chore: fix test, refactor to untangle circular imports

pyproject.toml

@@ -160,6 +160,7 @@ licensecheck = "licensecheck"  # run this when you add new deps
 addopts = "--cov-report=term-missing:skip-covered"
 filterwarnings = [
     "ignore::DeprecationWarning:bokeh.core.*",
+    "ignore::DeprecationWarning:jupyter_client.*",
 ]
 
 [tool.coverage.run]

src/metador_core/container/drivers.py

@@ -5,7 +5,7 @@
 import h5py
 
 from ..ih5.container import IH5Record
-from .protocols import H5FileLike, OpenMode
+from ..util.types import H5FileLike, OpenMode
 
 
 class MetadorDriverEnum(Enum):

src/metador_core/container/interface.py

@@ -30,6 +30,7 @@
 from ..schema import MetadataSchema
 from ..schema.plugins import PluginPkgMeta, PluginRef
 from ..schema.types import SemVerTuple
+from ..util.types import H5DatasetLike, H5FileLike, H5GroupLike
 from . import utils as M
 from .drivers import (
     METADOR_DRIVERS,
@@ -38,7 +39,6 @@
     get_driver_type,
     get_source,
 )
-from .protocols import H5DatasetLike, H5FileLike, H5GroupLike
 
 if TYPE_CHECKING:
     from .wrappers import MetadorContainer, MetadorNode

src/metador_core/container/wrappers.py

@@ -6,10 +6,10 @@
 import h5py
 import wrapt
 
+from ..util.types import H5DatasetLike, H5FileLike, H5GroupLike, H5NodeLike, OpenMode
 from . import utils as M
 from .drivers import MetadorDriver, to_h5filelike
 from .interface import MetadorContainerTOC, MetadorMeta, NodeAcl, NodeAclFlags
-from .protocols import H5DatasetLike, H5FileLike, H5GroupLike, H5NodeLike, OpenMode
 
 
 class UnsupportedOperationError(AttributeError):

src/metador_core/ih5/overlay.py

@@ -24,10 +24,10 @@
 import h5py
 import numpy as np
 
-from ..container.protocols import H5DatasetLike
+from ..util.types import H5DatasetLike
 
 if TYPE_CHECKING:
-    from ..container.protocols import H5GroupLike
+    from ..util.types import H5GroupLike
     from .record import IH5Record
 else:
     IH5Record = Any
@@ -346,8 +346,11 @@ def _find(self, key: str) -> Optional[int]:
     def get(self, key: str, default=None):
         try:
             return self[key]
-        except KeyError:
-            return default
+        except KeyError as e:
+            if str(e).find("not open") < 0:
+                return default
+            else:
+                raise
 
     def __getitem__(self, key: str):
         self._guard_open()

src/metador_core/ih5/record.py

@@ -23,9 +23,9 @@
 from pydantic import BaseModel, Field, PrivateAttr
 from typing_extensions import Annotated, Final
 
-from ..container.protocols import _OPEN_MODES, OpenMode
 from ..schema.types import QualHashsumStr
 from ..util.hashsums import qualified_hashsum
+from ..util.types import OPEN_MODES, OpenMode
 from .overlay import IH5Group, h5_copy_from_to
 
 # the magic string we use to identify a valid container
@@ -472,7 +472,7 @@ def __init__(
             paths = None
             path: Path = Path(record)
 
-        if mode not in _OPEN_MODES:
+        if mode not in OPEN_MODES:
             raise ValueError(f"Unknown file open mode: {mode}")
 
         if mode[0] == "w" or mode == "x":

src/metador_core/container/protocols.py → src/metador_core/util/types.py

@@ -20,7 +20,12 @@
     runtime_checkable,
 )
 
-from typing_extensions import get_args
+from .typing import get_args
+
+OpenMode = Literal["r", "r+", "a", "w", "w-", "x"]
+"""User open modes that can be passed during initialization."""
+
+OPEN_MODES = list(get_args(OpenMode))
 
 
 @runtime_checkable
@@ -138,11 +143,6 @@ def copy(self, source, dest, **kwargs) -> None:
         ...
 
