Feature: Add SavingOptions to save_result API

glotaran/builtin/io/ascii/wavelength_time_explicit_file.py

@@ -279,6 +279,7 @@ def save_dataset(
         dataset: xr.DataArray,
         file_name: str,
         *,
+        data_filter: list[str] = None,
         comment: str = "",
         file_format: DataFileType = DataFileType.time_explicit,
         number_format: str = "%.10e",

glotaran/builtin/io/folder/folder_plugin.py

@@ -9,15 +9,18 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+from glotaran.io import SAVING_OPTIONS_DEFAULT
 from glotaran.io import save_dataset
 from glotaran.io import save_model
 from glotaran.io import save_parameters
+from glotaran.io import save_result
 from glotaran.io import save_scheme
 from glotaran.io.interface import ProjectIoInterface
-from glotaran.plugin_system.project_io_registration import SAVING_OPTIONS_DEFAULT
 from glotaran.plugin_system.project_io_registration import register_project_io
 
 if TYPE_CHECKING:
+    from os import PathLike
+
     from glotaran.plugin_system.project_io_registration import SavingOptions
     from glotaran.project import Result
 
@@ -33,8 +36,10 @@ class FolderProjectIo(ProjectIoInterface):
     def save_result(
         self,
         result: Result,
-        result_path: str,
+        result_path: str | PathLike[str],
+        format_name: str = None,
         *,
+        allow_overwrite: bool = False,
         saving_options: SavingOptions = SAVING_OPTIONS_DEFAULT,
     ) -> list[str]:
         """Save the result to a given folder.
@@ -57,11 +62,16 @@ def save_result(
         Parameters
         ----------
         result : Result
-            Result instance to be saved.
-        result_path : str
-            The path to the folder in which to save the result.
+            :class:`Result` instance to write.
+        result_path : str | PathLike[str]
+            Path to write the result data to.
+        format_name : str
+            Format the result should be saved in, if not provided and it is a file
+            it will be inferred from the file extension.
+        allow_overwrite : bool
+            Whether or not to allow overwriting existing files, by default False
         saving_options : SavingOptions
-            Options for saving the the result.
+            Options for the saved result.
 
 
         Returns
@@ -77,52 +87,106 @@ def save_result(
         result_folder = Path(result_path)
         if result_folder.is_file():
             raise ValueError(f"The path '{result_folder}' is not a directory.")
-        result_folder.mkdir(parents=True, exist_ok=True)
-
-        paths = []
-        if saving_options.report:
-            report_path = result_folder / "result.md"
-            report_path.write_text(str(result.markdown()))
-            paths.append(report_path.as_posix())
-
-        model_path = result_folder / "model.yml"
-        save_model(result.scheme.model, model_path, allow_overwrite=True)
-        paths.append(model_path.as_posix())
-
-        initial_parameters_path = f"initial_parameters.{saving_options.parameter_format}"
-        save_parameters(
-            result.scheme.parameters,
-            result_folder / initial_parameters_path,
-            format_name=saving_options.parameter_format,
-            allow_overwrite=True,
+
+        return save_result(
+            result,
+            result_folder / "glotaran_result.yml",
+            allow_overwrite=allow_overwrite,
+            saving_options=saving_options,
         )
-        paths.append((result_folder / initial_parameters_path).as_posix())
 
