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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
45 stars 9 forks source link

Packaging Python script #34

Open traneric opened 2 years ago

traneric commented 2 years ago

Hello PoonLab. Do you have any plans to package OpenRDP to make it pip or conda installable? I'm trying to incorporate recombination detection into my workflow within our organization's computer cluster. RDP4/5 being available as Window's binaries make this impossible as we're running on Linux servers. Your re-implementation of RDP looks extremely promising and capable of being integrated into a high-throughput command line workflow. Do you plan to actively maintain OpenRDP?

ArtPoon commented 2 years ago

Hi @traneric - thanks for your feedback. OpenRDP was primarily implemented by @kwade4 who has since graduated and I haven't been able to assume the role of package maintainer, as I'm spread thin on other projects like CoVizu, gromstole and duotang. We are getting some help from another student, @dpannguyen, to work on OpenRDP issues like #32. As for pip or conda distributions, I haven't been planning to contribute OpenRDP to either repository, since it's a fairly simple standalone package. Since you're asking, though, I'll look into submitting to PyPI.

ArtPoon commented 2 years ago

Also, I'd rather hold off on packaging until we can resolve the speed and memory usage issues. I also want to modify the main function so that it returns a Python object that can optionally be displayed via stdout, to make this easier to integrate into a pipeline.

ArtPoon commented 1 year ago

About time to revisit packaging OpenRDP for PyPI, now that we've refactored the interface and are nearly done fixing memory issues

ArtPoon commented 1 year ago

See #50