Enhance Docker workflow and entry script for improved testing and compatibility

- Updated GitHub Actions workflow to use newer versions of Docker actions and added smoke test steps.
- Modified Dockerfile to include additional environment variables and install pytest.
- Created new smoke tests for ARC and RMG-Py functionalities.
- Refined entrywrapper.sh for better command handling and user experience.

Author: calvinp0

.github/workflows/docker_build.yml

@@ -32,33 +32,68 @@ jobs:
           large-packages: true
           docker-images: false
           swap-storage: true
+
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v5.0.0
 
+      - name: Set up Buildx
+        uses: docker/setup-buildx-action@v3.11.1
+      
+      # ----- PR and non-main branch steps -----
+      # For PRs: Build image but do not push and run smoke tests
       - name: Build Docker Image (No Push)
         if: github.event_name == 'pull_request' || (github.event_name == 'push' && github.ref != 'refs/heads/main')
-        uses: docker/build-push-action@v5.1.0
+        uses: docker/build-push-action@v6.18.0
         with:
           context: .
           file: ./Dockerfile
           push: false
+          load: true
+          tags: arc:test
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Run Smoke Tests
+        if: github.event_name == 'pull_request' || (github.event_name == 'push' && github.ref != 'refs/heads/main')
+        run: |
+          docker run --rm bash arc:test -lc \
+            "cd /home/mambauser/Code/ARC && micromamba run -n arc_env pytest dockerfiles/docker_tests/test_docker_smoke.py -m smoke -q"
+
+      # ----- Main branch only steps -----
+      # For pushes to main: Build, run smoke tests, and push to Docker Hub
+      - name: Build test stage (main)
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: docker/build-push-action@v6.18.0
+        with:
+          context: .
+          file: ./Dockerfile
+          load: true
+          tags: arc:final-${{ github.sha }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Run smoke (main, test stage)
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        run: |
+          docker run --rm arc:final-${{ github.sha }} bash -lc \
+            "cd /home/mambauser/Code/ARC && micromamba run -n arc_env pytest dockerfiles/docker_tests/test_docker_smoke.py -m smoke -q"
 
       - name: Login to Docker Hub
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/login-action@v3.0.0
+        uses: docker/login-action@v3.5.0
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
-      - name: Set up Docker Buildx
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/setup-buildx-action@v3.0.0
-
-      - name: Build and Push Docker Image
+      - name: Build final and push (main)
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/build-push-action@v5.1.0
+        uses: docker/build-push-action@v6.18.0
         with:
           context: .
           file: ./Dockerfile
           push: true
-          tags: ${{ secrets.DOCKERHUB_USERNAME }}/arc:latest
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/arc:latest
+            ${{ secrets.DOCKERHUB_USERNAME }}/arc:${{ github.sha }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

Dockerfile

@@ -1,7 +1,7 @@
-# Stage 1: RMG setup
-# RMG Dockerfile
+# Stage 1: RMG setup & ARC setup
 # 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.
+# Installation of ARC will also be done in this stage.
 FROM --platform=linux/amd64 mambaorg/micromamba:2.2-ubuntu24.04 AS builder
 
 # Set ARGS
@@ -51,19 +51,24 @@ RUN micromamba create -y -n rmg_env -f /home/mambauser/Code/RMG-Py/environment.y
 
 WORKDIR /home/mambauser/Code/ARC
 RUN micromamba create -y -n arc_env -f environment.yml --channel-priority flexible && \
+    micromamba install -y -n arc_env -c conda-forge pytest && \
     micromamba clean --all -f -y && \
     micromamba run -n arc_env bash -euxo pipefail -c \
       "make compile && bash ./devtools/install_pyrdl.sh" && \
     micromamba clean --all --yes
 
