File IO command line options revision #372
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #372 +/- ##
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- Coverage 94.32% 94.00% -0.32%
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Files 12 12
Lines 1039 1067 +28
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+ Hits 980 1003 +23
- Misses 59 64 +5 ☔ View full report in Codecov by Sentry. |
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Lilferrit
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casanovo/casanovo.py
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| if not output_path.is_dir(): | ||
| output_path.mkdir(parents=True) | ||
| logger.warning( | ||
| f"Target output directory {output_dir} does not exists, " |
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nitpick: Use %s instead of f-string for logging.
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Removed the
model_save_folder_pathoption in favor of the new--output_rootand--ouput_dircommand line options as written in the Casanovo File IO specification document, and introduced a new--overwriteflag that is required to be set in order to overwrite any output files. The--validation_peak_pathoption is now optional during training. If the--validation_peak_pathoption is not set thetrain_peak_pathwill be used to validate the model. In this case all spectra files intrain_peak_pathmust have peptide annotations.