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Add BioBlend tests #18975

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Oct 11, 2024
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80 changes: 80 additions & 0 deletions .github/workflows/bioblend.yaml
Original file line number Diff line number Diff line change
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name: BioBlend Tests
on:
pull_request:
paths:
- .github/workflows/bioblend.yaml
- lib/galaxy/schema/**
- lib/galaxy/webapps/galaxy/api/**
- lib/galaxy/webapps/galaxy/services/**
workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
runs-on: ubuntu-latest
services:
postgres:
image: postgres
# Provide the password for postgres
env:
POSTGRES_PASSWORD: postgres
# Set health checks to wait until postgres has started
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
- 5432:5432
strategy:
fail-fast: false
matrix:
tox_env: [py313]
galaxy_python_version: ["3.8"]
steps:
- name: Checkout Galaxy
uses: actions/checkout@v4
with:
fetch-depth: 1
path: galaxy
- name: Checkout Bioblend
uses: actions/checkout@v4
with:
repository: galaxyproject/bioblend
path: bioblend
- name: Cache pip dir
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.tox_env }}
- name: Calculate Python version for BioBlend from tox_env
id: get_bioblend_python_version
run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
- name: Set up Python for BioBlend
uses: actions/setup-python@v5
with:
python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
- name: Install tox
run: |
python3 -m pip install --upgrade pip setuptools
python3 -m pip install 'tox>=1.8.0' 'virtualenv>=20.0.14'
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- name: Set up Python for Galaxy
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.galaxy_python_version }}
- name: Run tests
env:
PGPASSWORD: postgres
PGPORT: 5432
PGHOST: localhost
run: |
# Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
createdb -U postgres galaxy
export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
./bioblend/run_bioblend_tests.sh -g galaxy -v python${{ matrix.galaxy_python_version }} -e ${{ matrix.tox_env }}
- name: The job has failed
if: ${{ failure() }}
run: |
cat galaxy/*.log
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