Correctly clone fixed versions in tests, adjusted fixed values to match, set default git clone temp dir from config variables

nwb_linkml/src/nwb_linkml/config.py

@@ -33,6 +33,12 @@ class Config(BaseSettings):
         """Directory to store generated pydantic models"""
         return self.cache_dir / 'pydantic'
 
+    @computed_field
+    @property
+    def git_dir(self) -> Path:
+        """Directory for :class:`nwb_linkml.providers.git.GitRepo` to clone to"""
+        return self.cache_dir / 'git'
+
 
     @field_validator('cache_dir', mode='before')
     @classmethod
@@ -46,5 +52,6 @@ class Config(BaseSettings):
         self.cache_dir.mkdir(exist_ok=True)
         self.linkml_dir.mkdir(exist_ok=True)
         self.pydantic_dir.mkdir(exist_ok=True)
+        self.git_dir.mkdir(exist_ok=True)
 
 

nwb_linkml/src/nwb_linkml/io/schema.py

@@ -87,7 +87,7 @@ def load_namespace_adapter(
         namespaces = _load_namespaces(path)
     elif isinstance(namespace, NamespaceRepo):
         path = namespace.provide_from_git(commit=version)
-        namespaces = _load_namespaces(namespace)
+        namespaces = _load_namespaces(path)
 
     elif isinstance(namespace, Namespaces):
         namespaces = namespace

nwb_linkml/src/nwb_linkml/providers/git.py

@@ -11,6 +11,8 @@ import shutil
 
 from pydantic import BaseModel, HttpUrl, FilePath, DirectoryPath, Field
 
+from nwb_linkml.config import Config
+
 class NamespaceRepo(BaseModel):
     """
     Definition of one NWB namespaces file to import from a git repository
@@ -55,11 +57,24 @@ class GitRepo:
     """
     Manage a temporary git repository that provides the NWB yaml files
     """
-    def __init__(self, namespace:NamespaceRepo, commit:str|None=None):
-        self._temp_directory = None
+    def __init__(
+            self,
+            namespace:NamespaceRepo,
+            commit:str|None=None,
+            path: Optional[Path] = None
+    ):
+        """
+        Args:
+            namespace (:class:`.NamespaceRepo`): The namespace repository to clone!
+            commit (str): A specific commit or tag to check out
+            path (:class:`pathlib.Path`): A directory to clone to - if ``None``, use :attr:`~.Config.git_dir` / :attr:`.NamespaceRepo.name`
+        """
+        self._temp_directory = path
         self.namespace = namespace
         self._commit = commit
 
+
+
     def _git_call(self, *args) -> subprocess.CompletedProcess:
         res = subprocess.run(
             ['git', '-C', self.temp_directory, *args],
@@ -75,7 +90,8 @@ class GitRepo:
         Temporary directory where this repository will be cloned to
         """
         if self._temp_directory is None:
-            self._temp_directory = Path(tempfile.gettempdir()) / f'nwb_linkml__{self.namespace.name}'
+            git_dir = Config().git_dir
+            self._temp_directory = git_dir / self.namespace.name
             if not self._temp_directory.exists():
                 self._temp_directory.mkdir(parents=True)
 
@@ -222,12 +238,20 @@ class GitRepo:
         # otherwise we're good
         return True
 
-    def cleanup(self):
+    def cleanup(self, force: bool=False):
         """
         Delete contents of temporary directory
+
+        If the temp_directory is outside the system temporary directory or
+
+        Args:
+            force (bool): If ``True``, remove git directory no matter where it is
         """
-        if not str(self.temp_directory).startswith(tempfile.gettempdir()):
-            warnings.warn('Temp directory is outside of the system temp dir, not deleting in case this has been changed by mistake')
+        if not force and not (
+                str(self.temp_directory).startswith(tempfile.gettempdir()) or
+                str(self.temp_directory).startswith(str(Config().git_dir))
+        ):
+            warnings.warn('Temp directory is outside of the system temp dir or git directory set by environmental variables, not deleting in case this has been changed by mistake')
             self._temp_directory = None
             return
 

nwb_linkml/tests/conftest.py

@@ -0,0 +1,8 @@
+import os
+import pytest
+
+from .fixtures import tmp_output_dir
+
+@pytest.fixture(autouse=True, scope='session')
+def set_config_vars(tmp_output_dir):
+    os.environ['NWB_LINKML_CACHE_DIR'] = str(tmp_output_dir)

nwb_linkml/tests/fixtures.py

@@ -45,9 +45,6 @@ def tmp_output_dir_mod(tmp_output_dir) -> Path:
     subpath.mkdir()
     return subpath
 
