initial support for Dask DataFrames in obsm/varm

docs/release-notes/1880.feature.md

@@ -0,0 +1 @@
+Add support for Dask DataFrames in `.obsm` and `.varm` ({user}`ilia-kats`)

src/anndata/_core/aligned_mapping.py

@@ -264,7 +264,16 @@ def to_df(self) -> pd.DataFrame:
     def _validate_value(self, val: Value, key: str) -> Value:
         if isinstance(val, pd.DataFrame):
             raise_value_error_if_multiindex_columns(val, f"{self.attrname}[{key!r}]")
-            if not val.index.equals(self.dim_names):
+            if (
+                not val.index.equals(self.dim_names)
+                and (
+                    val.index.dtype != "string"
+                    and self.dim_names.dtype != "O"
+                    or val.index.dtype != "O"
+                    and self.dim_names.dtype != "string"
+                )
+                and (val.index != self.dim_names).any()
+            ):
                 # Could probably also re-order index if it’s contained
                 try:
                     pd.testing.assert_index_equal(val.index, self.dim_names)

src/anndata/_core/file_backing.py

@@ -8,7 +8,7 @@
 
 import h5py
 
-from ..compat import AwkArray, DaskArray, ZarrArray, ZarrGroup
+from ..compat import AwkArray, DaskArray, DaskDataFrame, ZarrArray, ZarrGroup
 from .sparse_dataset import BaseCompressedSparseDataset
 
 if TYPE_CHECKING:
@@ -143,7 +143,8 @@ def _(x: BaseCompressedSparseDataset, *, copy: bool = False):
 
 
 @to_memory.register(DaskArray)
-def _(x: DaskArray, *, copy: bool = False):
+@to_memory.register(DaskDataFrame)
+def _(x: DaskArray | DaskDataFrame, *, copy: bool = False):
     return x.compute()
 
 

src/anndata/_core/storage.py

@@ -7,7 +7,7 @@
 import pandas as pd
 from scipy import sparse
 
-from anndata.compat import CSArray
+from anndata.compat import CSArray, DaskDataFrame
 
 from .._warnings import ImplicitModificationWarning
 from ..utils import (
@@ -51,7 +51,7 @@ def coerce_array(
     if any(is_non_csc_r_array_or_matrix):
         msg = f"Only CSR and CSC {'matrices' if isinstance(value, sparse.spmatrix) else 'arrays'} are supported."
         raise ValueError(msg)
-    if isinstance(value, pd.DataFrame):
+    if isinstance(value, pd.DataFrame | DaskDataFrame):
         if allow_df:
             raise_value_error_if_multiindex_columns(value, name)
         return value if allow_df else ensure_df_homogeneous(value, name)

src/anndata/_io/specs/methods.py

@@ -29,6 +29,7 @@
     CupyCSCMatrix,
     CupyCSRMatrix,
     DaskArray,
+    DaskDataFrame,
     H5Array,
     H5File,
     H5Group,
@@ -896,6 +897,19 @@ def write_dataframe(
         )
 
