Make VectorData and VectorIndex generics to ensure coercion to VectorData for declared columns

nwb_linkml/pyproject.toml

@@ -36,14 +36,10 @@ plot = [
     "dash-cytoscape<1.0.0,>=0.3.0",
 ]
 tests = [
-    "nwb-linkml[plot]",
+    "nwb-linkml",
     "pytest<8.0.0,>=7.4.0",
     "pytest-depends<2.0.0,>=1.0.1",
-    "coverage<7.0.0,>=6.1.1",
-    "pytest-md<1.0.0,>=0.2.0",
     "pytest-cov<5.0.0,>=4.1.0",
-    "coveralls<4.0.0,>=3.3.1",
-    "pytest-profiling<2.0.0,>=1.7.0",
     "sybil<6.0.0,>=5.0.3",
     "requests-cache>=1.2.1",
 ]

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -116,6 +116,7 @@ class NWBPydanticGenerator(PydanticGenerator):
     def after_generate_class(self, cls: ClassResult, sv: SchemaView) -> ClassResult:
         """Customize dynamictable behavior"""
         cls = AfterGenerateClass.inject_dynamictable(cls)
+        cls = AfterGenerateClass.wrap_dynamictable_columns(cls, sv)
         return cls
 
     def before_render_template(self, template: PydanticModule, sv: SchemaView) -> PydanticModule:
@@ -278,6 +279,28 @@ class AfterGenerateClass:
 
         return cls
 
+    @staticmethod
+    def wrap_dynamictable_columns(cls: ClassResult, sv: SchemaView) -> ClassResult:
+        """
+        Wrap NDArray columns inside of dynamictables with ``VectorData`` or
+        ``VectorIndex``, which are generic classes whose value slot is
+        parameterized by the NDArray
+        """
+        if cls.source.is_a == "DynamicTable" or "DynamicTable" in sv.class_ancestors(
+            cls.source.name
+        ):
+            for an_attr in cls.cls.attributes:
+                if "NDArray" in (slot_range := cls.cls.attributes[an_attr].range):
+                    if an_attr.endswith("_index"):
+                        cls.cls.attributes[an_attr].range = "".join(
+                            ["VectorIndex[", slot_range, "]"]
+                        )
+                    else:
+                        cls.cls.attributes[an_attr].range = "".join(
+                            ["VectorData[", slot_range, "]"]
+                        )
+        return cls
+
 
 def compile_python(
     text_or_fn: str, package_path: Path = None, module_name: str = "test"

nwb_linkml/src/nwb_linkml/includes/hdmf.py

@@ -2,15 +2,18 @@
 Special types for mimicking HDMF special case behavior
 """
 
+import sys
 from typing import (
     TYPE_CHECKING,
     Any,
     ClassVar,
     Dict,
+    Generic,
     Iterable,
     List,
     Optional,
     Tuple,
+    TypeVar,
     Union,
     overload,
 )
@@ -33,6 +36,9 @@ from pydantic import (
 if TYPE_CHECKING:
     from nwb_linkml.models import VectorData, VectorIndex
 
+T = TypeVar("T", bound=NDArray)
+T_INJECT = 'T = TypeVar("T", bound=NDArray)'
+
 
 class DynamicTableMixin(BaseModel):
     """
@@ -219,20 +225,28 @@ class DynamicTableMixin(BaseModel):
         anything in :attr:`.NON_COLUMN_FIELDS` to determine order implied from passage order
         """
         if "colnames" not in model:
-            colnames = [
-                k for k in model if k not in cls.NON_COLUMN_FIELDS and not k.endswith("_index")
-            ]
-            model["colnames"] = colnames
-        else:
-            # add any columns not explicitly given an order at the end
             colnames = [
                 k
                 for k in model
                 if k not in cls.NON_COLUMN_FIELDS
                 and not k.endswith("_index")
-                and k not in model["colnames"]
+                and not isinstance(model[k], VectorIndexMixin)
             ]
-            model["colnames"].extend(colnames)
+            model["colnames"] = colnames
+        else:
+            # add any columns not explicitly given an order at the end
+            colnames = model["colnames"].copy()
+            colnames.extend(
+                [
+                    k
+                    for k in model
+                    if k not in cls.NON_COLUMN_FIELDS
+                    and not k.endswith("_index")
+                    and k not in model["colnames"]
+                    and not isinstance(model[k], VectorIndexMixin)
+                ]
+            )
+            model["colnames"] = colnames
         return model
 
