[main] Add Sphinx documentation (ReadTheDocs) - #78
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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.
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yes, adding a reference to the chaikin algorithm
| * - ``--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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EliHei2
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Sep 15, 2026
| the segger assignment as `segger_cell_id` (plus `row_index`), a sibling column in the spirit of SOPA's | ||
| `sopa_prior`, so it merges onto an existing transcripts dataframe by `row_index` without overwriting | ||
| the vendor `cell_id`; its values match the `cell_id` in the other two files. No newline at end of file | ||
| TODO: citation |
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is this intentional? no citation to preprint? / also a contributions note I think is good.
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…rence, common-issues) and rewrite README/CONTRIBUTING Adds ReadTheDocs-built Sphinx docs covering installation, a How To guide (segger segment and segger export), outputs, hand-written CLI API reference tables (autodoc was too fragile against segger's CUDA-only import graph), and a common-issues page (gene dropout, filtering, CUDA 13, multi-GPU). Rewrites README.md as a short pointer to the docs plus the paper abstract and overview figure, adds CONTRIBUTING.md, and bumps the changelog/version to 0.3.0. Co-authored-by: Elyas Heidari <55977725+EliHei2@users.noreply.github.com>
…verview figure Adds notebooks/quickstart.ipynb (segment, export, load outputs, GPU cluster, visualize a crop), referenced from the docs. Adds a local pre-commit hook that strips notebook outputs down to stdout text and images (drops stderr/warnings, error tracebacks, execution counts) before commit, and segger_overview.png for the README/docs. Trims boilerplate .gitignore sections and tidies the xeniumranger run-artifact entry.
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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 exportessentiallyThanks @EliHei2 for your revisions.
closes #75