Update pytorch lightning requirement

.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

@@ -42,7 +42,7 @@ 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

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
 

docs/getting_started.md

@@ -81,9 +81,12 @@ This model file or a custom one can then be specified using the `--model` comman
 
 Not all releases will have a model file included on the [Releases page](https://github.com/Noble-Lab/casanovo/releases), in which case model weights for alternative releases with the same major version number can be used.
 
-The most recent model weights for Casanovo version 3.x are currently provided under [Casanovo v3.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v3.0.0):
-- `casanovo_massivekb.ckpt`: Default Casanovo weights to use when analyzing tryptic data. These weights will be downloaded automatically if no weights are explicitly specified.
-- `casanovo_non-enzy.checkpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually.
+The most recent model weights for Casanovo version 4.2 and above are currently provided under [Casanovo v4.2.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.2.0):
+- `casanovo_v4_2_0.ckpt`: Default Casanovo weights to use as described in [Melendez et al.](https://pubs.acs.org/doi/full/10.1021/acs.jproteome.4c00422). These weights will be downloaded automatically if no weights are explicitly specified.
+
+Alternatively, model weigths for Casanovo version 4.x as described in [Yilmaz et al.](https://www.nature.com/articles/s41467-024-49731-x) are currently provided under [Casanovo v4.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.0.0):
+- `casanovo_massivekb.ckpt`: Casanovo weights to use when analyzing tryptic data. These weights need to be downloaded manually.
+- `casanovo_nontryptic.ckpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually.
 
 ## Running Casanovo