-        optimized_parameters_path = f"optimized_parameters.{saving_options.parameter_format}"
-        save_parameters(
-            result.optimized_parameters,
-            result_folder / optimized_parameters_path,
-            format_name=saving_options.parameter_format,
+
+def save_result_to_folder(
+    result: Result,
+    result_path: str | PathLike[str],
+    saving_options: SavingOptions,
+) -> list[str]:
+    """Save the result to a given folder.
+
+    Returns a list with paths of all saved items.
+    The following files are saved if not configured otherwise:
+    * `result.md`: The result with the model formatted as markdown text.
+    * `model.yml`: Model spec file.
+    * `scheme.yml`: Scheme spec file.
+    * `initial_parameters.csv`: Initially used parameters.
+    * `optimized_parameters.csv`: The optimized parameter as csv file.
+    * `parameter_history.csv`: Parameter changes over the optimization
+    * `{dataset_label}.nc`: The result data for each dataset as NetCDF file.
+
+    Note
+    ----
+    As a side effect it populates the file path properties of ``result`` which can be
+    used in other plugins (e.g. the ``yml`` save_result).
+
+    Parameters
+    ----------
+    result : Result
+        :class:`Result` instance to write.
+    result_path : str | PathLike[str]
+        Path to write the result data to.
+    saving_options : SavingOptions
+        Options for the saved result.
+
+    Returns
+    -------
+    list[str]
+        List of file paths which were created.
+
+    Raises
+    ------
+    ValueError
+        If ``result_path`` is a file.
+    """
+    result_folder = Path(result_path)
+    if result_folder.is_file():
+        raise ValueError(f"The path '{result_folder}' is not a directory.")
+    result_folder.mkdir(parents=True, exist_ok=True)
+
+    paths = []
+    if saving_options.report:
+        report_path = result_folder / "result.md"
+        report_path.write_text(str(result.markdown()))
+        paths.append(report_path.as_posix())
+
+    model_path = result_folder / "model.yml"
+    save_model(result.scheme.model, model_path, allow_overwrite=True)
+    paths.append(model_path.as_posix())
+
+    initial_parameters_path = f"initial_parameters.{saving_options.parameter_format}"
+    save_parameters(
+        result.scheme.parameters,
+        result_folder / initial_parameters_path,
+        format_name=saving_options.parameter_format,
+        allow_overwrite=True,
+    )
+    paths.append((result_folder / initial_parameters_path).as_posix())
+
+    optimized_parameters_path = f"optimized_parameters.{saving_options.parameter_format}"
+    save_parameters(
+        result.optimized_parameters,
+        result_folder / optimized_parameters_path,
+        format_name=saving_options.parameter_format,
+        allow_overwrite=True,
+    )
+    paths.append((result_folder / optimized_parameters_path).as_posix())
+
+    scheme_path = result_folder / "scheme.yml"
+    save_scheme(result.scheme, scheme_path, allow_overwrite=True)
+    paths.append(scheme_path.as_posix())
+
+    parameter_history_path = result_folder / "parameter_history.csv"
+    result.parameter_history.to_csv(parameter_history_path)
+    paths.append(parameter_history_path.as_posix())
+
+    for label, dataset in result.data.items():
+        data_path = result_folder / f"{label}.{saving_options.data_format}"
+        save_dataset(
+            dataset,
+            data_path,
+            format_name=saving_options.data_format,
             allow_overwrite=True,
+            data_filters=saving_options.data_filter,
         )
-        paths.append((result_folder / optimized_parameters_path).as_posix())
-
-        scheme_path = result_folder / "scheme.yml"
-        save_scheme(result.scheme, scheme_path, allow_overwrite=True)
-        paths.append(scheme_path.as_posix())
-
-        parameter_history_path = result_folder / "parameter_history.csv"
-        result.parameter_history.to_csv(parameter_history_path)
-        paths.append(parameter_history_path.as_posix())
-
-        for label, dataset in result.data.items():
-            data_path = result_folder / f"{label}.{saving_options.data_format}"
-            save_dataset(
-                dataset,
-                data_path,
-                format_name=saving_options.data_format,
-                allow_overwrite=True,
-            )
-            paths.append(data_path.as_posix())
-
-        return paths
+        paths.append(data_path.as_posix())
+
+    return paths

glotaran/builtin/io/folder/test/test_folder_plugin.py

@@ -18,7 +18,7 @@ def dummy_result():
     yield optimize(SCHEME, raise_exception=True)
 
 
-@pytest.mark.parametrize("format_name", ("folder", "legacy"))
+@pytest.mark.parametrize("format_name", ["folder", "legacy"])
 def test_save_result_folder(
     tmp_path: Path,
     dummy_result: Result,
@@ -27,6 +27,7 @@ def test_save_result_folder(
     """Check all files exist."""
 
     result_dir = tmp_path / "testresult"
+    assert not result_dir.exists()
     save_paths = save_result(
         result_path=str(result_dir), format_name=format_name, result=dummy_result
     )
@@ -45,15 +46,15 @@ def test_save_result_folder(
         assert (result_dir / wanted).as_posix() in save_paths
 
 
-@pytest.mark.parametrize("format_name", ("folder", "legacy"))
+@pytest.mark.parametrize("format_name", ["folder", "legacy"])
 def test_save_result_folder_error_path_is_file(
     tmp_path: Path,
     dummy_result: Result,
     format_name: Literal["folder", "legacy"],
 ):
     """Raise error if result_path is a file without extension and overwrite is true."""
 
-    result_dir = tmp_path / "testresult"
+    result_dir = tmp_path / "testresulterror"
     result_dir.touch()
 
     with pytest.raises(ValueError, match="The path '.+?' is not a directory."):

glotaran/builtin/io/yml/test/test_save_result.py

@@ -16,8 +16,8 @@
 @pytest.fixture(scope="session")
 def dummy_result():
     """Dummy result for testing."""
+    print(SCHEME.data["dataset_1"])
     scheme = replace(SCHEME, maximum_number_function_evaluations=1)
-    print(scheme.data["dataset_1"])
     yield optimize(scheme, raise_exception=True)
 
 
@@ -58,4 +58,7 @@ def test_save_result_yml(
     assert (result_dir / "dataset_1.nc").exists()
 
     # We can't check equality due to numerical fluctuations
-    assert expected in (result_dir / "result.yml").read_text()
+    got = (result_dir / "result.yml").read_text()
+    print(got)
+    assert expected in got
+    save_result(result_path=tmp_path / "result.yml", result=dummy_result)

glotaran/builtin/io/yml/yml.py

@@ -6,11 +6,12 @@
 from ruamel.yaml import YAML
 from ruamel.yaml.compat import StringIO
 
