Adds support for relative paths for custom files (#163)

DrPaulSharp · web-flow · commit e6ae4dee289e · 2025-06-18T11:09:40.000+01:00
* Adds support for relative paths for custom files

* Bug fix

* Changes checks in save and load to parent directories

* Adds test for relative path
diff --git a/RATapi/examples/absorption/absorption.py b/RATapi/examples/absorption/absorption.py
@@ -108,7 +108,7 @@ def absorption():
         name="DPPC absorption",
         filename="volume_thiol_bilayer.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     # Finally add the contrasts
diff --git a/RATapi/examples/absorption/volume_thiol_bilayer.py b/RATapi/examples/absorption/volume_thiol_bilayer.py
@@ -133,7 +133,7 @@ def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
 
     CW = [cwThick, bulk_out[contrast], 0, bilayerRough]
 
-    if contrast == 0 or contrast == 2:
+    if contrast == 1 or contrast == 3:
         output = [alloyUp, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
     else:
         output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
diff --git a/RATapi/examples/domains/domains_custom_XY.py b/RATapi/examples/domains/domains_custom_XY.py
@@ -35,7 +35,7 @@ def domains_custom_XY():
         name="Domain Layer",
         filename="domains_XY_model.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     # Make contrasts
diff --git a/RATapi/examples/domains/domains_custom_layers.py b/RATapi/examples/domains/domains_custom_layers.py
@@ -32,7 +32,7 @@ def domains_custom_layers():
         name="Alloy domains",
         filename="alloy_domains.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     # Make a contrast
diff --git a/RATapi/examples/languages/run_custom_file_languages.py b/RATapi/examples/languages/run_custom_file_languages.py
@@ -7,7 +7,7 @@
 
 import RATapi as RAT
 
-path = pathlib.Path(__file__).parent.resolve()
+path = pathlib.Path(__file__).parent
 
 project = setup_problem.make_example_problem()
 controls = RAT.Controls()
diff --git a/RATapi/examples/languages/setup_problem.py b/RATapi/examples/languages/setup_problem.py
@@ -55,7 +55,7 @@ def make_example_problem():
         name="DSPC Model",
         filename="custom_bilayer.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     # Also, add the relevant background parameters - one each for each contrast:
diff --git a/RATapi/examples/normal_reflectivity/DSPC_custom_XY.py b/RATapi/examples/normal_reflectivity/DSPC_custom_XY.py
@@ -75,7 +75,7 @@ def DSPC_custom_XY():
         name="DSPC Model",
         filename="custom_XY_DSPC.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     # Also, add the relevant background parameters - one each for each contrast:
diff --git a/RATapi/examples/normal_reflectivity/DSPC_custom_layers.py b/RATapi/examples/normal_reflectivity/DSPC_custom_layers.py
@@ -52,7 +52,7 @@ def DSPC_custom_layers():
         name="DSPC Model",
         filename="custom_bilayer_DSPC.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     # Also, add the relevant background parameters - one each for each contrast:
diff --git a/RATapi/examples/normal_reflectivity/DSPC_function_background.py b/RATapi/examples/normal_reflectivity/DSPC_function_background.py
@@ -148,7 +148,7 @@ def DSPC_function_background():
         name="D2O Background Function",
         filename="background_function.py",
         language="python",
-        path=pathlib.Path(__file__).parent.resolve(),
+        path=pathlib.Path(__file__).parent,
     )
 
     problem.background_parameters.append(name="Fn Ao", min=5e-7, value=8e-6, max=5e-5)
diff --git a/RATapi/models.py b/RATapi/models.py
@@ -304,7 +304,13 @@ class CustomFile(RATModel):
     filename: str = ""
     function_name: str = ""
     language: Languages = Languages.Python
-    path: pathlib.Path = pathlib.Path(".")
+    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()
 
     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
@@ -868,7 +868,8 @@ def write_item(item):
                     + f"'filename': '{item.filename}', "
                     + f"'function_name': '{item.function_name}', "
                     + f"'language': '{str(item.language)}', "
-                    + f"'path': '{str(item.path)}'"
+                    # Raw string to ensure backslash is not interpreted as escape
+                    + f"'path': r'{str(try_relative_to(item.path, script_path.parent))}'"
                     + "}"
                 )
                 return item_str
@@ -932,7 +933,7 @@ def make_custom_file_dict(item):
                         "name": item.name,
                         "filename": item.filename,
                         "language": item.language,
-                        "path": try_relative_to(item.path, filepath),
+                        "path": try_relative_to(item.path, filepath.parent),
                     }
 
                 json_dict["custom_files"] = [make_custom_file_dict(file) for file in attr]
@@ -968,7 +969,7 @@ def load(cls, path: Union[str, Path]) -> "Project":
         # file paths are saved as relative to the project directory
         for file in model_dict["custom_files"]:
             if not Path(file["path"]).is_absolute():
-                file["path"] = Path(path, file["path"])
+                file["path"] = Path(path.parent, file["path"]).resolve()
 
         return cls.model_validate(model_dict)
 