     @model_validator(mode="after")
@@ -322,7 +336,7 @@ class DynamicTableMixin(BaseModel):
             )
 
 
-class VectorDataMixin(BaseModel):
+class VectorDataMixin(BaseModel, Generic[T]):
     """
     Mixin class to give VectorData indexing abilities
     """
@@ -330,7 +344,7 @@ class VectorDataMixin(BaseModel):
     _index: Optional["VectorIndex"] = None
 
     # redefined in `VectorData`, but included here for testing and type checking
-    value: Optional[NDArray] = None
+    value: Optional[T] = None
 
     def __init__(self, value: Optional[NDArray] = None, **kwargs):
         if value is not None and "value" not in kwargs:
@@ -373,13 +387,13 @@ class VectorDataMixin(BaseModel):
             return len(self.value)
 
 
-class VectorIndexMixin(BaseModel):
+class VectorIndexMixin(BaseModel, Generic[T]):
     """
     Mixin class to give VectorIndex indexing abilities
     """
 
     # redefined in `VectorData`, but included here for testing and type checking
-    value: Optional[NDArray] = None
+    value: Optional[T] = None
     target: Optional["VectorData"] = None
 
     def __init__(self, value: Optional[NDArray] = None, **kwargs):
@@ -649,8 +663,10 @@ DYNAMIC_TABLE_IMPORTS = Imports(
             module="typing",
             objects=[
                 ObjectImport(name="ClassVar"),
+                ObjectImport(name="Generic"),
                 ObjectImport(name="Iterable"),
                 ObjectImport(name="Tuple"),
+                ObjectImport(name="TypeVar"),
                 ObjectImport(name="overload"),
             ],
         ),
@@ -677,6 +693,7 @@ VectorData is purposefully excluded as an import or an inject so that it will be
 resolved to the VectorData definition in the generated module
 """
 DYNAMIC_TABLE_INJECTS = [
+    T_INJECT,
     VectorDataMixin,
     VectorIndexMixin,
     DynamicTableRegionMixin,
@@ -689,13 +706,27 @@ TSRVD_IMPORTS = Imports(
         Import(
             module="typing",
             objects=[
-                ObjectImport(name="overload"),
+                ObjectImport(name="Generic"),
                 ObjectImport(name="Iterable"),
                 ObjectImport(name="Tuple"),
+                ObjectImport(name="TypeVar"),
+                ObjectImport(name="overload"),
             ],
         ),
         Import(module="pydantic", objects=[ObjectImport(name="model_validator")]),
     ]
 )
 """Imports for TimeSeriesReferenceVectorData"""
-TSRVD_INJECTS = [VectorDataMixin, TimeSeriesReferenceVectorDataMixin]
+TSRVD_INJECTS = [T_INJECT, VectorDataMixin, TimeSeriesReferenceVectorDataMixin]
+
+if "pytest" in sys.modules:
+    # during testing define concrete subclasses...
+    class VectorData(VectorDataMixin):
+        """VectorData subclass for testing"""
+
+        pass
+
+    class VectorIndex(VectorIndexMixin):
+        """VectorIndex subclass for testing"""
+
+        pass

nwb_linkml/src/nwb_linkml/io/schema.py

@@ -114,7 +114,7 @@ def load_namespace_adapter(
     for ns in namespaces.namespaces:
         for schema in ns.schema_:
             if schema.source is None:
-                if imported is None and schema.namespace == "hdmf-common":
+                if imported is None and schema.namespace == "hdmf-common" and ns.name == "core":
                     # special case - hdmf-common is imported by name without location or version,
                     # so to get the correct version we have to handle it separately
                     imported = _resolve_hdmf(namespace, path)

nwb_linkml/tests/test_includes/test_hdmf.py

@@ -1,5 +1,9 @@
 import numpy as np
 import pandas as pd
+from numpydantic import NDArray, Shape
+
+from nwb_linkml.includes import hdmf
+from nwb_linkml.includes.hdmf import DynamicTableMixin, VectorDataMixin, VectorIndexMixin
 
