Add warning deprecation message to top-level commands #3036
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mashehu
approved these changes
Jun 25, 2024
ewels
reviewed
Jun 25, 2024
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+2254
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| from nf_core.pipelines.schema import PipelineSchema | ||
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| schema_obj = PipelineSchema() | ||
| try: | ||
| schema_obj.get_schema_path(pipeline) | ||
| # Load and check schema | ||
| schema_obj.load_lint_schema() | ||
| except AssertionError as e: | ||
| log.error(e) | ||
| sys.exit(1) | ||
| schema_obj.load_input_params(params) | ||
| try: | ||
| schema_obj.validate_params() | ||
| except AssertionError: | ||
| sys.exit(1) |
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Click CLI is just Python functions, so I don't think that you need to repeat this code. I think you can just call the new validate_schema() command with the supplied parameters directly (and same for the others).
Better to reduce code duplication and risk of error that way.
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oh ok! I didn't know that, makes sense 😄
This was referenced Jun 25, 2024
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Let top-level pipeline commands work to avoid breaking pipelines CI