Add environment validation and error handling to RMS installation script

.github/workflows/CI.yml

@@ -2,7 +2,7 @@
 # This file contains the script used by GitHub actions to execute the Continuous Integration (CI)
 # for RMG-Py. This includes building RMG and its dependencies, executing the unit tests,
 # functional tests, database tests, and regression tests.
-# 
+#
 # This will run automatically on any push to any branch, but will only run one instance of
 # itself at a time per branch (to avoid spawning tons of runners, which prevents them from
 # executing).
@@ -14,7 +14,7 @@
 #
 #
 # Changelog:
-# 2023-04    - Jackson Burns - Added this header, regression tests, cleanup of action in 
+# 2023-04    - Jackson Burns - Added this header, regression tests, cleanup of action in
 #              in general, and documentation throughout the file.
 # 2023-05    - added Docker build steps
 # 2023-05-12 - added changes to allow running on forks
@@ -54,6 +54,8 @@ env:
   RMG_DATABASE_BRANCH: main
   # RMS branch to use for ReactionMechanismSimulator installation
   RMS_BRANCH: for_rmg
+  # RMS mode used for install_rms.sh
+  RMS_MODE: CI
   # julia parallel pre-compilation leads to race conditions and hangs, so we limit it to run in serial
   JULIA_NUM_PRECOMPILE_TASKS: 1
 
@@ -64,7 +66,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9"]
-        os: [macos-13, macos-latest, ubuntu-latest]
+        os: [macos-13, macos-latest, ubuntu-20.04, ubuntu-22.04, ubuntu-latest]
         include-rms: ["", "with RMS"]
         exclude:
           - os: macos-13  # GitHub's runners just aren't up to the task of installing Julia
@@ -131,7 +133,7 @@ jobs:
     name: Regression Test
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
-    env: 
+    env:
       # This is true only if this is a reference case for the regression testing:
       REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
     defaults:
@@ -167,7 +169,7 @@ jobs:
 
       # RMG build step
       - run: make install
-      
+
       - name: Make separate No-RMS conda env
         run: |
           conda create --name rmg_env_without_rms --clone rmg_env
@@ -269,7 +271,7 @@ jobs:
           REFERENCE: stable_regression_results
         run: |
           conda activate rmg_env_without_rms
-          
+
           exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout)
           mkdir -p "test/regression-diff"
           for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface;

Dockerfile

@@ -77,9 +77,11 @@ RUN make
 # 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}
+ENV RMS_MODE=CI
 # 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"
+ENV JULIA_PYTHONCALL_EXE="/miniconda/envs/rmg_env/bin/python"
 RUN source install_rms.sh
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run

install_rms.sh

@@ -39,16 +39,36 @@ echo "Julia 1.10 binary path: $julia_path"
 
 # Get current conda environment name
 current_env=$(conda info --envs | grep '\*' | awk '{print $1}')
-echo "Current conda environment: $current_env"
+
+# Ask the user to confirm RMS is being installed in the correct
+# conda environemnt. Skip if this is run under CI.
+if [ "$RMS_MODE" != "CI" ]; then
+    echo "    Please confirm that you want to install RMS into the current conda environment: '$current_env'"
+    echo "    If this is not correct, abort and activate the correct environment before rerunning."
+    read -p "Proceed with installation in '$current_env'? (y/N): " confirm
+    case "$confirm" in
+    [yY][eE][sS]|[yY])
+        echo "✅ Proceeding with installation in '$current_env'"
+        ;;
+    *)
+        echo "❌ Aborted. Please activate the correct conda environment and try again."
+        exit 1
+        ;;
+    esac
+else
+    echo "Current conda environment: $current_env"
+fi
 
 # 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_CONDAPKG_EXE=$(which conda)
 conda env config vars set JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python
 conda env config vars set PYTHON_JULIAPKG_EXE=$(which julia)
 conda env config vars set PYTHON_JULIAPKG_PROJECT=$CONDA_PREFIX/julia_env
 # Also export for current shell/session (needed for Docker/non-interactive use)
 export JULIA_CONDAPKG_BACKEND=Null
+export JULIA_CONDAPKG_EXE="$(which conda)"
 export JULIA_PYTHONCALL_EXE="$CONDA_PREFIX/bin/python"
 export PYTHON_JULIAPKG_EXE="$(which julia)"
 export PYTHON_JULIAPKG_PROJECT="$CONDA_PREFIX/julia_env"
@@ -58,11 +78,101 @@ conda install -y conda-forge::pyjuliacall
 echo "Environment variables referencing JULIA:"
 env | grep JULIA
 