-
-RUN rm -rf ~/.cache ~/.npm ~/.yarn /tmp/* && \
-    find /opt/conda -name '*.a' -delete && \
-    find /opt/conda -name '*.pyc' -delete && \
-    find /opt/conda -name '__pycache__' -type d -exec rm -rf {} +
-
+# Stage 2: Final image
+# The final image is based on the same micromamba image, but we copy over the installed RMG and ARC from the builder stage.
+# This keeps the final image size smaller and avoids unnecessary layers.
 FROM --platform=linux/amd64 mambaorg/micromamba:2.2-ubuntu24.04
 
+ENV MAMBA_ROOT_PREFIX=/opt/conda
+ENV PATH=$MAMBA_ROOT_PREFIX/bin:/home/mambauser/.juliaup/bin:/home/mambauser/Code/RMG-Py:/home/mambauser/Code/ARC:$PATH
+ENV PYTHONPATH="/home/mambauser/Code/RMG-Py:/home/mambauser/Code/ARC"
+ENV RMG_PY_DIR="/home/mambauser/Code/RMG-Py"
+ENV ARC_DIR="/home/mambauser/Code/ARC"
+ENV MAMBA_DOCKERFILE_ACTIVATE=1
+
 USER root
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -79,18 +84,9 @@ COPY --from=builder --chown=mambauser:mambauser /opt/conda /opt/conda
 COPY --from=builder --chown=mambauser:mambauser /home/mambauser/.juliaup /home/mambauser/.juliaup
 COPY --from=builder --chown=mambauser:mambauser /home/mambauser/Code /home/mambauser/Code
 
-
-ENV MAMBA_ROOT_PREFIX=/opt/conda
-ENV PATH=$MAMBA_ROOT_PREFIX/bin:/home/mambauser/.juliaup/bin:/home/mambauser/Code/RMG-Py:$PATH
-ENV PYTHONPATH="/home/mambauser/Code/RMG-Py:/home/mambauser/Code/ARC"
-ENV RMG_PY_DIR="/home/mambauser/Code/RMG-Py"
-ENV ARC_DIR="/home/mambauser/Code/ARC"
-ENV MAMBA_DOCKERFILE_ACTIVATE=1
-
 # --- Entry wrapper ----------------------------------------------------------
 COPY --chmod=755  dockerfiles/entrywrapper.sh  /usr/local/bin/entrywrapper.sh
 COPY --chmod=644  dockerfiles/aliases.sh       /etc/profile.d/aliases.sh
 COPY --chmod=755  dockerfiles/aliases_print.sh /usr/local/bin/aliases
 
 ENTRYPOINT ["/usr/local/bin/entrywrapper.sh"]
-# -----------------------------------------------------------------------------

