ancestral: Implement --config - #2041
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Enables configuration via a YAML file in addition to CLI arguments. All options available in the CLI are also available in the YAML file, but an option cannot be set in both simultaneously. Updated help text to reference both CLI and YAML syntax, now that both are valid options. Implemented using a new dependency, ConfigArgParse. It handles the YAML configuration within argparse so that the rest of the code can continue referencing the values from argparse. Note that it doesn't make sense to use ConfigArgParse with augur subsample because the YAML config used in that command has a nested structure, opposed to the flat structure implicitly supported by the CLI. This commit just adds the functionality and a test. More to come in the following commits.
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## victorlin/refine-config #2041 +/- ##
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Coverage 73.37% 73.38%
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This will be useful as a basis for documentation, and validation by pathogen workflows. Done with a new script that inspects the argparse parser object so that all the logic and help text can stay in register_parser().
The schema by itself isn't very useful for users. A table describing the available options is much more decipherable. Luckily we already do something for augur subsample's config docs. I've generalized an existing helper function to work with any flat JSON schema.
Adds the --config option to augur ancestral using patterns from augur refine's --config option. Updated help text to reference both CLI and YAML syntax, now that both are valid options. Added code to handle enums in the schema generating script, since enums are used in ancestral and not refine.
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Description of proposed changes
Adds the --config option to augur ancestral using patterns from augur refine's --config option.
Updated help text to reference both CLI and YAML syntax, now that both are valid options.
Added code to handle enums in the schema generating script, since enums are used in ancestral and not refine.
Docs preview: https://nextstrain--2041.org.readthedocs.build/projects/augur/en/2041/usage/cli/ancestral.html#configuration
Related issue(s)
#1987
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