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readme.py
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readme.py
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import os
import re
def readme(self):
"""Repository ``README.md`` tests
The ``README.md`` files for a project are very important and must meet some requirements:
* Nextflow badge
* If no Nextflow badge is found, a warning is given
* If a badge is found but the version doesn't match the minimum version in the config file, the test fails
* Example badge code:
.. code-block:: md
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)
* Bioconda badge
* If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required
* Required badge code:
.. code-block:: md
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
.. note:: These badges are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.
"""
passed = []
warned = []
failed = []
# Remove field that should be ignored according to the linting config
ignore_configs = self.lint_config.get("readme", [])
with open(os.path.join(self.wf_path, "README.md"), "r") as fh:
content = fh.read()
if "nextflow_badge" not in ignore_configs:
# Check that there is a readme badge showing the minimum required version of Nextflow
# [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
# and that it has the correct version
nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
match = re.search(nf_badge_re, content)
if match:
nf_badge_version = match.group(1).strip("'\"")
try:
if nf_badge_version != self.minNextflowVersion:
raise AssertionError()
except (AssertionError, KeyError):
failed.append(
f"README Nextflow minimum version badge does not match config. Badge: `{nf_badge_version}`, "
f"Config: `{self.minNextflowVersion}`"
)
else:
passed.append(
f"README Nextflow minimum version badge matched config. Badge: `{nf_badge_version}`, "
f"Config: `{self.minNextflowVersion}`"
)
else:
warned.append("README did not have a Nextflow minimum version badge.")
# Check that the minimum version mentioned in the quick start section is consistent
# Looking for: "1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)"
nf_version_re = r"1\.\s*Install\s*\[`Nextflow`\]\(https://www.nextflow.io/docs/latest/getstarted.html#installation\)\s*\(`>=(\d*\.\d*\.\d*)`\)"
match = re.search(nf_version_re, content)
if match:
nf_quickstart_version = match.group(1)
try:
if nf_quickstart_version != self.minNextflowVersion:
raise AssertionError()
except (AssertionError, KeyError):
failed.append(
f"README Nextflow minimium version in Quick Start section does not match config. README: `{nf_quickstart_version}`, Config `{self.minNextflowVersion}`"
)
else:
passed.append(
f"README Nextflow minimum version in Quick Start section matched config. README: `{nf_quickstart_version}`, Config: `{self.minNextflowVersion}`"
)
else:
warned.append("README did not have a Nextflow minimum version mentioned in Quick Start section.")
return {"passed": passed, "warned": warned, "failed": failed}