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add h5ad assert test #16392

add h5ad assert test

add h5ad assert test #16392

name: CWL conformance
on:
push:
paths-ignore:
- 'client/**'
- 'doc/**'
- 'lib/galaxy_test/selenium/**'
pull_request:
paths-ignore:
- 'client/**'
- 'doc/**'
- 'lib/galaxy_test/selenium/**'
env:
GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
name: Test
if: ${{ false }}
runs-on: ubuntu-latest
continue-on-error: ${{ startsWith(matrix.marker, 'red') }}
strategy:
fail-fast: false
matrix:
python-version: ['3.8']
marker: ['green', 'red and required', 'red and not required']
conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
services:
postgres:
image: postgres:13
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
POSTGRES_DB: postgres
ports:
- 5432:5432
steps:
- 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))')" >> $GITHUB_OUTPUT
- name: Cache pip dir
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: pip-cache-${{ 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') }}-api
- name: Run tests
run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
working-directory: 'galaxy root'
- uses: codecov/codecov-action@v3
with:
flags: cwl-conformance
working-directory: 'galaxy root'
- uses: actions/upload-artifact@v4
if: failure()
with:
name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})
path: 'galaxy root/run_cwl_tests.html'