TIR-Learner step crashes with KeyError: 0 due to Pandas 2.0+ incompatibility

[lorenzopenone]

When running the EDTA.sif Apptainer container on the TIR step, the pipeline crashes with a KeyError: 0. This is caused by TIR-Learner3.0 using deprecated positional indexing (x[0]) on a Pandas Series in check_TIR_TSD.py. Python 3.12 and Pandas 2.0+ strictly forbid this fallback behavior.

For anyone encountering this, you can extract check_TIR_TSD.py, run sed -i 's/x\[\([0-9]\+\)\]/x.iloc[\1]/g' check_TIR_TSD.py, and bind-mount the fixed file when running Apptainer: apptainer exec --bind $PWD/check_TIR_TSD.py:/usr/local/share/TIR-Learner3.0/bin/check_TIR_TSD.py EDTA.sif ...

[linyuiz]

When running the EDTA.sif Apptainer container on the TIR step, the pipeline crashes with a KeyError: 0. This is caused by TIR-Learner3.0 using deprecated positional indexing (x[0]) on a Pandas Series in check_TIR_TSD.py. Python 3.12 and Pandas 2.0+ strictly forbid this fallback behavior.

For anyone encountering this, you can extract check_TIR_TSD.py, run sed -i 's/x\[\([0-9]\+\)\]/x.iloc[\1]/g' check_TIR_TSD.py, and bind-mount the fixed file when running Apptainer: apptainer exec --bind $PWD/check_TIR_TSD.py:/usr/local/share/TIR-Learner3.0/bin/check_TIR_TSD.py EDTA.sif ...

Maybe you can try this: https://github.com/linyuiz/EDTA_update/releases/tag/v2.3.0-4

[oushujun]

Hello @lorenzopenone,

The current version should be more stable. Can you please try again?

Thanks!
Shujun