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https://github.com/MillironX/nf-core_modules.git
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ab67a1d41b
* Update fastqc to produce multi-version versions.yml * Update readme and pull request template * Fix markdownlint * remove variable * Change publish dir to lowercase * Re-add getSoftwareName * Add custom pytest-workflow test to ensure versions.yml is valid * Add docstring * Remove __init__.py as it is not needed * Remove changes to README, since this part went to nf-co.re * Add NF_CORE_TEST env var * Fix editorconfig * Add additional consistency checks for versions.yml * Update multiqc module * Fix output channel
40 lines
1.5 KiB
Python
40 lines
1.5 KiB
Python
from pathlib import Path
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import pytest
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import yaml
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import re
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def _get_workflow_names():
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"""Get all names of all workflows which have a test.yml in the tests directory.
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To do so, recursively finds all test.yml files and parses their content.
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"""
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here = Path(__file__).parent.resolve()
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pytest_workflow_files = here.glob("**/test.yml")
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for f in pytest_workflow_files:
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test_config = yaml.safe_load(f.read_text())
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for workflow in test_config:
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yield workflow["name"]
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@pytest.mark.workflow(*_get_workflow_names())
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def test_ensure_valid_version_yml(workflow_dir):
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workflow_dir = Path(workflow_dir)
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software_name = workflow_dir.name.split("_")[0].lower()
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versions_yml = (workflow_dir / f"output/{software_name}/versions.yml").read_text()
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assert (
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"END_VERSIONS" not in versions_yml
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), "END_VERSIONS detected in versions.yml. END_VERSIONS being in the text is a sign of an ill-formatted HEREDOC"
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# Raises an exception if yaml is not valid
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versions = yaml.safe_load(versions_yml)
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try:
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software_versions = versions[software_name.upper()]
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except KeyError:
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raise AssertionError("There is no entry `<SOFTWARE>` in versions.yml. ")
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assert len(software_versions), "There must be at least one version emitted."
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for tool, version in software_versions.items():
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assert re.match(
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r"^\d+.*", str(version)
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), f"Version number for {tool} must start with a number. "
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