h5netcdf 1.7.1__tar.gz → 1.7.3__tar.gz

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/CHANGELOG.rst

@@ -1,6 +1,17 @@
 Change Log
 ----------
 
+Version 1.7.3 (October 21st, 2025):
+
+- Fix indexing with empty arrays and lists (:pull:``).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+Version 1.7.2 (October 17th, 2025):
+
+- Fix regression where format was requested from group instance instead of _root. Simplify logic to check and raise ``CompatibilityError``. (:issue:`293`, :pull:`294`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_
+
+
 Version 1.7.1 (October 16th, 2025):
 
 - Fix regression where attributes with list of strings were written with h5py low-level API instead of high-level API (:issue:`291`, :pull:`292`).

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5netcdf
-Version: 1.7.1
+Version: 1.7.3
 Summary: netCDF4 via h5py
 Author-email: Stephan Hoyer <shoyer@gmail.com>, Kai Mühlbauer <kmuehlbauer@wradlib.org>
 Maintainer-email: h5netcdf developers <devteam@h5netcdf.org>

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/h5netcdf/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.7.1'
-__version_tuple__ = version_tuple = (1, 7, 1)
+__version__ = version = '1.7.3'
+__version_tuple__ = version_tuple = (1, 7, 3)
 
-__commit_id__ = commit_id = 'g251854355'
+__commit_id__ = commit_id = 'g6bd08d40a'

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/h5netcdf/core.py

@@ -12,7 +12,7 @@ from packaging import version
 
 from . import __version__
 from .attrs import Attributes
-from .dimensions import Dimension, Dimensions
+from .dimensions import Dimension, Dimensions, _check_classic_unlimited
 from .utils import (
     CompatibilityError,
     Frozen,
@@ -55,20 +55,13 @@ def _invalid_netcdf_feature(feature, allow):
 
 def _transform_1d_boolean_indexers(key):
     """Find and transform 1D boolean indexers to int"""
-    # return key, if not iterable
-    try:
-        key = [
-            (
-                np.asanyarray(k).nonzero()[0]
-                if isinstance(k, (np.ndarray, list)) and type(k[0]) in (bool, np.bool_)
-                else k
-            )
-            for k in key
-        ]
-    except TypeError:
-        return key
-
-    return tuple(key)
+    # Convert 1D boolean arrays/lists to integer indices,
+    # leaving all other types unchanged
+    return tuple(
+        np.flatnonzero(arr) if arr.dtype == bool else k
+        for k in key
+        for arr in [np.asanyarray(k)]
+    )
 
 
 def _expanded_indexer(key, ndim):
@@ -526,13 +519,27 @@ class BaseVariable(BaseObject):
             h5ds_shape = self._h5ds.shape
             shape = self.shape
 
-            # check for ndarray and list
             # see https://github.com/pydata/xarray/issues/7154
+            # see https://github.com/pydata/xarray/issues/10867
             # first get maximum index
-            max_index = [
-                max(k) + 1 if isinstance(k, (np.ndarray, list)) else k.stop
-                for k in key0
-            ]
+            def _get_max_index(k):
+                # Return the maximum index for ndarray, list, slice, or int,
+                # handling empty arrays/lists safely
+                if isinstance(k, np.ndarray):
+                    if k.size == 0:
+                        return None
+                    return k.max() + 1
+                elif isinstance(k, list):
+                    return max(k) + 1 if k else None
+                elif isinstance(k, slice):
+                    return k.stop
+                elif isinstance(k, int):
+                    return k + 1
+                else:
+                    return None
+
+            max_index = [_get_max_index(k) for k in key0]
+
             # second convert to max shape
             # we take the minimum of shape vs max_index to not return
             # slices larger than expected data
@@ -1030,12 +1037,8 @@ class Group(Mapping):
 
     @dimensions.setter
     def dimensions(self, value):
-        if self._format == "NETCDF4_CLASSIC":
-            unlimited_dims = list(filter(lambda s: s in [None, 0], value.values()))
-            if len(unlimited_dims) > 1:
-                raise CompatibilityError(
-                    "NETCDF4_CLASSIC format only allows one unlimited dimension."
-                )
+        if self._root._format == "NETCDF4_CLASSIC":
+            _check_classic_unlimited(value)
 
         for k, v in self._all_dimensions.maps[0].items():
             if k in value:

