Dockerfile (#710)

This PR includes a Dockerfile for ARC as well as a new CI for the
Dockerfile build and push

.github/workflows/docker_build.yml

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+name: Docker Image Build and Push
+
+on:
+  schedule:
+    - cron: "0 0 */7 * *" # every 7 days
+  push:
+    branches:
+        - main
+  pull_request:
+    branches:
+        - main
+    paths:
+        - './Dockerfile'
+jobs:
+  ci-check:
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build ARC
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          push: false
+
+  build-and-push:
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Login to Docker Hub
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v1
+    - name: Build and push ARC
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        file: ./Dockerfile
+        push: true
+        tags: ${{ secrets.DOCKERHUB_USERNAME }}/arc:latest
+

Dockerfile

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+# Stage 1: RMG setup
+# RMG Dockerfile 
+# The parent image is the base image that the Dockerfile builds upon.
+# The RMG installation instructions suggest Anaconda for installation by source, however, we use micromamba for the Docker image due to its smaller size and less overhead.
+# https://hub.docker.com/layers/mambaorg/micromamba/1.4.3-jammy/images/sha256-0c7c97be938c5522dcb9e1737bfa4499c53f6cf9e32e53897607a57ba8b148d5?context=explore
+# We are using the sha256 hash to ensure that the image is not updated without our knowledge. It considered best practice to use the sha256 hash
+FROM --platform=linux/amd64 mambaorg/micromamba@sha256:20fb02f2d1160265f7fabaf1601707a902ae65c6dc9e053d305441182450c368 AS rmg-stage
+
+# Set the user as root
+USER root
+
+# Create a login user named rmguser
+# Create a login user named rmguser
+ARG NEW_MAMBA_USER=rmguser
+ARG NEW_MAMBA_USER_ID=1000
+ARG NEW_MAMBA_USER_GID=1000
+RUN usermod "--login=${NEW_MAMBA_USER}" "--home=/home/${NEW_MAMBA_USER}" \
+        --move-home "-u ${NEW_MAMBA_USER_ID}" "${MAMBA_USER}" && \
+    groupmod "--new-name=${NEW_MAMBA_USER}" \
+             "-g ${NEW_MAMBA_USER_GID}" "${MAMBA_USER}" && \
+    echo "${NEW_MAMBA_USER}" > "/etc/arg_mamba_user" && \
+    :
+
+# Set the environment variables
+ARG MAMBA_ROOT_PREFIX=/opt/conda
+ENV MAMBA_USER=$NEW_MAMBA_USER
+ENV BASE=$MAMBA_ROOT_PREFIX
+
+# Install system dependencies
+#
+# List of deps and why they are needed:
+#  - make, gcc, g++ for building RMG
+#  - git for downloading RMG respoitories
+#  - wget for downloading conda install script
+#  - libxrender1 required by RDKit
+# Clean up the apt cache to reduce the size of the image
+RUN apt-get update && apt-get install -y \
+    git \
+    gcc \
+    g++ \
+    make \
+    libgomp1\
+    libxrender1 \
+    sudo \
+    && apt-get clean \
+    && apt-get autoclean \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/*\
+    && echo "${NEW_MAMBA_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+# Change user to the non-root user
+USER $MAMBA_USER
+
+# Make directory for RMG-Py and RMG-database
+RUN mkdir -p /home/rmguser/Code
+
+# Change working directory to Code
+WORKDIR /home/rmguser/Code
+
+# Clone the RMG base and database repositories. The pulled branches are only the main branches.
+RUN git clone -b main https://github.com/ReactionMechanismGenerator/RMG-Py.git \ 
+    && git clone -b main https://github.com/ReactionMechanismGenerator/RMG-database.git
+
+# cd into RMG-Py
+WORKDIR /home/rmguser/Code/RMG-Py
+
+# Install RMG-Py and then clean up the micromamba cache
+RUN micromamba create -y -f environment.yml && \
+    micromamba install -n rmg_env -c conda-forge conda && \
+    micromamba clean --all -f -y
