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Update job_dispatch and nwb_units #42

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Update job_dispatch and nwb_units #42

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4 changes: 2 additions & 2 deletions docs/source/parameters.rst
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion environment/Dockerfile_base
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Expand Up @@ -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 && \
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3 changes: 1 addition & 2 deletions environment/push_all.sh
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Expand Up @@ -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
docker push --all-tags ghcr.io/allenneuraldynamics/aind-ephys-spikesort-spykingcircus2
4 changes: 2 additions & 2 deletions environment/requirements.txt
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@@ -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
6 changes: 3 additions & 3 deletions pipeline/capsule_versions.env
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@@ -1,5 +1,5 @@
JOB_DISPATCH=18d3fa32828e18b7f871b2a86d0a93c88f0b081b
PREPROCESSING=9d57dfcd5f0e3e95191fb5d0ef6dac1c0c096a2a
JOB_DISPATCH=78d29b83f2878ef3980a49dcd0c20581bb79c37b
PREPROCESSING=fb9b1f65d31ea0371611f127077ede9e3ee5814f
SPIKESORT_KS4=d463c618881f9d073ed51ca84f3474ee3eaee47a
SPIKESORT_KS25=a29823ff57047f59fcdb9864010a6cbdc0d2c725
SPIKESORT_SC2=892b3bacabf5310255325ab6e0cdb7797b55cb32
Expand All @@ -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