DynaRef 6.2.0__tar.gz → 6.3.0__tar.gz

{dynaref-6.2.0/src/DynaRef.egg-info → dynaref-6.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: DynaRef
-Version: 6.2.0
+Version: 6.3.0
 Summary: Dyna: X-ray magnetic reflectivity simulation
 Author-email: Stephane Grenier <stephane.grenier@neel.cnrs.fr>
 License-Expression: GPL-2.0-or-later
@@ -14,6 +14,7 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: matplotlib
 Requires-Dist: PyQt5
+Requires-Dist: PyYAML
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
@@ -97,11 +98,12 @@ result = run_reflectivity(SampleIni(), experiment)
 print(result.x, result.intensity)
 ```
 
-For reproducible batch calculations, use a JSON configuration such as
-`examples/stepanov-angle.json`:
+For reproducible batch calculations, use a JSON or YAML configuration such as
+`examples/stepanov-angle.json` or `examples/stepanov-angle.yaml`:
 
 ```console
 dyna-sim examples/stepanov-angle.json --output reflectivity.csv
+dyna-sim examples/stepanov-angle.yaml --output reflectivity.csv
 dyna-sim examples/stepanov-angle.json --output reflectivity.npz
 ```
 
@@ -114,6 +116,21 @@ result = load_config("examples/stepanov-angle.json").run()
 result.save("reflectivity.csv")
 ```
 
+Headless fitting is also available from JSON or YAML:
+
+```console
+dyna-sim fit examples/fit-angle.json --summary fit-summary.json --output fitted.csv
+dyna-sim fit examples/fit-angle.yaml --summary fit-summary.json --output fitted.csv
+```
+
+More ready-to-adapt examples are available in `examples/README.md`.
+
+The graphical interface can also save and load Dyna projects as YAML files.
+This is the recommended project format for editable samples and experimental
+parameters; legacy project files can still be loaded. The GUI also provides
+sample-only YAML import/export actions for reusing the same layer stack across
+several projects.
+
 ### Features
 
 * magnetic-sensitive susceptibility, arbitrary magnetic moment direction described by Euler angles, with the limitation of neglictible spin-orbit coupling in the valence states

{dynaref-6.2.0 → dynaref-6.3.0}/README.md

@@ -73,11 +73,12 @@ result = run_reflectivity(SampleIni(), experiment)
 print(result.x, result.intensity)
 ```
 
-For reproducible batch calculations, use a JSON configuration such as
-`examples/stepanov-angle.json`:
+For reproducible batch calculations, use a JSON or YAML configuration such as
+`examples/stepanov-angle.json` or `examples/stepanov-angle.yaml`:
 
 ```console
 dyna-sim examples/stepanov-angle.json --output reflectivity.csv
+dyna-sim examples/stepanov-angle.yaml --output reflectivity.csv
 dyna-sim examples/stepanov-angle.json --output reflectivity.npz
 ```
 
@@ -90,6 +91,21 @@ result = load_config("examples/stepanov-angle.json").run()
 result.save("reflectivity.csv")
 ```
 
+Headless fitting is also available from JSON or YAML:
+
+```console
+dyna-sim fit examples/fit-angle.json --summary fit-summary.json --output fitted.csv
+dyna-sim fit examples/fit-angle.yaml --summary fit-summary.json --output fitted.csv
+```
+
+More ready-to-adapt examples are available in `examples/README.md`.
+
+The graphical interface can also save and load Dyna projects as YAML files.
+This is the recommended project format for editable samples and experimental
+parameters; legacy project files can still be loaded. The GUI also provides
+sample-only YAML import/export actions for reusing the same layer stack across
+several projects.
+
 ### Features
 
 * magnetic-sensitive susceptibility, arbitrary magnetic moment direction described by Euler angles, with the limitation of neglictible spin-orbit coupling in the valence states

{dynaref-6.2.0 → dynaref-6.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "DynaRef"
-version = "6.2.0"
+version = "6.3.0"
 description = "Dyna: X-ray magnetic reflectivity simulation"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -19,6 +19,7 @@ dependencies = [
     "scipy",
     "matplotlib",
     "PyQt5",
+    "PyYAML",
 ]
 
 [project.urls]

{dynaref-6.2.0 → dynaref-6.3.0/src/DynaRef.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: DynaRef
-Version: 6.2.0
+Version: 6.3.0
 Summary: Dyna: X-ray magnetic reflectivity simulation
 Author-email: Stephane Grenier <stephane.grenier@neel.cnrs.fr>
 License-Expression: GPL-2.0-or-later
@@ -14,6 +14,7 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: matplotlib
 Requires-Dist: PyQt5
+Requires-Dist: PyYAML
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
@@ -97,11 +98,12 @@ result = run_reflectivity(SampleIni(), experiment)
 print(result.x, result.intensity)
 ```
 
-For reproducible batch calculations, use a JSON configuration such as
-`examples/stepanov-angle.json`:
+For reproducible batch calculations, use a JSON or YAML configuration such as
+`examples/stepanov-angle.json` or `examples/stepanov-angle.yaml`:
 
