Add a small system test for sage2lib #9
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #9 +/- ##
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+ Coverage 43.20% 60.86% +17.66%
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Files 8 8
Lines 250 253 +3
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+ Hits 108 154 +46
+ Misses 142 99 -43 ☔ View full report in Codecov by Sentry. |
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Hmm... the Windows error here seems to originate from Pyteomics within ms2ml 🤔 Do we actually care about supporting Windows here? Probably not. |
| @@ -24,7 +24,11 @@ def read_peptides(peptides, qvalue): | |||
| polars.DataFrame | |||
| The parsed and filtered peptides. | |||
| """ | |||
| peptide_df = pl.read_csv(peptides, separator="\t") | |||
| try: | |||
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Request: Could we add an error/warning message saying the fallback is occurring?
| peptide_df = pl.read_csv(peptides, separator="\t") | ||
| try: | ||
| peptide_df = pl.read_parquet(peptides) | ||
| except pl.exceptions.ComputeError: |
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R: Can we add a check of the error to make sure the compute error comes from the parsing and not anywhere else?
| import pytest | ||
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| @pytest.mark.parametrize("ftype", ["parquet", "csv"]) |
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Note: Since the whole XZ situation ive become a bit more paranoid ... we whould make a PR so the .parquet is generated from a .csv ... just to have no binaries in source control.
This PR adds a very small test for sage2lib.