environment_yml

ModuleLint.environment_yml(module: NFCoreComponent, allow_missing: bool = False, fix_version: bool = False, progress_bar: Progress | None = None) → None

Lint an environment.yml file.

The lint test checks that the dependencies section in the environment.yml file is valid YAML and that it is sorted alphabetically.

The following checks are performed:

• environment_yml_exists: The environment.yml file must exist, unless the module has a Dockerfile. If neither environment.yml nor a Dockerfile is present, the test fails.
• environment_yml_dockerfile_conflict: A module must not have both an environment.yml and a Dockerfile; Remove the Dockerfile if present.
• environment_yml_valid: The environment.yml must be valid according to the JSON schema defined at https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json.
• environment_yml_sorted: The dependencies listed in environment.yml must be sorted alphabetically. If they are not, they will be sorted automatically.
• bioconda_version: The version specified for each bioconda package must be a valid, known version available in the bioconda channel.
• bioconda_latest: Each bioconda package should be pinned to the latest available version. A warning is raised (or the version updated if fix_version is set) when a newer version exists.