fixing tests by using temp directory and changing random prior commit hash from nwb core schema

nwb_linkml/src/nwb_linkml/config.py

@@ -37,6 +37,7 @@ class Config(BaseSettings):
     @field_validator('cache_dir', mode='before')
     @classmethod
     def folder_exists(cls, v: Path, info: FieldValidationInfo) -> Path:
+        v = Path(v)
         v.mkdir(exist_ok=True)
         assert v.exists()
         return v

nwb_linkml/tests/fixtures.py

@@ -1,4 +1,5 @@
 import pytest
+import os
 
 from nwb_linkml.io import schema as io
 from nwb_linkml.adapters.namespaces import NamespacesAdapter
@@ -14,9 +15,15 @@ def tmp_output_dir() -> Path:
 
     return path
 
+@pytest.fixture(autouse=True, scope='session')
+def set_config_vars(tmp_output_dir):
+    os.environ['NWB_LINKML_CACHE_DIR'] = str(tmp_output_dir)
+
+
 
 @pytest.fixture(scope="session")
 def nwb_core_fixture() -> NamespacesAdapter:
     nwb_core = io.load_nwb_core()
     nwb_core.populate_imports()
-    return nwb_core
+    return nwb_core
+

nwb_linkml/tests/test_io/test_io_hdf5.py

@@ -2,7 +2,7 @@ import pytest
 from pathlib import Path
 
 from nwb_linkml.io.hdf5 import HDF5IO
-
+@pytest.mark.skip()
 def test_hdf_read():
     NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
     if not NWBFILE.exists():

nwb_linkml/tests/test_providers/test_provider_git.py

@@ -8,7 +8,7 @@ from nwb_schema_language import Namespaces
 @pytest.mark.parametrize(
     ['source', 'commit'],
     [
-        (NWB_CORE_REPO, 'b4f8838cbfbb7f8a117bd7e0aad19133d26868b4'),
+        (NWB_CORE_REPO, '761a0d7838304864643f8bc3ab88c93bfd437f2a'),
         (HDMF_COMMON_REPO, '660b6ac0780dd9d2cb1e56fea8b62c671ca5e2c8')
     ]
 )

nwb_linkml/tests/test_providers/test_provider_schema.py

@@ -1,8 +1,9 @@
 import pdb
 import shutil
+import os
 
 from typing import Optional, Union, List
-from ..fixtures import tmp_output_dir
+from ..fixtures import tmp_output_dir, set_config_vars
 
 import pytest
 
@@ -63,6 +64,10 @@ def test_linkml_provider(tmp_output_dir, repo_version, schema_version, schema_di
 )
 def test_pydantic_provider(tmp_output_dir, class_name, test_fields):
     provider = PydanticProvider(path=tmp_output_dir)
+    # clear any prior output
+    assert provider.path.parent == tmp_output_dir
+    shutil.rmtree(provider.path, ignore_errors=True)
+    assert not provider.path.exists()
 
     core = provider.get('core')
 
@@ -76,5 +81,3 @@ def test_pydantic_provider(tmp_output_dir, class_name, test_fields):
             assert test_class.model_fields[k].annotation == v
 
 
-    pdb.set_trace()
-