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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #428 +/- ##
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+ Coverage 65.79% 68.03% +2.23%
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Files 26 26
Lines 3263 3272 +9
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+ Hits 2147 2226 +79
+ Misses 1116 1046 -70
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- transcripts: make `gene` a known categorical before PointsModel.parse so categories are not inferred from the first dask partition (which can drop genes absent from partition 0); pass sort=True and drop the redundant post-parse re-cast - table: store X as csr_matrix like the other scverse readers (MERSCOPE matrices are ~10% dense; ~1GB -> ~200MB on a 960-gene panel) - read the micron-to-pixel transform only when present, else fall back to an identity transform with a warning, so table/transcripts-only reads work - handle a missing images/ directory in merscope() with a warning - sort channel names for a deterministic image channel order - accept string paths in vpt_outputs dict mode (wrap in Path) - normalise boundary geometries to MultiPolygon so plain Polygons don't crash Add merscope reader-fix tests to tests/test_merscope.py.
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Audited
merscope()against real Vizgen data (Figshare VPT output: 137k cells / 70.5M transcripts / 960-gene panel; the Vizgen showcase mosaic images; GSE241870 for the counted-cell-without-polygon case). Each fix has a regression test (fails onmain, passes here).genewas passed toPointsModel.parseas object dtype, leaving dask categories "unknown"; spatialdata then infers them from the first partition only, turning genes absent from partition 0 intoNaN. Now a known categorical before parse;sort=Truedrops a redundant eager index scan.int64. Nowcsr_matrixlike the other scverse readers (~1,057 MB → ~197 MB on the Figshare panel); also removes the deprecatedAnnData(dtype=...)arg.images/. The micron→pixel transform was read unconditionally; table/transcripts-only reads now fall back to an identity transform with a warning.list(set(...)),PYTHONHASHSEED-dependent) →sorted().'str' object has no attribute 'exists') → values wrapped inPath.Polygonboundaries crashedMultiPolygon(x.geoms)→ geometries normalised to MultiPolygon.No public API changes. Adds
tests/test_merscope.py(self-contained synthetic fixtures). ruff / ruff-format / mypy clean.