Implement --config for various commands - #2041
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## victorlin/refine-config #2041 +/- ##
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+ Coverage 73.42% 73.44% +0.01%
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Files 86 86
Lines 10895 10902 +7
Branches 2129 2129
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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.
Change the default from False to implicit None, since the option should take a file path not boolean.
The default is already rendered in both CLI help text and docs.
Adds the --config option to augur align using patterns from augur refine's --config option.
Adds the --config option to augur mask using patterns from augur refine's --config option.
Adds the --config option to augur tree using patterns from augur refine's --config option. Updated help text to reference both CLI and YAML syntax, now that both are valid options.
Adds the --config option to augur translate using patterns from augur refine's --config option. Updated help text to reference both CLI and YAML syntax, now that both are valid options.
This keeps the test focused on command-specific functionality rather than parser specifics which change over time.
Adds the --config option to augur traits using patterns from augur refine's --config option.
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Description of proposed changes
Adds the --config option to align, ancestral, mask, traits, translate, and tree using patterns from #2040.
Docs preview: https://nextstrain--2041.org.readthedocs.build/projects/augur/en/2041/usage/cli/ancestral.html#configuration
Related issue(s)
Closes #1987
Checklist