 
+@_REGISTRY.register_write(H5Group, DaskDataFrame, IOSpec("dataframe", "0.2.0"))
+@_REGISTRY.register_write(ZarrGroup, DaskDataFrame, IOSpec("dataframe", "0.2.0"))
+def write_dask_dataframe(
+    f: GroupStorageType,
+    key: str,
+    df: DaskDataFrame,
+    *,
+    _writer: Writer,
+    dataset_kwargs: Mapping[str, Any] = MappingProxyType({}),
+):
+    _writer.write_elem(f, key, df.compute(), dataset_kwargs=dataset_kwargs)
+
+
 @_REGISTRY.register_read(H5Group, IOSpec("dataframe", "0.2.0"))
 @_REGISTRY.register_read(ZarrGroup, IOSpec("dataframe", "0.2.0"))
 def read_dataframe(elem: GroupStorageType, *, _reader: Reader) -> pd.DataFrame:
@@ -1051,6 +1065,12 @@ def read_partial_categorical(elem, *, items=None, indices=(slice(None),)):
 @_REGISTRY.register_write(
     ZarrGroup, pd.arrays.StringArray, IOSpec("nullable-string-array", "0.1.0")
 )
+@_REGISTRY.register_write(
+    H5Group, pd.arrays.ArrowStringArray, IOSpec("nullable-string-array", "0.1.0")
+)
+@_REGISTRY.register_write(
+    ZarrGroup, pd.arrays.ArrowStringArray, IOSpec("nullable-string-array", "0.1.0")
+)
 def write_nullable(
     f: GroupStorageType,
     k: str,
@@ -1073,7 +1093,7 @@ def write_nullable(
     g = f.require_group(k)
     values = (
         v.to_numpy(na_value="")
-        if isinstance(v, pd.arrays.StringArray)
+        if isinstance(v, pd.arrays.StringArray | pd.arrays.ArrowStringArray)
         else v.to_numpy(na_value=0, dtype=v.dtype.numpy_dtype)
     )
     _writer.write_elem(g, "values", values, dataset_kwargs=dataset_kwargs)

src/anndata/compat/__init__.py

@@ -100,13 +100,19 @@
     from dask.array.core import Array as DaskArray
 elif find_spec("dask"):
     from dask.array import Array as DaskArray
+    from dask.dataframe import DataFrame as DaskDataFrame
 else:
 
     class DaskArray:
         @staticmethod
         def __repr__():
             return "mock dask.array.core.Array"
 
+    class DaskDataFrame:
+        @staticmethod
+        def __repr__():
+            return "mock dask.dataframe.dask_expr._collection.DataFrame"
+
 
 # https://github.com/scverse/anndata/issues/1749
 def is_cupy_importable() -> bool:

src/anndata/tests/helpers.py

@@ -32,6 +32,7 @@
     CupyCSRMatrix,
     CupySparseMatrix,
     DaskArray,
+    DaskDataFrame,
     ZarrArray,
 )
 from anndata.utils import asarray
@@ -644,8 +645,13 @@ def assert_equal_h5py_dataset(
 
 
 @assert_equal.register(DaskArray)
+@assert_equal.register(DaskDataFrame)
 def assert_equal_dask_array(
-    a: DaskArray, b: object, *, exact: bool = False, elem_name: str | None = None
+    a: DaskArray | DaskDataFrame,
+    b: object,
+    *,
+    exact: bool = False,
+    elem_name: str | None = None,
 ):
     assert_equal(b, a.compute(), exact=exact, elem_name=elem_name)
 

src/anndata/utils.py

@@ -13,7 +13,7 @@
 import anndata
 
 from ._core.sparse_dataset import BaseCompressedSparseDataset
-from .compat import CSArray, CupyArray, CupySparseMatrix, DaskArray
+from .compat import CSArray, CupyArray, CupySparseMatrix, DaskArray, DaskDataFrame
 from .logging import get_logger
 
 if TYPE_CHECKING:
@@ -115,6 +115,11 @@ def axis_len(x, axis: Literal[0, 1]) -> int | None:
     return x.shape[axis]
 
 
+@axis_len.register(DaskDataFrame)
+def axis_len_dask_df(df, axis: Literal[0, 1]) -> int | None:
+    return df.shape[axis].compute()
+
+
 try:
     from .compat import awkward as ak
 

tests/test_dask.py

@@ -11,7 +11,7 @@
 
 import anndata as ad
 from anndata._core.anndata import AnnData
-from anndata.compat import CupyArray, DaskArray
+from anndata.compat import CupyArray, DaskArray, DaskDataFrame
 from anndata.experimental.merge import as_group
 from anndata.tests.helpers import (
     GEN_ADATA_DASK_ARGS,
@@ -74,6 +74,7 @@ def test_dask_X_view():
 
 def test_dask_write(adata, tmp_path, diskfmt):
     import dask.array as da
+    import dask.dataframe as ddf
     import numpy as np
 