 ```console
 dyna-sim examples/stepanov-angle.json --output reflectivity.csv
+dyna-sim examples/stepanov-angle.yaml --output reflectivity.csv
 dyna-sim examples/stepanov-angle.json --output reflectivity.npz
 ```
 
@@ -114,6 +116,21 @@ result = load_config("examples/stepanov-angle.json").run()
 result.save("reflectivity.csv")
 ```
 
+Headless fitting is also available from JSON or YAML:
+
+```console
+dyna-sim fit examples/fit-angle.json --summary fit-summary.json --output fitted.csv
+dyna-sim fit examples/fit-angle.yaml --summary fit-summary.json --output fitted.csv
+```
+
+More ready-to-adapt examples are available in `examples/README.md`.
+
+The graphical interface can also save and load Dyna projects as YAML files.
+This is the recommended project format for editable samples and experimental
+parameters; legacy project files can still be loaded. The GUI also provides
+sample-only YAML import/export actions for reusing the same layer stack across
+several projects.
+
 ### Features
 
 * magnetic-sensitive susceptibility, arbitrary magnetic moment direction described by Euler angles, with the limitation of neglictible spin-orbit coupling in the valence states

{dynaref-6.2.0 → dynaref-6.3.0}/src/DynaRef.egg-info/SOURCES.txt

@@ -17,6 +17,8 @@ src/dyna/cli.py
 src/dyna/config.py
 src/dyna/configuration.py
 src/dyna/constants.py
+src/dyna/fitting.py
+src/dyna/project.py
 src/dyna/simulation.py
 src/dyna/Samples/Samples.py
 src/dyna/Samples/__init__.py
@@ -1162,10 +1164,13 @@ tests/test_ConfigurationCLI.py
 tests/test_DynaGraphTabs.py
 tests/test_ElzoRef_vs_StepanovRef.py
 tests/test_FaradayLiteratureBenchmark.py
+tests/test_GUIProjectYAML.py
+tests/test_HeadlessFittingAPI.py
 tests/test_HeadlessSimulationAPI.py
 tests/test_KerrLiteratureBenchmark.py
 tests/test_OptimisationLoadData.py
 tests/test_PhysicsModuleAPI.py
+tests/test_ProjectYAML.py
 tests/test_layerManager.py
 tests/test_optimization_no_data.py
 tests/test_simBox.py

{dynaref-6.2.0 → dynaref-6.3.0}/src/DynaRef.egg-info/requires.txt

@@ -2,6 +2,7 @@ numpy
 scipy
 matplotlib
 PyQt5
+PyYAML
 
 [dev]
 pytest

{dynaref-6.2.0 → dynaref-6.3.0}/src/dyna/__init__.py

@@ -112,9 +112,25 @@ from dyna.configuration import (
     SimulationConfig,
     load_config,
 )
+from dyna.fitting import (
+    FitConfig,
+    FitParameter,
+    FitResult,
+    load_fit_config,
+    run_fit,
+)
+from dyna.project import (
+    load_project_yaml,
+    load_sample_yaml,
+    save_project_yaml,
+    save_sample_yaml,
+)
 
 __all__ = [
     "Experiment",
+    "FitConfig",
+    "FitParameter",
+    "FitResult",
     "Formalism",
     "LayerConfig",
     "ReflectivityResult",
@@ -122,9 +138,15 @@ __all__ = [
     "ScanRange",
     "SimulationConfig",
     "build_scattering_factors",
+    "load_fit_config",
     "load_config",
+    "load_project_yaml",
+    "load_sample_yaml",
+    "run_fit",
     "run_reflectivity",
+    "save_project_yaml",
     "save_result",
+    "save_sample_yaml",
 ]
 
 

{dynaref-6.2.0 → dynaref-6.3.0}/src/dyna/cli.py

@@ -1,6 +1,7 @@
 """Command-line interface for headless Dyna simulations."""
 
 import argparse
+import json
 from pathlib import Path
 import sys
 
@@ -8,6 +9,7 @@ import numpy as np
 
 from dyna import __version__
 from dyna.configuration import load_config
+from dyna.fitting import load_fit_config
 
 
 def build_parser() -> argparse.ArgumentParser:
@@ -26,7 +28,32 @@ def build_parser() -> argparse.ArgumentParser:
     return parser
 
 
+def build_fit_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="dyna-sim fit",
+        description="Fit a Dyna reflectivity simulation without the GUI.",
+    )
+    parser.add_argument("config", type=Path, help="JSON fitting configuration")
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=Path,
+        help="optional fitted curve path (.csv, .txt, or .npz)",
+    )
+    parser.add_argument(
+        "--summary",
+        type=Path,
+        help="optional JSON fit summary path; stdout is used by default",
+    )
+    parser.add_argument("--version", action="version", version=f"%(prog)s {__version__}")
+    return parser
+
+
 def main(argv=None) -> int:
+    argv = list(sys.argv[1:] if argv is None else argv)
+    if argv[:1] == ["fit"]:
+        return _fit_main(argv[1:])
+
     parser = build_parser()
     args = parser.parse_args(argv)
 
