q2-2023.5 nopython keyword argument

Technical Support
1

Hi,
I have installed q2-2023.5 which was released today, and I geut the following warnings.
They showed up using these plugins (I did not test all plugins...)
q2 composition ancombc
q2 diversity
q2 cutadapt

E.g. qiime composition ancombc
/home/bt140047/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See Deprecation Notices — Numba 0.57.0+0.g4fd4e39c6.dirty documentation for details.
@numba.jit()
/home/bt140047/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See Deprecation Notices — Numba 0.57.0+0.g4fd4e39c6.dirty documentation for details.
@numba.jit()
/home/bt140047/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See Deprecation Notices — Numba 0.57.0+0.g4fd4e39c6.dirty documentation for details.
@numba.jit()
/home/bt140047/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See Deprecation Notices — Numba 0.57.0+0.g4fd4e39c6.dirty documentation for details.
@numba.jit()

So far, the analyses completed without problems, including the q2 compostions da-barplot. Thanks for fixing this issue in this release.

Best,

Update after trying to install clawback plugin (conda install -c kaehler -c conda-forge q2-clawback); see error message in the txt file:

q2-2023.5-referesh-cache.txt (6.5 KB)

1 Like
2

Hi @arwqiime,

Thanks for reaching out and for bringing this to our attention!

We were able to reproduce this on our end, and are looking into a fix for these warnings today. In the meantime, you can set an environment variable to suppress these (harmless but annoying) warnings:

export PYTHONWARNINGS="ignore"

Thanks for your patience while we get this sorted!

1 Like
3

Hi @arwqiime,

We have rolled back a couple of our dependencies, which should resolve this issue. If you already added that environment variable, you can go ahead and remove it now and re-install QIIME 2 2023.5, and these warnings should now be removed. Thanks for your patience, and for bringing this to our attention!

Cheers :lizard:

1 Like
4

Hi @lizgehret
Re-installed the new release and it worked just fine!
Thank you for your fast response!
Best,

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