refactor: restructure the api docs (4/4) - #1287
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## feat/enum-to-literal #1287 +/- ##
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Coverage ? 79.18%
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Files ? 65
Lines ? 9545
Branches ? 1584
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Misses ? 1455
Partials ? 532
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so I talked with @timtreis and we pointed out a +/- expanding bug. Plus maybe adding these rules about Params, Fits and Results into a contribution guideline. |
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The API page was one flat list per area, every line repeating the module it belonged to, and `experimental` was a single block interleaving `im`, `tl` and `pl`. Group it: every section names its module, `experimental` splits by submodule and then by what the entries are for, and `neighbors` moves under Graph so `GraphMatrixT` is documented once rather than beside the `gr` functions, where a bare type variable read as public API. `squidpy.types` gains the two result tuples alongside the parameter bags, and the params leave `im`/`tl`'s `__all__` so it is the single public route to them. Nine names were public but absent from the page, among them `detect_tissue`, `make_tiles` and `qc_image`. Docs machinery, so the above renders: attributes inline with their types rather than an untyped summary table, `navigation_depth` at 5 so a section unfolds to its pages instead of stopping at the sub-section, and page titles as the bare name rather than the dotted path repeated in every nav entry. `typeddict.rst` goes: it was byte-identical to the built-in `base.rst` it shadowed, so it rendered nothing the default did not.
The Python domain renders a typed field inline as ``name (type) - description`` inside a two-column grid, so the three things a reader scans for share one run-on line indented behind the "Parameters:" label. A doctree transform splits each entry into ``name : type`` and its prose, and the field list is laid out as blocks rather than a grid. ``typehints_defaults`` puts each default next to its type. The signature line gets the name at a size worth landing on, with the module path receding behind it.
``pl.qc_image`` respelled every type the annotation already gives and named its return twice; ``tl.make_stitched_labels`` and ``pl.tiling_qc`` documented no return at all. Each parameter now renders its own ``(default: x)``, so the inline ``(default)`` markers duplicate it -- the computed ones, which no signature can show, stay. ``QCMetric`` is a fifteen-value alias that ``qc_image`` spelled out twice; it renders by name.
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4th step of #1279