pandas is incompatible with numpy < 1.20.3

[YiqianGu]

Hi team,

My singularity version is 3.8.5, and I used SAW_7.1.sif. When I run this pipeline, an error happened. I copied the error part and upload a log file. I really appreciate your help!

Thanks, Yiqian

Traceback (most recent call last): File "v3.4.2/Tissuecut.py", line 261, in File "v3.4.2/Tissuecut.py", line 257, in main File "v3.4.2/Tissuecut.py", line 236, in tslib File "v3.4.2/Tissuecut.py", line 33, in drawStatImg File "/usr/local/python3/lib/python3.8/site-packages/seaborn/init.py", line 2, in from .rcmod import * # noqa: F401,F403 File "/usr/local/python3/lib/python3.8/site-packages/seaborn/rcmod.py", line 7, in from . import palettes File "/usr/local/python3/lib/python3.8/site-packages/seaborn/palettes.py", line 9, in from .utils import desaturate, get_color_cycle File "/usr/local/python3/lib/python3.8/site-packages/seaborn/utils.py", line 11, in import pandas as pd File "/usr/local/python3/lib/python3.8/site-packages/pandas/init.py", line 22, in from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 File "/usr/local/python3/lib/python3.8/site-packages/pandas/compat/init.py", line 18, in from pandas.compat.numpy import ( File "/usr/local/python3/lib/python3.8/site-packages/pandas/compat/numpy/init.py", line 23, in raise ImportError( ImportError: this version of pandas is incompatible with numpy < 1.20.3 your numpy version is 1.20.0.

Please upgrade numpy to >= 1.20.3 to use this pandas version

script.log

[Clouate]

Hi, It is recommended that upgrade the numpy package in your environment, or change to a clean environment(such as using conda) to run SAW.

[YiqianGu]

Hi Clouate, I guess this error is not related with my environment. Instead, it shows that the version of numpy from SAW_7.1.sif is not compatible with the pandas from SAW_7.1.sif.

[YiqianGu]

solved by "singularity exec SAW_7.1.sif pip3 install numpy==1.20.3"