[main] Add Sphinx documentation (ReadTheDocs) - #78
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August 25, 2026 10:25
…eference Autodoc was too fragile against segger's heavy/CUDA-only import graph (PEP 604 unions on mocked types, mocked numpy.ndarray breaking singledispatch, stale docstrings with wrong defaults). Replaced with plain parameter tables read directly from segger/cli/segment.py and segger/cli/export.py.
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Aug 25, 2026
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I think, aside from the 2-3 detailed comments I noted, this looks very nice and minimalist.
| segger export | ||
| ============== | ||
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| Positional arguments select which elements to write: ``anndata``, ``transcripts``, |
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I believe it's worth mentioning what transcripts mean --> the additional cell column (mvp!)
| * - ``--method`` | ||
| - delaunay | ||
| - Cell-polygon method for boundaries (``delaunay`` or ``convex_hull``). | ||
| * - ``--chaikin-iterations`` |
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again worth clarifying this, what it is exaclty and a reference maybe.
| * - ``--include-all-transcripts`` | ||
| - False | ||
| - Keep every cell-assigned transcript, ignoring the similarity threshold. | ||
| * - ``--min-similarity`` |
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worth mentioning highly recommended not to change.
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| About | |||
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maybe a contribution note would be nice, but could do later.
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…ent sdata.zarr export Filtering no longer needs a join with source transcripts now that x/y/feature_name/filtered are inline. Also document segger export spatialdata, which adds segger's elements to an existing SpatialData Zarr store.
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Summary
Added minimal, highly focused docs.
Important notes:
Expect the following changes:
--save-anndata, consider replacing this with an automatic pipe throughsegger exportessentiallycloses #75