Close sequencefile if an error happens in open_reader #106
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #106 +/- ##
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+ Coverage 87.53% 87.57% +0.03%
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Files 15 15
Lines 634 636 +2
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+ Hits 555 557 +2
Misses 79 79
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Need #107 to fix RTD checks |
ctb
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Nov 25, 2023
luizirber
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Nov 25, 2023
Address #974 (comment), down from 281 warnings to 24 after dib-lab/screed#106 is merged and a new `screed` version is available. Most warnings were `ResourceWarnings` for unclosed files in tests, but there were a couple in `src/sourmash` too. Preferred to use a context manager with `screed.open` or when passing the file to another library (like `numpy`), but for tests changed a lot of code to use `Path(...).read_text().splitlines()` instead. The remaining 24 warnings are due to duplicate files in `ZipStorage`, punting it for later because they will require more attention when modifying `src/sourmash/sbt_storage.py`.
ctb
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Mar 9, 2024
Fixes #2869 Screed release: https://github.com/dib-lab/screed/releases The only really interesting/important update between 1.1.2 and 1.1.3 is dib-lab/screed#106, which removes an unnecessary warning when running tests.
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When running downstream projects with
PYTHONDEVMODE=1there is aResourceWarningfor unclosed files:Turns out we didn't close the
sequencefilein theopen_readermethod ofscreed.openscreed.Openfor two error cases before raising an exception, and with the fix in this PR the warnings disappear.