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firasmidani / amiga

Analysis of Microbial Growth Assays
https://firasmidani.github.io/amiga/
GNU General Public License v3.0
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Issue with pandas? #3

Closed bholt20 closed 3 years ago

bholt20 commented 3 years ago
Screen Shot 2021-03-26 at 10 00 55 AM

I'm fairly new to python based programming, so this might be a quick fix, but I continue to get this error during while working through the tutorial from git. A little googling lead me to this thread https://github.com/pandas-dev/pandas/issues/36522

The error arrived when running: python amiga.py -i examples/randomii --only-basic-summary

I installed the requirements.txt and ran into two issues that were quickly resolved by uninstalling and reinstalling numpy and pandas. Python is 3.8.5

firasmidani commented 3 years ago

Thanks for bringing this to my attention. You are correct; this seems to be an issue due to a difference in the behavior of pandas.replace() based on the installed version of pandas. There are also many known issues with numpy and pandas that can be simply resolved by reinstallation.

I have patched the issue. In short, instead of passing a type int to pandas.replace(), I now pass a dictionary which explicitly defines the replacement values for existing values. The updated code should now be compatible with versions of pandas 0.24 or higher.

By the way, I expect to push a new update to AMiGA over the next 1-2 weeks, with major performance improvements, more thorough documentations, and cleaner command-line interface.

Don’t hesitate to open more issues or ask questions; I appreciate your feedback.