chore: auto-generate scripts from notebooks

Support all Cellpose v4 models (SAM + DINO) in GPU-resident segmentat…

…ion (#51)

* feat(segmentation): support all Cellpose v4 models in GPU-resident path

Rename the GPU-resident entry point to segment_cellpose and cover every
Cellpose v4 model -- the SAM backbone (cpsam, cpsam_v2) and the DINOv3
backbones (cpdino, cpdino-vitb). The backbones differ only in the default
tile size (256 for sam_vitl, 384 for dino_*) and share the (flow, style)
forward contract, so the resident path needs only to expose bsize and
thread it through _run_net_gpu, with cellpose's sam_vitl->256 guard.

segment_cpsam is kept as a deprecated alias (warns, slated for removal
after 0.8). Parity tests confirm resident masks match stock
CellposeModel.eval (AP >= 0.95) for all four models in 2D and 3D.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* chore(deps): add cellpose-dino extra and require cellpose>=4.2.0

The DINO models (cpdino, cpdino-vitb) and cpsam_v2 first ship in cellpose
4.2.0, and the DINO backbones additionally need the dinov3 dependency from
cellpose's `dino` extra. Bump the base cellpose extra to >=4.2.0 and add a
cellpose-dino extra (cubic[cellpose] + cellpose[dino]>=4.2.0), documenting
both install paths in the README.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* refactor(segmentation): centralize backbone tile-size resolution

The default tile size (256 for SAM, 384 for DINO) and the SAM-pinned-to-256
guard were encoded separately in _run_net_gpu and segment_cellpose -- two
sources of truth for the same backbone->tile-size rule. Extract _resolve_bsize
to own both; segment_cellpose resolves bsize once and passes the concrete value
down, so _run_net_gpu no longer needs the backbone argument.

Replace the GPU-only bsize-guard test with a fast pure-function unit test that
covers the full resolution matrix (defaults per backbone + the SAM guard),
removing a heavyweight model load for a string-compare assertion.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* test(segmentation): share CellposeModel instances across tests

The GPU parity tests each constructed their own CellposeModel, reloading the
same weights repeatedly (cpsam alone was built ~8 times). Add a module-scoped
factory fixture that caches one model per backbone and route every GPU test
through it. eval/segment_cellpose are read-only inference, so a shared instance
is safe; the fixture is lazy, so no-GPU/no-cellpose runs never construct a model
and free VRAM on teardown.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* chore: bump version to 0.8.0a1

First alpha of the 0.8 cycle, which adds DINO-model support to the
GPU-resident segmentation path and deprecates segment_cpsam.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(segmentation): mention DINO in _require_cellpose error message

The ImportError raised when cellpose is missing still said "(SAM)" only,
while _check_gpu_precondition was already updated to "(SAM or DINO)". Align
the message and point DINO users at the dinov3 install note in the README.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* chore(deps): drop unusable cellpose[dino] extra; document dinov3 install

Published cellpose (4.2.1.1) does not expose a `dino` extra, and dinov3 is
git-only (pip install git+https://github.com/facebookresearch/dinov3), so it
cannot be declared as a dependency of a PyPI package. The cellpose-dino extra
therefore pulled no dinov3 (uv warned the extra did not exist). Remove it and
document the manual dinov3 install in the README for the DINO backbones.

Regenerate uv.lock, which was stale against the cellpose>=4.2.0 bump (it still
recorded >=4.0 and resolved cellpose 4.1.1, predating cpsam_v2/cpdino).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(segmentation): reject non-positive bsize for DINO backbones

bsize is now part of the public segment_cellpose API, but _resolve_bsize
passed any explicit value straight through for DINO backbones, so bsize<=0
reached make_tiles/run_net_gpu and caused divide-by-zero / invalid tiling.
Validate it as a positive integer and fail fast with a clear error.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

---------

Co-authored-by: Alexandr Kalinin <alxndrkalinin@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

v0.7.0a7 — expose MicroSSIM alpha_min/alpha_max kwargs

cubic 0.7.0a6 — torch CUDA → cupy zero-copy fix