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/h5netcdf/dimensions.py

@@ -1,12 +1,24 @@
 import weakref
 from collections import OrderedDict
-from collections.abc import MutableMapping
+from collections.abc import Mapping, MutableMapping
 
 import numpy as np
 
 from .utils import CompatibilityError
 
 
+def _check_classic_unlimited(value, unlimited=None):
+    if isinstance(value, Mapping):
+        multiple_unlimited_dimensions = sum(v in (None, 0) for v in value.values()) > 1
+    else:
+        multiple_unlimited_dimensions = unlimited and value in (None, 0)
+
+    if multiple_unlimited_dimensions:
+        raise CompatibilityError(
+            "Only one unlimited dimension allowed in the NETCDF4_CLASSIC format."
+        )
+
+
 class Dimensions(MutableMapping):
     def __init__(self, group):
         self._group_ref = weakref.ref(group)
@@ -25,14 +37,8 @@ class Dimensions(MutableMapping):
             raise RuntimeError("H5NetCDF: Write to read only")
         if name in self._objects:
             raise ValueError(f"dimension {name!r} already exists")
-        if (
-            size in [0, None]
-            and self._unlimited()
-            and self._group._format == "NETCDF4_CLASSIC"
-        ):
-            raise CompatibilityError(
-                "Only one unlimited dimension allowed in the NETCDF4_CLASSIC format."
-            )
+        if self._group._root._format == "NETCDF4_CLASSIC":
+            _check_classic_unlimited(size, self._unlimited())
 
         self._objects[name] = Dimension(self._group, name, size, create_h5ds=True)
 

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/h5netcdf/tests/test_h5netcdf.py

@@ -211,7 +211,7 @@ def write_h5netcdf(tmp_netcdf, compression="gzip", format="NETCDF4"):
     if ds.data_model == "NETCDF4_CLASSIC":
         with raises(
             CompatibilityError,
-            match="NETCDF4_CLASSIC format only allows one unlimited dimension.",
+            match="Only one unlimited dimension allowed",
         ):
             ds.dimensions = {"x": 4, "y": 5, "z": 6, "unlimited": None, "empty": 0}
 
@@ -1973,6 +1973,13 @@ def test_fancy_indexing(tmp_local_or_remote_netcdf):
         np.testing.assert_array_equal(ds["hello"][[4, 5, 6], 1], [41, 0, 0])
         np.testing.assert_array_equal(ds["hello"][slice(4, 7), 1], [41, 0, 0])
 
+        # test empty slices
+        # regression test for https://github.com/pydata/xarray/pull/10870
+        empty = np.empty(0, dtype="int64")
+        np.testing.assert_array_equal(ds["hello"][1, []], empty)
+        np.testing.assert_array_equal(ds["hello"][1, np.array([], dtype="int")], empty)
+        np.testing.assert_array_equal(ds["hello"][1, slice(0, 0)], empty)
+
 
 def test_h5py_chunking(tmp_local_netcdf):
     with h5netcdf.File(tmp_local_netcdf, "w") as ds:
@@ -2903,7 +2910,7 @@ def test_raise_on_closed_file(tmp_local_netcdf):
     v = f.create_variable("hello", ("x",), float)
     v[:] = np.ones(5)
     f.close()
-    with pytest.raises(
+    with raises(
         ValueError,
         match=f"I/O operation on <Closed h5netcdf.File>: '{tmp_local_netcdf}'",
     ):
@@ -3013,3 +3020,30 @@ def test_attributes_list(tmp_local_netcdf, attr):
         assert hf.attrs["foo"][0] == attr[0]
         assert hf.attrs["foo"][1] == attr[1]
         assert isinstance(hf.attrs["foo"], list)
+
+
+def test_group_dimensions(tmp_local_netcdf):
+    # regression test for https://github.com/h5netcdf/h5netcdf/issues/293
+    with h5netcdf.File(tmp_local_netcdf, mode="w") as f:
+        group = f.create_group("data")
+        dims = {"y": 3, "x": 3, "z": None, "z1": None}
+        group.dimensions = dims
+        assert list(group.dimensions) == ["y", "x", "z", "z1"]
+        group.dimensions["z2"] = None
+        assert list(group.dimensions) == ["y", "x", "z", "z1", "z2"]
+
+
+def test_group_dimensions_classic(tmp_local_netcdf):
+    # regression test for https://github.com/h5netcdf/h5netcdf/issues/293
+    with h5netcdf.File(tmp_local_netcdf, mode="w", format="NETCDF4_CLASSIC") as f:
+        group = f.create_group("data")
+        dims = {"y": 3, "x": 3, "z": None, "z1": None}
+        with raises(CompatibilityError, match=r"Only one unlimited dimension allowed"):
+            group.dimensions = dims
+        assert list(group.dimensions) == []
+        dims = {"y": 3, "x": 3, "z": None}
+        group.dimensions = dims
+        assert list(group.dimensions) == ["y", "x", "z"]
+        with raises(CompatibilityError, match=r"Only one unlimited dimension allowed"):
+            group.dimensions["z1"] = None
+        assert list(group.dimensions) == ["y", "x", "z"]

{h5netcdf-1.7.1 → h5netcdf-1.7.3}/h5netcdf.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5netcdf
-Version: 1.7.1
+Version: 1.7.3
 Summary: netCDF4 via h5py
 Author-email: Stephan Hoyer <shoyer@gmail.com>, Kai Mühlbauer <kmuehlbauer@wradlib.org>
 Maintainer-email: h5netcdf developers <devteam@h5netcdf.org>