Add source namespace to all generated linkml schemas

change `namespace` annotation to `is_namespace` and use `namespace` for name of namespace
dont change commit when commit is None - otherwise always reset to recent version when we don't intend to

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -73,14 +73,14 @@ class NamespacesAdapter(Adapter):
             if progress is not None:
                 try:
                     progress.update(sch.namespace, action=sch.name)
-                except KeyError:
-                    # happens when we skip builds due to cachine
+                except KeyError: # pragma: no cover
+                    # happens when we skip builds due to caching
                     pass
             sch_result += sch.build()
             if progress is not None:
                 try:
                     progress.update(sch.namespace, advance=1)
-                except KeyError:
+                except KeyError: # pragma: no cover
                     # happens when we skip builds due to caching
                     pass
 
@@ -113,7 +113,7 @@ class NamespacesAdapter(Adapter):
                 description = ns.doc,
                 version = ns.version,
                 imports=ns_schemas,
-                annotations=[{'tag': 'namespace', 'value': True}]
+                annotations=[{'tag': 'is_namespace', 'value': True}, {'tag': 'namespace', 'value': ns.name}]
             )
             sch_result.schemas.append(ns_schema)
 

nwb_linkml/src/nwb_linkml/adapters/schema.py

@@ -72,7 +72,7 @@ class SchemaAdapter(Adapter):
         for group in self.groups:
             res += GroupAdapter(cls=group).build()
 
-        if len(res.slots) > 0:
+        if len(res.slots) > 0: # pragma: no cover - hard to induce this error because the child classes don't fuck up like this
             raise RuntimeError('Generated schema in this translation can only have classes, all slots should be attributes within a class')
 
         sch = SchemaDefinition(
@@ -82,7 +82,8 @@ class SchemaAdapter(Adapter):
             classes=res.classes,
             slots=res.slots,
             types=res.types,
-            version=self.version
+            version=self.version,
+            annotations=[{'tag': 'is_namespace', 'value': False}, {'tag': 'namespace', 'value': self.namespace}]
         )
         # every schema needs the language elements
         sch.imports.append('.'.join([self.namespace, 'nwb.language']))

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -328,7 +328,7 @@ class NWBPydanticGenerator(PydanticGenerator):
         if not self.split:
             # we are compiling this whole thing in one big file so we don't import anything
             return {}
-        if 'namespace' in sv.schema.annotations.keys() and sv.schema.annotations['namespace']['value'] == 'True':
+        if 'is_namespace' in sv.schema.annotations.keys() and sv.schema.annotations['is_namespace']['value'] == 'True':
             return self._get_namespace_imports(sv)
 
         all_classes = sv.all_classes(imports=True)

nwb_linkml/src/nwb_linkml/providers/git.py

@@ -135,18 +135,16 @@ class GitRepo:
 
     @commit.setter
     def commit(self, commit:str|None):
-        # first get out of a potential detached head state
-        # that would cause a call to "HEAD" to fail in unexpected ways
-        if self.detached_head:
-            self._git_call('checkout', self.default_branch)
+        # setting commit as None should do nothing if we have already cloned,
+        # and if we are just cloning we will always be at the most recent commit anyway
+        if commit is not None:
+            # first get out of a potential detached head state
+            # that would cause a call to "HEAD" to fail in unexpected ways
+            if self.detached_head:
+                self._git_call('checkout', self.default_branch)
 
-        if commit is None:
-            if len(self.namespace.versions) > 0:
-                self._git_call('checkout', self.namespace.versions[-1])
-            else:
-                self._git_call('checkout', "HEAD")
-        else:
             self._git_call('checkout', commit)
+
         self._git_call('submodule', 'update', '--init', '--recursive')
         self._commit = commit
 
@@ -277,7 +275,6 @@ class GitRepo:
                     self.cleanup()
                 else:
                     # already have it, just ensure commit and return
-
                     self.commit = self.commit
                     return
         elif self.temp_directory.exists():

nwb_linkml/src/nwb_linkml/providers/schema.py

@@ -384,7 +384,7 @@ class LinkMLProvider(Provider):
         # write schemas to yaml files
         build_result = {}
 
-        namespace_sch = [sch for sch in built.schemas if 'namespace' in sch.annotations.keys()]
+        namespace_sch = [sch for sch in built.schemas if sch.annotations.get('is_namespace', False) and sch.annotations['is_namespace'].value == 'True']
         for ns_linkml in namespace_sch:
             version = ns_adapter.versions[ns_linkml.name]
             version_path = self.namespace_path(ns_linkml.name, version, allow_repo=False)

nwb_linkml/tests/fixtures.py

@@ -220,7 +220,7 @@ def linkml_schema_bare() -> TestSchemas:
             id="namespace",
             version="1.1.1",
             default_prefix="namespace",
-            annotations={'namespace': {'tag': 'namespace', 'value': 'True'}},
+            annotations=[{'tag': 'is_namespace', 'value': 'True'}, {'tag': 'namespace', 'value': 'core'}],
             description="A namespace package that should import all other classes",
             imports=['core', 'imported']
         )

nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

@@ -1,3 +1,5 @@
+import pdb
+
 import pytest
 from ..fixtures import nwb_core_fixture
 from nwb_schema_language import Dataset, Group
@@ -32,4 +34,14 @@ def test_populate_imports(nwb_core_fixture):
 
 
 def test_build(nwb_core_fixture):
-    pass
+    pass
+
+def test_skip_imports(nwb_core_fixture):
+    """
+    We can build just the namespace in question without also building the other namespaces that it imports
+    """
+    res = nwb_core_fixture.build(skip_imports=True)
+
+    # we shouldn't have any of the hdmf-common schema in with us
+    namespaces = [sch.annotations['namespace'].value for sch in res.schemas]
+    assert all([ns == 'core' for ns in namespaces])

nwb_linkml/tests/test_adapters/test_adapter_schema.py

@@ -11,4 +11,15 @@ from nwb_schema_language import Dataset, Group, Schema
 )
 def test_schema_build(nwb_core_fixture, schema_name):
     schema = [sch for sch in nwb_core_fixture.schemas if sch.name == schema_name][0]
-    res = schema.build()
+    res = schema.build()
+
+
+
+def test_schema_repr(nwb_core_fixture):
+    """
+    Doesn't really make sense to test the string repr matches any particular value because it's
+    strictly cosmetic, but we do test that it can be done
+    """
+    sch = nwb_core_fixture.schemas[0]
+    repr_str = sch.__repr__()
+    assert isinstance(repr_str, str)