Can package dependencies be loosened?

[JacobHayes]

Hi, I'm trying to install ont-bonito into an existing virtualenv, but the package dependencies (base ones here) are specified quite precisely (==), causing conflicts with other packages I'm using. Eg: requests==2.25.1 (released in 2020); pysam==0.18.0 (I was using new properties in 0.19), etc

Could the requirements files be relaxed to >=MAJOR for most deps (and only upper bound pins for known incompatibilities, if any)?

side question: is onnxruntime used by the lib (anymore)? I see the dep but not sure use in the code after a quick search side question 2: It seems this can only be installed on linux (not Mac, even for CPU only) due to ont-koi only having manylinux wheels - is this expected? (not a blocker, just curious)

Thanks!

[iiSeymour]

Hey @JacobHayes

I can upgrade pysam and requests. Bonito doesn't use onnxruntime directly but it's used when calling mods (it's a [unpinned] dependancy of remora). Yes, you are correct w.r.t ont-koi... many of these issues we are aiming to alleviate with dorado.

[iiSeymour]

Bonito is now using the latest pysam.