     pth = tmp_path / f"test_write.{diskfmt}"
@@ -84,6 +85,12 @@ def test_dask_write(adata, tmp_path, diskfmt):
     adata.obsm["a"] = da.random.random((M, 10))
     adata.obsm["b"] = da.random.random((M, 10))
     adata.varm["a"] = da.random.random((N, 10))
+    adata.varm["b"] = ddf.from_pandas(
+        pd.DataFrame(
+            {"A": np.arange(N), "B": np.random.randint(1e6, size=N)},
+            index=adata.var_names,
+        )
+    )
 
     orig = adata
     write(orig, pth)
@@ -93,6 +100,7 @@ def test_dask_write(adata, tmp_path, diskfmt):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
+    assert_equal(orig.varm["b"], orig.varm["b"])
     assert_equal(curr.obsm["a"], orig.obsm["a"])
 
     assert isinstance(curr.X, np.ndarray)
@@ -105,6 +113,7 @@ def test_dask_write(adata, tmp_path, diskfmt):
 
 def test_dask_distributed_write(adata, tmp_path, diskfmt):
     import dask.array as da
+    import dask.dataframe as ddf
     import dask.distributed as dd
     import numpy as np
 
@@ -119,6 +128,12 @@ def test_dask_distributed_write(adata, tmp_path, diskfmt):
         adata.obsm["a"] = da.random.random((M, 10))
         adata.obsm["b"] = da.random.random((M, 10))
         adata.varm["a"] = da.random.random((N, 10))
+        adata.varm["b"] = ddf.from_pandas(
+            pd.DataFrame(
+                {"A": np.arange(N), "B": np.random.randint(1e6, size=N)},
+                index=adata.var_names,
+            )
+        )
         orig = adata
         if diskfmt == "h5ad":
             with pytest.raises(ValueError, match=r"Cannot write dask arrays to hdf5"):
@@ -131,6 +146,7 @@ def test_dask_distributed_write(adata, tmp_path, diskfmt):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
+    assert_equal(orig.varm["b"], curr.varm["b"])
     assert_equal(curr.obsm["a"], orig.obsm["a"])
 
     assert isinstance(curr.X, np.ndarray)
@@ -143,6 +159,7 @@ def test_dask_distributed_write(adata, tmp_path, diskfmt):
 
 def test_dask_to_memory_check_array_types(adata, tmp_path, diskfmt):
     import dask.array as da
+    import dask.dataframe as ddf
     import numpy as np
 
     pth = tmp_path / f"test_write.{diskfmt}"
@@ -153,6 +170,12 @@ def test_dask_to_memory_check_array_types(adata, tmp_path, diskfmt):
     adata.obsm["a"] = da.random.random((M, 10))
     adata.obsm["b"] = da.random.random((M, 10))
     adata.varm["a"] = da.random.random((N, 10))
+    adata.varm["b"] = ddf.from_pandas(
+        pd.DataFrame(
+            {"A": np.arange(N), "B": np.random.randint(1e6, size=N)},
+            index=adata.var_names,
+        )
+    )
 
     orig = adata
     write(orig, pth)
@@ -161,6 +184,7 @@ def test_dask_to_memory_check_array_types(adata, tmp_path, diskfmt):
     assert isinstance(orig.X, DaskArray)
     assert isinstance(orig.obsm["a"], DaskArray)
     assert isinstance(orig.varm["a"], DaskArray)
+    assert isinstance(orig.varm["b"], DaskDataFrame)
 
     mem = orig.to_memory()
 
@@ -171,20 +195,25 @@ def test_dask_to_memory_check_array_types(adata, tmp_path, diskfmt):
     assert_equal(curr.obsm["a"], orig.obsm["a"])
     assert_equal(mem.obsm["a"], orig.obsm["a"])
     assert_equal(mem.varm["a"], orig.varm["a"])
+    assert_equal(orig.varm["b"], mem.varm["b"])
 
