Fix bugs in filter_features command line utility. - #660
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- Convert any labels specified on the command line using `safe_float()` just like the labels that are read by all of the FeatureSet reader classes. This ensures that something like `-L 0 1` is interpreted correctly.
- Right now, the input and output file need to be specified _before_ any optional arguments which is unintuitive. This commit makes it such that the files also require flags but they are required.
- Add new tests to check that the label conversion works correctly. - Update existing tests to use the new command line argument flags.
- Update the command line arguments. - Add a warning explaining the backwards incompatibility and changes that will be coming up in v2.5.
Codecov Report
@@ Coverage Diff @@
## main #660 +/- ##
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Coverage 95.09% 95.10%
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Files 27 27
Lines 3101 3104 +3
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+ Hits 2949 2952 +3
Misses 152 152
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aoifecahill
approved these changes
Feb 4, 2021
mulhod
approved these changes
Feb 5, 2021
mulhod
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Looks good to me!
One very minor editing comment. Address if you have the inclination.
Co-authored-by: Matt Mulholland <mulhodm@gmail.com>
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This PR closes #598.
-Lthroughsafe_float()to make sure that they are converted in the same way that the FeatureSet reader classes do for any feature files (see issue for more details).filter_featuresto make them more intuitive to newcomers. This breaks backwards compatibility but it's worth it. Specifically, input and output files must be specified using-iand-orespectively, and inversion is now effected by using--inverse.filter_featuretests to use the new command line arguments.filter_featuresdocumentation with the new arguments as well as by adding a new warning.