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Noble-Lab / casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
https://casanovo.readthedocs.io
Apache License 2.0
102 stars 37 forks source link

Fix documentation of --output and updated output settings. #348

Closed Lilferrit closed 2 weeks ago

Lilferrit commented 3 months ago

In order to introduce some of the features/changes requested in #241 and the comments of PR #276 a branch from the output branch was created and some new command line features were introduced.

First, the --root_ckpt_name option was added to the train sub-command. This option, if set, will add a root name to the checkpoint files, e.g. if the option is set as --root_ckpt_name foobar than the checkpoint filenames will have the format foobar.epoch=2-step=150000.ckpt. Otherwise the checkpoint files will have the original default format. The checkpoint files will still be saved to the model_save_folder_path set in the config file.

Additionally a --overwrite_output boolean flag was added to all of the sub commands which produce .log and .mztab output files. If this flag isn't set then the Casanovo CLI will raise an error if one of the output files already exists, otherwise it will overwrite the output files with the new output.

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 89.89%. Comparing base (ac2ddec) to head (84b85c3).

:exclamation: Current head 84b85c3 differs from pull request most recent head 18c95fb

Please upload reports for the commit 18c95fb to get more accurate results.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #348 +/- ## ========================================== + Coverage 89.77% 89.89% +0.11% ========================================== Files 12 12 Lines 929 940 +11 ========================================== + Hits 834 845 +11 Misses 95 95 ```

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Lilferrit commented 2 weeks ago

Duplicate of #372.