possible numpy-related issue

[gregcaporaso]

A numpy-related failure was brought up in the context of DEICODE's rpca action on the QIIME 2 Forum here. @cameronmartino thought it might also impact gemelli, so I'm posting this here. See the forum post for the command and traceback.

[cherman2]

Seems like a user did observe this issue in q2-gemelli. (Same link as Greg used above) Here is the code they reported:
qiime gemelli rpca --i-table DADA2_denoising_output/table_filtered_v2.qza --p-min-feature-count 10 --p-min-sample-count 47500 --o-biplot core_metrics_47500/Aitchison_ordination.qza --o-distance-matrix core_metrics_47500/Aitchison_distance.qza --verbose &> core_metrics_47500_Aitchison_samples.log

Here is the error:

Plugin error from gemelli:

module 'numpy' has no attribute 'int'.
np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
NumPy 1.20.0 Release Notes — NumPy v2.0.dev0 Manual

[cameronmartino]

Hi @gregcaporaso & @cherman2, thanks for posting this, will work on patching it in the next version. Thanks!!

[cameronmartino]

Hi @gregcaporaso and @cherman2,

This is now fixed in the new release of Gemelli merged today. I will update the original thread on the forums too. Thanks!!

Cameron

[cameronmartino]

@gregcaporaso or @cherman2

Actually, looks like the forum question was closed here and I can't re-open it. If you could open or update the original thread, that would be great. Thanks!!

[cherman2]

Thanks for the update! I posted the update in the original thread.

[gregcaporaso]

Thanks for the update and fix @cameronmartino!