General purpose sq.tl.align() function with STAlign core logic#1162
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timtreis wants to merge 7 commits intoscverse:mainfrom
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General purpose sq.tl.align() function with STAlign core logic#1162timtreis wants to merge 7 commits intoscverse:mainfrom
sq.tl.align() function with STAlign core logic#1162timtreis wants to merge 7 commits intoscverse:mainfrom
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Introduces a backend-agnostic alignment API (align_obs, align_images, align_by_landmarks) with STalign and landmark backends, lazy JAX imports, and e2e tests. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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- Replace private `sdata._gen_elements()` with public `gen_elements()` - Replace dict-style `sdata[key]` lookup with explicit element-type search - Add subprocess timeout (30s) to lazy-import hygiene test - Document shallow X sharing in `materialise_obs` docstring - Document JAX array retention in stalign metadata comment - Document camelCase convention in STalignRegistrationConfig docstring - Broaden landmark type hints to accept Sequence and np.ndarray - Remove stale TODO comment from _stalign_helpers.py Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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- Resolve JAX_DTYPE lazily via jax_dtype() to respect runtime x64 config - Replace 14-line config field unpack with dataclasses.asdict(registration) - Remove unreachable ValueError in _writeback (already validated upstream) - Remove task-tracking comment from moscot stub - Clean up PR-line-number reference in stalign comment Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Adds a hatch-test.py3.13-stable-jax environment that installs the [jax] optional extra so the STalign solver and e2e alignment tests run in CI. Excluded from macOS to avoid doubling runner cost. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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sq.tl.align() function with STAlign core logic
- align_obs: default output_mode="obs" (was "affine", which crashed with the default stalign backend). Auto-generate key_added from query name when not provided for SpatialData inputs. - align_by_landmarks: make cs_name_ref/query and landmarks_ref/query keyword-only required args (were Optional with None defaults that immediately errored). Remove unused scale_ref/scale_query params. Wire get_extent validation for landmark bounds checking against cs extent. Fix docstring (y, x) -> (x, y). - align_images: make img_ref/query_name keyword-only required. Remove from public __all__ (no backend implements it yet). - align_obs docstring: note that inplace only affects SpatialData. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
JAX selects the appropriate device based on its install (CPU/GPU) and runtime context managers. The explicit device arg added unnecessary complexity with no benefit over JAX's built-in device management. Removes device from: align_obs, align_images, AlignBackend protocol, StAlignBackend, MoscotBackend, and require_jax. Simplifies require_jax to a pure import guard. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Implements the following functions:
This registers a spatialdata Affine transformation on every element in cs_b, mapping it into cs_a. After the call, sdata is updated in-place, all elements in section_b now know how to transform into section_a's coordinate system.
output_mode controls what you get back:
Currently dead but will be implemente via STalign. Already in here to better align function internals