init public release

tests/conftest.py

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+"""Shared test setup.
+
+Several modules under test import first-party packages (`graphCreation`,
+`fhirImport`, `schema_config_generation`, `mdm2neo4j`) and heavy third-party
+ones (`biocypher`, `dotenv`) at import time. ``_ensure`` uses the *real*
+module when it can be imported and falls back to a lightweight stub only when
+it can't. That way the same suite runs in a full checkout (everything present)
+and in a minimal environment (only the module under test available). As you
+add real packages, the stubs simply stop being used -- no edits needed here.
+"""
+
+import importlib
+import sys
+import types
+from pathlib import Path
+
+# Make the repo root importable. Adjust if your tests live elsewhere.
+ROOT = Path(__file__).resolve().parents[1]
+if str(ROOT) not in sys.path:
+    sys.path.insert(0, str(ROOT))
+
+
+def _stub(name, **attrs):
+    module = types.ModuleType(name)
+    for key, value in attrs.items():
+        setattr(module, key, value)
+    sys.modules[name] = module
+    return module
+
+
+def _noop(*_args, **_kwargs):
+    return None
+
+
+def _ensure(name, **stub_attrs):
+    """Import the real module if available; otherwise register a stub."""
+    try:
+        return importlib.import_module(name)
+    except Exception:
+        return _stub(name, **stub_attrs)
+
+
+# External deps that are irrelevant to the pure logic under test.
+_ensure("dotenv", load_dotenv=_noop)
+_ensure("biocypher", BioCypher=object)
+_ensure("schema_config_generation", write_automated_schema=_noop)
+_ensure("fhirImport", get_patient_everything=_noop, get_bundle=_noop)
+
+# First-party graph helpers. create_graph is real and tested directly; the
+# reference/convolution modules are stubbed only if they're not on disk yet.
+_ensure("graphCreation")
+_ensure("graphCreation.create_graph", add_json_to_networkx=_noop)
+_ensure("graphCreation.process_references", process_references=_noop)
+_ensure("graphCreation.property_convolution", property_convolution=_noop)
+
+# mdm2neo4j XML-processor chain (imported by multiple_adapters).
+_ensure("mdm2neo4j")
+_ensure("mdm2neo4j.src")
+_ensure("mdm2neo4j.src.xml_processor")
+_ensure(
+    "mdm2neo4j.src.xml_processor.xml_processor",
+    parse_xml_generate_nodes=_noop,
+    parse_xml_generate_edges=_noop,
+)