Remove/disable Julia/decapodes/forecast_hub in new Dockerfile.light f…

…ile (#139)

Dockerfile

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+Dockerfile.light

Dockerfile.full

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+FROM ghcr.io/darpa-askem/askem-julia:8.0.1 AS JULIA_BASE_IMAGE
+FROM ghcr.io/darpa-askem/askem-forecast-hub:latest AS FORECAST_HUB_BASE
+
+FROM python:3.10
+
+USER root
+
+# Install custom Julia
+ENV JULIA_PATH=/usr/local/julia
+ENV JULIA_DEPOT_PATH=/usr/local/julia
+ENV JULIA_PROJECT=/home/jupyter/.julia/environments/askem
+
+# Install r-lang and kernel
+RUN apt update && \
+    apt install -y r-base r-cran-irkernel \
+        graphviz libgraphviz-dev \
+        libevent-core-2.1-7 libevent-pthreads-2.1-7 \
+        lsof && \
+    apt clean -y && \
+    apt autoclean -y \
+    apt autoremove -y
+
+# # Install forecast hub requirements from precompiled image (Rlang)
+COPY --chown=1000:1000 --from=FORECAST_HUB_BASE /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/
+
+RUN apt-get install -y build-essential make gcc g++ git gfortran npm \
+        gdal-bin libgdal-dev python3-all-dev libspatialindex-dev && \
+    npm install -g typescript
+ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
+ENV C_INCLUDE_PATH=/usr/include/gdal
+
+COPY --chown=1000:1000 --from=JULIA_BASE_IMAGE /usr/local/julia /usr/local/julia
+COPY --chown=1000:1000 --from=JULIA_BASE_IMAGE /Project.toml /Manifest.toml /home/jupyter/.julia/environments/askem/
+RUN chmod -R 777 /usr/local/julia/logs
+RUN ln -sf /usr/local/julia/bin/julia /usr/local/bin/julia
+
+# Switch to non-root user. It is crucial for security reasons to not run jupyter as root user!
+RUN useradd -m jupyter
+USER jupyter
+
+# Install PyCIEMSS from GitHub
+RUN pip install --no-cache-dir git+https://github.com/ciemss/pyciemss.git@9aa5d8849c630e8d2b208d25464d7b006fcd4d60 --use-pep517
+
+
+# Install Mira from github, with cache-bust
+ADD https://api.github.com/repos/DARPA-ASKEM/askem-beaker/git/refs/heads/main bust-cache.json
+
+RUN git clone https://github.com/indralab/mira.git /home/jupyter/mira && \
+    pip install --no-cache-dir /home/jupyter/mira/"[ode,tests,dkg-client,sbml]" && \
+    rm -r /home/jupyter/mira
+
+# Install Gilda - Mira Dependency 
+RUN pip install gilda==1.2.1
+
+#### START Installs for PySB context
+# Install project requirements
+USER root
+WORKDIR /tmp
+RUN wget https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.2/BioNetGen-2.9.2-linux.tar.gz && \
+    tar -xzf BioNetGen-2.9.2-linux.tar.gz && \
+    mv BioNetGen-2.9.2 /usr/local/share/BioNetGen && \
+    rm BioNetGen-2.9.2-linux.tar.gz
+
+WORKDIR /opt/stochkit
+ENV STOCHKIT_HOME=/opt/stochkit
+RUN git clone https://github.com/StochSS/StochKit.git /opt/stochkit
+RUN bash ./install.sh
+USER jupyter
+ENV PATH=$PATH:$STOCHKIT_HOME/bin
+RUN pip install --no-cache-dir beaker-pysb
+####  END  Installs for PySB context
+
+# Install project requirements
+COPY --chown=1000:1000 pyproject.toml README.md hatch_build.py /home/jupyter/askem_beaker/
+RUN mkdir -p /home/jupyter/askem_beaker/src/askem_beaker && touch /home/jupyter/askem_beaker/src/askem_beaker/__init__.py
+RUN pip install --no-cache-dir --upgrade -e /home/jupyter/askem_beaker
+
+COPY --chown=1000:1000 . /home/jupyter/askem_beaker/
+
+# Installs the askem specific subkernels
+RUN pip install --no-cache-dir --upgrade /home/jupyter/askem_beaker
+
+#WORKDIR /askem_beaker
+WORKDIR /home/jupyter
+RUN unzip /home/jupyter/askem_beaker/resources/chromadb_functions_mira.zip \
+    && mv /home/jupyter/chromadb_functions /home/jupyter/chromadb_functions_mira && ls
+RUN unzip /home/jupyter/askem_beaker/resources/chromadb_functions_chirho.zip \
+    && mv /home/jupyter/chromadb_functions /home/jupyter/chromadb_functions_chirho && ls
+RUN unzip /home/jupyter/askem_beaker/resources/chromadb_functions_mimi.zip
+
+# Install Julia kernel (as user jupyter)
+RUN /usr/local/julia/bin/julia -e 'using IJulia; IJulia.installkernel("julia"; julia=`/usr/local/julia/bin/julia --threads=4`)'
+
+RUN mkdir /home/jupyter/workspace
+WORKDIR /home/jupyter/workspace
+
+CMD ["python", "-m", "beaker_kernel.server.main", "--ip", "0.0.0.0"]

