Merge pull request #118 from gaelforget/dev_jupyter_kernel_fix

Dev jupyter kernel fix

Author: gaelforget

Dockerfile

@@ -2,28 +2,18 @@ FROM jupyter/base-notebook:latest
 
 USER root
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends build-essential && \
-    apt-get install -y --no-install-recommends vim && \
-    apt-get install -y --no-install-recommends curl && \
-    apt-get install -y --no-install-recommends git-all && \
-    apt-get install -y --no-install-recommends unzip && \
-    apt-get install -y --no-install-recommends gfortran && \
-    apt-get install -y --no-install-recommends openmpi-bin && \
-    apt-get install -y --no-install-recommends libopenmpi-dev && \
-    apt-get install -y --no-install-recommends libnetcdf-dev && \
-    apt-get install -y --no-install-recommends libnetcdff-dev && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
+ENV mainpath=/home/jovyan/
+RUN mkdir -p ${mainpath}
 
-USER ${NB_USER}
+RUN apt-get update
 
-ENV mainpath=/home/${NB_USER}
+RUN apt-get install -y --no-install-recommends build-essential && \
+    apt-get install -y --no-install-recommends vim && \
+    apt-get install -y --no-install-recommends git && \
+    apt-get install -y --no-install-recommends curl && \
+    apt-get install -y --no-install-recommends unzip
 
-RUN echo 'alias julia="${mainpath}/.juliaup/bin/julia --project=${mainpath}"' >> ~/.bashrc
-RUN curl -fsSL https://install.julialang.org | sh -s -- --yes
-
-USER root
-RUN ln -s ${mainpath}/.juliaup/bin/julia /usr/local/bin/julia
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*
 
 USER ${NB_USER}
 
@@ -32,20 +22,21 @@ COPY --chown=${NB_USER}:users ./src/plutoserver ${mainpath}/plutoserver
 
 RUN cp ${mainpath}/src/setup.py ${mainpath}/setup.py
 RUN cp ${mainpath}/src/runpluto.sh ${mainpath}/runpluto.sh
-RUN cp ${mainpath}/src/environment.yml ${mainpath}/environment.yml
 RUN cp ${mainpath}/src/Project.toml ${mainpath}/Project.toml
-RUN cp ${mainpath}/src/Manifest.toml ${mainpath}/Manifest.toml
+ 
+RUN echo 'alias julia="${mainpath}/.juliaup/bin/julia --project=${mainpath}"' >> ~/.bashrc
 
-RUN ${mainpath}/.juliaup/bin/julia -e "import Pkg; Pkg.update(); Pkg.instantiate();"
+RUN conda config --env --add channels conda-forge
+RUN conda config --env --add channels r
+
+RUN curl -fsSL https://install.julialang.org | sh -s -- --yes
+
+RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} -e "import Pkg; Pkg.update(); Pkg.instantiate();"
+RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} ${mainpath}/src/download_notebooks.jl
+RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} ${mainpath}/src/warmup1.jl
 
 RUN jupyter lab build && \
     jupyter lab clean && \
     pip install ${mainpath} --no-cache-dir && \
     rm -rf ~/.cache
 
-RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath}/src ${mainpath}/src/warmup1.jl
-RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath}/src ${mainpath}/src/download_notebooks.jl
-
-RUN mkdir .dev
-RUN mv build plutoserver.egg-info .dev
-