Reduce image size

d4science-base/Dockerfile

@@ -1,7 +1,9 @@
-# 4d70cf8da953 has python3.10.11
+# Using julia-1.12.4 / python3.13
 # Using that to ensure the image remains the same
-FROM jupyter/datascience-notebook:4d70cf8da953
-ARG julia_version="1.9.3"
+FROM quay.io/jupyter/datascience-notebook@sha256:7e4d915319d998c5dbca911ae8ea3d7c59193aad598c75f8bf272a57d5ddfca2
+
+#FROM jupyter/datascience-notebook:4d70cf8da953
+#ARG julia_version="1.9.3"
 
 USER root
 
@@ -17,58 +19,16 @@ RUN apt-get -qq update \
 RUN curl https://raw.githubusercontent.com/kadwanev/retry/master/retry \
          -o /usr/local/bin/retry && chmod +x /usr/local/bin/retry
 
-# -----------------------------------------------------------------------------
-# Julia setup - we need a newer version than the one in the base
-# Julia dependencies
-# install Julia packages in /opt/julia instead of ${HOME}
-ENV JULIA_DEPOT_PATH=/opt/julia \
-    JULIA_PKGDIR=/opt/julia \
-    JULIA_VERSION="${julia_version}"
-
-WORKDIR /tmp
-
-# hadolint ignore=SC2046
-RUN set -x && \
-    julia_arch=$(uname -m) && \
-    julia_short_arch="${julia_arch}" && \
-    if [ "${julia_short_arch}" == "x86_64" ]; then \
-      julia_short_arch="x64"; \
-    fi; \
-    julia_installer="julia-${JULIA_VERSION}-linux-${julia_arch}.tar.gz" && \
-    julia_major_minor=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2) && \
-    mkdir "/opt/julia-${JULIA_VERSION}" && \
-    wget -q "https://julialang-s3.julialang.org/bin/linux/${julia_short_arch}/${julia_major_minor}/${julia_installer}" && \
-    tar xzf "${julia_installer}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
-    rm "${julia_installer}" && \
-    ln -fs /opt/julia-${JULIA_VERSION}/bin/julia /usr/local/bin/julia
-
-# Show Julia where conda libraries are \
-RUN rm -rf /etc/julia && mkdir /etc/julia && \
-    echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl && \
-    # Create JULIA_PKGDIR \
-    rm -rf "${JULIA_PKGDIR}" && \
-    mkdir "${JULIA_PKGDIR}" && \
-    chown "${NB_USER}" "${JULIA_PKGDIR}" && \
-    fix-permissions "${JULIA_PKGDIR}"
-
 USER $NB_UID
 
 # Add Julia packages.
-# Install IJulia as jovyan and then move the kernelspec out
-# to the system share location. Avoids problems with runtime UID change not
-# taking effect properly on the .local folder in the jovyan home dir.
 RUN julia -e 'import Pkg; Pkg.update()' && \
-    julia -e 'import Pkg; Pkg.add("HDF5")' && \
-    julia -e 'using Pkg; pkg"add IJulia"; pkg"precompile"' && \
-    # move kernelspec out of home \
-    mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
-    chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
-    rm -rf "${HOME}/.local" && \
-    fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
-
-# end Julia Setup
-# -----------------------------------------------------------------------------
-
+    julia --eval 'using Pkg; Pkg.add(["Images","VideoIO"])' && \
+    julia --eval 'using Pkg; Pkg.add(url="https://github.com/gher-uliege/OceanPlot.jl",rev="master")'
+    julia --eval 'using Pkg; Pkg.add(name="DIVAnd", version="2.7.14")' && \
+    julia --eval 'using Pkg; Pkg.add(["JSON", "PyCall", "PyPlot", "Glob", "DataStructures", "NCDatasets"])' && \
+    julia --eval 'using Pkg; Pkg.add(url="https://github.com/Alexander-Barth/CoastalCurrents.jl")' && \
+    julia --eval 'using Pkg; Pkg.add("PhysOcean")'
 
 RUN mamba install --channel conda-forge -y -q \
         rdflib \
@@ -89,8 +49,6 @@ RUN mamba install --channel conda-forge -y -q \
         netcdf4 \
         aiohttp \
         graph-tool \
-        scikit-learn \
-        scikit-mobility \
         dask-jobqueue \
         fs \
         rasterio \

single-user-d4science/Dockerfile

@@ -16,16 +16,16 @@ RUN apt-get -qq update \
 
 USER $NB_UID
 
-RUN conda create --quiet --yes -n java8 \
-    && mamba install -n java8 --yes openjdk=8 \
-    && conda clean -tipy
+#RUN conda create --quiet --yes -n java8 \
+#    && mamba install -n java8 --yes openjdk=8 \
+#    && conda clean -tipy
 
 ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
 ENV C_INCLUDE_PATH=/usr/include/gdal
 
 # Installing torch explictly to have only CPU version
-RUN pip install --index-url https://download.pytorch.org/whl/cpu \
-	torch torchvision torchaudio
+#RUN pip install --index-url https://download.pytorch.org/whl/cpu \
+#	torch torchvision torchaudio
 
 
 # cdlib[C]==0.2.3 is too old for this env, so unpinning
@@ -60,31 +60,12 @@ RUN pip install --no-cache-dir \
         GDAL==$(gdal-config --version) \
         copernicusmarine
 
-# Julia Updates and packages installations
-# See https://support.d4science.org/issues/22065
-RUN julia --eval 'using Pkg; Pkg.pin("IJulia")' \
-    && julia --eval "using Pkg; Pkg.update()" \
-    && julia --eval 'using Pkg; Pkg.add(["Images","VideoIO"])' \
-    && julia --eval 'using Pkg; Pkg.add(url="https://github.com/gher-ulg/DIVAndNN.jl")' \
-    && julia --eval 'using Pkg; Pkg.add(name="DIVAnd", version="2.7.9")' \
-    && julia --eval 'using Pkg; Pkg.add(["JSON", "PyCall", "PyPlot", "Glob", "DataStructures", "NCDatasets"])' \
-    && julia --eval 'using Pkg; Pkg.add(url="https://github.com/Alexander-Barth/CoastalCurrents.jl")' \
-    && julia --eval 'using Pkg; Pkg.add("PhysOcean")' \
-    && julia --eval 'using Pkg; \
-                     Pkg.add(["CSV", "DataFrames", "Revise", "Compat", "Dates", \
-                              "Statistics", "Logging", "Random", "Printf", "FileIO", \
-			      "Missings", "Distributed", "Profile", "StatsBase", \
-			      "JLD2", "Interpolations"]);' \
-    && cd /tmp \
-    && git clone https://github.com/Alexander-Barth/CoastalCurrents.jl \
-    && cd CoastalCurrents.jl \
-    && julia --project=. --eval "using Pkg; Pkg.instantiate()"
-
 # -------------------------------
 # JupyterLab extensions
 # -------------------------------
 RUN pip install --no-cache-dir \
     jupyterlab-topbar \
-    jupyterlab-system-monitor
-RUN jupyter labextension disable @jupyterlab/filebrowser-extension:share-file
-RUN jupyter lab build
+    jupyterlab-system-monitor \
+    && jupyter labextension disable @jupyterlab/filebrowser-extension:share-file \
+    && jupyter lab build \
+    && jupyter lab clean