fix(ci): remove echo command in pytest CI #56
Workflow file for this run
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name: CI | |
# Enable Buildkit and let compose use it to speed up image building | |
env: | |
DOCKER_BUILDKIT: 1 | |
COMPOSE_DOCKER_CLI_BUILD: 1 | |
CONDA_ENV_NAME: clim-recal | |
MIN_PYTHON_VERSION: 3.9 | |
PYTHON_MODULE_FOLDER: /home/jovyan/python/ | |
COVERAGE_SVG_FOLDER: docs/assets/ | |
COVERAGE_SVG_FILE_NAME: coverage.svg | |
# replace below with references to previous config lines | |
COVERAGE_SVG_PATH: docs/assets/coverage.svg | |
GH_PAGE_PATH: _gh-page | |
on: | |
pull_request: | |
branches: ['main', 'doc-deploy', 'ruth-notebook-for-workshop', 'r-docker-refactor'] | |
paths-ignore: ['docs/**'] | |
push: | |
branches: ['main', 'doc-deploy', 'ruth-notebook-for-workshop', 'r-docker-refactor'] | |
concurrency: | |
group: ${{ github.head_ref || github.run_id }} | |
cancel-in-progress: true | |
permissions: | |
contents: write | |
jobs: | |
linter: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Code Repository | |
uses: actions/checkout@main | |
- name: Set up Python | |
uses: actions/setup-python@main | |
with: | |
python-version: ${{ env.MIN_PYTHON_VERSION }} | |
- name: Run pre-commit | |
uses: pre-commit/action@main | |
- name: Update pre-commit | |
uses: pre-commit-ci/[email protected] | |
if: always() | |
# With no caching at all the entire ci process takes 4m 30s to complete! | |
pytest: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Code Repository | |
uses: actions/checkout@main | |
- name: Build, Test and Save Test Coverage | |
run: | | |
docker compose build jupyter | |
docker compose up jupyter --detach | |
docker compose exec -u 0 jupyter bash -c "conda run -n ${{ env.CONDA_ENV_NAME }} --cwd python pytest" | |
export JUPYTER_ID=$(docker compose ps -q jupyter) | |
echo "jupyter_id=$JUPYTER_ID" >> $GITHUB_ENV | |
- name: Check accessing saved jupyter_id | |
run: | | |
echo ${{ env.jupyter_id }} | |
- name: Copy test coverage results | |
run: | | |
docker cp ${{ env.jupyter_id }}:${{ env.PYTHON_MODULE_FOLDER }}${{ env.COVERAGE_SVG_PATH }} ${{ env.COVERAGE_SVG_FOLDER }} | |
- name: Archive coverage svg | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage-badge | |
path: ${{ env.COVERAGE_SVG_PATH }} | |
- name: Tear down the Stack | |
run: docker compose down | |
docs: | |
needs: [linter, pytest] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Download coverage svg | |
uses: actions/download-artifact@v3 | |
with: | |
name: coverage-badge | |
path: ${{ env.GH_PAGE_PATH }}${{ env.COVERAGE_SVG_PATH }} | |
# Other options for documentation build for future testing outside docker | |
# - name: Set up conda environment | |
# uses: conda-incubator/setup-miniconda@v2 | |
# with: | |
# activate-environment: environment.yml | |
# | |
# From https://github.com/r-lib/actions/tree/v2-branch/setup-r | |
# - name: Setup R | |
# uses: r-lib/actions/setup-r@v2 | |
# Potentially necessary for future interactive documentation builds following uatk-spc | |
# - name: Install node | |
# uses: actions/setup-node@v2 | |
# with: | |
# node-version: 18.x | |
# cache: 'npm' | |
# cache-dependency-path: web/package-lock.json | |
# | |
# - name: Build web app | |
# run: | | |
# cd web | |
# npm ci | |
# npm run build --if-present | |
# mv dist ../docs/_book/app | |
- name: Build docker quarto | |
run: | | |
# A potentially quicker build option to try in future, requires running in detatched mode | |
# DOCKER_BUILDKIT=1 docker build --no-cache -f compose/docs/Dockerfile --target builder --tag 'clim-recal-docs' . | |
docker compose build docs | |
docker compose up --detach | |
docker cp $(docker compose ps -q docs):/usr/local/apache2/htdocs/ ${{ env.GH_PAGE_PATH }} | |
- name: Publish | |
uses: peaceiris/actions-gh-pages@v3 | |
with: | |
github_token: ${{ secrets.GITHUB_TOKEN }} | |
publish_dir: ${{ env.GH_PAGE_PATH }} | |
keep_files: false |