Support groups with HDF5 reader.

virtualizarr/backend.py

@@ -177,11 +177,12 @@ def open_virtual_dataset(
 
             virtual_vars = virtual_vars_from_hdf(
                 path=filepath,
+                group=group,
                 drop_variables=drop_variables + loadable_variables,
                 reader_options=reader_options,
             )
             ds_attrs = attrs_from_root_group(
-                path=filepath, reader_options=reader_options
+                path=filepath, reader_options=reader_options, group=group
             )
             coord_names = ds_attrs.pop("coordinates", [])
         # we currently read every other filetype using kerchunks various file format backends

virtualizarr/readers/hdf.py

@@ -209,6 +209,7 @@ def _dataset_to_variable(path: str, dataset: h5py.Dataset) -> Optional[xr.Variab
 
 def virtual_vars_from_hdf(
     path: str,
+    group: Optional[str] = None,
     drop_variables: Optional[List[str]] = None,
     reader_options: Optional[dict] = {
         "storage_options": {"key": "", "secret": "", "anon": True}
@@ -220,11 +221,17 @@ def virtual_vars_from_hdf(
         filepath=path, reader_options=reader_options
     )
     f = h5py.File(open_file, mode="r")
+    if group:
+        g = f[group]
+        if not isinstance(g, h5py.Group):
+            raise ValueError("The provided group is not an HDF group")
+    else:
+        g = f
     variables = {}
-    for key in f.keys():
+    for key in g.keys():
         if key not in drop_variables:
-            if isinstance(f[key], h5py.Dataset):
-                variable = _dataset_to_variable(path, f[key])
+            if isinstance(g[key], h5py.Dataset):
+                variable = _dataset_to_variable(path, g[key])
                 if variable is not None:
                     variables[key] = variable
             else:
@@ -235,6 +242,7 @@ def virtual_vars_from_hdf(
 
 def attrs_from_root_group(
     path: str,
+    group: Optional[str] = None,
     reader_options: Optional[dict] = {
         "storage_options": {"key": "", "secret": "", "anon": True}
     },
@@ -243,5 +251,11 @@ def attrs_from_root_group(
         filepath=path, reader_options=reader_options
     )
     f = h5py.File(open_file, mode="r")
-    attrs = _extract_attrs(f)
+    if group:
+        g = f[group]
+        if not isinstance(g, h5py.Group):
+            raise ValueError("The provided group is not an HDF group")
+    else:
+        g = f
+    attrs = _extract_attrs(g)
     return attrs

virtualizarr/tests/test_backend.py

@@ -293,9 +293,9 @@ def test_explicit_filetype(self, netcdf4_file):
             open_virtual_dataset(netcdf4_file, filetype="grib")
 
     def test_group_kwarg(self, hdf5_groups_file):
-        with pytest.raises(ValueError, match="Multiple HDF Groups found"):
+        with pytest.raises(NotImplementedError, match="Nested groups"):
             open_virtual_dataset(hdf5_groups_file)
-        with pytest.raises(ValueError, match="not found in"):
+        with pytest.raises(KeyError, match="doesn't exist"):
             open_virtual_dataset(hdf5_groups_file, group="doesnt_exist")
 
         vars_to_load = ["air", "time"]
@@ -321,6 +321,7 @@ def test_open_virtual_dataset_passes_expected_args(
         open_virtual_dataset(netcdf4_file, indexes={}, reader_options=reader_options)
         args = {
             "path": netcdf4_file,
+            "group": None,
             "drop_variables": [],
             "reader_options": reader_options,
         }

virtualizarr/tests/test_readers/conftest.py

@@ -118,7 +118,20 @@ def root_attributes_hdf5_file(tmpdir):
 def group_hdf5_file(tmpdir):
     filepath = f"{tmpdir}/group.nc"
     f = h5py.File(filepath, "w")
-    f.create_group("group")
+    g = f.create_group("group")
+    data = np.random.random((10, 10))
+    g.create_dataset("data", data=data)
+    return filepath
+
+
+@pytest.fixture
+def nested_group_hdf5_file(tmpdir):
+    filepath = f"{tmpdir}/nested_group.nc"
+    f = h5py.File(filepath, "w")
+    g = f.create_group("group")
+    data = np.random.random((10, 10))
+    g.create_dataset("data", data=data)
+    g.create_group("nested_group")
     return filepath
 
 

virtualizarr/tests/test_readers/test_hdf.py

@@ -113,10 +113,20 @@ def test_variable_with_dimensions(self, chunked_dimensions_netcdf4_file):
         variables = virtual_vars_from_hdf(chunked_dimensions_netcdf4_file)
         assert len(variables) == 3
 
-    def test_groups_not_implemented(self, group_hdf5_file):
+    def test_nested_groups_not_implemented(self, nested_group_hdf5_file):
         with pytest.raises(NotImplementedError):
-            virtual_vars_from_hdf(group_hdf5_file)
+            virtual_vars_from_hdf(path=nested_group_hdf5_file, group="group")
 
     def test_drop_variables(self, multiple_datasets_hdf5_file):
-        variables = virtual_vars_from_hdf(multiple_datasets_hdf5_file, ["data2"])
+        variables = virtual_vars_from_hdf(
+            path=multiple_datasets_hdf5_file, drop_variables=["data2"]
+        )
         assert "data2" not in variables.keys()
+
+    def test_dataset_in_group(self, group_hdf5_file):
+        variables = virtual_vars_from_hdf(path=group_hdf5_file, group="group")
+        assert len(variables) == 1
+
+    def test_non_group_error(self, group_hdf5_file):
+        with pytest.raises(ValueError):
+            virtual_vars_from_hdf(path=group_hdf5_file, group="group/data")