@@ -50,5 +77,23 @@ def main(argv=None) -> int:
     return 0
 
 
+def _fit_main(argv) -> int:
+    parser = build_fit_parser()
+    args = parser.parse_args(argv)
+
+    try:
+        result = load_fit_config(args.config).run()
+        if args.output is not None:
+            result.simulation.save(args.output)
+        summary = json.dumps(result.to_dict(), indent=2, sort_keys=True) + "\n"
+        if args.summary is not None:
+            args.summary.write_text(summary, encoding="utf-8")
+        else:
+            sys.stdout.write(summary)
+    except (OSError, ValueError) as exc:
+        parser.exit(2, f"{parser.prog}: error: {exc}\n")
+    return 0
+
+
 if __name__ == "__main__":
     raise SystemExit(main())

{dynaref-6.2.0 → dynaref-6.3.0}/src/dyna/configuration.py

@@ -2,11 +2,14 @@
 
 from __future__ import annotations
 
+from collections.abc import Mapping as MappingABC
 from dataclasses import dataclass
 import json
 from pathlib import Path
 from typing import Any, Mapping, Sequence
 
+import yaml
+
 from dyna.ExperimentClass import Experiment
 from dyna.LayerClass import Layer
 from dyna.simulation import Formalism, ReflectivityResult, run_reflectivity
@@ -45,8 +48,12 @@ class LayerConfig:
     @classmethod
     def from_mapping(cls, values: Mapping[str, Any]) -> LayerConfig:
         _reject_unknown(values, cls.__dataclass_fields__, "layer")
+        normalized = dict(values)
+        for name in ("density", "thickness", "roughness", "mms", "phi", "gamma"):
+            if name in normalized:
+                normalized[name] = _current_value(normalized[name])
         try:
-            return cls(**values)
+            return cls(**normalized)
         except TypeError as exc:
             raise ValueError(f"invalid layer configuration: {exc}") from exc
 
@@ -188,14 +195,15 @@ class SimulationConfig:
 
 
 def load_config(path: str | Path) -> SimulationConfig:
-    """Load a JSON simulation configuration from disk."""
+    """Load a JSON or YAML simulation configuration from disk."""
     source = Path(path)
-    try:
-        values = json.loads(source.read_text(encoding="utf-8"))
-    except json.JSONDecodeError as exc:
-        raise ValueError(f"invalid JSON in {source}: {exc.msg}") from exc
+    values = _load_mapping_file(source, "simulation configuration")
     if not isinstance(values, dict):
-        raise ValueError("simulation configuration must be a JSON object")
+        raise ValueError("simulation configuration must be a JSON/YAML object")
+    if "simulation" in values:
+        if not isinstance(values["simulation"], dict):
+            raise ValueError("simulation section must be a JSON/YAML object")
+        values = values["simulation"]
     return SimulationConfig.from_mapping(values)
 
 
@@ -231,12 +239,50 @@ def _fixed(value: float) -> list[float]:
     return [number, number, number]
 
 
+def _current_value(value) -> float:
+    if isinstance(value, MappingABC):
+        if "value" in value:
+            return float(value["value"])
+        if "current" in value:
+            return float(value["current"])
+        raise ValueError("range mappings must contain a value field")
+    if isinstance(value, list | tuple):
+        if len(value) == 3:
+            return float(value[1])
+        if len(value) == 1:
+            return float(value[0])
+        raise ValueError("range lists must contain either one or three numbers")
+    return float(value)
+
+
 def _reject_unknown(values: Mapping[str, Any], accepted, name: str) -> None:
     unknown = sorted(set(values) - set(accepted))
     if unknown:
         raise ValueError(f"unknown {name} field(s): {', '.join(unknown)}")
 
 
+def _load_mapping_file(path: Path, description: str) -> Mapping[str, Any]:
+    suffix = path.suffix.lower()
+    text = path.read_text(encoding="utf-8")
+    if suffix == ".json":
+        try:
+            values = json.loads(text)
+        except json.JSONDecodeError as exc:
+            raise ValueError(f"invalid JSON in {path}: {exc.msg}") from exc
+    elif suffix in (".yaml", ".yml"):
+        try:
+            values = yaml.safe_load(text)
+        except yaml.YAMLError as exc:
+            raise ValueError(f"invalid YAML in {path}: {exc}") from exc
+    else:
+        raise ValueError(f"{description} path must end in .json, .yaml, or .yml")
+    if values is None:
+        values = {}
+    if not isinstance(values, MappingABC):
+        raise ValueError(f"{description} must be a JSON/YAML object")
+    return values
+
+
 __all__ = [
     "LayerConfig",
     "SampleConfig",