+
+# Activate the RMG environment
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+ENV ENV_NAME=rmg_env
+
+# Set environment variables
+# These need to be set in the Dockerfile so that they are available to the build process
+ENV PATH /opt/conda/envs/rmg_env/bin:$PATH
+ENV PYTHONPATH /home/rmguser/Code/RMG-Py:$PYTHONPATH
+ENV PATH /home/rmguser/Code/RMG-Py:$PATH
+
+# Build RMG
+RUN make \
+    && echo "export PYTHONPATH=/home/rmguser/Code/RMG-Py" >> ~/.bashrc \
+    && echo "export PATH=/home/rmguser/Code/RMG-Py:$PATH" >> ~/.bashrc
+
+# Install RMS
+# The extra arguments are required to install PyCall and RMS in this Dockerfile. Will not work without them.
+# Final command is to compile the RMS during Docker build - This will reduce the time it takes to run RMS for the first time
+RUN touch /opt/conda/envs/rmg_env/condarc-julia.yml
+RUN CONDA_JL_CONDA_EXE=/bin/micromamba julia -e 'ENV["CONDA_JL_CONDA_EXE"]="/opt/conda/envs/rmg_env/bin/conda";using Pkg;Pkg.add(PackageSpec(name="PyCall", rev="master")); Pkg.build("PyCall"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="main"))' \
+    && python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" \
+    && python-jl -c "from pyrms import rms"
+
+# Add alias to bashrc - rmge to activate the environment
+# These commands are not necessary for the Docker image to run, but they are useful for the user
+RUN echo "alias rmge='micromamba activate rmg_env'" >> ~/.bashrc \
+    && echo "alias rmg='python-jl /home/rmguser/Code/RMG/rmg.py input.py'" >> ~/.bashrc \
+    && echo "alias deact='micromamba deactivate'" >> ~/.bashrc \
+    && echo "export rmgpy_path='/home/rmguser/Code/RMG-Py/'" >> ~/.bashrc \
+    && echo "export rmgdb_path='/home/rmguser/Code/RMG-database/'" >> ~/.bashrc \
+    && echo "alias rmgcode='cd \$rmgpy_path'" >> ~/.bashrc \
+    && echo "alias rmgdb='cd \$rmgdb_path'" >> ~/.bashrc \
+    && echo "alias conda='micromamba'" >> ~/.bashrc \
+    && echo "alias mamba='micromamba'" >> ~/.bashrc 
+
+# Set the entrypoint to bash
+ENTRYPOINT ["/bin/bash", "--login"]
+
+FROM rmg-stage AS arc-stage
+
+# Log in as rmguser
+USER rmguser
+
+# Installing ARC
+# Change directory to Code
+WORKDIR /home/rmguser/Code
+
+# Clone main branch ARC repository from GitHub and set as working directory
+RUN git clone -b main https://github.com/ReactionMechanismGenerator/ARC.git
+WORKDIR /home/rmguser/Code/ARC
+
+# Set environment variables for the Docker run and container
+ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/ARC"
+ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/AutoTST"
+ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/TS-GCN"
+ENV PATH /home/rmguser/Code/ARC:$PATH
+
+# Install ARC Environment
+RUN micromamba create -y -f environment.yml && \
+    micromamba clean --all -f -y && \
+    rm -rf /home/rmguser/.cache/yarn \
+    rm -rf /home/rmguser/.cache/pip &&\
+    rm -rf /home/rmguser/.cache/pip && \
+    find -name '*.a' -delete && \
+    find -name '*.pyc' -delete && \
+    find -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
+    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/scipy -name 'tests' -type d -exec rm -rf '{}' '+' && \
+    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/numpy -name 'tests' -type d -exec rm -rf '{}' '+' && \
+    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/pandas -name 'tests' -type d -exec rm -rf '{}' '+' && \
+    find /opt/conda/envs/arc_env/lib/python3.7/site-packages -name '*.pyx' -delete && \
+    rm -rf /opt/conda/envs/arc_env/lib/python3.7/site-packages/uvloop/loop.c &&\
+    make clean
+
+# Activate the ARC environment
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+ENV ENV_NAME=arc_env