Deprecate petablint with individual tables #274
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #274 +/- ##
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- Coverage 76.30% 76.09% -0.22%
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Files 36 36
Lines 3224 3233 +9
Branches 783 786 +3
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Hits 2460 2460
- Misses 559 568 +9
Partials 205 205 ☔ View full report in Codecov by Sentry. |
dilpath
approved these changes
Jun 25, 2024
| dest="yaml_file_name", | ||
| help="PEtab YAML problem filename", | ||
| nargs="?", |
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I wonder if it's possible to say yaml_file_name_deprecated takes 0 arguments, i.e. it's treated as just a "flag", and instead its argument then gets treated as a positional argument, and hence saved to yaml_file_name. Anyway, not important
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It can be done and would slightly simplify the code, but the petablint --help output would be more confusing, I think.
dilpath
reviewed
Jun 25, 2024
Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
dweindl
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I think the main use case is running petablint on a full petab problem, so we don't need the option to pass individual tables. To support individual tables with the upcoming petab v2, we'd have to extend the list of files and require a version number. I don't it's worth maintaining this functionality (correct me if I am wrong), since validation of individual files is anyways rather limited.
Therefore, this adds deprecation warnings to command line arguments for individual PEtab tables and for the
-y--yamlflags, which are no longer required, and the removal of which will makepetablinteasier to use.Related to #271