Merge pull request #385 from Noble-Lab/lightning_version_fix

Update pytorch lightning requirement

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
 

pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
 requires-python = ">=3.8"
 dependencies = [
     "appdirs",
-    "lightning>=2.0",
+    "lightning>=2.1",
     "click",
     "depthcharge-ms>=0.2.3,<0.3.0",
     "natsort",