Add load_dataset and save_dataset functions

sgkit/__init__.py

@@ -1,6 +1,7 @@
 from pkg_resources import DistributionNotFound, get_distribution
 
 from .display import display_genotypes
+from .io.dataset import load_dataset, save_dataset
 from .io.vcfzarr_reader import read_vcfzarr
 from .model import (
     DIM_ALLELE,
@@ -59,4 +60,6 @@
     "variables",
     "pca",
     "window",
+    "load_dataset",
+    "save_dataset",
 ]

sgkit/io/dataset.py

@@ -0,0 +1,53 @@
+from typing import Any
+
+import xarray as xr
+from xarray import Dataset
+
+from sgkit.typing import PathType
+
+
+def save_dataset(ds: Dataset, path: PathType, **kwargs: Any) -> None:
+    """Save a dataset to Zarr storage.
+
+    This function is a thin wrapper around :meth:`xarray.Dataset.to_zarr`
+    that uses sensible defaults and makes it easier to use in a pipeline.
+
+    Parameters
+    ----------
+    ds
+        Dataset to save.
+    path
+        Path to directory in file system to save to.
+    kwargs
+        Additional arguments to pass to :meth:`xarray.Dataset.to_zarr`.
+    """
+    store = str(path)
+    for v in ds:
+        # Workaround for https://github.com/pydata/xarray/issues/4380
+        ds[v].encoding.pop("chunks", None)
+    ds.to_zarr(store, **kwargs)
+
+
+def load_dataset(path: PathType) -> Dataset:
+    """Load a dataset from Zarr storage.
+
+    This function is a thin wrapper around :meth:`xarray.open_zarr`
+    that uses sensible defaults and makes it easier to use in a pipeline.
+
+    Parameters
+    ----------
+    path
+        Path to directory in file system to load from.
+
+    Returns
+    -------
+    Dataset
+        The dataset loaded from the file system.
+    """
+    store = str(path)
+    ds: Dataset = xr.open_zarr(store, concat_characters=False)  # type: ignore[no-untyped-call]
+    for v in ds:
+        # Workaround for https://github.com/pydata/xarray/issues/4386
+        if v.endswith("_mask"):  # type: ignore
+            ds[v] = ds[v].astype(bool)  # type: ignore[no-untyped-call]
+    return ds

sgkit/tests/io/test_dataset.py

@@ -0,0 +1,24 @@
+import xarray as xr
+from xarray import Dataset
+
+from sgkit import load_dataset, save_dataset
+from sgkit.testing import simulate_genotype_call_dataset
+
+
+def assert_identical(ds1: Dataset, ds2: Dataset) -> None:
+    """Assert two Datasets are identical, including dtypes for all variables."""
+    xr.testing.assert_identical(ds1, ds2)  # type: ignore[no-untyped-call]
+    assert all([ds1[v].dtype == ds2[v].dtype for v in ds1.data_vars])
+
+
+def test_save_and_load_dataset(tmp_path):
+    path = str(tmp_path / "ds.zarr")
+    ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10)
+    save_dataset(ds, path)
+    ds2 = load_dataset(path)
+    assert_identical(ds, ds2)
+
+    # save and load again to test https://github.com/pydata/xarray/issues/4386
+    path2 = str(tmp_path / "ds2.zarr")
+    save_dataset(ds2, path2)
+    assert_identical(ds, load_dataset(path2))