Docker build updates

.github/workflows/CI.yml

@@ -48,9 +48,12 @@ env:
   # if running on RMG-Py but requiring changes on an un-merged branch of RMG-database, replace
   # main with the name of the branch
   RMG_DATABASE_BRANCH: main
+  # RMS branch to use for ReactionMechanismSimulator installation
+  RMS_BRANCH: for_rmg
   # julia parallel pre-compilation leads to race conditions and hangs, so we limit it to run in serial
   JULIA_NUM_PRECOMPILE_TASKS: 1
 
+
 jobs:
   build-and-test:
     strategy:
@@ -400,7 +403,10 @@ jobs:
     # taken from https://github.com/docker/build-push-action
     needs: [build-and-test, regression-test]
     runs-on: ubuntu-latest
-    if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
+    # Run on push to main or on pull requests from official fork.
+    if: |
+      (github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py') ||
+      (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == 'ReactionMechanismGenerator/RMG-Py')
     steps:
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
@@ -409,15 +415,20 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Login to Docker Hub
+        if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
-      - name: Build and Push
+      - name: Build (and Push if on main)
         uses: docker/build-push-action@v6
+        env:
+          BUILDKIT_PROGRESS: plain
         with:
-          push: true
+          push: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
           tags: reactionmechanismgenerator/rmg:latest
           build-args: |
-            RMS_Branch=for_rmg
+            RMG_Py_Branch=${{ github.head_ref || github.ref_name }}
+            RMG_Database_Branch=${{ env.RMG_DATABASE_BRANCH }}
+            RMS_Branch=${{ env.RMS_BRANCH }}

Dockerfile

@@ -11,31 +11,43 @@ RUN ln -snf /bin/bash /bin/sh
 #  - git for downloading RMG respoitories
 #  - wget for downloading conda install script
 #  - libxrender1 required by RDKit
+#  - ca-certificates added for HTTPS downloads
 RUN apt-get update && \
     apt-get install -y \
         make \
         gcc \
         wget \
         git \
         g++ \
-        libxrender1 && \
+        libxrender1 \
+        ca-certificates && \
     apt-get autoremove -y && \
     apt-get clean -y
 
+
+# Install Julia 1.10 using juliaup
+RUN wget -qO- https://install.julialang.org | sh -s -- --yes --default-channel 1.10 && \
+    /root/.juliaup/bin/juliaup add 1.10 && \
+    /root/.juliaup/bin/juliaup default 1.10 && \
+    /root/.juliaup/bin/juliaup list && \
+    rm -rf /root/.juliaup/downloads /root/.juliaup/tmp
+ENV PATH="/root/.juliaup/bin:$PATH"
+
 # Install conda
 RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
     bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda && \
     rm Miniconda3-latest-Linux-x86_64.sh
-ENV PATH="$PATH:/miniconda/bin"
+ENV PATH="/miniconda/bin:$PATH"
 
 # Set Bash as the default shell for following commands
 SHELL ["/bin/bash", "-c"]
 
 # Add build arguments for RMG-Py, RMG-database, and RMS branches.
+# The defaults are set here, but they can be overridden at build time
+# using the --build-arg option, or in the continous integration CI.yml file.
 ARG RMG_Py_Branch=main
 ARG RMG_Database_Branch=main
-ARG RMS_Branch=main
-ENV rmsbranch=${RMS_Branch}
+ARG RMS_Branch=for_rmg
 
 # cd
 WORKDIR /rmg
@@ -45,8 +57,11 @@ RUN git clone --single-branch --branch ${RMG_Py_Branch} --depth 1 https://github
     git clone --single-branch --branch ${RMG_Database_Branch} --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git
 
 WORKDIR /rmg/RMG-Py
+
 # build the conda environment
 RUN conda env create --file environment.yml
+# Remove conda package cache to reduce image size
+RUN rm -rf /miniconda/pkgs
 
