[python] Add cell and transcript ingestion for Xenium #3893
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| if isinstance(platform_config, dict): | ||
| platform_config.setdefault("tiledb", dict()) | ||
| if isinstance(platform_config["tiledb"], dict): | ||
| platform_config["tiledb"].setdefault("create", dict()) | ||
| if isinstance(platform_config["tiledb"]["create"], dict): | ||
| platform_config["tiledb"]["create"].setdefault( | ||
| "allows_duplicates", True | ||
| ) |
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I think you want to get rid of the isinstance checks in here. I might be mistaken, but I think they should always evaluate to True since you setdefault first. If not, then you are failing to set allows_duplicates to True by default.
| return xenium_path | ||
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| @pytest.mark.skip(reason="Missing test dataset") |
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We need to add the test data to the test data repo before we fully release the Xenium reader. I added a shortcut story for this.
| @@ -8,7 +8,9 @@ namespace tiledbsoma { | |||
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| class OutlineTransformer : public Transformer { | |||
| public: | |||
| OutlineTransformer(SOMACoordinateSpace coordinate_space); | |||
| OutlineTransformer( | |||
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Could you add some docs either here or above the columns private member on what columns is and how it is used?
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #3893 +/- ##
===========================================
- Coverage 89.18% 66.29% -22.90%
===========================================
Files 57 156 +99
Lines 6901 20627 +13726
Branches 0 1205 +1205
===========================================
+ Hits 6155 13674 +7519
- Misses 746 6543 +5797
- Partials 0 410 +410
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| from .ingest import ( | ||
| VisiumPaths, | ||
| XeniumPaths, | ||
| from_visium, | ||
| from_xenium, | ||
| register_visium_datasets, | ||
| ) | ||
| from .outgest import to_spatialdata | ||
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| __all__ = ["to_spatialdata", "from_visium", "register_visium_datasets", "VisiumPaths"] | ||
| __all__ = [ | ||
| "to_spatialdata", | ||
| "from_visium", | ||
| "register_visium_datasets", | ||
| "VisiumPaths", | ||
| "from_xenium", | ||
| "XeniumPaths", | ||
| ] |
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Let's not add from_xenium and XeniumPaths to the module until it's fully implemented.
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De-prioritized for now. We can re-open later when we have more resources to dedicate towards spatial io. |
Issue and/or context: sc-52730
Changes:
Notes for Reviewer: