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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Pandas version issue when installing using conda/mamba #154

Closed tianrenmaogithub closed 11 months ago

tianrenmaogithub commented 11 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 11 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 11 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.