Add test of dev container

.github/workflows/dev_container.yml

@@ -0,0 +1,25 @@
+name: Test research template dev container
+
+on:
+  schedule:
+    - cron: "18 8 * * *"
+  workflow_dispatch:
+
+jobs:
+  dev-container:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout research-template repository
+        uses: actions/checkout@v4
+        with:
+          repository: 'opensafely/research-template'
+
+      - name: Checkout research-template-docker repository in subdirectory
+        uses: actions/checkout@v4
+        with:
+          path: 'research-template/research-template-docker'
+
+      - name: Test dev container
+        uses: devcontainers/ci@a56d055efecd725e8cfe370543b6071b79989cc8 # v0.3.1900000349
+        with:
+          runCmd: ./research-template/research-template-docker/tests/dev_container.sh

.github/workflows/main.yml

@@ -3,6 +3,7 @@ name: CI
 
 env:
   IMAGE_NAME: research-template
+  IMAGE_VERSION: v0
   PUBLIC_IMAGE_NAME: ghcr.io/opensafely-core/research-template
   REGISTRY: ghcr.io
 
@@ -15,7 +16,7 @@ on:
     - cron: "0 12 * * SUN"
 
 jobs:
-  build-and-test:
+  build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -30,23 +31,53 @@ jobs:
       - name: Build docker image
         run: just build
 
-      - name: Test docker image
-        run: just smoke-test
-
       - name: Save docker image
         run: |
-          docker save research-template | gzip > /tmp/research-template.tar.gz
+          docker save research-template | pigz --fast > /tmp/research-template.tar.gz
 
       - name: Upload docker image
         uses: actions/upload-artifact@v4
         with:
             name: research-template-image
             path: /tmp/research-template.tar.gz
+            # Disable compression; the file is already compressed
+            compression-level: 0
+
+  test-docker-image:
+    needs: build
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install just
+      uses: "opensafely-core/setup-action@v1"
+      with:
+        install-just: true
+
+    - name: Download Docker image
+      uses: actions/download-artifact@v4
+      with:
+        name: research-template-image
+        path: /tmp/image
+
+    - name: Import Docker image
+      run: docker image load --input /tmp/image/research-template.tar.gz
+
+    - name: Test Python installation
+      run: just test-python-install
+
+    - name: Test R Studio installation
+      run: just test-rstudio-install
+
+    - name: Test packages
+      run: just test-packages
 
   publish:
-    needs: [build-and-test]
+    needs: [build, test-docker-image]
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     permissions:
       contents: read
@@ -67,12 +98,12 @@ jobs:
             path: /tmp/image
 
       - name: Import docker image
-        run: gunzip -c /tmp/image/research-template.tar.gz | docker load
+        run: docker image load --input /tmp/image/research-template.tar.gz
 
       - name: Publish image
         run: |
-            echo ${{ secrets.GITHUB_TOKEN }} | docker login $REGISTRY -u ${{ github.actor }} --password-stdin
-            docker tag $IMAGE_NAME $PUBLIC_IMAGE_NAME:v0
-            docker tag $IMAGE_NAME $PUBLIC_IMAGE_NAME:latest
-            docker push $PUBLIC_IMAGE_NAME:v0
-            docker push $PUBLIC_IMAGE_NAME:latest
+            echo ${{ secrets.GITHUB_TOKEN }} | docker login "$REGISTRY" -u ${{ github.actor }} --password-stdin
+            docker tag "$IMAGE_NAME" "$PUBLIC_IMAGE_NAME:$IMAGE_VERSION"
+            docker tag "$IMAGE_NAME" "$PUBLIC_IMAGE_NAME:latest"
+            docker push "$PUBLIC_IMAGE_NAME:$IMAGE_VERSION"
+            docker push "$PUBLIC_IMAGE_NAME:latest"