 
-OpenMode = Literal["r", "r+", "a", "w", "w-", "x"]
-"""User open modes that can be passed during initialization."""
-_OPEN_MODES = list(get_args(OpenMode))
-
-
 @runtime_checkable
 class H5FileLike(H5GroupLike, Protocol):  # pragma: no cover
     """A HDF5 File acts like the root group and has some extra features."""
@@ -163,4 +163,4 @@ def __exit__(self, ex_type, ex_value, ex_traceback) -> None:
         ...
 
 
-__all__ = ["H5FileLike", "H5GroupLike", "H5DatasetLike", "H5NodeLike", "OpenMode"]
+__all__ = ["H5FileLike", "H5GroupLike", "H5DatasetLike", "H5NodeLike"]

tests/container/test_container_protocols_drivers.py → tests/container/test_container_drivers.py

@@ -7,55 +7,7 @@
     get_source,
     to_h5filelike,
 )
-from metador_core.container.protocols import (
-    H5DatasetLike,
-    H5FileLike,
-    H5GroupLike,
-    H5NodeLike,
-)
-
-
-def check_protocols_for(f):
-    # create group and dataset node
-    f["group/dataset"] = 123
-
-    # check that behavior is correct:
-
-    # file-like:
-    assert isinstance(f, H5NodeLike)
-    assert isinstance(f, H5FileLike)
-    assert isinstance(f, H5GroupLike)
-    assert not isinstance(f, H5DatasetLike)
-
-    # group-like:
-    g = f["group"]
-    assert isinstance(f, H5NodeLike)
-    assert not isinstance(g, H5FileLike)
-    assert isinstance(g, H5GroupLike)
-    assert not isinstance(g, H5DatasetLike)
-
-    # dataset-like:
-    d = g["dataset"]
-    assert isinstance(f, H5NodeLike)
-    assert not isinstance(d, H5FileLike)
-    assert not isinstance(d, H5GroupLike)
-    assert isinstance(d, H5DatasetLike)
-
-
-def test_instance_checks(fresh_mc):
-    # Check that all driver classes work correctly with the protocol types.
-    #
-    # Expected relationships (< = base_class_of):
-    #  H5DatasetLike > H5NodeLike < H5GroupLike < H5FileLike
-    check_protocols_for(fresh_mc.__wrapped__)
-
-
-def test_instance_checks_wrapped(fresh_mc):
-    # same, but wrapped with MetadorContainer
-    check_protocols_for(fresh_mc)
-
-
-# ----
+from metador_core.util.types import H5DatasetLike, H5GroupLike
 
 
 def test_driver_type_detection(tmp_mc_path, mc_driver):

tests/container/test_container_types.py

@@ -0,0 +1,41 @@
+from metador_core.util.types import H5DatasetLike, H5FileLike, H5GroupLike, H5NodeLike
+
+
+def check_protocols_for(f):
+    # create group and dataset node
+    f["group/dataset"] = 123
+
+    # check that behavior is correct:
+
+    # file-like:
+    assert isinstance(f, H5NodeLike)
+    assert isinstance(f, H5FileLike)
+    assert isinstance(f, H5GroupLike)
+    assert not isinstance(f, H5DatasetLike)
+
+    # group-like:
+    g = f["group"]
+    assert isinstance(f, H5NodeLike)
+    assert not isinstance(g, H5FileLike)
+    assert isinstance(g, H5GroupLike)
+    assert not isinstance(g, H5DatasetLike)
+
+    # dataset-like:
+    d = g["dataset"]
+    assert isinstance(f, H5NodeLike)
+    assert not isinstance(d, H5FileLike)
+    assert not isinstance(d, H5GroupLike)
+    assert isinstance(d, H5DatasetLike)
+
+
+def test_instance_checks(fresh_mc):
+    # Check that all driver classes work correctly with the protocol types.
+    #
+    # Expected relationships (< = base_class_of):
+    #  H5DatasetLike > H5NodeLike < H5GroupLike < H5FileLike
+    check_protocols_for(fresh_mc.__wrapped__)
+
+
+def test_instance_checks_wrapped(fresh_mc):
+    # same, but wrapped with MetadorContainer
+    check_protocols_for(fresh_mc)

tests/ih5/test_ih5_overlay.py

@@ -560,7 +560,7 @@ def test_not_open_fail(dummy_ds_factory):
     ds.close()
 
     def assert_ex(f):
-        with pytest.raises(ValueError) as e:
+        with pytest.raises(KeyError) as e:
             f()
         assert str(e).lower().find("not open") >= 0