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ShobiStassen / VIA

trajectory inference
https://pyvia.readthedocs.io/en/latest/
MIT License
78 stars 20 forks source link

Documentation #13

Open GreenGilad opened 2 years ago

GreenGilad commented 2 years ago

I find it difficult to understand how the package works, how to set the different parameters and which attribute is set in which operation. Is it possible to add function documentation and type hinting to the main functions?

ShobiStassen commented 2 years ago

hi again,

Yes sure let me add that over the next week or two - i agree that would be helpful!

pavsol commented 1 year ago

Hi, I agree with @GreenGilad. The documentation is absolutely insufficient. The package looks very promising regarding my data structure, but it is unusable without proper documentation. It would be really useful to add a detailed description of the attributes and parameters. Please take an example of CellRank documentation which is remarkable in my opinion.

ShobiStassen commented 1 year ago

@pavsol Hi Pavel, ahhh I know we need some proper API documentation. I'm actually working on it now (you can see some "under construction" doc generation in the Readthedocs page, so hopefully I can have something basic up soon). I'll try to do so without perturbing the current implementation and usage too much.

pavsol commented 1 year ago

Glad to hear that. It seems that VIA can resolve the pseudotime in my data well. I was able to resolve it with Slingshot only partially due to its divergence-convergence structure but VIA seems working nicely. I believe that a lot of others would benefit from the proper documentation of this promising tool.