Fix parse fix dates (take 2) #878
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Updates functional tests for the parse command to use the `--fix-dates` argument and updates the corresponding initial sequence data to include a sequence with an incomplete date value that needs to be fixed. This functional test fails, recapitulating issue #873. Also, updates the unit tests for the `fix_dates` function to explicitly check for warning messages when users provide invalid dates. These tests now include an example where a user may provide a valid ambiguous date that currently produces a warning and shouldn't.
Renames the `fix_dates` argument of `parse_sequence` to `fix_dates_format`. This name is a slightly more accurate description of the variable and also prevents the overwriting of the `fix_dates` function by a function argument. Fixes #873
Checks whether dates that could not be parsed by pandas are still valid ambiguous dates for Augur (e.g., "2020-XX-XX") and does not warn users about these ambiguous dates. Also, prints warnings to stderr where users should expect to find them instead of stdout.
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Codecov Report
@@ Coverage Diff @@
## master #878 +/- ##
==========================================
- Coverage 34.28% 33.75% -0.53%
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Files 41 41
Lines 5942 6213 +271
Branches 1521 1673 +152
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+ Hits 2037 2097 +60
- Misses 3823 3999 +176
- Partials 82 117 +35
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rneher
approved these changes
Mar 31, 2022
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Description of proposed changes
An alternate solution to #874 that prefers renaming the
parse_sequenceargument fromfix_datestofix_dates_formatto fix #873.As part of this fix, I also noticed undesirable behavior from the
fix_datesfunction (which we wouldn't have noticed, since the function hasn't been getting called!) where users are warned about valid ambiguous dates (e.g., "2020-XX-XX").Related issue(s)
Fixes #873
Related to #874
Testing
This PR adds functional tests for the original issue and unit tests for the second issue and then adds the code to make these tests pass.