search

kipoi / kipoiseq

Standard set of data-loaders for training and making predictions for DNA sequence-based models.
https://kipoi.org/kipoiseq/
MIT License
77 stars 13 forks source link

pyranges import #95

Closed haimasree closed 3 years ago

haimasree commented 3 years ago

pyranges is not part of requirements here. This leads to a build error in website repo's nightly test. Using pip to install pyranges and cython from setup.py does not work either (tested on mac and ubuntu 18.04 and python 3.7). I suggest either to remove pyranges from top level import in sequence.py if possible or maybe add

Karollus commented 3 years ago

Sorry for the very late reply, I somehow didnt get notifications for all these issues.

If this is resolved already, then ignore.

Otherwise, I would think pyranges should be a global dependency of kipoiseq at this point, because so many of its components require it and simply won't work without it I think

Hoeze commented 3 years ago

+1 on the global dependency of pyranges

haimasree commented 3 years ago

I dont fully remember the context but seems like I added pyranges to requirements.txt at some point. I moved pyranges to top level import in sequence.py here