Resolve DeprecationWarnings and fix CodeCov

[shralex]

Resolves observed DeprecationWarning in integration tests by replacing deprecated .value access on nnx Variables with [...] and updating _object__state to _pytree__state. Fix CodeCov, that recently stopped running.

Tests

Tested on TPU VM

Checklist

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[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 5 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/maxtext/layers/nnx_wrappers.py	61.53%	4 Missing and 1 partial ⚠️

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