CTM-575 Preparations to update terra-base

.github/workflows/test-terra-base.yml

@@ -0,0 +1,43 @@
+name: Test terra-base
+# Smoke-test the terra-base image on pull requests that touch it.
+
+on:
+  pull_request:
+    branches: [ master ]
+
+  workflow_dispatch:
+    # Allows manually triggering the workflow on a selected branch via the GitHub Actions tab.
+
+jobs:
+
+  test_docker_image:
+    runs-on: self-hosted
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v7
+
+    - name: Build the terra-base image locally
+      run: |
+        docker build --pull ./terra-base --tag terra-base:smoke-test
+
+    - name: Test Python version
+      run: |
+        version=$(docker run --rm --entrypoint="" terra-base:smoke-test python --version)
+        echo "$version"
+        [[ "$version" == "Python 3.10"* ]]
+
+    - name: Test OS version
+      run: |
+        version=$(docker run --rm --entrypoint="" terra-base:smoke-test \
+                    bash -c 'source /etc/os-release && echo "$VERSION"')
+        echo "$version"
+        [[ "$version" == "22.04"* ]]
+
+    - name: Smoke test
+      run: |
+        docker run --rm \
+          --volume "$GITHUB_WORKSPACE/terra-base/tests:/tests:ro" \
+          --entrypoint="" \
+          terra-base:smoke-test \
+          /etc/jupyter/bin/python /tests/smoke_test.py

build_all.sh

@@ -13,7 +13,7 @@
 # 8- terra-jupyter-bioconductor
 # 9- terra-rstudio-aou
 # 10- wondershaper
-images=("terra-base", "terra-jupyter-base" "terra-jupyter-python" "terra-jupyter-r" "terra-jupyter-gatk" "terra-jupyter-hail" "terra-jupyter-aou" "terra-jupyter-bioconductor" "terra-rstudio-aou" "wondershaper")
+images=("terra-base" "terra-jupyter-base" "terra-jupyter-python" "terra-jupyter-r" "terra-jupyter-gatk" "terra-jupyter-hail" "terra-jupyter-aou" "terra-jupyter-bioconductor" "terra-rstudio-aou" "wondershaper")
 
 # Loop over each image to build in the correct order
 for image in "${images[@]}"; do

terra-base/tests/smoke_test.py

@@ -0,0 +1,87 @@
+"""Smoke tests for the terra-base image.
+
+Verifies that both the user-facing conda kernel env and the Jupyter server venv run the
+image's target Python (the PYTHON_VERSION set in the Dockerfile), and that the Jupyter
+stack and the Terra (Leonardo) notebook extensions import on that Python.
+
+Has no third-party dependencies, so CI can run it without installing anything:
+
+    docker run --rm --entrypoint="" terra-base:smoke-test \
+        /etc/jupyter/bin/python /tests/smoke_test.py
+
+Run it with the Jupyter *server* venv python (it shells out to check the kernel env too).
+The functions are also pytest-discoverable if pytest is available in that interpreter.
+"""
+import os
+import subprocess
+import sys
+
+# The Jupyter server runs in this venv; user notebook code runs in the conda kernel env.
+SERVER_PY = "/etc/jupyter/bin/python"
+KERNEL_PY = "/home/jupyter/.envs/python3/bin/python"
+# Where the Dockerfile copies the Leonardo extensions (loaded via run-jupyter.sh).
+CUSTOM_DIR = "/etc/jupyter/custom"
+
+
+def _target_version():
+    """The image's target Python as 'major.minor' (from ENV PYTHON_VERSION), or None."""
+    return os.environ.get("PYTHON_VERSION", "").strip() or None
+
+
+def _minor(python_path):
+    out = subprocess.check_output(
+        [python_path, "-c", "import sys; print('%d.%d' % sys.version_info[:2])"]
+    )
+    return out.decode().strip()
+
+
+def test_kernel_env_matches_target():
+    target = _target_version()
+    got = _minor(KERNEL_PY)
+    if target:
+        assert got == target, f"conda kernel env is Python {got}, expected {target}"
+
+
+def test_server_venv_matches_target():
+    target = _target_version()
+    got = _minor(SERVER_PY)
+    if target:
+        assert got == target, f"jupyter server venv is Python {got}, expected {target}"
+
+
+def test_server_and_kernel_agree():
+    assert _minor(SERVER_PY) == _minor(KERNEL_PY), "server venv and kernel env Python differ"
+
+
+def test_jupyter_stack_imports():
+    # Runs under the server venv python, where the Jupyter stack lives.
+    import notebook  # noqa: F401
+    import jupyterlab  # noqa: F401
+    import jupyter_server  # noqa: F401
+    import nbclassic  # noqa: F401
+    import jupyter_core  # noqa: F401
+    import traitlets  # noqa: F401
+    import notebook.utils  # noqa: F401  exercises the distutils->setuptools shim on 3.12+
+
+
+def test_terra_extensions_import():
+    sys.path.insert(0, CUSTOM_DIR)
+    import jupyter_localize_extension  # noqa: F401
+    import jupyter_delocalize  # noqa: F401
+
+
+if __name__ == "__main__":
+    import traceback
+
+    tests = [v for k, v in sorted(globals().items()) if k.startswith("test_") and callable(v)]
+    failed = 0
+    for test in tests:
+        try:
+            test()
+            print(f"PASS {test.__name__}")
+        except Exception:
+            failed += 1
+            print(f"FAIL {test.__name__}")
+            traceback.print_exc()
+    print(f"\n{len(tests) - failed}/{len(tests)} passed")
+    sys.exit(1 if failed else 0)