8c5d04732af5fc +NWB_UNITS=d0eb99e6334e6051fb7fa195583be9825a48394f SPIKEINTERFACE_VERSION=0.102.1 \ No newline at end of file