diff --git a/docs/getting_started.md b/docs/getting_started.md index 73cbd5f0..78163ac2 100644 --- a/docs/getting_started.md +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index f2871087..3967bf05 100644 --- a/pyproject.toml +++ b/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",