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LooseLab / readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers
https://looselab.github.io/readfish/
GNU General Public License v3.0
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Dev branch - numpy versioning clash #173

Closed lfearnley closed 2 years ago

lfearnley commented 2 years ago

Hi all!

Hopefully an easy one - I'm following the readfish dev branch install instructions in a conda environment, and I'm seeing a dependency issue when running the commands as specified:

pip install git+https://github.com/nanoporetech/read_until_api@v3.0.0 installs and requires numpy==1.17.4. pip install git+https://github.com/LooseLab/readfish@dev installs numpy==1.22.2 and generates an incompatibility warning.

What's the cleanest way to resolve this? Will readfish run without issues on numpy 1.17.4/pandas 1.3.x?

alexomics commented 2 years ago

Sorry for the slow response. We don't have a hard requirement for numpy v1.22.2 on the dev branch. pip should, in this scenario, downgrade numpy to the pinned version used by the read_until_api but (as you mention) pandas is preventing this.

I think the solution here is ensuring that pandas is set to ==1.3.?. I have tried 1.3.1 and 1.3.3 which both install successfully. Please let me know how you get along with this

lfearnley commented 2 years ago

Hi @alexomics! Sorry about the delay - I've had a bit of a gap where I didn't want to touch the readfish install.

Setting pandas to 1.3 seems to be working ok in simulation, though I'm noticing a bit of a slowdown using guppy 6.0.6 relative to older versions of readfish - I think this might be a guppy issue though, as it's occuring on both a 2080Ti and an RTX A5000.