deprecate, rename and check config entries

[FabianHofmann]

Add scheme for deprecating config entries and warn for config validation

This PR introduces specific warning classes for deprecated and invalid configuration entries. A scheme is proposed to deprecate and optionally rename config entries through the config/deprecations.yaml.

Like this snakemake raises:

• a DeprecationConfigWarning for deprecated config entries
• a InvalidConfigWarning for unsupported/invalid config entries which are not included in config.default.yaml

Testing

Added assertions to verify warning classes in:

• test_config_deprecations()
• test_config_invalid_entries()

Open points

• extend this to capture scenario config.

Checklist

• I tested my contribution locally and it works as intended.
• Code and workflow changes are sufficiently documented.
• Changed dependencies are added to envs/environment.yaml.
• Changes in configuration options are added in config/config.default.yaml.
• Changes in configuration options are documented in doc/configtables/*.csv.
• Sources of newly added data are documented in doc/data_sources.rst.
• A release note doc/release_notes.rst is added.

[github-actions]

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Last updated on 2025-01-26 15:45:50 CET.