annotate_nhood error

[ali-harasty]

annotate_nhood error

[emdann]

Hi @ali-harasty, thanks for reporting. This has to do with some recent change in rpy2, and it's also breaking the tests in github actions. I won't be able to work on a patch today but I'll get to it ASAP.

For now I would suggest downgrading to rpy2 < 3.5.5, although you might need to make a new environment for that (where you install r-base first and then rpy2 ). You can use the following environment.yml:

name: milopy-env
channels:
  - conda-forge
  - bioconda
dependencies:
  - r-base
  - bioconductor-edger
  - rpy2==3.5.4
  - notebook
  - pip
  - pip:
      - scanpy
      - git+https://github.com/emdann/milopy

[ali-harasty]

Thank you so much!