nf-core_modules/tests/test_versions_yml.py
2022-06-10 11:01:40 +00:00

60 lines
2.3 KiB
Python

from pathlib import Path
import pytest
import yaml
import re
from textwrap import dedent
def _get_workflow_names():
"""Get all names of all workflows which have a test.yml in the tests directory.
To do so, recursively finds all test.yml files and parses their content.
"""
here = Path(__file__).parent.resolve()
pytest_workflow_files = here.glob("modules/**/test.yml")
for f in pytest_workflow_files:
# test_config = yaml.safe_load(f.read_text())
test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
for workflow in test_config:
# https://github.com/nf-core/modules/pull/1242 - added to cover tests
# that expect an error and therefore will not generate a versions.yml
if 'exit_code' not in workflow:
yield workflow["name"]
@pytest.mark.workflow(*_get_workflow_names())
def test_ensure_valid_version_yml(workflow_dir):
workflow_dir = Path(workflow_dir)
software_name = workflow_dir.name.split("_")[0].lower()
try:
versions_yml_file = workflow_dir / f"output/{software_name}/versions.yml"
versions_yml = versions_yml_file.read_text()
except FileNotFoundError:
raise AssertionError(
dedent(
f"""\
`versions.yml` not found in the output directory.
Expected path: `{versions_yml_file}`
This can have multiple reasons:
* The test-workflow failed before a `versions.yml` could be generated.
* The workflow name in `test.yml` does not start with the tool name.
"""
)
)
assert (
"END_VERSIONS" not in versions_yml
), "END_VERSIONS detected in versions.yml. This is a sign of an ill-formatted HEREDOC"
# Raises an exception if yaml is not valid
versions = yaml.safe_load(versions_yml)
assert (
len(versions) == 1
), "The top-level of versions.yml must contain exactly one entry: the process name as dict key"
software_versions = next(iter(versions.values()))
assert len(software_versions), "There must be at least one version emitted."
for tool, version in software_versions.items():
assert re.match(
r"^\d.*|^[a-f0-9]{40}$", str(version)
), f"Version number for {tool} must start with a number, or be a Git SHA commit id. "