make error a warning if can't clone when installed as package, simpli…

…fy error message, fix tests which are improperly accessing dunder methods.

src/pynwb/__init__.py

@@ -158,6 +158,10 @@ def load_namespaces(**kwargs):
     namespace_path = getargs('namespace_path', kwargs)
     return __TYPE_MAP.load_namespaces(namespace_path)
 
+def available_namespaces():
+    """Returns all namespaces registered in the namespace catalog"""
+    return __NS_CATALOG.namespaces
+
 
 def _git_cmd(*args) -> subprocess.CompletedProcess:
     """
@@ -183,9 +187,7 @@ def _clone_submodules():
                 'Exception while initializing submodules, got:\n'
                 'stdout:\n' + ('-'*20) + res.stdout + "\nstderr:\n" + ('-'*20) + res.stderr)
     else:  # pragma: no cover
-        raise RuntimeError("'core' is not a registered namespace, and pynwb doesn't seem to be installed"
-                           "from a cloned repository so the submodules can't be initialized. "
-                           "Something has gone terribly wrong. maybe try reinstalling???")
+        raise RuntimeError("Package is not installed from a git repository, can't clone submodules")
 
 
 def _load_core_namespace(final:bool=False):
@@ -234,19 +236,20 @@ def _load_core_namespace(final:bool=False):
     else:
         try:
             _clone_submodules()
-        except (FileNotFoundError, OSError):  # pragma: no cover
-            raise RuntimeError(
-                "'core' is not a registered namespace. If you installed PyNWB locally using a git clone, you need to "
-                "use the --recurse_submodules flag when cloning. See developer installation instructions here: "
-                "https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository"
-            )
+        except (FileNotFoundError, OSError, RuntimeError) as e:  # pragma: no cover
+            if 'core' not in available_namespaces():
+                warnings.warn(
+                    "'core' is not a registered namespace. If you installed PyNWB locally using a git clone, "
+                    "you need to use the --recurse_submodules flag when cloning. "
+                    "See developer installation instructions here: "
+                    "https://pynwb.readthedocs.io/en/stable/install_developers.html#install-from-git-repository\n"
+                    f"Got exception: \n{e}"
+                )
         if not final:
             _load_core_namespace(final=True)
 _load_core_namespace()
 
-def available_namespaces():
-    """Returns all namespaces registered in the namespace catalog"""
-    return __NS_CATALOG.namespaces
+
 
 
 # a function to register a container classes with the global map

tests/unit/test_import.py

@@ -11,6 +11,7 @@
 except ImportError:
     from importlib_resources import files
 
+import pynwb
 from pynwb.testing import TestCase
 
 class TestPyNWBSubmoduleClone(TestCase):
@@ -23,9 +24,7 @@ def setUp(self):
 
         # remove cache files if they exist
         self.typemap_cache = Path(files('pynwb') / 'core_typemap.pkl')
-        self.nscatalog_cache = Path(files('pynwb') / 'core_nscatalog.pkl')
         self.typemap_cache.unlink(missing_ok=True)
-        self.nscatalog_cache.unlink(missing_ok=True)
 
 
     def tearDown(self) -> None:
@@ -40,11 +39,9 @@ def test_clone_on_import(self):
         we should try and import it
         """
         assert not self.repo_dir.exists()
-        assert not self.nscatalog_cache.exists()
         assert not self.typemap_cache.exists()
 
         with self.assertWarns(Warning) as clone_warning:
-            import pynwb
             importlib.reload(pynwb)
 
             # there can be other warnings, but we should get at least one
@@ -53,7 +50,6 @@ def test_clone_on_import(self):
             assert any(['initializing submodules' in msg for msg in messages])
 
         assert self.repo_dir.exists()
-        assert self.nscatalog_cache.exists()
         assert self.typemap_cache.exists()
 
         # we should also get the namespaces correctly too
@@ -72,5 +68,4 @@ def test_typemap_ns_match(self):
         The global __NS_CATALOG and the one contained within the global __TYPE_MAP
         should be the same object after importing
         """
-        import pynwb
-        assert id(pynwb.__TYPE_MAP.namespace_catalog) == id(pynwb.__NS_CATALOG)
+        assert id(getattr(pynwb, '__TYPE_MAP').namespace_catalog) == id(getattr(pynwb, '__NS_CATALOG'))