0

Same problem as defined in this post, but there has been no solved answer. Wondering if there is something going on between pyarrow and feather.

I tried environments where:

  • I installed with conda install feather-format -c conda-forge

  • Installed with pip install feather-format

The error is occurring when calling:

from feather.compat import pdapi

I tried switching feather to pyarrow as a last resort with no luck.

Having trouble with line 14 from the MicrobiomeHD source code

Failures with a Python 2.7 environment as described in the readme, as well as a Python 3 environment

Any ideas what the issue is?

WRosko
  • 73
  • 10

2 Answers2

1

For anyone else using microbiomeHD in the future, replace line 14:

from pyarrow.compat import pdapi

with:

from pandas.core import common as pdapi

in src/data/clean_otu_and_metadata.py

GS1
  • 13
  • 3
  • Cool, thanks for adding that. Have you found this to be able to run without fail and further modification? – WRosko May 04 '21 at 15:17
  • Sure thing, It's a valuable resource so I figured I wouldn't be the only one still interested. I actually got hit with a division by zero error at the start of the analyses but the cleaned tables in feather format were produced so I didn't feel the need to continue. – GS1 May 05 '21 at 16:35
0

feather.compat no longer exists in feather 0.4.0. Most of the feather functionality has been moved to pyarrow, and feather itself is now a thin wrapper around pyarrow.feather. feather.compat was removed as part of that change. I don't think it was ever intended to be used from outside of feather itself.

New code you write should not rely on feather.compat, and old code will have to be adjusted.

user2357112
  • 260,549
  • 28
  • 431
  • 505
  • Alright, that clarifies the problem a bit and explains why there aren't many docs for `feather`. Will try modifying the file I linked to and update it for this application. – WRosko Jul 31 '18 at 20:32