feat: improvements to normalizing flow

[aseyboldt]

This repairs the householder transformation layers, changes the asymmetric transformation a bit and brings a couple more normalizing flow options for experimentation.

@jessegrabowski Maybe you want to check if this repairs your model with householder transforms...

[Copilot]

Pull Request Overview

This PR aims to improve the normalizing flow routines by repairing householder transformation layers, modifying the asymmetric transformation, and adding additional flow options for experimentation.

• Update to test configuration for Stan and PyMC models
• Enhancements to the transform adapter with new parameters and adjusted training thresholds
• Updates to project configuration files including Cargo.toml and CI workflows

Reviewed Changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_stan.py	Adds jax configuration management and test adjustments
tests/test_pymc.py	Simplifies normalization flow tests and reduces the number of draws
tests/reference/*.txt	Updates reference output files for deterministic sampling
python/nutpie/transform_adapter.py	Updates loss threshold, batch size, optimizer, and flow parameters
pyproject.toml	Updates Python requirement and adds a dependency for pytest-arraydiff
docs/.gitignore	Adds .quarto/ to the ignored files
Cargo.toml	Bumps tch version and increases opt-level
.github/workflows/ci.yml	Adds pytest-arraydiff flag to the CI pipeline
.gitattributes	Adds a highlighting configuration for SCM files

Comments suppressed due to low confidence (3)

python/nutpie/transform_adapter.py:682

• Ensure that changing the loss threshold from -5 to -4 is intentional, as this lower threshold may affect training termination behavior.

if np.isfinite(old_loss) and old_loss < -4 and self.index > 10:

tests/test_pymc.py:292

• [nitpick] Reducing the number of draws from 2000 to 500 may impact the statistical robustness of the test; please confirm that 500 draws are sufficient for your reproducibility requirements.

draws=500,

Cargo.toml:53

• [nitpick] Increasing opt-level to 3 can affect compile times and binary size; verify that this change aligns with production performance goals.

opt-level = 3

[Copilot]

[nitpick] The default batch size was updated from 100 to 128; consider updating any related documentation or comments to reflect this change.