Fix the phenix convergence trace in Figure 2D - #67

torchref/base/alignment/__init__.py:21:22: F401 `.scoring.binned_correlation` imported but unused; consider removing, adding to `__all__`, or using a redundant alias help: Add unused import `binned_correlation` to __all__

torchref/base/alignment/__init__.py:10:1: I001 Import block is un-sorted or un-formatted help: Organize imports

torchref/base/__init__.py:234:11: RUF022 `__all__` is not sorted help: Apply an isort-style sorting to `__all__`

torchref/base/__init__.py:192:5: F401 `.alignment.rotation_matrix_euler_zyz` imported but unused; consider removing, adding to `__all__`, or using a redundant alias help: Add unused import `rotation_matrix_euler_zyz` to __all__

torchref/base/__init__.py:191:5: F401 `.alignment.binned_correlation` imported but unused; consider removing, adding to `__all__`, or using a redundant alias help: Add unused import `binned_correlation` to __all__

torchref/base/__init__.py:57:1: I001 Import block is un-sorted or un-formatted help: Organize imports

torchref/_bootstrap.py:32:38: RUF013 PEP 484 prohibits implicit `Optional` help: Convert to `T | None`

torchref/__init__.py:123:11: RUF022 `__all__` is not sorted help: Apply an isort-style sorting to `__all__`

torchref/__init__.py:96:5: F401 `torchref.io.FcalcDataset` imported but unused; consider removing, adding to `__all__`, or using a redundant alias help: Add unused import `FcalcDataset` to __all__