refactor: move the demo blocks and script helpers out of the package

[Hendrik-code]

Stacked on #64. Last of the deduplication PRs.

Three __main__ blocks leave the shipped package

486 lines across transforms/gpu/transforms.py, transforms/gpu/transforms_list.py and transforms/cpu/transforms.py become one parameterised scripts/demo_augmentations.py.

None of them could run for anyone but their author. All three hardcoded absolute paths into one person's machine, and the two GPU blocks differed only in that path and in cuda(device=7) vs cuda() — otherwise a 205-line copy of each other. They also imported cv2, which is not a SmaugLab dependency, so they'd have failed at import for anyone who did try. The script writes PNGs through torchvision, which is a dependency.

The real cost was that they shipped in the wheel: 486 lines of dead demonstration code in the installed package. The wheel is now 26 modules.

Dropping them removes the only reason for the F811 ruff carve-out, so that goes too.

smauglab/utils/utils.py → scripts/_common.py

Nothing under smauglab/ imported it once the demo blocks were gone. It's MONAI training-loop helpers, argparse tuple parsers and a Dice function, used only by scripts/train_monai.py and scripts/generate_augmentations.py. config2parser and sig_fn had no callers at all.

Its normalize becomes normalize_percentile — three functions in this repo shared that name and two computed different things. The min-max one now lives in the demo script as normalize_minmax.

smauglab/utils/image.py deliberately stays. Five modules in the sibling segtransferaug repository import smauglab.utils.image.Image, so it is public API in practice despite having no in-package consumer.

Verification

• The 24-config seeded digests are unchanged.
• The wheel builds and carries 26 modules / 30 configs, with no utils/utils.py.
• Both scripts still import and parse their arguments (--help runs clean).
• Full suite: 105 passed, 199 subtests. ruff and mypy clean.

One subtest fewer than the parent, as expected: test_imports.py walks the package's modules, and there is one less module.

Usage

# GPU pipeline, two subjects batched together (what the old GPU demos did)
python scripts/demo_augmentations.py \
    --image sub-01_T1w.nii.gz --seg sub-01_dseg.nii.gz \
    --image sub-02_T2w.nii.gz --seg sub-02_dseg.nii.gz \
    --config smauglab/configs/transform_params_gpu.json --device cuda:0

# CPU pipeline, a grid of repeated draws (what the old CPU demo did)
python scripts/demo_augmentations.py --backend cpu --repeats 24 \
    --image sub-01_T1w.nii.gz --seg sub-01_dseg.nii.gz

The shape/NaN assertions the old demos made inline are kept — they're the reason the script is worth having, since a pipeline that changes shape or emits NaN is broken in a way the unit tests' 24-voxel volumes don't always surface.

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