Update EUKulele module

[danilodileo]

Description of feature

There should be another container version of EUKulele. check it out

[danilodileo]

testing EUKulele 2.0.9 container

4 - 02 - 2025

• Test failed with gtdb
• Test failed with gtdb-r220
• Test failed with phylodb
  Error message in log/tax_vis.out
  "One of the files, proteins.faa, in the sample directory did not complete successfully."
  Error message in log/tax_est_proteins.err
  "Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/EUKulele/manage_steps.py", line 589, in manageTaxEstimation
  curr_out = place_taxonomy(tax_tab, cutoff_file, consensus_cutoff, consensus_proportion,
  File "/usr/local/lib/python3.9/site-packages/EUKulele/tax_placement.py", line 297, in place_taxonomy
  tax_table, classes = read_in_taxonomy(tax_file)
  File "/usr/local/lib/python3.9/site-packages/EUKulele/tax_placement.py", line 64, in read_in_taxonomy
  (np.issubdtype(tax_out[str(c)].dtypes, np.float_)):
  File "/usr/local/lib/python3.9/site-packages/numpy/init.py", line 397, in getattr
  raise AttributeError(
  AttributeError: np.float_ was removed in the NumPy 2.0 release. Use np.float64 instead."
  Error message in tax_est_proteins.out
  "Taxonomic estimation did not complete successfully. Check log file for details.
  AttributeError('np.float_ was removed in the NumPy 2.0 release. Use np.float64 instead.')"

I tried also containers eukulele:2.0.7--pyh78b79e7_0 and I got the same error.
It looks like something it's broken and EUKulele can't reach the end of its workflow.
I am trying the docker container on my local machine to replicate the same error.

[erikrikarddaniel]

The messages you get above are perfect for the Eukulele developers. It seems it's a function call in a library that got updated. I don't think you need to spend much more time on that here, but instead report Eukulele issues to their repo and close them here, I think.

[danilodileo]

I am closing this issue as the new version in containers are currently broken, so we keep v2.0.5