 # FIXME: Make this just be the output of the provider by patching into import machinery
 from nwb_linkml.models.pydantic.core.v2_7_0.namespace import (
@@ -48,7 +52,7 @@ def test_dynamictable_indexing(electrical_series):
 
     # get a single column
     col = electrodes["y"]
-    assert all(col == [5, 6, 7, 8, 9])
+    assert all(col.value == [5, 6, 7, 8, 9])
 
     # get a single cell
     val = electrodes[0, "y"]
@@ -198,3 +202,104 @@ def test_aligned_dynamictable(intracellular_recordings_table):
     for i in range(len(stims)):
         assert isinstance(stims[i], VoltageClampStimulusSeries)
         assert all([i == val for val in stims[i][:]])
+
+
+# --------------------------------------------------
+# Direct mixin tests
+# --------------------------------------------------
+
+
+def test_dynamictable_mixin_indexing():
+    """
+    This is just a placeholder test to say that indexing is tested above
+    with actual model objects in case i ever ctrl+f for this
+    """
+    pass
+
+
+def test_dynamictable_mixin_colnames():
+    """
+    Should correctly infer colnames
+    """
+
+    class MyDT(DynamicTableMixin):
+        existing_col: NDArray[Shape["* col"], int]
+
+    new_col_1 = VectorDataMixin(value=np.arange(10))
+    new_col_2 = VectorDataMixin(value=np.arange(10))
+
+    inst = MyDT(existing_col=np.arange(10), new_col_1=new_col_1, new_col_2=new_col_2)
+    assert inst.colnames == ["existing_col", "new_col_1", "new_col_2"]
+
+
+def test_dynamictable_mixin_colnames_index():
+    """
+    Exclude index columns in colnames
+    """
+
+    class MyDT(DynamicTableMixin):
+        existing_col: NDArray[Shape["* col"], int]
+
+    cols = {
+        "existing_col": np.arange(10),
+        "new_col_1": hdmf.VectorData(value=np.arange(10)),
+        "new_col_2": hdmf.VectorData(value=np.arange(10)),
+    }
+    # explicit index with mismatching name
+    cols["weirdname_index"] = VectorIndexMixin(value=np.arange(10), target=cols["new_col_1"])
+    # implicit index with matching name
+    cols["new_col_2_index"] = VectorIndexMixin(value=np.arange(10))
+
+    inst = MyDT(**cols)
+    assert inst.colnames == ["existing_col", "new_col_1", "new_col_2"]
+
+
+def test_dynamictable_mixin_colnames_ordered():
+    """
+    Should be able to pass explicit order to colnames
+    """
+
+    class MyDT(DynamicTableMixin):
+        existing_col: NDArray[Shape["* col"], int]
+
+    cols = {
+        "existing_col": np.arange(10),
+        "new_col_1": hdmf.VectorData(value=np.arange(10)),
+        "new_col_2": hdmf.VectorData(value=np.arange(10)),
+        "new_col_3": hdmf.VectorData(value=np.arange(10)),
+    }
+    order = ["new_col_2", "existing_col", "new_col_1", "new_col_3"]
+
+    inst = MyDT(**cols, colnames=order)
+    assert inst.colnames == order
+
+    # this should get reflected in the columns selector and the df produces
+    assert all([key1 == key2 for key1, key2 in zip(order, inst._columns)])
+    assert all(inst[0].columns == order)
+
+    # partial lists should append unnamed columsn at the end
+    partial_order = ["new_col_3", "new_col_2"]
+    inst = MyDT(**cols, colnames=partial_order)
+    assert inst.colnames == [*partial_order, "existing_col", "new_col_1"]
+
+
+def test_dynamictable_mixin_getattr():
+    """
+    Dynamictable should forward unknown getattr requests to the df
+    """
+
+    class MyDT(DynamicTableMixin):
+        existing_col: NDArray[Shape["* col"], int]
+
+    class AModel(DynamicTableMixin):
+        col: hdmf.VectorData[NDArray[Shape["3, 3"], int]]
+
+    col = hdmf.VectorData(value=np.arange(10))
+    inst = MyDT(existing_col=col)
+    # regular lookup for attrs that exist
+
+    # pdb.set_trace()
+    # inst.existing_col
+    # assert inst.existing_col == col
+    # df lookup otherwise
+    # inst.columns