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Add jupyterlab_h5web package #242

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Add jupyterlab_h5web package #242

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2deba0b
Add `jupyterlab_h5web`
kabilar Feb 27, 2025
780134b
Remove `jupyterlab_h5web` from `Dockerfile.gpu.allensdk`
kabilar Feb 27, 2025
f076f8a
Remove packages from `Dockerfile.gpu.allensdk`
kabilar Feb 27, 2025
5d1e1e6
Remove packages
kabilar Feb 27, 2025
f1d3f46
Remove packages
kabilar Feb 27, 2025
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2 changes: 1 addition & 1 deletion images/Dockerfile
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Expand Up @@ -56,7 +56,7 @@ RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller data
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata
tensorstore anndata jupyterlab_h5web

RUN pip install --no-cache-dir multiscale_spatial_image jupyterlab-git \
datalad-fuse
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2 changes: 1 addition & 1 deletion images/Dockerfile.allensdk
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Expand Up @@ -64,7 +64,7 @@ RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller data
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata
tensorstore anndata jupyterlab_h5web

RUN pip install --no-cache-dir multiscale_spatial_image jupyterlab-git \
datalad-fuse
2 changes: 1 addition & 1 deletion images/Dockerfile.gpu
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Expand Up @@ -56,7 +56,7 @@ RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller data
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata && rm -rf /tmp/*
tensorstore anndata jupyterlab_h5web && rm -rf /tmp/*

RUN mamba install --yes -c "nvidia/label/cuda-12.6.3" cuda-toolkit cudnn \
&& conda clean --all -f -y && rm -rf /tmp/*
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13 changes: 4 additions & 9 deletions images/Dockerfile.gpu.allensdk
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Expand Up @@ -59,15 +59,10 @@ RUN mamba install --yes datalad rclone 'h5py>3.3=mpi*' ipykernel zarr blosc ecco
RUN /opt/conda/envs/allen/bin/python -m ipykernel install --user --name allen \
--display-name="Allen SDK"

RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller datalad_container \
datalad-osf dandi pybids spikeinterface neo itkwidgets \
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata && rm -rf /tmp/*
RUN pip install --no-cache-dir -U plotly jupyter_bokeh nbgitpuller \
dandi pybids itkwidgets jupyterlab-git \
'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf \
ipywidgets && rm -rf /tmp/*

RUN mamba install --yes -c "nvidia/label/cuda-11.8.0" cuda-toolkit cudnn \
&& conda clean --all -f -y && rm -rf /tmp/*

RUN pip install --no-cache-dir multiscale_spatial_image jupyterlab-git \
datalad-fuse jupyterlab_nvdashboard
2 changes: 1 addition & 1 deletion images/Dockerfile.gpu.matlab
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Expand Up @@ -77,7 +77,7 @@ RUN pip install --no-cache-dir plotly jupyter_bokeh jupytext nbgitpuller datalad
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata "tensorflow[and-cuda]==2.14"
tensorstore anndata jupyterlab_h5web "tensorflow[and-cuda]==2.14"

# Ensure OpenSSL is up-to-date
RUN pip install -U pyopenssl
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2 changes: 1 addition & 1 deletion images/Dockerfile.matlab
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@@ -1,5 +1,5 @@
ARG MATLAB_RELEASE=r2024b
FROM --platform=linux/amd64 ghcr.io/mathworks-ref-arch/matlab-integration-for-jupyter/jupyter-matlab-notebook:${MATLAB_RELEASE}

Check warning on line 2 in images/Dockerfile.matlab

View workflow job for this annotation

GitHub Actions / docker-test (latest-matlab, Dockerfile.matlab)

FROM --platform flag should not use a constant value 

FromPlatformFlagConstDisallowed: FROM --platform flag should not use constant value "linux/amd64"
More info: https://docs.docker.com/go/dockerfile/rule/from-platform-flag-const-disallowed/

USER root

Expand All @@ -16,7 +16,7 @@
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata tensorflow
tensorstore anndata jupyterlab_h5web tensorflow

# Install the required Toolboxes with user root
# Optimization toolbox is a required dependency
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2 changes: 1 addition & 1 deletion images/Dockerfile.openscope
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Expand Up @@ -56,7 +56,7 @@ RUN pip install --no-cache-dir -U plotly jupyter_bokeh jupytext nbgitpuller data
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
aicsimageio kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr \
webio_jupyter_extension https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip \
tensorstore anndata
tensorstore anndata jupyterlab_h5web

RUN pip install --no-cache-dir multiscale_spatial_image jupyterlab-git \
datalad-fuse
Expand Down
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