common.smk: use update_config to simplify merge_configs
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@ -10,7 +10,7 @@ import os, sys, glob
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path = workflow.source_path("../scripts/_helpers.py")
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sys.path.insert(0, os.path.dirname(path))
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from _helpers import validate_checksum
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from snakemake.utils import update_config
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def get_config(config, keys, default=None):
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@ -29,11 +29,7 @@ def get_config(config, keys, default=None):
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def merge_configs(base_config, scenario_config):
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"""Merge base config with a specific scenario without modifying the original."""
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merged = copy.deepcopy(base_config)
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for key, value in scenario_config.items():
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if key in merged and isinstance(merged[key], dict):
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merged[key] = merge_configs(merged[key], value)
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else:
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merged[key] = value
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update_config(merged, scenario_config)
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return merged
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