mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
1d59dcb409
Fix ``test_singularity_container_test`` unit test, which failed with:
```
test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py:48:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py:62: in singularity_container_test
check_output(exec_command.extend(["bash", "-c", test_command]), stderr=subprocess.STDOUT)
/usr/lib/python3.8/subprocess.py:415: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
/usr/lib/python3.8/subprocess.py:493: in run
with Popen(*popenargs, **kwargs) as process:
/usr/lib/python3.8/subprocess.py:858: in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
> args = list(args)
E TypeError: 'NoneType' object is not iterable
/usr/lib/python3.8/subprocess.py:1569: TypeError
```
Broken in commit 1dc1e5f219 .
Also:
- Use `tmp_path` pytest fixture.
- Add type annotations.
- Code refactorings.
- Install singularity in the mulled GitHub workflow so that the 2 singularity
unit tests are not skipped any more.
57 lines
1.7 KiB
YAML
57 lines
1.7 KiB
YAML
name: Mulled Unit Tests
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on:
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push:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'lib/galaxy_test/selenium/**'
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pull_request:
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paths-ignore:
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- 'client/**'
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- 'doc/**'
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- 'lib/galaxy_test/selenium/**'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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test:
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name: Test
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.7']
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steps:
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- uses: actions/checkout@v3
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with:
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path: 'galaxy root'
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Get full Python version
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id: full-python-version
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shell: bash
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run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
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- name: Cache pip dir
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
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- name: Cache tox env
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uses: actions/cache@v3
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with:
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path: .tox
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key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
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- name: Install Apptainer's singularity
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uses: eWaterCycle/setup-apptainer@v2
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- name: Install tox
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run: pip install tox
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- name: Run tests
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run: tox -e mulled
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working-directory: 'galaxy root'
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- uses: actions/upload-artifact@v3
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if: failure()
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with:
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name: Mulled unit test results (${{ matrix.python-version }})
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path: 'galaxy root/run_unit_tests.html'
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