search

phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
111 stars 31 forks source link

Pandas version issue when installing using conda/mamba #154

Closed tianrenmaogithub closed 6 months ago

tianrenmaogithub commented 7 months ago

I used mamba to install it with python version 3.9, but it installed pandas 2.1.3 and returned an error. You required pandas >= 0.22.0,<=1.05 but it was not effective in conda. I solved it by manually installing pandas 1.0.5 in python 3.8.

kbessonov1984 commented 7 months ago

We restricted pandas version due to EmptyDataError (empty dataframe error) we had before (now all exceptions reside in pandas.errors). See issues #70 and #63. Since then we updated code to make it compatible with newer pandas versions but did not extensively tested it. Please install mob_suite in a separate environment to avoid pandas versions conflicting requirements. In future releases will relax pandas requirement version range

kbessonov1984 commented 6 months ago

Relaxed pandas to 1.5.3 or lower version in mob_suite v3.1.8 build 1 conda recipe (https://github.com/bioconda/bioconda-recipes/pull/44947) to make it more install flexible (https://anaconda.org/bioconda/mob_suite/files). pandas >=1.5.3 is not supported yet in the mob_suite code and would cause issues due to deprecation of some parameters in some key functions.