     assert isinstance(curr.X, np.ndarray)
     assert isinstance(curr.obsm["a"], np.ndarray)
     assert isinstance(curr.varm["a"], np.ndarray)
+    assert isinstance(curr.varm["b"], pd.DataFrame)
     assert isinstance(mem.X, np.ndarray)
     assert isinstance(mem.obsm["a"], np.ndarray)
     assert isinstance(mem.varm["a"], np.ndarray)
+    assert isinstance(mem.varm["b"], pd.DataFrame)
     assert isinstance(orig.X, DaskArray)
     assert isinstance(orig.obsm["a"], DaskArray)
     assert isinstance(orig.varm["a"], DaskArray)
+    assert isinstance(orig.varm["b"], DaskDataFrame)
 
 
 def test_dask_to_memory_copy_check_array_types(adata, tmp_path, diskfmt):
     import dask.array as da
+    import dask.dataframe as ddf
     import numpy as np
 
     pth = tmp_path / f"test_write.{diskfmt}"
@@ -195,6 +224,12 @@ def test_dask_to_memory_copy_check_array_types(adata, tmp_path, diskfmt):
     adata.obsm["a"] = da.random.random((M, 10))
     adata.obsm["b"] = da.random.random((M, 10))
     adata.varm["a"] = da.random.random((N, 10))
+    adata.varm["b"] = ddf.from_pandas(
+        pd.DataFrame(
+            {"A": np.arange(N), "B": np.random.randint(1e6, size=N)},
+            index=adata.var_names,
+        )
+    )
 
     orig = adata
     write(orig, pth)
@@ -209,25 +244,36 @@ def test_dask_to_memory_copy_check_array_types(adata, tmp_path, diskfmt):
     assert_equal(curr.obsm["a"], orig.obsm["a"])
     assert_equal(mem.obsm["a"], orig.obsm["a"])
     assert_equal(mem.varm["a"], orig.varm["a"])
+    assert_equal(orig.varm["b"], mem.varm["b"])
 
     assert isinstance(curr.X, np.ndarray)
     assert isinstance(curr.obsm["a"], np.ndarray)
     assert isinstance(curr.varm["a"], np.ndarray)
+    assert isinstance(curr.varm["b"], pd.DataFrame)
     assert isinstance(mem.X, np.ndarray)
     assert isinstance(mem.obsm["a"], np.ndarray)
     assert isinstance(mem.varm["a"], np.ndarray)
+    assert isinstance(mem.varm["b"], pd.DataFrame)
     assert isinstance(orig.X, DaskArray)
     assert isinstance(orig.obsm["a"], DaskArray)
     assert isinstance(orig.varm["a"], DaskArray)
+    assert isinstance(orig.varm["b"], DaskDataFrame)
 
 
 def test_dask_copy_check_array_types(adata):
     import dask.array as da
+    import dask.dataframe as ddf
 
     M, N = adata.X.shape
     adata.obsm["a"] = da.random.random((M, 10))
     adata.obsm["b"] = da.random.random((M, 10))
     adata.varm["a"] = da.random.random((N, 10))
+    adata.varm["b"] = ddf.from_pandas(
+        pd.DataFrame(
+            {"A": np.arange(N), "B": np.random.randint(1e6, size=N)},
+            index=adata.var_names,
+        )
+    )
 
     orig = adata
     curr = adata.copy()
@@ -236,14 +282,17 @@ def test_dask_copy_check_array_types(adata):
         assert_equal(curr.obsm["a"], curr.obsm["b"])
 
     assert_equal(curr.varm["a"], orig.varm["a"])
+    assert_equal(orig.varm["b"], curr.varm["b"])
     assert_equal(curr.obsm["a"], orig.obsm["a"])
 
     assert isinstance(curr.X, DaskArray)
     assert isinstance(curr.obsm["a"], DaskArray)
     assert isinstance(curr.varm["a"], DaskArray)
+    assert isinstance(curr.varm["b"], DaskDataFrame)
     assert isinstance(orig.X, DaskArray)
     assert isinstance(orig.obsm["a"], DaskArray)
     assert isinstance(orig.varm["a"], DaskArray)
+    assert isinstance(orig.varm["b"], DaskDataFrame)
 
 
 def test_assign_X(adata):