Add smoke tests for terra-jupyter-python and terra-jupyter-aou (DataB…

…iosphere#199)

* Initial commit of terra-jupyter-python smoke tests.

* Fix test volume.

* Remove flag for BigQuery magic, it isn't needed until the next PR.

* Disable tests that are expected to fail.

* Remove debugging code from workflow.

* Capture results from all notebook-based tests as a workflow artifact, regardless of success or failure of those tests.

* Add smoke tests for terra-jupyter-aou.

* Build base images, if needed.

Also move tests into a subdir.

* Add errexit.

* Remove the workflow triggers added for testing purposes.

.github/workflows/test-terra-jupyter-aou.yml

@@ -0,0 +1,106 @@
+name: Test terra-jupyter-aou
+# Perform smoke tests on the terra-jupyter-aou Docker image to have some amount of confidence that
+# Python package versions are compatible.
+#
+# To configure the minimal auth needed for these tests to be able to read public data from Google Cloud Platform:
+# Step 1: Create a service account per these instructions:
+#         https://github.com/google-github-actions/setup-gcloud/blob/master/setup-gcloud/README.md
+# Step 2: Give the service account the following permissions within the project: BigQuery User
+# Step 3: Store its key and project id as GitHub repository secrets GCP_SA_KEY and GCP_PROJECT_ID.
+#         https://docs.github.com/en/free-pro-team@latest/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository
+
+on:
+  pull_request:
+    branches: [ master ]
+    paths:
+    - 'terra-jupyter-aou/**'
+    - '.github/workflows/test-terra-jupyter-aou.yml'
+    # Note: secrets are not passed to pull requests from forks, so the dev team will need to use the manual workflow
+    # dispatch trigger when receiving community contributions.
+
+  workflow_dispatch:
+    # Allows manually triggering of workflow on a selected branch via the GitHub Actions tab.
+    # GitHub blog demo: https://github.blog/changelog/2020-07-06-github-actions-manual-triggers-with-workflow_dispatch/.
+
+env:
+  GOOGLE_PROJECT: ${{ secrets.GCP_PROJECT_ID }}
+
+jobs:
+
+  test_docker_image:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+
+    - name: Set up Cloud SDK
+      uses: google-github-actions/setup-gcloud@master
+      with:
+        project_id: ${{ secrets.GCP_PROJECT_ID }}
+        service_account_key: ${{ secrets.GCP_SA_KEY }}
+        export_default_credentials: true
+
+    - name: Build Docker image and base images too, if needed
+      run: |
+        gcloud auth configure-docker
+        ./build_smoke_test_image.sh terra-jupyter-aou
+
+    - name: Run Python code specific to notebooks with nbconvert
+      # Run all notebooks from start to finish, regardles of error, so that we can capture the
+      # result as a workflow artifact.
+      # See also https://github.com/marketplace/actions/run-notebook if a more complicated
+      # workflow for notebooks is needed in the future.
+      run: |
+        chmod a+w -R $GITHUB_WORKSPACE
+        docker run \
+          --env GOOGLE_PROJECT \
+          --volume "${{ env.GOOGLE_APPLICATION_CREDENTIALS }}:/tmp/credentials.json:ro" \
+          --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \
+          --volume $GITHUB_WORKSPACE:/tests \
+          --workdir=/tests \
+          --entrypoint="" \
+          terra-jupyter-aou:smoke-test \
+          /bin/bash -c 'for nb in {terra-jupyter-python/tests,terra-jupyter-aou/tests}/*ipynb ; do jupyter nbconvert --to html --ExecutePreprocessor.allow_errors=True --execute "${nb}" ; done'
+
+    - name: Upload workflow artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: notebook-execution-results
+        path: |
+          terra-jupyter-python/tests/*.html
+          terra-jupyter-aou/tests/*.html
+        retention-days: 30
+
+    - name: Test Python code with pytest
+      run: |
+        docker run \
+          --env GOOGLE_PROJECT \
+          --volume "${{ env.GOOGLE_APPLICATION_CREDENTIALS }}:/tmp/credentials.json:ro" \
+          --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \
+          --volume $GITHUB_WORKSPACE:/tests \
+          --workdir=/tests \
+          --entrypoint="" \
+          terra-jupyter-aou:smoke-test \
+          /bin/bash -c 'pip3 install pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-aou/tests/'
+
+    - name: Test Python code specific to notebooks with nbconvert
+      # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite.
+      # If the tests throw any exceptions, execution of the notebooks will halt at that point. Look at the workflow
+      # artifacts to understand if there are more failures than just the one that caused this task to halt.
+      run: |
+        docker run \
+          --env GOOGLE_PROJECT \
+          --volume "${{ env.GOOGLE_APPLICATION_CREDENTIALS }}:/tmp/credentials.json:ro" \
+          --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \
+          --volume $GITHUB_WORKSPACE:/tests \
+          --workdir=/tests \
+          --entrypoint="" \
+          terra-jupyter-aou:smoke-test \
+          /bin/bash -c 'for nb in {terra-jupyter-python/tests,terra-jupyter-aou/tests}/*ipynb ; do jupyter nbconvert --to html --execute "${nb}" ; done'
+

