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Migrate MATLAB Docker image to MATLAB 2025b #282

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43 changes: 22 additions & 21 deletions images/Dockerfile.matlab
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Original file line number Diff line number Diff line change
@@ -1,12 +1,11 @@
ARG MATLAB_RELEASE=r2024b
ARG MATLAB_RELEASE=r2025b
FROM --platform=linux/amd64 ghcr.io/mathworks-ref-arch/matlab-integration-for-jupyter/jupyter-matlab-notebook:${MATLAB_RELEASE}

USER root

# install extra apps, add extra folder and fix ownership in case apt-get messed with it
# install extra apps, add extra folder and fix ownership in case apt messed with it
ARG EXTRA_DIR=/opt/extras
RUN df -h && apt-get update \
&& apt-get install -y \
RUN df -h && apt update \
&& apt install -y \
htop \
libnss-wrapper \
curl \
Expand All @@ -17,12 +16,13 @@ RUN df -h && apt-get update \
&& chown -R $NB_UID:$NB_GID $HOME ${EXTRA_DIR}

RUN df -h && pip install --no-cache-dir datalad 'h5py>3.3' zarr pyopenssl plotly jupyter_bokeh jupytext nbgitpuller datalad_container \
datalad-osf dandi nibabel nilearn pybids spikeinterface neo \
'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 && \
rm -rf /tmp/*
datalad-osf dandi nibabel nilearn pybids spikeinterface neo \
'pydra>=0.25' 'pynwb>=2.8.3' 'nwbwidgets>=0.10.2' hdf5plugin s3fs h5netcdf "xarray[io]" \
lxml kerchunk 'neuroglancer>=2.28' cloud-volume ipywidgets ome-zarr webio_jupyter_extension \
tensorstore anndata tensorflow \
xmlschema \
&& pip install --no-cache-dir https://github.com/balbasty/dandi-io/archive/refs/heads/main.zip --no-deps && \
rm -rf /tmp/*

# Install the required Toolboxes with user root
# Optimization toolbox is a required dependency
Expand All @@ -32,13 +32,13 @@ ARG TOOLBOXES="Bioinformatics_Toolbox \
Curve_Fitting_Toolbox \
Deep_Learning_Toolbox \
Econometrics_Toolbox \
Financial_Toolbox \
Image_Processing_Toolbox \
Optimization_Toolbox \
Statistics_and_Machine_Learning_Toolbox \
Signal_Processing_Toolbox \
Parallel_Computing_Toolbox \
Financial_Toolbox \
Signal_Processing_Toolbox \
Statistics_and_Machine_Learning_Toolbox \
Wavelet_Toolbox \
Optimization_Toolbox \
Deep_Learning_Toolbox_Converter_for_TensorFlow_models"
RUN df -h && wget -q https://www.mathworks.com/mpm/glnxa64/mpm && \
chmod +x mpm && \
Expand All @@ -48,15 +48,15 @@ RUN df -h && wget -q https://www.mathworks.com/mpm/glnxa64/mpm && \
--products ${TOOLBOXES} && \
rm -f mpm /tmp/mathworks_root.log

# Switch to NB_USER for addons and live-scripts installations
USER $NB_USER
# Switch to NB_UID for addons and live-scripts installations
USER $NB_UID

## Adds add-ons and register them in the Matlab instance
# Patch startup.m to automatically register the addons
# The registration process simply iterate over all entries from the ADDONS_DIR folder
# and add them to the "path"
ARG ADDONS_DIR=${EXTRA_DIR}/dandi
ARG STARTUP_SCRIPT=/opt/conda/lib/python3.11/site-packages/matlab_proxy/matlab/startup.m
ARG STARTUP_SCRIPT=/opt/conda/lib/python3.13/site-packages/matlab_proxy/matlab/startup.m

# Generate MATLAB startup script
RUN df -h && echo -e "\n\
Expand Down Expand Up @@ -84,8 +84,7 @@ end \n\
clear" >> ${STARTUP_SCRIPT}

# Variables for addons management that are tied to a specific release or commit
ARG ADDONS_RELEASES="https://github.com/NeurodataWithoutBorders/matnwb/archive/2c3a4e13c9504724c08f3d937c08c730accf7685.zip \
https://github.com/schnitzer-lab/EXTRACT-public/archive/refs/heads/master.zip \
ARG ADDONS_RELEASES="https://github.com/schnitzer-lab/EXTRACT-public/archive/refs/heads/master.zip \
https://github.com/bahanonu/ciatah/archive/refs/heads/master.zip"

# Add add-ons for Dandi: create the addons folder and download/unzip the addons
Expand All @@ -98,7 +97,9 @@ RUN df -h && mkdir -p ${ADDONS_DIR} && \
done

# Variables for addons management that always takes the last release
ARG ADDONS_LATEST="https://github.com/emeyers/Brain-Observatory-Toolbox"
ARG ADDONS_LATEST="https://github.com/NeurodataWithoutBorders/matnwb \
https://github.com/MATLAB-Community-Toolboxes-at-INCF/Brain-Observatory-Toolbox \
https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB"

# Add add-ons for Dandi: detect/download/unzip the last release version
RUN df -h && cd ${ADDONS_DIR} && \
Expand Down
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