@@ -1038,7 +1039,7 @@ def try_relative_to(path: Path, relative_to: Path) -> str:
         return str(path.relative_to(relative_to))
     else:
         warnings.warn(
-            "Could not save custom file path as relative to the project directory, "
+            "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.",
             stacklevel=2,
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -6858,7 +6858,7 @@ def r1_monolayer():
         ),
         custom_files=RATapi.ClassList(
             RATapi.models.CustomFile(
-                name="Model_IIb", filename="Model_IIb.m", function_name="Model_IIb", language="matlab", path=""
+                name="Model_IIb", filename="Model_IIb.m", function_name="Model_IIb", language="matlab"
             )
         ),
     )
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
@@ -663,7 +663,7 @@ def test_append_data_background_error():
 
 
 def test_get_python_handle():
-    path = pathlib.Path(__file__).parent.resolve()
+    path = pathlib.Path(__file__).parent
     assert RATapi.inputs.get_python_handle("utils.py", "dummy_function", path).__code__ == dummy_function.__code__
 
 
diff --git a/tests/test_models.py b/tests/test_models.py
@@ -1,5 +1,6 @@
 """Test the pydantic models."""
 
+import pathlib
 import re
 from typing import Callable
 
@@ -100,6 +101,13 @@ 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_data_eq() -> None:
     """If we use the Data.__eq__ method with an object that is not a pydantic BaseModel, we should return
     "NotImplemented".
diff --git a/tests/test_project.py b/tests/test_project.py
@@ -1590,10 +1590,6 @@ def test_save_load(project, request):
             original_project.save(path)
         converted_project = RATapi.Project.load(path)
 
-    # resolve custom files in case the original project had unresolvable relative paths
-    for file in original_project.custom_files:
-        file.path = file.path.resolve()
-
     for field in RATapi.Project.model_fields:
         assert getattr(converted_project, field) == getattr(original_project, field)
 
@@ -1614,7 +1610,7 @@ def test_relative_paths_warning():
     relative_path = "/tmp/project/project_path/myproj.dat"
 
     with pytest.warns(
-        match="Could not save custom file path as relative to the project directory, "
+        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.",
     ):

Original file line number	Diff line number	Diff line change
`@@ -108,7 +108,7 @@ def absorption():`
`108`	`108`	`name="DPPC absorption",`
`109`	`109`	`filename="volume_thiol_bilayer.py",`
`110`	`110`	`language="python",`
`111`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`111`	`+ path=pathlib.Path(__file__).parent,`
`112`	`112`	`)`
`113`	`113`
`114`	`114`	`# Finally add the contrasts`
Original file line number	Diff line number	Diff line change
`@@ -35,7 +35,7 @@ def domains_custom_XY():`
`35`	`35`	`name="Domain Layer",`
`36`	`36`	`filename="domains_XY_model.py",`
`37`	`37`	`language="python",`
`38`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`38`	`+ path=pathlib.Path(__file__).parent,`
`39`	`39`	`)`
`40`	`40`
`41`	`41`	`# Make contrasts`
Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@ def domains_custom_layers():`
`32`	`32`	`name="Alloy domains",`
`33`	`33`	`filename="alloy_domains.py",`
`34`	`34`	`language="python",`
`35`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`35`	`+ path=pathlib.Path(__file__).parent,`
`36`	`36`	`)`
`37`	`37`
`38`	`38`	`# Make a contrast`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ def make_example_problem():`
`55`	`55`	`name="DSPC Model",`
`56`	`56`	`filename="custom_bilayer.py",`
`57`	`57`	`language="python",`
`58`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`58`	`+ path=pathlib.Path(__file__).parent,`
`59`	`59`	`)`
`60`	`60`
`61`	`61`	`# Also, add the relevant background parameters - one each for each contrast:`
Original file line number	Diff line number	Diff line change
`@@ -75,7 +75,7 @@ def DSPC_custom_XY():`
`75`	`75`	`name="DSPC Model",`
`76`	`76`	`filename="custom_XY_DSPC.py",`
`77`	`77`	`language="python",`
`78`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`78`	`+ path=pathlib.Path(__file__).parent,`
`79`	`79`	`)`
`80`	`80`
`81`	`81`	`# Also, add the relevant background parameters - one each for each contrast:`
Original file line number	Diff line number	Diff line change
`@@ -52,7 +52,7 @@ def DSPC_custom_layers():`
`52`	`52`	`name="DSPC Model",`
`53`	`53`	`filename="custom_bilayer_DSPC.py",`
`54`	`54`	`language="python",`
`55`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`55`	`+ path=pathlib.Path(__file__).parent,`
`56`	`56`	`)`
`57`	`57`
`58`	`58`	`# Also, add the relevant background parameters - one each for each contrast:`
Original file line number	Diff line number	Diff line change
`@@ -148,7 +148,7 @@ def DSPC_function_background():`
`148`	`148`	`name="D2O Background Function",`
`149`	`149`	`filename="background_function.py",`
`150`	`150`	`language="python",`
`151`		`- path=pathlib.Path(__file__).parent.resolve(),`
	`151`	`+ path=pathlib.Path(__file__).parent,`
`152`	`152`	`)`
`153`	`153`
`154`	`154`	`problem.background_parameters.append(name="Fn Ao", min=5e-7, value=8e-6, max=5e-5)`