dockerfiles/docker_tests/test_docker_smoke.py

@@ -0,0 +1,75 @@
+import pytest
+import subprocess
+import tempfile
+import pathlib
+import textwrap
+
+
+@pytest.mark.smoke
+def test_import_arc():
+    """Test that ARC can be imported in the docker image."""
+    try:
+        import arc
+        assert hasattr(arc, '__version__')
+    except ImportError as e:
+        pytest.fail(f"ImportError: {e}")
+
+
+@pytest.mark.smoke
+def test_arc_cli_help_runs():
+    """Test that ARC CLI help runs in the docker image."""
+    cmd = ["bash","-lc","micromamba run -n arc_env python -m ARC --help || true"]
+    p = subprocess.run(cmd, capture_output=True, text=True)
+    # Just ensure it executes and prints usage/help
+    assert "help" in (p.stdout + p.stderr).lower()
+
+
+@pytest.mark.smoke
+def test_arkane_cli_help_runs():
+    """Test that Arkane CLI help runs in the docker image."""
+    cmd = ["bash","-lc","micromamba run -n rmg_env python -m arkane --help || true"]
+    p = subprocess.run(cmd, capture_output=True, text=True)
+    # Just ensure it executes and prints usage/help
+    assert "arkane" in (p.stdout + p.stderr).lower()
+
+
+@pytest.mark.smoke
+def test_arc_can_execute_arkane_minimal():
+    """Test that ARC can execute Arkane with a minimal input in the docker image."""
+    arkane_input = textwrap.dedent("""\
+    #!/usr/bin/env python
+    modelChemistry = 'wb97m-v/def2-tzvpd'  # irrelevant here, just parseable
+    useHinderedRotors = False
+    thermo('H2', 'H298')
+    """)
+    with tempfile.TemporaryDirectory() as td:
+        inp = pathlib.Path(td, "input.py")
+        inp.write_text(arkane_input)
+        # Call arkane via rmg_env the same way ARC would (subprocess)
+        cmd = ["bash", "-lc", f"micromamba run -n rmg_env python -m arkane {inp} || true"]
+        p = subprocess.run(cmd, capture_output=True, text=True)
+        # We only assert it runs and produces any Arkane header/output (no heavy calc)
+        assert "arkane" in (p.stdout + p.stderr).lower()
+
+
+@pytest.mark.smoke
+def test_rmgpy_imports():
+    """Test that RMG-Py can be imported in the docker image."""
+    code = r"""
+import importlib, sys
+m = importlib.import_module('rmgpy')
+print('rmgpy OK', getattr(m, '__version__', 'unknown'))
+"""
+    cmd = ["bash","-lc", f"micromamba run -n rmg_env python - <<'PY'\n{code}\nPY"]
+    p = subprocess.run(cmd, capture_output=True, text=True)
+    assert p.returncode == 0, p.stderr
+    assert "rmgpy OK" in p.stdout
+
+
+@pytest.mark.smoke
+def test_rmg_cli_help_runs():
+    """Test that RMG CLI help runs in the docker image."""
+    cmd = ["bash", "-lc", "micromamba run -n rmg_env rmg --help || true"]
+    p = subprocess.run(cmd, capture_output=True, text=True)
+    # Just ensure it executes and prints usage/help
+    assert "rmg" in (p.stdout + p.stderr).lower()

dockerfiles/entrywrapper.sh

@@ -1,34 +1,32 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-# 1) Micromamba setup (for both interactive & non-interactive)
-eval "$(micromamba shell hook --shell bash)"
-
-# 1.1) Ensure the Code directory is owned by mambauser
-if [ ! -O /home/mambauser/Code ]; then
-  chown -R mambauser:mambauser /home/mambauser/Code
+# 0) Only try chown if we're root (bind-mounts may be root-owned)
+if [[ "$(id -u)" -eq 0 ]] && [[ ! -O /home/mambauser/Code ]]; then
+  chown -R mambauser:mambauser /home/mambauser/Code || true
 fi
 
-# 2) Interactive mode: login shells or docker exec … bash
-if [ -t 0 ] && [ -t 1 ]; then
-#   # Show the aliases cheat-sheet
-#   /home/rmguser/.aliases_print.sh
-  # Drop into an interactive Bash
+# 1) If no args → interactive shell (when run with -it)
+if [[ $# -eq 0 ]]; then
   exec /bin/bash -l
 fi
 
-# 3) Non-interactive command mode: rmg or arc
-case "${1:-}" in
+# 2) Subcommands: rmg / arc
+cmd="$1"; shift || true
+case "$cmd" in
   rmg)
-    micromamba activate rmg_env
-    exec python /home/mambauser/Code/RMG-Py/rmg.py "${2:-input.py}"
+    exec micromamba run -n rmg_env python /home/mambauser/Code/RMG-Py/rmg.py "${@:-input.py}"
     ;;
   arc)
-    micromamba activate arc_env
-    exec python /home/mambauser/Code/ARC/ARC.py "${2:-input.yml}"
+    exec micromamba run -n arc_env python /home/mambauser/Code/ARC/ARC.py "${@:-input.yml}"
     ;;
   *)
-    echo "Usage: <rmg|arc> [input-file]" >&2
-    exit 1
+    # 3) Pass-through: run arbitrary commands (keeps CI 'bash -lc "...") working
+    exec "$cmd" "$@"
     ;;
 esac
+
+if [[ $# -eq 0 ]] && [[ ! -t 1 ]]; then
+  echo "Usage: <rmg|arc> [input-file]  or pass a shell command (e.g., bash -lc '…')" >&2
+  exit 1
+fi