diff --git a/config/__init__.py b/config/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/config/test/__init__.py b/config/test/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/setup.py b/setup.py
index 424d4acd6..8e62d7edc 100644
--- a/setup.py
+++ b/setup.py
@@ -8,8 +8,7 @@
 
 setup(
     name="deepreg",
-    packages=find_packages(exclude=["test", "test.unit"]),
-    package_data={"deepreg": ["config/*.yaml", "config/test/*.yaml"]},
+    packages=find_packages(exclude=["test", "test.unit", "test.output"]),
     include_package_data=True,
     version="0.1.0b1",
     license="apache-2.0",