 # This runs all subsequent commands inside the rmg_env conda environment
 #
@@ -61,19 +76,25 @@ RUN conda clean --all --yes
 ENV RUNNER_CWD=/rmg
 ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 
-# 1. Build RMG
-# 2. Install and link Julia dependencies for RMS
+# Build RMG
+RUN make
+
+# Install and link Julia dependencies for RMS
 # setting this env variable fixes an issue with Julia precompilation on Windows
 ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
+ENV RMS_BRANCH=${RMS_Branch}
+# Usually this is set automatically, but we're not actually running
+# in an active conda environment when building the Docker so we need to set it manually
+ENV PYTHON_JULIAPKG_PROJECT="/miniconda/envs/rmg_env/julia_env"
 RUN source install_rms.sh
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
-RUN python rmg.py examples/rmg/minimal/input.py
-# delete the results, preserve input.py
-RUN mv examples/rmg/minimal/input.py . && \
-    rm -rf examples/rmg/minimal/* && \
-    mv input.py examples/rmg/minimal/
+RUN python rmg.py examples/rmg/rms_constant_V/input.py
+# delete the results, restore input.py from git
+RUN rm -rf examples/rmg/rms_constant_V/* && \
+    git checkout -- examples/rmg/rms_constant_V/
 
 # when running this image, open an interactive bash terminal inside the conda environment
-RUN echo "source activate rmg_env" >~/.bashrc
+RUN conda init
+RUN echo "conda activate rmg_env" >> ~/.bashrc
 ENTRYPOINT ["/bin/bash", "--login"]

install_rms.sh

@@ -41,18 +41,28 @@ echo "Julia 1.10 binary path: $julia_path"
 current_env=$(conda info --envs | grep '\*' | awk '{print $1}')
 echo "Current conda environment: $current_env"
 
-# Set environment variables for the current environment
+# Set environment variables for the current environment, for future uses
 # https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-Python-and-required-Python-packages-installed
 conda env config vars set JULIA_CONDAPKG_BACKEND=Null
 conda env config vars set JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python
 conda env config vars set PYTHON_JULIAPKG_EXE=$(which julia)
-
-# Reactivate the current environment to apply the new variables
-conda deactivate
-conda activate $current_env
+conda env config vars set PYTHON_JULIAPKG_PROJECT=$CONDA_PREFIX/julia_env
+# Also export for current shell/session (needed for Docker/non-interactive use)
+export JULIA_CONDAPKG_BACKEND=Null
+export JULIA_PYTHONCALL_EXE="$CONDA_PREFIX/bin/python"
+export PYTHON_JULIAPKG_EXE="$(which julia)"
+export PYTHON_JULIAPKG_PROJECT="$CONDA_PREFIX/julia_env"
 
 conda install -y conda-forge::pyjuliacall
 
-julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl.git", rev="for_rmg")); using ReactionMechanismSimulator; Pkg.instantiate()' || echo "RMS install error - continuing anyway ¯\_(ツ)_/¯"
+echo "Environment variables referencing JULIA:"
+env | grep JULIA
+
+# Use RMS_BRANCH environment variable if set, otherwise default to for_rmg
+RMS_BRANCH=${RMS_BRANCH:-for_rmg}
+echo "Installing ReactionMechanismSimulator from branch: $RMS_BRANCH"
+
+julia -e "using Pkg; Pkg.add(Pkg.PackageSpec(name=\"ReactionMechanismSimulator\", url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl.git\", rev=\"$RMS_BRANCH\")); using ReactionMechanismSimulator; Pkg.instantiate()" || echo "RMS install error - continuing anyway ¯\_(ツ)_/¯"
 
+echo "Checking if ReactionMechanismSimulator is installed in the current conda environment for Python usage..."
 python -c "from juliacall import Main; import sys; sys.exit(0 if Main.seval('Base.identify_package(\"ReactionMechanismSimulator\") !== nothing') and print('ReactionMechanismSimulator is installed in $current_env') is None else 1)"