.github/workflows/test-terra-jupyter-python.yml

@@ -0,0 +1,104 @@
+name: Test terra-jupyter-python
+# Perform smoke tests on the terra-jupyter-python Docker image to have some amount of confidence that
+# Python package versions are compatible.
+#
+# To configure the minimal auth needed for these tests to be able to read public data from Google Cloud Platform:
+# Step 1: Create a service account per these instructions:
+#         https://github.com/google-github-actions/setup-gcloud/blob/master/setup-gcloud/README.md
+# Step 2: Give the service account the following permissions within the project: BigQuery User
+# Step 3: Store its key and project id as GitHub repository secrets GCP_SA_KEY and GCP_PROJECT_ID.
+#         https://docs.github.com/en/free-pro-team@latest/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository
+
+on:
+  pull_request:
+    branches: [ master ]
+    paths:
+    - 'terra-jupyter-python/**'
+    - '.github/workflows/test-terra-jupyter-python.yml'
+    # Note: secrets are not passed to pull requests from forks, so the dev team will need to use the manual workflow
+    # dispatch trigger when receiving community contributions.
+
+  workflow_dispatch:
+    # Allows manually triggering of workflow on a selected branch via the GitHub Actions tab.
+    # GitHub blog demo: https://github.blog/changelog/2020-07-06-github-actions-manual-triggers-with-workflow_dispatch/.
+
+env:
+  GOOGLE_PROJECT: ${{ secrets.GCP_PROJECT_ID }}
+
+jobs:
+
+  test_docker_image:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+
+    - name: Set up Cloud SDK
+      uses: google-github-actions/setup-gcloud@master
+      with:
+        project_id: ${{ secrets.GCP_PROJECT_ID }}
+        service_account_key: ${{ secrets.GCP_SA_KEY }}
+        export_default_credentials: true
+
+    - name: Build Docker image and base images too, if needed
+      run: |
+        gcloud auth configure-docker
+        ./build_smoke_test_image.sh terra-jupyter-python
+
+    - name: Run Python code specific to notebooks with nbconvert
+      # Run all notebooks from start to finish, regardles of error, so that we can capture the
+      # result as a workflow artifact.
+      # See also https://github.com/marketplace/actions/run-notebook if a more complicated
+      # workflow for notebooks is needed in the future.
+      run: |
+        chmod a+w $GITHUB_WORKSPACE/terra-jupyter-python/tests
+        docker run \
+          --env GOOGLE_PROJECT \
+          --volume "${{ env.GOOGLE_APPLICATION_CREDENTIALS }}:/tmp/credentials.json:ro" \
+          --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \
+          --volume $GITHUB_WORKSPACE/terra-jupyter-python/tests:/tests \
+          --workdir=/tests \
+          --entrypoint="" \
+          terra-jupyter-python:smoke-test \
+          /bin/sh -c 'for nb in *ipynb ; do jupyter nbconvert --to html --ExecutePreprocessor.allow_errors=True --execute "${nb}" ; done'
+
+    - name: Upload workflow artifacts
+      uses: actions/upload-artifact@v2
+      with:
+        name: notebook-execution-results
+        path: terra-jupyter-python/tests/*.html
+        retention-days: 30
+
+    - name: Test Python code with pytest
+      run: |
+        docker run \
+          --env GOOGLE_PROJECT \
+          --volume "${{ env.GOOGLE_APPLICATION_CREDENTIALS }}:/tmp/credentials.json:ro" \
+          --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \
+          --volume $GITHUB_WORKSPACE/terra-jupyter-python/tests:/tests \
+          --workdir=/tests \
+          --entrypoint="" \
+          terra-jupyter-python:smoke-test \
+          /bin/sh -c "pip3 install pytest; pytest"
+
+    - name: Test Python code specific to notebooks with nbconvert
+      # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite.
+      # If the tests throw any exceptions, execution of the notebooks will halt at that point. Look at the workflow
+      # artifacts to understand if there are more failures than just the one that caused this task to halt.
+      run: |
+        chmod a+w $GITHUB_WORKSPACE/terra-jupyter-python
+        docker run \
+          --env GOOGLE_PROJECT \
+          --volume "${{ env.GOOGLE_APPLICATION_CREDENTIALS }}:/tmp/credentials.json:ro" \
+          --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \
+          --volume $GITHUB_WORKSPACE/terra-jupyter-python/tests:/tests \
+          --workdir=/tests \
+          --entrypoint="" \
+          terra-jupyter-python:smoke-test \
+          /bin/sh -c 'for nb in *ipynb ; do jupyter nbconvert --to html --execute "${nb}" ; done'

