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[24.1] Determine expression tool output extension when input terminal #31952

[24.1] Determine expression tool output extension when input terminal

[24.1] Determine expression tool output extension when input terminal #31952

Workflow file for this run

name: Integration
on:
push:
paths-ignore:
- 'client/**'
- 'doc/**'
- 'lib/galaxy_test/selenium/**'
pull_request:
paths-ignore:
- 'client/**'
- 'doc/**'
- 'lib/galaxy_test/selenium/**'
schedule:
# Run at midnight UTC every Tuesday
- cron: '0 0 * * 2'
env:
GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//'
GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1'
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
name: Test
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
python-version: ['3.8']
chunk: ['0', '1', '2', '3']
services:
postgres:
image: postgres:13
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
POSTGRES_DB: postgres
ports:
- 5432:5432
rabbitmq:
image: rabbitmq
ports:
- 5672:5672
steps:
- if: github.event_name == 'schedule'
run: |
echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
# Skip outputs_to_working_directory: true in integration tests, doesn't work with pulsar
# echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
- name: Prune unused docker image, volumes and containers
run: docker system prune -a -f
- name: Clean dotnet folder for space
run: rm -Rf /usr/share/dotnet
- name: Install packages
# conntrack: mandatory for later k8s versions
# ffmpeg: ffprobe needed by media datatypes
run: sudo apt-get update && sudo apt-get -y install conntrack ffmpeg
- name: Setup Minikube
uses: medyagh/setup-minikube@latest
with:
driver: none
kubernetes-version: '1.23.0'
- name: Check pods
run: kubectl get pods -A
- uses: actions/checkout@v4
with:
path: 'galaxy root'
- uses: actions/setup-node@v4
with:
node-version: '18.12.1'
cache: 'yarn'
cache-dependency-path: 'galaxy root/client/yarn.lock'
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Get full Python version
id: full-python-version
shell: bash
run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
- name: Cache pip dir
uses: actions/cache@v4
id: pip-cache
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Cache galaxy venv
uses: actions/cache@v4
with:
path: 'galaxy root/.venv'
key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration
- name: Install Apptainer's singularity
uses: eWaterCycle/setup-apptainer@v2
- name: Run tests
run: |
. .ci/minikube-test-setup/start_services.sh
./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v3
with:
flags: integration
working-directory: 'galaxy root'
- uses: actions/upload-artifact@v4
if: failure()
with:
name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
path: 'galaxy root/run_integration_tests.html'