diff --git a/pyproject.toml b/pyproject.toml
index 85d6e16..c68585c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = "ratapi"
-version = "0.0.0.dev11"
+version = "0.0.0.dev12"
 description = "Python extension for the Reflectivity Analysis Toolbox (RAT)"
 readme = "README.md"
 requires-python = ">=3.10"
diff --git a/ratapi/models.py b/ratapi/models.py
index 7d0d4f7..755ea97 100644
--- a/ratapi/models.py
+++ b/ratapi/models.py
@@ -313,13 +313,7 @@ class CustomFile(RATModel):
     filename: str = ""
     function_name: str = ""
     language: Languages = Languages.Python
-    path: pathlib.Path = pathlib.Path(".").resolve()
-
-    @field_validator("path")
-    @classmethod
-    def resolve_relative_paths(cls, path: pathlib.Path) -> pathlib.Path:
-        """Return the absolute path of the given path."""
-        return path.resolve()
+    path: pathlib.Path = pathlib.Path(".")
 
     def model_post_init(self, __context: Any) -> None:
         """Autogenerate the function name from the filename if not set.
diff --git a/ratapi/project.py b/ratapi/project.py
index fcbbaf8..b8ca49f 100644
--- a/ratapi/project.py
+++ b/ratapi/project.py
@@ -956,12 +956,16 @@ def make_data_dict(item):
             elif field == "custom_files":
 
                 def make_custom_file_dict(item):
-                    return {
+                    file_dict = {
                         "name": item.name,
                         "filename": item.filename,
                         "language": item.language,
                         "path": try_relative_to(item.path, filepath.parent),
                     }
+                    if item.name != item.function_name:
+                        file_dict["function_name"] = item.function_name
+
+                    return file_dict
 
                 json_dict["custom_files"] = [make_custom_file_dict(file) for file in attr]
 
@@ -1062,7 +1066,9 @@ def try_relative_to(path: Path, relative_to: Path) -> str:
     """
     path = Path(path)
     relative_to = Path(relative_to)
-    if path.is_relative_to(relative_to):
+    if not path.is_absolute():
+        return str(path)
+    elif path.is_relative_to(relative_to):
         return str(path.relative_to(relative_to))
     else:
         warnings.warn(
diff --git a/tests/conftest.py b/tests/conftest.py
index b717ec4..0f3b356 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8537,3 +8537,11 @@ def absorption():
     """The project from the absorption example."""
     project, _ = ratapi.examples.absorption()
     return project
+
+
+@pytest.fixture
+def absorption_different_function():
+    """The project from the absorption example with a function name different from filename."""
+    project, _ = ratapi.examples.absorption()
+    project.custom_files[0].function_name = "test_func"
+    return project
diff --git a/tests/test_models.py b/tests/test_models.py
index 906a5d6..949cf5a 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -1,6 +1,5 @@
 """Test the pydantic models."""
 
-import pathlib
 import re
 from collections.abc import Callable
 
@@ -101,11 +100,11 @@ def test_initialise_with_extra_fields(self, model: Callable, model_params: dict)
             model(new_field=1, **model_params)
 
 
-def test_custom_file_path_is_absolute() -> None:
-    """If we use provide a relative path to the custom file model, it should be converted to an absolute path."""
-    relative_path = pathlib.Path("./relative_path")
-    custom_file = ratapi.models.CustomFile(path=relative_path)
-    assert custom_file.path.is_absolute()
+# def test_custom_file_path_is_absolute() -> None:
+#     """If we use provide a relative path to the custom file model, it should be converted to an absolute path."""
+#     relative_path = pathlib.Path("./relative_path")
+#     custom_file = ratapi.models.CustomFile(path=relative_path)
+#     assert custom_file.path.is_absolute()
 
 
 def test_data_eq() -> None:
diff --git a/tests/test_project.py b/tests/test_project.py
index 31e1376..35d5864 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -1616,6 +1616,7 @@ def test_wrap_extend(test_project, class_list: str, model_type: str, field: str,
         "domains_custom_layers",
         "domains_custom_xy",
         "absorption",
+        "absorption_different_function",
     ],
 )
 def test_save_load(project, request):
@@ -1637,24 +1638,25 @@ def test_save_load(project, request):
 def test_relative_paths():
     """Test that ``try_relative_to`` correctly creates relative paths to subfolders."""
 
-    with tempfile.TemporaryDirectory() as tmp:
-        data_path = Path(tmp, "data/myfile.dat")
+    cur_path = Path(".").resolve()
+    data_path = cur_path / "data/myfile.dat"
+    assert Path(ratapi.project.try_relative_to(data_path, cur_path)) == Path("data/myfile.dat")
 
-        assert Path(ratapi.project.try_relative_to(data_path, tmp)) == Path("data/myfile.dat")
+    # relative path will be left relative.
+    data_path = "data/myfile.dat"
+    assert Path(ratapi.project.try_relative_to(data_path, cur_path)) == Path("data/myfile.dat")
 
 
 def test_relative_paths_warning():
     """Test that we get a warning for trying to walk up paths."""
 
-    data_path = "/tmp/project/data/mydata.dat"
-    relative_path = "/tmp/project/project_path/myproj.dat"
+    cur_path = Path(".").resolve()
+    data_path = cur_path / "tmp/project/data/mydata.dat"
+    relative_path = cur_path / "tmp/project/project_path/myproj.dat"
 
     with pytest.warns(
         match="Could not write custom file path as relative to the project directory, "
         "which means that it may not work on other devices. If you would like to share your project, "
         "make sure your custom files are in a subfolder of the project save location.",
     ):
-        assert (
-            Path(ratapi.project.try_relative_to(data_path, relative_path))
-            == Path("/tmp/project/data/mydata.dat").resolve()
-        )
+        assert Path(ratapi.project.try_relative_to(data_path, relative_path)) == data_path