search

phac-nml / sistr_cmd

SISTR (Salmonella In Silico Typing Resource) command-line tool
Apache License 2.0
25 stars 9 forks source link

SISTR v1.1.1 is not compatible with pandas >= 1.1.0 due to failed EmptyDataError exception import #44

Closed kbessonov1984 closed 3 years ago

kbessonov1984 commented 4 years ago

Just for future reference, in pandas 1.1.0 the EmptyDataError exception definition is no longer defined in pandas/io/common.py submodule causing from pandas.io.common import EmptyDataError statement, defined in sistr/src/blast_wrapper/__init__.py, to fail. The import statement requires to be changed to from pandas.errors import EmptyDataError. Could be addressed in next SISTR release. This is now handled by new conda recipe v1.1.1 build 2 restricting pandas version to <= 1.0.5

apetkau commented 4 years ago

Thanks @kbessonov1984 👍

flashton2003 commented 4 years ago

Amazing! Just came across this bug, your fix worked for me thanks @kbessonov1984

apetkau commented 3 years ago

Just a note for this issue. If you already have a conda environment with pandas > 1.0.5 and then install sistr (via conda) it does not downgrade pandas to 1.0.5. But if you install sistr to a new environment it will install pandas 1.0.5.