Clean up Dockerfile

.github/workflows/build.yml

@@ -7,9 +7,8 @@ on:
     branches: [ "master" ]
   workflow_dispatch:
 
-
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:

.github/workflows/container.yml

@@ -7,6 +7,10 @@ on:
     branches: [ "master" ]
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 env:
     IMAGE_NAME: pynucleus
     IMAGE_TAGS: latest ${{ github.sha }}

.github/workflows/documentation-ci.yml

@@ -5,6 +5,10 @@ on:
     branches: [ "master" ]
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 permissions:
   contents: read
   id-token: write

Dockerfile

@@ -8,10 +8,12 @@ LABEL maintainer Christian Glusa
 
 # install packages needed for build
 RUN sed -i 's/Components: main/Components: main contrib non-free/' /etc/apt/sources.list.d/debian.sources \
-  && apt-get update && \
-  DEBIAN_FRONTEND=noninteractive apt-get install -y \
+  && apt-get update \
+  && DEBIAN_FRONTEND=noninteractive apt-get dist-upgrade -y \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -y \
         gcc g++ make gfortran \
         libssl-dev ca-certificates \
+        ccache \
         git less nano \
         libopenblas0-serial \
         libmetis-dev libparmetis-dev \
@@ -37,30 +39,33 @@ WORKDIR /pynucleus
 
 ARG PYNUCLEUS_BUILD_PARALLELISM=1
 
-# Build PyNucleus
-RUN make prereq PIP_FLAGS="--no-cache-dir --break-system-packages" && \
-    make prereq-extra PIP_FLAGS="--no-cache-dir --break-system-packages" && \
-    make install PIP_INSTALL_FLAGS="--no-cache-dir --break-system-packages" && \
-    make docs && \
-    find . -type f -name '*.c' -exec rm {} + && \
-    find . -type f -name '*.cpp' -exec rm {} + && \
-    rm -rf build packageTools/build base/build metisCy/build fem/build multilevelSolver/build nl/build
+# Install dependencies
+# RUN --mount=type=cache,target=/root/.ccache --mount=type=cache,target=/root/.cache/pip \
+RUN \
+    make prereq PIP_FLAGS=" --break-system-packages" \
+    && make prereq-extra PIP_FLAGS=" --break-system-packages"
 
-# Set up Jupyter notebooks, greeting, some bash things
-RUN python -m pip install --no-cache-dir --break-system-packages ipykernel && \
-    python -m ipykernel install --name=PyNucleus && \
-    echo '[ ! -z "$TERM" -a -r /pynucleus/README.container.rst ] && printf "\e[32m" && cat /pynucleus/README.container.rst && printf "\e[0m"' >> /etc/bash.bashrc && \
-    echo "alias ls='ls --color=auto -FN'" >> /etc/bash.bashrc && \
-    echo "set completion-ignore-case On" >> /etc/inputrc
+# Build PyNucleus
+# RUN --mount=type=cache,target=/root/.ccache --mount=type=cache,target=/root/.cache/pip \
+RUN \
+    make install PIP_INSTALL_FLAGS=" --break-system-packages" \
+    && find . -type f -name '*.c' -exec rm {} + \
+    && find . -type f -name '*.cpp' -exec rm {} + \
+    && rm -rf build packageTools/build base/build metisCy/build fem/build multilevelSolver/build nl/build \
+    && ccache -s
 
-WORKDIR /root
+# Generate documentation and examples
+RUN make docs \
+    && rm examples/test.hdf5
 
-# Copy examples and drivers to user home, launch Jupyter notebook server
-ENTRYPOINT mkdir -p /root/examples && \
-           mkdir -p /root/drivers && \
-           cp -r --update=none /pynucleus/examples/* /root/examples && \
-           cp -r --update=none /pynucleus/drivers/* /root/drivers && \
-           jupyter notebook --port=8889 --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token='' --NotebookApp.password='' --notebook-dir=/root/ --KernelSpecManager.ensure_native_kernel=False --KernelSpecManager.allowed_kernelspecs=pynucleus > /dev/null 2>&1 & \
-           /bin/bash
+# Set up greeting, settings
+RUN \
+    echo '[ ! -z "$TERM" -a -r /pynucleus/README.container.rst ] && printf "\e[32m" && cat /pynucleus/README.container.rst && printf "\e[0m"' >> /etc/bash.bashrc \
+    && echo "alias ls='ls --color=auto -FN'" >> /etc/bash.bashrc \
+    && echo "set completion-ignore-case On" >> /etc/inputrc
 
+# Set up entrypoint with jupyter notebook
+COPY entrypoint.sh /usr/local/bin/
+ENTRYPOINT ["entrypoint.sh"]
+WORKDIR /root
 EXPOSE 8889

compose.yaml

@@ -24,7 +24,9 @@ services:
       # Expose a Jupyter notebook server from the container
       - 8889:8889
     network_mode: host
+    user: root
     hostname: pynucleus-container
+    command: bash
 
   tests:
     image: ghcr.io/sandialabs/pynucleus:latest

entrypoint.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+set -e
+
+mkdir -p ~/examples
+mkdir -p ~/drivers
+cp -r --update=none /pynucleus/examples/* ~/examples
+cp -r --update=none /pynucleus/drivers/* ~/drivers
+
+jupyter notebook --port=8889 --no-browser --allow-root --ip=0.0.0.0 \
+        --NotebookApp.token='' --NotebookApp.password='' \
+        --notebook-dir=/root  > /dev/null 2>&1 &
+
+exec "$@"