[augur ancestral] arg parsing improvements #1344
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Additional details and impacted files@@ Coverage Diff @@
## master #1344 +/- ##
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+ Coverage 65.80% 65.94% +0.14%
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Files 68 68
Lines 7153 7156 +3
Branches 1756 1758 +2
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+ Hits 4707 4719 +12
+ Misses 2182 2173 -9
Partials 264 264 ☔ View full report in Codecov by Sentry. |
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victorlin
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Check that provided arguments are compatible. Where possible we use argparse built-ins, but they don't cover everything we want to check. This checking isn't intended to replace conditional checks in the code which check for arg existence (as demonstrated by the additional conditional added here), however by checking for invalid combinations up-front we can exit quickly.
This is consistent with augur's general behaviour of "request a file for it to be produced". Moreover, the previous code would ~always result in the VCF input file being overwritten. This is potentially a backwards compatible change. The number of users expected to be affected is minimal (perhaps zero). Closes #1343.
This is the preferred method rather than printing to STDERR and exiting
For VCF alignments, `--vcf-reference` becomes the 'ref' variable and for FASTA alignments, `--root-sequence` becomes the 'ref' variable. If both was provided then (previously) one was silently ignored, but they are now mutually exclusive. The argument help messages are also improved.
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victorlin
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The move to "Creating files in the initial working directory" is motivated by <#1344 (comment)> and <#1176>. Additionally, I remove the pushd commands which were confusing (there were multiple!) and use variables to refer to common directories to improve readability.
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The move to "Creating files in the initial working directory" is motivated by <#1344 (comment)> and <#1176>. Additionally, I remove the pushd commands which were confusing (there were multiple!) and use variables to refer to common directories to improve readability.
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ThreeFour small commits - see messages in each for details.This PR is potentially a backwards incompatible change, and the changelog has been updated accordingly.
Closes #1343