Merge branch 'dev' into dev_db_search

.github/ISSUE_TEMPLATE/bug_report_template.md

@@ -0,0 +1,55 @@
+---
+name: Bug Report
+about: Submit a Casanovo Bug Report
+labels: bug
+---
+
+## Describe the Issue
+A clear and concise description of what the issue/bug is.
+
+## Steps To Reproduce
+Steps to reproduce the incorrect behavior.
+
+## Expected Behavior
+A clear and concise description of what you expected to happen.
+
+## Terminal Output (If Applicable)
+Provide any applicable console output in between the tick marks below.
+
+```
+
+```
+
+## Environment:
+- OS: [e.g. Windows 11, Windows 10, macOS 14, Ubuntu 24.04]
+- Casanovo Version: [e.g. 4.2.1]
+- Hardware Used (CPU or GPU, if GPU also GPU model and CUDA version): [e.g. GPU: NVIDIA GeForce RTX 2070, CUDA Version: 12.5]
+
+### Checking GPU Version
+
+The GPU model can be checked by typing `nvidia-smi` into a terminal/console window.
+An example of how to use this command is shown below.
+In this case, the CUDA version is 12.5 and the GPU model is GeForce RTX 2070.
+
+
+```
+(casanovo_env) C:\Users\<user>\OneDrive\Documents\casanovo>nvidia-smi
+Fri Aug  2 12:34:57 2024       
++-----------------------------------------------------------------------------------------+
+| NVIDIA-SMI 555.99                 Driver Version: 555.99         CUDA Version: 12.5     |
+|-----------------------------------------+------------------------+----------------------+
+| GPU  Name                  Driver-Model | Bus-Id          Disp.A | Volatile Uncorr. ECC |
+| Fan  Temp   Perf          Pwr:Usage/Cap |           Memory-Usage | GPU-Util  Compute M. |
+|                                         |                        |               MIG M. |
+|=========================================+========================+======================|
+|   0  NVIDIA GeForce RTX 2070 ...  WDDM  |   00000000:01:00.0  On |                  N/A |
+| N/A   60C    P8             16W /   90W |    1059MiB /   8192MiB |      0%      Default |
+|                                         |                        |                  N/A |
++-----------------------------------------+------------------------+----------------------+
+```
+
+## Additional Context
+Add any other context about the problem here.
+
+## Attach Files
+Please attach all input files used and the full Casanovo log file.

.github/workflows/tests.yml

@@ -26,7 +26,11 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
-
+    - name: Set up Java
+      uses: actions/setup-java@v3
+      with:
+        distribution: 'zulu'
+        java-version: '22'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -42,7 +46,8 @@ jobs:
       run: |
         pytest --cov=casanovo tests/
     - 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
+

CHANGELOG.md

@@ -8,7 +8,32 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ### Added
 
-- A deprecation warning will be issued when depecrated config options are used in the config file or in the model weights file.
+- During training, model checkpoints will be saved at the end of each training epoch in addition to the checkpoints saved at the end of every validation run.
+- Besides as a local file, model weights can be specified from a URL. Upon initial download, the weights file is cached for future re-use.
+
+### Changed
+
+- Removed the `evaluate` sub-command, and all model evaluation functionality has been moved to the `sequence` command using the new `--evaluate` flag.
+
+### Fixed
+
+- Precursor charges are exported as integers instead of floats in the mzTab output file, in compliance with the mzTab specification.
+
+### Removed
+
+- Removed the `save_top_k` option from the Casanovo config, the model with the lowest validation loss during training will now be saved to a fixed filename `<output_root>.best.ckpt`. 
+
+## [4.2.1] - 2024-06-25
+
+### Fixed
+
+- Pin NumPy version to below v2.0 to ensure compatibility with current DepthCharge version.
+
+## [4.2.0] - 2024-05-14
+
+### Added
+
+- A deprecation warning will be issued when deprecated config options are used in the config file or in the model weights file.
 
 ### Changed
 
@@ -246,7 +271,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 - Initial Casanovo version.
 
-[Unreleased]: https://github.com/Noble-Lab/casanovo/compare/v4.1.0...HEAD
+[Unreleased]: https://github.com/Noble-Lab/casanovo/compare/v4.2.1...HEAD
+[4.2.1]: https://github.com/Noble-Lab/casanovo/compare/v4.2.0...v4.2.1
+[4.2.0]: https://github.com/Noble-Lab/casanovo/compare/v4.1.0...v4.2.0
 [4.1.0]: https://github.com/Noble-Lab/casanovo/compare/v4.0.1...v4.1.0
 [4.0.1]: https://github.com/Noble-Lab/casanovo/compare/v4.0.0...v4.0.1
 [4.0.0]: https://github.com/Noble-Lab/casanovo/compare/v3.5.0...v4.0.0

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