Fix type errors in titer models #1688
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1688 +/- ##
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+ Coverage 72.31% 72.79% +0.48%
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Files 79 79
Lines 8271 8271
Branches 1691 1691
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+ Hits 5981 6021 +40
+ Misses 2005 1961 -44
- Partials 285 289 +4 ☔ View full report in Codecov by Sentry. |
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Adds unit tests for validation of both tree and substitution titer models including public test data from Bedford et al. 2014 (titers and sequences). These tests cover code that is only accessible through the Python API and which previously had type errors caused by changes in core Python since the code was last run (probably circa late 2016). Several doctest updates in this commit reflect the change of test titer data.
Fixes type errors in titer model code that is only accessible through the developer's Python API but which prevented me from running cross-validation of titer models with that API. It looks like these were the only references to the dictionary methods of keys and values that didn't get updated in the past.
Fixes a type error "Population must be a sequence. For dicts or sets, use sorted(d)."
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Description of proposed changes
Adds unit tests to catch type errors in titer model code and adds fixes for that code. The affected code is only accessible through the developer's Python API but these type errors prevented me from running cross-validation of titer models with that API.
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