Comments (5)
Currently, when no config file is given, the code tries to find a default config file in the same directory as the script. If we don't package a (fully functional) config file with Casanovo, this doesn't make a lot of sense imo.
We could:
- Include a default config file. It might be a bit challenging to come up with sensible default values for all options, but it's probably possible.
- Change the code so that it gives a more informative error message, rather than look for a non-existing file.
- In each case, update the documentation accordingly so that this is more clearly described.
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I updated the tutorial to tell the user how to make their own config file. However, a default already exists and it is supposed to be accessed with these lines:
if config_path == None:
abs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.yaml')
with open(abs_path) as f:
config = yaml.safe_load(f)
You can see the file here: https://github.com/Noble-Lab/casanovo/blob/main/casanovo/config.yaml
from casanovo.
There are two problems with the default config file:
- It's not packaged along with the source code, so will not be available by default after installing with pip.
- It does not always work out of the box (i.e. fails if you don't have a GPU). Especially when the config file is hidden in some internal package directory, this is challenging for people to find and modify.
from casanovo.
How can I modify the repo so that the config.yaml is packaged and placed in its proper place with a pip install? I'll also update the default values.
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You have to specify non-Python files you want included using a MANIFEST.in file.
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Related Issues (20)
- how to train casanovo v4 on huge dataset like massive-kb from scratch? HOT 3
- What is the criteria of saving the top k models in Casanovo version 4? HOT 1
- add additional inputs to encoder and decoder HOT 1
- Add contrastive loss term
- Implement bidirectional decoding HOT 1
- Add rotary embeddings
- mzTab validation
- Automate mzTab validation HOT 7
- More information about the train/val/test split HOT 2
- WARNING: Skipped spectra with invalid precursor info HOT 1
- Export casanovo to torchscript/onnx HOT 1
- ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() HOT 3
- Make Casanovo produce Skyline compatible output
- 9-Species Benchmark Set: Data Preprocessing Step? HOT 5
- Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo HOT 3
- Is there a way to know which spectras are ITMS instead of FTMS? HOT 3
- Numpy release 2.0.0 breaks depthcharge dependency HOT 2
- Use Fourier embeddings
- Add mzTab validator to github actions HOT 1
- Make Casanovo model compatible with torch.compile
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