-@pytest.fixture(autouse=True, scope='session')
-def set_config_vars(tmp_output_dir):
-    os.environ['NWB_LINKML_CACHE_DIR'] = str(tmp_output_dir)
 
 
 
@@ -59,6 +56,9 @@ def set_config_vars(tmp_output_dir):
 def nwb_core_fixture(request) -> NamespacesAdapter:
     nwb_core = io.load_nwb_core(**request.param)
     nwb_core.populate_imports()
+    assert request.param['core_version'] in nwb_core.versions['core'] # 2.6.0 is actually 2.6.0-alpha
+    assert nwb_core.versions['hdmf-common'] == request.param['hdmf_version']
+
     return nwb_core
 
 

nwb_linkml/tests/test_adapters/test_adapter.py

@@ -16,14 +16,19 @@ def test_walk(nwb_core_fixture):
     Not sure exactly what should be tested here, for now just testing that we get an expected value
     """
     everything = nwb_core_fixture.walk(nwb_core_fixture)
-    assert len(list(everything)) == 9959
+
+    # number of items obviously changes based on what version we're talking about
+    # this is configured as a test matrix on the nwb_core_fixture, currently only testing the latest version
+    if nwb_core_fixture.versions['core'] == '2.6.0-alpha' and nwb_core_fixture.versions['hdmf-common'] == '1.5.0':
+
+        assert len(list(everything)) == 9908
 
 @pytest.mark.parametrize(
     ['walk_class', 'known_number'],
     [
-        (Dataset, 211),
+        (Dataset, 210),
         (Group, 144),
-        ((Dataset, Group), 355),
+        ((Dataset, Group), 354),
         (Schema, 19)
     ]
 )
@@ -48,7 +53,7 @@ def test_walk_field_values(nwb_core_fixture):
     text_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, 'dtype', value='text'))
     assert all([d.dtype == 'text' for d in text_models])
     # 135 known value from regex search
-    assert len(text_models) == len([d for d in dtype_models if d.dtype == 'text']) == 135
+    assert len(text_models) == len([d for d in dtype_models if d.dtype == 'text']) == 134
 
 
 def test_build_result(linkml_schema_bare):

nwb_linkml/tests/test_config.py

@@ -0,0 +1,37 @@
+import pytest
+import tempfile
+from pathlib import Path
+import os
+import shutil
+
+from nwb_linkml.config import Config
+
+
+def test_config_dir():
+    """Ensure that the temporary directory is the same across multiple instantiations of the singleton-like config object"""
+    c1 = Config()
+    c2 = Config()
+    assert c1.cache_dir == c2.cache_dir
+
+def test_config_env():
+    """
+    Base cache dir can be overridden by environmental variable
+    """
+
+    orig_env = os.environ['NWB_LINKML_CACHE_DIR']
+
+    new_temp = Path(tempfile.gettempdir()) / 'test_tmp_dir'
+    new_temp.mkdir()
+
+    try:
+        assert Path(orig_env) != new_temp
+
+        os.environ['NWB_LINKML_CACHE_DIR'] = str(new_temp)
+
+        conf = Config()
+
+        assert conf.cache_dir == new_temp
+    finally:
+        shutil.rmtree(new_temp)
+        os.environ['NWB_LINKML_CACHE_DIR'] = orig_env
+

nwb_linkml/tests/test_io/test_io_hdf5.py

@@ -5,7 +5,7 @@ import pytest
 from pathlib import Path
 import numpy as np
 
-from ..fixtures import tmp_output_dir, set_config_vars, data_dir
+from ..fixtures import tmp_output_dir, data_dir
 
 from nwb_linkml.io.hdf5 import HDF5IO
 from nwb_linkml.io.hdf5 import truncate_file

nwb_linkml/tests/test_providers/test_provider_schema.py

@@ -6,7 +6,7 @@ import warnings
 from pathlib import Path
 
 from typing import Optional, Union, List
-from ..fixtures import tmp_output_dir, set_config_vars
+from ..fixtures import tmp_output_dir
 
 import pytest