.gitignore

@@ -3,4 +3,6 @@
 .DS_Store
 node_modules/
 package-lock.json
-.dotty-ide-disabled
+.dotty-ide-disabled
+.ipynb_checkpoints
+*html

build_smoke_test_image.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+# Perform a local build of an image for smoke-testing purposes. Also build its tree of base images, when missing.
+#
+# Example: ./build_smoke_test_image terra-jupyter-python  
+#
+# Current working directory must be the directory in which this script resides (one level above all the Dockerfiles).
+# It walks down each relevant image directory, making changes to the FROM statements,
+# as needed, to refer to locally built base images.
+
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace 
+
+build_smoke_test_image() {
+  local IMAGE_TYPE=$1
+  pushd ${IMAGE_TYPE}
+  local BASE_IMAGES=$( egrep '^FROM (\S+)' Dockerfile |tr -s ' ' | cut -d ' ' -f 2 )
+
+  local BASE_IMAGE
+  for BASE_IMAGE in ${BASE_IMAGES}; do
+    local PULL_RESULT=$( docker pull -q $BASE_IMAGE )
+
+    if [[ -n "${PULL_RESULT}" ]]; then
+      echo "${BASE_IMAGE} exists"
+    else
+      echo "${BASE_IMAGE} does not exist, building it locally"
+      local BASE_IMAGE_TYPE=$( echo ${BASE_IMAGE} | cut -d '/' -f 3 | cut -d ':' -f 1)
+      local LOCAL_BASE_IMAGE=${BASE_IMAGE_TYPE}:smoke-test
+      # Call this function recursively to build base images for however many levels down we need to go.
+      popd
+      build_smoke_test_image ${BASE_IMAGE_TYPE}
+      pushd ${IMAGE_TYPE}
+      # Edit our local copy of the Dockerfile to use the locally built base image.
+      sed -i "s;${BASE_IMAGE};${LOCAL_BASE_IMAGE};g" Dockerfile
+    fi
+  done
+
+  docker build . --file Dockerfile --tag ${IMAGE_TYPE}:smoke-test
+  popd
+}
+
+build_smoke_test_image $1