Hello Q2 Developer Community 
For the upcoming full release, we attempted some pretty major environment file upgrades (Python 3.12; NumPy/SciPy/pandas; scikit-bio; scikit-learn; vsearch) plus several plugin transitions (q2-fastp -> moshpit, q2-boots/q2-kmerizer -> amplicon). A few critical test issues still remain, so we’ve decided to defer these dependency updates to 2026.4. This allows us more time to work through the remaining issues while ensuring we are continuing work on new feature development for 2025.10.
Remaining failures we’re still working on:
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q2-sample-classifier: different RFECV(RandomForestClassifier) results on ARM vs x86 architecture.
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q2-vsearch: uchime2/uchime3 now matching uchime output (previously producing differing results); awaiting developer confirmation for expected behavior.
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q2-feature-classifier & q2-phylogeny: intermittent <SIGABRT 6> on macOS runners, likely resource-related.
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q2-diversity: index/value mismatches in test outputs.
Next steps we’ll be working on during the 2026.4 development cycle (Oct -> April):
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Investigate potential NumPy 2.x effects on result differences.
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Optimize tests for performance and runner constraints.
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Coordinate with vsearch maintainers on uchime* behavior.
We recognize that many developers are eager to utilize the new functionality that’s provided with these updates. Our decision to delay these updates by one full release cycle ensures we have stability in our distribution builds, and provides us with enough time to balance the time these updates take along with our regularly scheduled development.
In the meantime, you can utilize any of our available per-distro Development Environments, and these will remain stable through the 2025.10 release - so you can continue your own regularly scheduled feature development as needed.
Thanks for your patience and understanding, and as always, happy QIIMEing! 