refactor: Clean up DB sessions consistently #2229
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name: CI | |
on: | |
pull_request_target: | |
types: [assigned, opened, synchronize, reopened] | |
push: | |
branches: | |
- main | |
env: | |
GCS_PROJECT: qc-oss-mamba-org-quetz-dev | |
GCS_TOKEN: /home/runner/gcs/token.json | |
GCS_TOKEN_CONTENT: ${{ secrets.gcs_token_content }} | |
jobs: | |
test_quetz: | |
# timeout for the whole job | |
timeout-minutes: 10 | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest] | |
test_database: ["sqlite", "postgres"] | |
db_init: ["use-migrations", "create-tables"] | |
services: | |
postgres: | |
image: postgres | |
env: | |
POSTGRES_PASSWORD: mysecretpassword | |
POSTGRES_USER: postgres | |
POSTGRES_DB: postgres | |
ports: | |
- 5432/tcp | |
# Set health checks to wait until postgres has started | |
options: >- | |
--health-cmd pg_isready | |
--health-interval 10s | |
--health-timeout 5s | |
--health-retries 5 | |
redis: | |
image: redis | |
options: >- | |
--health-cmd "redis-cli ping" | |
--health-interval 10s | |
--health-timeout 5s | |
--health-retries 5 | |
ports: | |
- 6379:6379 | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
ref: ${{ github.event.pull_request.head.sha }} | |
- name: write gcs token file | |
run: | | |
mkdir $(dirname "${GCS_TOKEN}") | |
echo "${GCS_TOKEN_CONTENT}" > "${GCS_TOKEN}" | |
- name: install mamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: environment.yml | |
- name: test quetz | |
shell: bash -l -eo pipefail {0} | |
env: | |
TEST_DB_BACKEND: ${{ matrix.test_database }} | |
QUETZ_TEST_DBINIT: ${{ matrix.db_init }} | |
POSTGRES_HOST: localhost | |
POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} | |
S3_ACCESS_KEY: ${{ secrets.s3_access_key }} | |
S3_SECRET_KEY: ${{ secrets.s3_secret_key }} | |
S3_ENDPOINT: https://s3.sbg.cloud.ovh.net/ | |
S3_REGION: sbg | |
S3_BUCKET_NAME: quetz | |
run: | | |
# install dev dependencies | |
pip install -e .[all,dev] | |
pip install redis rq | |
pip install pytest-github-actions-annotate-failures | |
- name: Testing server | |
shell: bash -l -eo pipefail {0} | |
# timeout for the step | |
timeout-minutes: 5 | |
env: | |
TEST_DB_BACKEND: ${{ matrix.test_database }} | |
QUETZ_TEST_DBINIT: ${{ matrix.db_init }} | |
POSTGRES_HOST: localhost | |
POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} | |
S3_ACCESS_KEY: ${{ secrets.s3_access_key }} | |
S3_SECRET_KEY: ${{ secrets.s3_secret_key }} | |
S3_ENDPOINT: https://s3.sbg.cloud.ovh.net/ | |
S3_REGION: sbg | |
S3_BUCKET_NAME: quetz | |
run: | | |
if [ "$TEST_DB_BACKEND" == "postgres" ]; then | |
export QUETZ_TEST_DATABASE="postgresql://postgres:mysecretpassword@${POSTGRES_HOST}:${POSTGRES_PORT}/postgres" | |
echo "Running with postgres" | |
fi | |
if [ "$QUETZ_TEST_DBINIT" == "use-migrations" ]; then | |
echo "Using migrations" | |
fi | |
export QUETZ_IS_TEST=1 | |
pytest -v ./quetz/tests/ --cov-config=pyproject.toml --cov=. --cov-report=xml --capture=no | |
- name: Test the plugins | |
shell: bash -l -eo pipefail {0} | |
env: | |
TEST_DB_BACKEND: ${{ matrix.test_database }} | |
QUETZ_TEST_DBINIT: ${{ matrix.db_init }} | |
POSTGRES_HOST: localhost | |
POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} | |
S3_ACCESS_KEY: ${{ secrets.s3_access_key }} | |
S3_SECRET_KEY: ${{ secrets.s3_secret_key }} | |
S3_ENDPOINT: https://s3.sbg.cloud.ovh.net/ | |
S3_REGION: sbg | |
S3_BUCKET_NAME: quetz | |
run: | | |
if [ "$TEST_DB_BACKEND" == "postgres" ]; then | |
export QUETZ_TEST_DATABASE="postgresql://postgres:mysecretpassword@${POSTGRES_HOST}:${POSTGRES_PORT}/postgres" | |
echo "Running with postgres" | |
fi | |
# add micromamba to path | |
export PATH=$(dirname $MAMBA_EXE):$PATH | |
echo "adding micromamba to path: $MAMBA_EXE" | |
pip install --no-deps git+https://[email protected]/regro/libcflib@master | |
for f in ./plugins/quetz_* | |
do | |
echo "::group::Testing plugin ${f}" | |
quetz plugin install $f | |
# We want to test all the plugins, regardless of whether one fails | |
set +e | |
pytest -v $f | |
pytest_exit_code=$? | |
set -e | |
echo "::endgroup::" | |
if [ $pytest_exit_code -ne 0 ]; then | |
echo "::error::Tests for plugin $f failed!" | |
tests_failed="true" | |
fi | |
done | |
if [ "$tests_failed" == "true" ]; then | |
echo "::error::Some plugin tests failed!" | |
exit 1 | |
fi | |
- uses: codecov/codecov-action@v1 | |
with: | |
verbose: true | |
file: ./coverage.xml | |
test_release: | |
runs-on: ubuntu-latest | |
permissions: | |
contents: write | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: "3.10" | |
- name: install missing dependency | |
run: pip install ipython_genutils | |
- name: Get branch name | |
id: branch-name | |
uses: tj-actions/branch-names@eee8675bd61ec38bcfbfedd504d8473292ba649e | |
- name: Check Release | |
uses: jupyter-server/jupyter_releaser/.github/actions/check-release@v2 | |
with: | |
token: ${{ secrets.GITHUB_TOKEN }} |