Merge branch 'codecov-fix' into 322-mztab-validation

Noble-Lab · Aug 5, 2024 · c96040e · c96040e
2 parents 13e9bec + 72ebdce
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -63,7 +63,7 @@ jobs:
           exit 1
         fi
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 If you use Casanovo in your work, please cite the following publications:
 
 - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html)
-- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621)
+- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x)
 
 ## Documentation
 

diff --git a/docs/index.md b/docs/index.md
@@ -7,7 +7,7 @@
 If you use Casanovo in your work, please cite the following publications:
 
 - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html)
-- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621)
+- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x)
 
 ```{toctree}
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