+from glotaran.builtin.io.folder.folder_plugin import save_result_to_folder
 from glotaran.deprecation.modules.builtin_io_yml import model_spec_deprecations
 from glotaran.deprecation.modules.builtin_io_yml import scheme_spec_deprecations
+from glotaran.io import SAVING_OPTIONS_DEFAULT
 from glotaran.io import ProjectIoInterface
 from glotaran.io import register_project_io
-from glotaran.io import save_result
 from glotaran.model import Model
 from glotaran.parameter import ParameterGroup
 from glotaran.project import Result
@@ -20,12 +21,15 @@
 from glotaran.utils.sanitize import sanitize_yaml
 
 if TYPE_CHECKING:
+    from os import PathLike
     from typing import Any
     from typing import Mapping
 
     from ruamel.yaml.nodes import ScalarNode
     from ruamel.yaml.representer import BaseRepresenter
 
+    from glotaran.plugin_system.project_io_registration import SavingOptions
+
 
 @register_project_io(["yml", "yaml", "yml_str"])
 class YmlProjectIo(ProjectIoInterface):
@@ -127,22 +131,66 @@ def load_result(self, result_path: str) -> Result:
         Result
             :class:`Result` instance created from the saved format.
         """
+
         spec = self._load_yml(result_path)
         return fromdict(Result, spec, folder=Path(result_path).parent)
 
-    def save_result(self, result: Result, result_path: str):
-        """Write a :class:`Result` instance to a spec file.
+    def save_result(
+        self,
+        result: Result,
+        result_path: str | PathLike[str],
+        format_name: str = None,
+        *,
+        allow_overwrite: bool = False,
+        saving_options: SavingOptions = SAVING_OPTIONS_DEFAULT,
+    ) -> list[str]:
+        """Save the result to a given folder.
+
+        Returns a list with paths of all saved items.
+        The following files are saved if not configured otherwise:
+        * `result.md`: The result with the model formatted as markdown text.
+        * `model.yml`: Model spec file.
+        * `scheme.yml`: Scheme spec file.
+        * `initial_parameters.csv`: Initially used parameters.
+        * `optimized_parameters.csv`: The optimized parameter as csv file.
+        * `parameter_history.csv`: Parameter changes over the optimization
+        * `{dataset_label}.nc`: The result data for each dataset as NetCDF file.
+
+        Note
+        ----
+        As a side effect it populates the file path properties of ``result`` which can be
+        used in other plugins (e.g. the ``yml`` save_result).
 
         Parameters
         ----------
         result : Result
             :class:`Result` instance to write.
         result_path : str | PathLike[str]
             Path to write the result data to.
+        format_name : str
+            Format the result should be saved in, if not provided and it is a file
+            it will be inferred from the file extension.
+        allow_overwrite : bool
+            Whether or not to allow overwriting existing files, by default False
+        saving_options : SavingOptions
+            Options for the saved result.
+
+
+        Returns
+        -------
+        list[str]
+            List of file paths which were created.
+
+        Raises
+        ------
+        ValueError
+            If ``result_path`` is a file.
         """
-        save_result(result, Path(result_path).parent.as_posix(), format_name="folder")
+        paths = save_result_to_folder(result, Path(result_path).parent.as_posix(), saving_options)
         result_dict = asdict(result, folder=Path(result_path).parent)
         write_dict(result_dict, file_name=result_path)
+        paths.append(result_path)
+        return paths
 
     def _load_yml(self, file_name: str) -> dict[str, Any]:
         yaml = YAML()

glotaran/io/__init__.py

@@ -6,8 +6,11 @@
 reexports functions from the pluginsystem from a common place.
 """
 
+from glotaran.io.interface import SAVING_OPTIONS_DEFAULT
+from glotaran.io.interface import SAVING_OPTIONS_MINIMAL
 from glotaran.io.interface import DataIoInterface
 from glotaran.io.interface import ProjectIoInterface
+from glotaran.io.interface import SavingOptions
 from glotaran.io.prepare_dataset import prepare_time_trace_dataset
 from glotaran.plugin_system.data_io_registration import data_io_plugin_table
 from glotaran.plugin_system.data_io_registration import get_dataloader
@@ -17,9 +20,6 @@
 from glotaran.plugin_system.data_io_registration import save_dataset
 from glotaran.plugin_system.data_io_registration import set_data_plugin
 from glotaran.plugin_system.data_io_registration import show_data_io_method_help
-from glotaran.plugin_system.project_io_registration import SAVING_OPTIONS_DEFAULT
-from glotaran.plugin_system.project_io_registration import SAVING_OPTIONS_MINIMAL
-from glotaran.plugin_system.project_io_registration import SavingOptions
 from glotaran.plugin_system.project_io_registration import get_project_io_method
 from glotaran.plugin_system.project_io_registration import load_model
 from glotaran.plugin_system.project_io_registration import load_parameters