subsample: Improve default search paths, allow customization - #1918
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1918 +/- ##
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+ Coverage 74.17% 74.25% +0.08%
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Files 82 82
Lines 8984 9052 +68
Branches 1827 1847 +20
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+ Hits 6664 6722 +58
- Misses 2017 2024 +7
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tsibley
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This is pretty close to what I meant when I was describing the approach!
A couple small niggles noted.
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This makes it easier to add/remove steps.
This will be used in a future commit.
Preparing to use the schema in another function.
Previously, the only search path was implicitly the current working directory. Make this explicit and add an option to search other paths before it. This means the notes in option descriptions mentioning cwd as search path are no longer accurate for augur subsample. Since the descriptions are shared with augur filter which does not allow custom search paths, I figured it'd be best to remove the notes entirely.
This allows more intuitive relative filepaths from the perspective of the config file.
Environment variables can be easier to use than CLI options in some situations.
This can be used by Snakemake workflows to declare input files for rules that call augur subsample.
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Description of proposed changes
Previously, the only search path was implicitly the current working directory.
This PR adds another default – the config file's parent directory – and prefers it over cwd. Custom search paths are supported via command line option and environment variable.
Related issue(s)
Notable review threads
str(Path)instead ofPath.as_posix()? yesAUGUR_SEARCH_PATHSin other commands? yesget_referenced_files()andaugur subsample? yesChecklist