justfile

@@ -7,5 +7,15 @@ default:
 build:
     docker build . -t research-template
 
-smoke-test:
-    docker run --rm research-template ls /opt/venv/bin/python3.10
+check-image-exists:
+    # Extra brackets are for Just escaping.
+    docker image inspect --format='{{{{.Id}}}}' research-template
+
+test-packages: check-image-exists
+    tests/packages.sh
+
+test-python-install: check-image-exists
+    docker run -i --entrypoint /bin/bash research-template < ./tests/python.sh
+
+test-rstudio-install: check-image-exists
+    docker run -i --entrypoint /bin/bash research-template < ./tests/r_studio.sh

tests/dev_container.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -euxo pipefail
+
+# Check the OpenSAFELY research-template example runs.
+opensafely run run_all
+
+# Check the RStudio server is running.
+curl -L 'http://localhost:8787' | grep 'RStudio'
+
+# This is a rudimentary placeholder test of the ehrQL installation.
+# We cannot easily run ehrQL because it requires Python 3.11 to be imported,
+# but the OpenSAFELY Python Docker image, and the dev container, uses Python 3.10.
+# In future, we could actually try and import ehrQL through Python.
+ls .devcontainer/ehrql-main/

tests/packages.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+set -euxo pipefail
+
+# This test requires:
+# * Docker
+# * the availability of the research-template Docker image
+research_template_image="research-template"
+docker image inspect "$research_template_image" > /dev/null
+
+# These checks assume that the packages do not change
+# between building the Docker image in this repository,
+# and checking the packages against the OpenSAFELY R and Python images.
+
+# Check that the R packages in the OpenSAFELY R image are available in the dev container.
+# The R setup we have leads to two sources of packages.
+# As a result, this only compares package names;
+# some packages are installed multiple times with different version numbers.
+# See https://github.com/opensafely-core/research-template-docker/issues/22
+
+# These packages are known to be extra to the local installation.
+r_installed_known_extra_packages=$(cat <<-END
+"docopt"
+"littler"
+"spatial"
+END
+)
+
+# This function expects a CSV format with header line:
+# "Package","Version"
+# "SomeRPackage","1.0"
+extract_quoted_package_names_from_csv() {
+    tail -n +2 | \
+    cut -d ',' -f1 | \
+    sort -u
+}
+
+r_docker_packages=$(curl 'https://raw.githubusercontent.com/opensafely-core/r-docker/main/packages.csv' |
+    extract_quoted_package_names_from_csv)
+r_installed_packages=$(docker run -i "$research_template_image" /bin/bash -c "Rscript -e 'write.csv(installed.packages()[, c(\"Package\", \"Version\")], row.names = FALSE)'" |
+    extract_quoted_package_names_from_csv)
+r_packages_extra_to_local_install=$(comm -13 <(echo "$r_docker_packages") <(echo "$r_installed_packages"))
+
+[ "$r_packages_extra_to_local_install" == "$r_installed_known_extra_packages" ]
+
+# Check that the Python packages in the OpenSAFELY Python image are available in the dev container.
+# This checks package names and versions.
+python_image_version='v2'
+python_image="ghcr.io/opensafely-core/python:$python_image_version"
+
+docker pull "$python_image"
+
+python_docker_packages=$(docker run "$python_image" python -m pip freeze)
+python_installed_packages=$(docker run "$research_template_image" /opt/venv/bin/python3.10 -m pip freeze)
+diff <(echo "$python_docker_packages") <(echo "$python_installed_packages")

tests/python.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+set -euxo pipefail
+
+/opt/venv/bin/python3.10 --version

tests/r_studio.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -euxo pipefail
+
+# Check that we are the rstudio user.
+[ "$(whoami)" == 'rstudio' ]
+
+# Check the RStudio server installation.
+sudo rstudio-server verify-installation
+sudo rstudio-server start
+
+# Check the RStudio server is running.
+curl -L 'http://localhost:8787' | grep 'RStudio'
+
+sudo rstudio-server stop