Changes checks in save and load to parent directories

Author: DrPaulSharp

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

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]

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

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

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()

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:

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:

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:

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)

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': r'{str(item.path)}'"  # Raw string to ensure backslash is not interpreted as escape
+                    # 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,