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Villen-Lab / pyAscore

A python package for fast post translational modification localization, powered by Cython.
https://pyascore.readthedocs.io/
MIT License
18 stars 5 forks source link

Get Peptide Scores for all peptides #41

Closed FloBay closed 1 year ago

FloBay commented 1 year ago

This fixes some compilation errors and returns a pep score even for unambiguous peptides: https://github.com/Villen-Lab/pyAscore/issues/40

AnthonyOfSeattle commented 1 year ago

Looks like the GCC version I used in the linux machines isn't available anymore. Let me fix that and then you can rebase.

Please also remove the numpy upgrades. The logic needs to be conditional to support other versions of python.

Update: you should be good to rebase and try again.

FloBay commented 1 year ago
AnthonyOfSeattle commented 1 year ago

Sweet, I think this all looks good. I think the logic for just always supplying a PepScore is sound.

Please go ahead and squash the commits down to 1 or 2 and write a more detailed commit message about what you did.

Once you merge, I will write a flag to allow users to run with infinite PepScores. Honestly, I may be the only one who uses that in any pipeline, though, so I can handle it. Your change will be available on main and released in minor version update after my updates.

FloBay commented 1 year ago

Hey.. sorry I was quite busy the last days...

You can absolutely squash all my commits into a single commit and merge it to your repository. I cannot do this unfortunately. Only people with write access can do this. Normally, it should like this for you: image

Regarding a commit massage, i would suggest the following line:

"Enable peptide score for all peptides regardless of the modification state"

AnthonyOfSeattle commented 1 year ago

Yeah, I can do this for you. I'm surprised that you don't have write access to main on your own fork. Usually squashes and rebases are performed with force pushes to a branch on your fork, and the updates will be reflected here.

AnthonyOfSeattle commented 1 year ago

Merged these changes as a squashed commit in linked PR