-# Use RMS_BRANCH environment variable if set, otherwise default to for_rmg
+# Defaults to "standard" if no arg provided
+RMS_MODE=${1:-standard}
+
+# Default RMS branch for standard install
 RMS_BRANCH=${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=\"$RMS_BRANCH\")); using ReactionMechanismSimulator; Pkg.instantiate()" || echo "RMS install error - continuing anyway ¯\_(ツ)_/¯"
+# Ask for local RMS path
+if [ "$RMS_MODE" = "developer" ]; then
+    echo "Using developer mode for RMS installation"
+    read -e -p "Please enter full path to your local RMS source code: " RMS_PATH
+    if [ ! -d "$RMS_PATH" ]; then
+        echo "ERROR: '$RMS_PATH' is not a valid directory."
+        exit 1
+    fi
+    echo "Using local RMS path: $RMS_PATH"
+fi
+
+# Initialize the Julia environment from Python using juliacall
+python << EOF
+import sys
+try:
+    from juliacall import Main
+    Main.seval('println("Active Julia environment: ", Base.active_project())')
+    Main.seval('println("Julia load path: ", Base.load_path())')
+    Main.seval('using Pkg')
+    Main.seval('Pkg.status()')
+except Exception as e:
+    print("❌ Error while initialize Julia environment:")
+    print(e)
+    sys.exit(1)
+EOF
+
+# Install RMS
+if [ "$RMS_MODE" = "standard" ] || [ "$RMS_MODE" = "CI" ]; then
+    echo "Installing RMS from branch: $RMS_BRANCH"
+    julia << EOF || echo "RMS standard install error - continuing anyway ¯\\_(ツ)_/¯"
+    using Pkg
+    Pkg.activate(ENV["PYTHON_JULIAPKG_PROJECT"])
+    Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl.git", rev="$RMS_BRANCH"))
+    Pkg.instantiate()
+    try
+        @info "Loading RMS"
+        using ReactionMechanismSimulator
+        @info "RMS loaded successfully!"
+    catch err
+        @error "Failed to load RMS" exception=err
+        Base.show_backtrace(stderr, catch_backtrace())
+        exit(1)
+    end
+EOF
+elif [ "$RMS_MODE" = "developer" ]; then
+    echo "Installing RMS in developer mode from path: $RMS_PATH"
+    julia << EOF || echo "RMS developer install error - continuing anyway ¯\\_(ツ)_/¯"
+    using Pkg
+    println(ENV["PYTHON_JULIAPKG_PROJECT"])
+    Pkg.activate(ENV["PYTHON_JULIAPKG_PROJECT"])
+    Pkg.develop(path="$RMS_PATH")
+    Pkg.instantiate()
+    try
+        @info "Loading RMS"
+        using ReactionMechanismSimulator
+        @info "RMS loaded successfully!"
+    catch err
+        @error "Failed to load RMS" exception=err
+        Base.show_backtrace(stderr, catch_backtrace())
+        exit(1)
+    end
+EOF
+else
+    echo "Unknown RMS_MODE: $RMS_MODE. Must be either 'CI', 'standard' or 'developer'."
+    exit 1
+fi
+
+julia_status=$?
+if [ $julia_status -ne 0 ]; then
+    echo "RMS installation failed!"
+    exit $julia_status
+fi
 
 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)"
+
+python << EOF
+import sys
+try:
+    from juliacall import Main
+    RMS_Pkg = Main.seval('Base.identify_package("ReactionMechanismSimulator")')
+    print("Package identify result: ", RMS_Pkg)
+    if RMS_Pkg is Main.nothing:
+        print("❌ ReactionMechanismSimulator is NOT installed correctly.")
+        sys.exit(1)
+    else:
+        print("✅ ReactionMechanismSimulator is succesfully installed!")
+        sys.exit(0)
+except Exception as e:
+    print("❌ Error while checking ReactionMechanismSimulator installation:")
+    print(e)
+    sys.exit(1)
+EOF