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Tests

Tests #220

Workflow file for this run

name: Tests
on:
push:
pull_request:
schedule:
# Run at midnight UTC every Tuesday
- cron: '0 0 * * 2'
concurrency:
group: test-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
if: github.event_name != 'schedule' || github.repository_owner == 'galaxyproject'
runs-on: ${{ matrix.os }}
services:
postgres:
image: postgres
# Provide the password for postgres
env:
POSTGRES_PASSWORD: postgres
# Set health checks to wait until postgres has started
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
- 5432:5432
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
tox_env: [py38]
galaxy_version:
- dev
- release_23.1
- release_23.0
- release_22.05
- release_22.01
- release_21.09
- release_21.05
- release_21.01
- release_20.09
- release_20.05
- release_20.01
- release_19.09
- release_19.05
include:
- os: ubuntu-latest
tox_env: py311
galaxy_version: dev
# Cannot test on macOS because service containers are not supported
# yet: https://github.community/t/github-actions-services-available-on-others-vms/16916
# - os: macos-latest
# tox_env: py38
# galaxy_version: dev
steps:
- uses: actions/checkout@v3
- name: Cache pip dir
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.tox_env }}-${{ matrix.galaxy_version }}
- name: Calculate Python version for BioBlend from tox_env
id: get_bioblend_python_version
run: echo "bioblend_python_version=$(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@v4
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'
- name: Determine Python version for Galaxy
id: get_galaxy_python_version
run: |
case ${{ matrix.galaxy_version }} in
release_19.05 | release_19.09 | release_20.0* )
# The minimum Python version supported by the 19.05 and 19.09
# releases is 2.7, but virtualenv dropped support for creating
# Python <3.7 environments in v20.22.0 .
# The minimum Python version supported by the 20.0* releases is
# 3.5, but the setup-python GitHub action dropped support for
# Python 3.5 and 3.6 on Ubuntu 22.04, see
# https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
galaxy_python_version=3.7
;;
release_21.0* )
# The minimum Python supported version by these releases is 3.6,
# but same as above.
galaxy_python_version=3.7
;;
release_22.0* | release_23.* | dev )
galaxy_python_version=3.7
esac
echo "galaxy_python_version=$galaxy_python_version" >> $GITHUB_OUTPUT
- name: Set up Python for Galaxy
uses: actions/setup-python@v4
with:
python-version: ${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
- name: Run tests
env:
PGPASSWORD: postgres
PGPORT: 5432
PGHOST: localhost
run: |
# Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
createdb -U postgres galaxy
# Run ToolShed tests only once per Python version
if [ "${{ matrix.galaxy_version }}" = 'dev' ]; then
export BIOBLEND_TOOLSHED_URL=https://testtoolshed.g2.bx.psu.edu/
fi
# Install Galaxy
GALAXY_DIR=galaxy-${{ matrix.galaxy_version }}
git clone --depth=1 -b ${{ matrix.galaxy_version }} https://github.com/galaxyproject/galaxy $GALAXY_DIR
export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
./run_bioblend_tests.sh -g $GALAXY_DIR -v python${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }} -e ${{ matrix.tox_env }}
- name: The job has failed
if: ${{ failure() }}
run: |
cat galaxy-${{ matrix.galaxy_version }}/*.log