Dockerfile.light

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+FROM python:3.10
+
+USER root
+
+
+# Install r-lang and kernel
+RUN apt update && \
+    apt install -y r-base r-cran-irkernel \
+        graphviz libgraphviz-dev \
+        libevent-core-2.1-7 libevent-pthreads-2.1-7 \
+        lsof && \
+    apt clean -y && \
+    apt autoclean -y \
+    apt autoremove -y
+
+RUN apt-get install -y build-essential make gcc g++ git gfortran npm \
+        gdal-bin libgdal-dev python3-all-dev libspatialindex-dev && \
+    npm install -g typescript
+ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
+ENV C_INCLUDE_PATH=/usr/include/gdal
+
+# Switch to non-root user. It is crucial for security reasons to not run jupyter as root user!
+RUN useradd -m jupyter
+USER jupyter
+
+# Install PyCIEMSS from GitHub
+RUN pip install --no-cache-dir git+https://github.com/ciemss/pyciemss.git@9aa5d8849c630e8d2b208d25464d7b006fcd4d60 --use-pep517
+
+RUN git clone https://github.com/indralab/mira.git /home/jupyter/mira && \
+    pip install --no-cache-dir /home/jupyter/mira/"[ode,tests,dkg-client,sbml]" && \
+    rm -r /home/jupyter/mira
+
+# Install Gilda - Mira Dependency 
+RUN pip install gilda==1.2.1
+
+#### START Installs for PySB context
+# Install project requirements
+USER root
+WORKDIR /tmp
+RUN wget https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.2/BioNetGen-2.9.2-linux.tar.gz && \
+    tar -xzf BioNetGen-2.9.2-linux.tar.gz && \
+    mv BioNetGen-2.9.2 /usr/local/share/BioNetGen && \
+    rm BioNetGen-2.9.2-linux.tar.gz
+
+WORKDIR /opt/stochkit
+ENV STOCHKIT_HOME=/opt/stochkit
+RUN git clone https://github.com/StochSS/StochKit.git /opt/stochkit
+RUN bash ./install.sh
+USER jupyter
+ENV PATH=$PATH:$STOCHKIT_HOME/bin
+RUN pip install --no-cache-dir beaker-pysb
+####  END  Installs for PySB context
+
+# Install project requirements
+COPY --chown=1000:1000 pyproject.toml README.md hatch_build.py /home/jupyter/askem_beaker/
+RUN mkdir -p /home/jupyter/askem_beaker/src/askem_beaker && touch /home/jupyter/askem_beaker/src/askem_beaker/__init__.py
+RUN pip install --no-cache-dir --upgrade -e /home/jupyter/askem_beaker
+
+COPY --chown=1000:1000 . /home/jupyter/askem_beaker/
+
+# Installs the askem specific subkernels
+RUN pip install --no-cache-dir --upgrade /home/jupyter/askem_beaker
+
+#WORKDIR /askem_beaker
+WORKDIR /home/jupyter
+RUN unzip /home/jupyter/askem_beaker/resources/chromadb_functions_mira.zip \
+    && mv /home/jupyter/chromadb_functions /home/jupyter/chromadb_functions_mira && ls
+RUN unzip /home/jupyter/askem_beaker/resources/chromadb_functions_chirho.zip \
+    && mv /home/jupyter/chromadb_functions /home/jupyter/chromadb_functions_chirho && ls
+
+RUN mkdir /home/jupyter/workspace
+WORKDIR /home/jupyter/workspace
+
+CMD ["python", "-m", "beaker_kernel.server.main", "--ip", "0.0.0.0"]