Modernize PyPythia - #24
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## Summary - restore the final commit omitted from #24 - complete the Pixi CI matrix for RAxML-NG 1.2.2 and 2.0.2 - update workflow actions, pre-commit hooks, documentation, and locked environments
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Summary
RAxML-NG compatibility
--adaptive offfor RAxML-NG 2 and newer to preserve reproducible predictions.--adaptiveoption for RAxML-NG 1.x.adaptivevalues.