fix tests, cant assign to tuple

nwb_linkml/pyproject.toml

@@ -76,9 +76,15 @@ addopts = [
     "--cov=nwb_linkml",
     "--cov-append",
     "--cov-config=.coveragerc",
-    "--doctest-modules"
+    "--doctest-modules",
+    "--ignore=tests/__tmp__"
 ]
 testpaths = [
     "tests",
     'nwb_linkml/tests'
 ]
+doctest_optionflags = "NORMALIZE_WHITESPACE"
+filterwarnings = [
+    "ignore:Deprecated NumPy 1.24:DeprecationWarning",
+    "ignore:parse_obj:pydantic.PydanticDeprecatedSince20"
+]

nwb_linkml/src/nwb_linkml/adapters/__init__.py

@@ -2,5 +2,6 @@ from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.classes import ClassAdapter
 from nwb_linkml.adapters.group import GroupAdapter
+from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter
 

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -61,7 +61,7 @@ class BuildResult:
 
         return out_str
 
-T = TypeVar('T', Dataset, Attribute, Schema, Group)
+T = TypeVar('T', Dataset, Attribute, Schema, Group, BaseModel)
 Ts = TypeVarTuple('Ts')
 
 class Adapter(BaseModel):

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -21,7 +21,7 @@ from nwb_schema_language import Namespaces
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.schema import SchemaAdapter
 from nwb_linkml.lang_elements import NwbLangSchema
-from nwb_linkml.providers.git import DEFAULT_REPOS
+
 
 from nwb_linkml.ui import AdapterProgress
 
@@ -47,6 +47,7 @@ class NamespacesAdapter(Adapter):
         with hdmf-common)
         """
         from nwb_linkml.io import schema as schema_io
+        from nwb_linkml.providers.git import DEFAULT_REPOS
         ns_adapter = schema_io.load_namespace_adapter(path)
 
         # try and find imported schema

nwb_linkml/src/nwb_linkml/providers/git.py

@@ -209,8 +209,7 @@ class GitRepo:
         try:
             # check our commit, this also checks if we're a git repo
             if self.active_commit != self.commit and self.commit is not None:
-                warnings.warn('At wrong commit')
-                return False
+                self.commit = self.commit
 
         except GitError:
             return False

nwb_linkml/tests/fixtures.py

@@ -1,11 +1,13 @@
 import pytest
 import os
-from typing import NamedTuple, Optional
+from typing import NamedTuple, Optional, List, Dict
+from dataclasses import dataclass, field
 
 from linkml_runtime.dumpers import yaml_dumper
 
 from nwb_linkml.io import schema as io
 from nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_schema_language import Schema, Group, Dataset, Attribute
 from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition, Prefix, TypeDefinition
 import shutil
 from pathlib import Path
@@ -65,7 +67,9 @@ def data_dir() -> Path:
     path = Path(__file__).parent.resolve() / 'data'
     return path
 
-class TestSchemas(NamedTuple):
+@dataclass
+class TestSchemas():
+    __test__ = False
     core: SchemaDefinition
     imported: SchemaDefinition
     namespace: SchemaDefinition
@@ -243,12 +247,51 @@ def linkml_schema(tmp_output_dir_mod, linkml_schema_bare) -> TestSchemas:
     imported_path = test_schema_path / 'imported.yaml'
     namespace_path = test_schema_path / 'namespace.yaml'
 
-    schema.core_path = core_path,
-    schema.imported_path = imported_path,
-    schema.namespace_path = namespace_path,
+    schema.core_path = core_path
+    schema.imported_path = imported_path
+    schema.namespace_path = namespace_path
 
     yaml_dumper.dump(schema.core, schema.core_path)
     yaml_dumper.dump(schema.imported, schema.imported_path)
     yaml_dumper.dump(schema.namespace, schema.namespace_path)
     return schema
 
+
+@dataclass
+class NWBSchemaTest():
+    datasets: Dict[str, Dataset] = field(default_factory=dict)
+    groups: Dict[str, Group] = field(default_factory=dict)
+
+@pytest.fixture()
+def nwb_schema() -> NWBSchemaTest:
+    """Minimal NWB schema for testing"""
+    image = Dataset(
+        neurodata_type_def="Image",
+        dtype="numeric",
+        neurodata_type_inc="NWBData",
+        dims=[['x', 'y'], ['x', 'y', 'r, g, b'], ['x', 'y', 'r, g, b, a']],
+        shape=[[None, None], [None, None, 3], [None, None, 4]],
+        doc="An image!",
+        attributes = [
+            Attribute(dtype="float32", name="resolution", doc="resolution!"),
+            Attribute(dtype="text", name="description", doc='Description!')
+        ]
+    )
+    images = Group(
+        neurodata_type_def='Images',
+        neurodata_type_inc='NWBDataInterface',
+        default_name="Images",
+        doc='Images!',
+        attributes=[
+            Attribute(dtype="text", name='description', doc="description!")
+        ],
+        datasets=[
+            Dataset(neurodata_type_inc='Image', quantity="+", doc="images!"),
+            Dataset(neurodata_type_inc='ImageReferences',
+                    name='order_of_images',
+                    doc="Image references!",
+                    quantity='?'
+            )
+        ]
+    )
+    return NWBSchemaTest(datasets=[image], groups=[images])

nwb_linkml/tests/test_adapters/test_adapter_classes.py

@@ -0,0 +1,9 @@
+import pytest
+
+from ..fixtures import linkml_schema_bare, linkml_schema, nwb_schema
+
+from nwb_linkml.adapters import DatasetAdapter, ClassAdapter
+
+def test_build_base(nwb_schema):
+
+    pass

nwb_linkml/tests/test_adapters/test_adapter_dataset.py

@@ -1,4 +1,10 @@
+import pdb
+
 import pytest
 
-def test_nothing():
+from ..fixtures import nwb_core_fixture
+
+from nwb_linkml.adapters import DatasetAdapter
+
+def test_nothing(nwb_core_fixture):
     pass

nwb_linkml/tests/test_generators/test_generator_pydantic.py

@@ -27,6 +27,7 @@ class TestModules(TypedDict):
     namespace: ModuleType
     split: bool
 
+TestModules.__test__ = False
 
 def generate_and_import(linkml_schema:TestSchemas, split:bool, generator_kwargs:Optional[dict]=None) -> TestModules:
     if generator_kwargs is None: