fix: ensure read_10x_mtx returns CSR format

src/scanpy/readwrite.py

@@ -593,6 +593,41 @@ def read_10x_mtx(
     return adata[:, gex_rows].copy()
 
 
+def _read_mtx(
+    filename: Path,
+    *,
+    dtype: str = "float32",
+    sparse_format: Literal["csr", "csc", "coo"] = "csc",
+) -> AnnData:
+    """Read `.mtx` file with configurable sparse format.
+
+    Inlines the logic from :func:`anndata.read_mtx` to allow choosing the
+    sparse format directly, avoiding unnecessary conversions when the result
+    will be transposed (e.g., for 10x data where ``CSC.T → CSR``).
+
+    Parameters
+    ----------
+    filename
+        Path to the ``.mtx`` file.
+    dtype
+        Numpy data type.
+    sparse_format
+        Sparse matrix format for the output. Defaults to ``'csc'`` so that
+        a subsequent ``.T`` produces a CSR matrix with no extra conversion.
+    """
+    from scipy.io import mmread
+    from scipy.sparse import csc_matrix, csr_matrix  # noqa: TID251
+
+    x = mmread(filename)
+    if x.dtype != np.dtype(dtype):
+        x = x.astype(dtype)
+    if sparse_format == "csr":
+        x = csr_matrix(x)
+    elif sparse_format == "csc":
+        x = csc_matrix(x)
+    return AnnData(x)
+
+
 def _read_10x_mtx(
     path: Path,
     *,
@@ -607,11 +642,28 @@ def _read_10x_mtx(
     """Read mex from output from Cell Ranger v2- or v3+."""
     # Only append .gz if not a legacy file AND compression is requested
     suffix = "" if is_legacy else (".gz" if compressed else "")
-    adata = read(
-        path / f"{prefix}matrix.mtx{suffix}",
-        cache=cache,
-        cache_compression=cache_compression,
-    ).T  # transpose the data
+    mtx_file = path / f"{prefix}matrix.mtx{suffix}"
+    ext = f"mtx{suffix}"
+
+    if cache:
+        path_cache: Path = settings.cachedir / _slugify(mtx_file).replace(
+            f".{ext}", ".h5ad"
+        )
+        if path_cache.is_file():
+            logg.info(f"... reading from cache file {path_cache}")
+            adata = read_h5ad(path_cache)
+        else:
+            adata = _read_mtx(mtx_file, sparse_format="csc")
+            if isinstance(cache_compression, Default):
+                cache_compression = settings.cache_compression
+            if not path_cache.parent.is_dir():
+                path_cache.parent.mkdir(parents=True)
+            adata.write(path_cache, compression=cache_compression)
+    else:
+        # Read MTX as CSC so that .T yields CSR (one conversion, not two)
+        adata = _read_mtx(mtx_file, sparse_format="csc")
+
+    adata = adata.T  # transpose: 10x stores var×obs, anndata uses obs×var
     genes = pd.read_csv(
         path / f"{prefix}{'genes' if is_legacy else 'features'}.tsv{suffix}",
         header=None,

tests/test_read_10x.py

@@ -11,6 +11,7 @@
 import pytest
 
 import scanpy as sc
+from scanpy._compat import CSRBase
 
 if TYPE_CHECKING:
     from typing import Literal
@@ -63,6 +64,9 @@ def test_read_10x(
     if "3.0.0" in str(h5_path):
         h5.var.drop(columns="genome", inplace=True)
 
+    # Verify CSR format (not CSC from transpose)
+    assert isinstance(mtx.X, CSRBase), f"Expected CSR matrix, got {type(mtx.X)}"
+
     # Check equivalence
     assert_anndata_equal(mtx, h5)