Fix test collection module errors & silence upstream Pytest warnings (#823)

* chore: add virtual environment and .env directories to gitignore

* test: filter upstream DeprecationWarning and UserWarning messages

* fix(namespace): remove empty __init__.py files to fix PEP 420 implicit namespace routing for trustgraph sub-packages

.gitignore

@@ -16,4 +16,7 @@ trustgraph-vertexai/trustgraph/vertexai_version.py
 trustgraph-unstructured/trustgraph/unstructured_version.py
 trustgraph-mcp/trustgraph/mcp_version.py
 trustgraph/trustgraph/trustgraph_version.py
-vertexai/
+vertexai/
+venv/
+.venv/
+.env

tests/pytest.ini

@@ -16,4 +16,10 @@ markers =
     unit: marks tests as unit tests
     contract: marks tests as contract tests (service interface validation)
     vertexai: marks tests as vertex ai specific tests
-    asyncio: marks tests that use asyncio
+    asyncio: marks tests that use asyncio
+filterwarnings =
+    ignore:Core Pydantic V1 functionality isn't compatible with Python 3.14.*:UserWarning
+    ignore:builtin type SwigPyPacked has no __module__ attribute:DeprecationWarning
+    ignore:builtin type SwigPyObject has no __module__ attribute:DeprecationWarning
+    ignore:builtin type swigvarlink has no __module__ attribute:DeprecationWarning
+    ignore:.*_UnionGenericAlias.*is deprecated and slated for removal in Python 3.17:DeprecationWarning