🩹 Fix Project.import_data path resolving for different script and cwd

changelog.md

@@ -28,6 +28,7 @@
 - 🩹 Fix yaml result saving with relative paths (#1199)
 - 🩹 Fix model markdown render for items without label (#1213)
 - 🩹 Fix wrong file loading due to partial filename matching in Project (#1212)
+- 🩹 Fix `Project.import_data` path resolving for different script and cwd (#1214)
 <!-- Fix within the 0.7.0 release cycle, therefore hidden:
 - 🩹 Fix the matrix provider alignment/reduction ('grouping') issues introduced in #1175 (#1190)
   -->

glotaran/plugin_system/data_io_registration.py

@@ -231,7 +231,7 @@ def save_dataset(
         by default True
     **kwargs : Any
         Additional keyword arguments passes to the ``write_dataset`` implementation
-        of the data io plugin. If you aren't sure about those use ``get_datawriter``
+        of the data io plugin. If you aren't sure about those use ``get_datasaver``
         to get the implementation with the proper help and autocomplete.
     """
     protect_from_overwrite(file_name, allow_overwrite=allow_overwrite)

glotaran/plugin_system/io_plugin_utils.py

@@ -6,6 +6,7 @@
 from collections.abc import Callable
 from functools import partial
 from functools import wraps
+from pathlib import Path
 from typing import TYPE_CHECKING
 from typing import Any
 from typing import TypeVar
@@ -94,6 +95,8 @@ def wrapper(*args: Any, **kwargs: Any) -> Any:
 def protect_from_overwrite(path: str | os.PathLike[str], *, allow_overwrite: bool = False) -> None:
     """Raise FileExistsError if files already exists and allow_overwrite isn't True.
 
+    As a side effect this also creates the parent directory of a file if it does not exist.
+
     Parameters
     ----------
     path : str
@@ -113,11 +116,14 @@ def protect_from_overwrite(path: str | os.PathLike[str], *, allow_overwrite: boo
         "If you are absolutely sure this is what you want and need to do you can "
         "use the argument 'allow_overwrite=True'."
     )
+    path = Path(path).resolve()
+    if path.parent.is_file() is False:
+        path.parent.mkdir(parents=True, exist_ok=True)
     if allow_overwrite:
         return
-    elif os.path.isfile(path):
+    elif path.is_file():
         raise FileExistsError(f"The file {path!r} already exists. \n{user_info}")
-    elif os.path.isdir(path) and os.listdir(str(path)):
+    elif path.is_dir() and os.listdir(str(path)):
         raise FileExistsError(
             f"The folder {path!r} already exists and is not empty. \n{user_info}"
         )

glotaran/plugin_system/test/test_data_io_registration.py

@@ -217,10 +217,11 @@ def test_protect_from_overwrite_write_functions(tmp_path: Path):
         save_dataset(xr.DataArray([1, 2]), str(file_path))
 
 
+@pytest.mark.parametrize("sub_dir", ("", "sub_dir"))
 @pytest.mark.usefixtures("mocked_registry")
-def test_write_dataset(tmp_path: Path):
+def test_write_dataset(tmp_path: Path, sub_dir: str):
     """All args and kwargs are passes correctly."""
-    file_path = tmp_path / "dummy.mock"
+    file_path = tmp_path / sub_dir / "dummy.mock"
 
     result: dict[str, Any] = {}
     save_dataset(

glotaran/plugin_system/test/test_project_io_registration.py

@@ -241,6 +241,7 @@ def test_load_functions(tmp_path: Path, load_function: Callable[..., Any]):
     assert result.source_path == Path(file_path).as_posix()
 
 
+@pytest.mark.parametrize("sub_dir", ("", "sub_dir"))
 @pytest.mark.parametrize(
     "save_function",
     (
@@ -253,10 +254,10 @@ def test_load_functions(tmp_path: Path, load_function: Callable[..., Any]):
 @pytest.mark.parametrize("update_source_path", (True, False))
 @pytest.mark.usefixtures("mocked_registry")
 def test_write_functions(
-    tmp_path: Path, save_function: Callable[..., Any], update_source_path: bool
+    tmp_path: Path, save_function: Callable[..., Any], update_source_path: bool, sub_dir: str
 ):
     """All args and kwargs are passes correctly."""
-    file_path = tmp_path / "model.mock"
+    file_path = tmp_path / "sub_dir" / "model.mock"
     mock_obj = MockFileLoadable()
 
     save_function(

glotaran/project/project_data_registry.py

@@ -46,6 +46,9 @@ def import_data(
         """
         path = Path(path)
 
+        if path.is_absolute() is False:
+            path = (self.directory.parent / path).resolve()
+
         name = name or path.stem
         data_path = self.directory / f"{name}.nc"
 

glotaran/project/test/test_project.py

@@ -1,12 +1,14 @@
 from __future__ import annotations
 
+import sys
 from importlib.metadata import distribution
 from pathlib import Path
 from shutil import rmtree
 from textwrap import dedent
 from typing import Literal
 
 import pytest
+from _pytest.monkeypatch import MonkeyPatch
 from _pytest.recwarn import WarningsRecorder
 from IPython.core.formatters import format_display_data
 
@@ -24,6 +26,7 @@
 from glotaran.testing.simulated_data.sequential_spectral_decay import (
     PARAMETERS as example_parameter,
 )
+from glotaran.utils.io import chdir_context
 
 
 @pytest.fixture(scope="module")
@@ -345,6 +348,37 @@ def test_generators_allow_overwrite(project_folder: Path, project_file: Path):
     assert len(list(filter(lambda p: p.label.startswith("rates"), parameters.all()))) == 3
 
 
+def test_import_data_relative_paths_script_folder_not_cwd(
+    tmp_path: Path, monkeypatch: MonkeyPatch
+):
+    """Import data using relative paths where cwd and script folder differ."""
+    script_folder = tmp_path / "project"
+    script_folder.mkdir(parents=True, exist_ok=True)
+    with chdir_context(tmp_path), monkeypatch.context() as m:
+        # Pretend the currently running script is located at ``script_folder / "script.py"``
+        m.setattr(
+            sys.modules[globals()["__name__"]],
+            "__file__",
+            (script_folder / "script.py").as_posix(),
+        )
+        cwd_data_import_path = "import_data.nc"
+        save_dataset(example_dataset, cwd_data_import_path)
+        assert (tmp_path / cwd_data_import_path).is_file() is True
+
+        script_folder_data_import_path = "original/import_data.nc"
+        save_dataset(example_dataset, script_folder / script_folder_data_import_path)
+        assert (script_folder / script_folder_data_import_path).is_file() is True
+
+        project = Project.open("project.gta")
+        assert (script_folder / "project.gta").is_file() is True
+
+        project.import_data(f"../{cwd_data_import_path}", name="dataset_1")
+        assert (script_folder / "data/dataset_1.nc").is_file() is True
+
+        project.import_data(script_folder_data_import_path, name="dataset_2")
+        assert (script_folder / "data/dataset_2.nc").is_file() is True
+
+
 def test_missing_file_errors(tmp_path: Path, project_folder: Path):
     """Error when accessing non existing files."""
     with pytest.raises(FileNotFoundError) as exc_info: