Merge pull request #98 from aglavic/release

Release version 1.1

HISTORY.rst

@@ -2,13 +2,30 @@
 History
 =======
 
+1.1.0 (2023-02-20)
+------------------
+
+* Introduction of simple model language that can be used to describe
+  sample structures. The module *orsopy.fileio.model_language* is used to implement
+  and parse the model language.
+  See https://www.reflectometry.org/projects/simple_model for specifications.
+  Sample model examples can be found in the examples folder together
+  with scripts using the orsopy module to parse and plot the data.
+* Add polarization channels for x-ray experiments
+* Implement ErrorValue class for optional description of errors
+  on values within the file header.
+* Update of .ort standard according to discussions with community.
+  (E.g. rename of column attribute "dimension" to "physical_quantity")
+
 1.0.1 (2022-06-28)
 ------------------
 
 * Fix bug that did allow some dictionary type values to be created in Sample.
 * Update the schema files for released .ort standard.
 * Sample.sample_parameters keys to be strings and values restricted to
   Value, ValueRange, ValueVector or ComplexValue.
+* Add *as_unit* method to value classes that uses the *pint* library to convert
+  values to supplied unit automatically.
 
 1.0.0 (2022-06-10)
 ------------------

examples/simple_model_example_3.yml

@@ -6,10 +6,10 @@ sample:
           substrate:
             sequence:
             - material: Si
-              sigma: 2
+              roughness: 2
             - material: SiO2
               thickness: 5
-              sigma: 3
+              roughness: 3
           film:
             repetitions: 5
             stack: head_group 4 | tail | tail | head_group 4
@@ -35,7 +35,7 @@ sample:
               H2O: 0.3
               D2O: 0.7
         globals:
-          sigma: {magnitude: 5, unit: angstrom}
+          roughness: {magnitude: 5, unit: angstrom}
           length_unit: angstrom
           mass_density_unit: g/cm^3
           sld_unit: 1/angstrom^2

orsopy/__init__.py

@@ -1,3 +1,3 @@
 """Top-level package for orsopy."""
 
-__version__ = "1.0.1"
+__version__ = "1.1.0"

orsopy/dataclasses.py

@@ -9,3 +9,14 @@
 
     def _field_init(f, frozen, locals, self_name):
         return _field_init_real(f, frozen, locals, self_name, False)
+
+
+elif sys.version_info < (3, 7, 0):
+    # fix bug in python 3.6 when using default_factory for dataclass objects
+    _orig_field = field
+
+    def field(*args, **opts):
+        if "default_factory" in opts and not opts["default_factory"] in [list, tuple]:
+            return opts["default_factory"]()
+        else:
+            return _orig_field(*args, **opts)

orsopy/fileio/model_language.py

@@ -8,6 +8,7 @@
 
 from typing import Any, Dict, List, Optional, Union
 
+from ..dataclasses import field
 from ..utils.chemical_formula import Formula
 from ..utils.density_resolver import DensityResolver
 from .base import ComplexValue, Header, Value, orsodataclass
@@ -26,12 +27,12 @@ def find_idx(string, start, value):
 
 @orsodataclass
 class ModelParameters(Header):
-    roughness: Optional[Value] = Value(0.3, "nm")
-    length_unit: Optional[str] = "nm"
-    mass_density_unit: Optional[str] = "g/cm^3"
-    number_density_unit: Optional[str] = "1/nm^3"
-    sld_unit: Optional[str] = "1/angstrom^2"
-    magnetic_moment_unit: Optional[str] = "muB"
+    roughness: Value = field(default_factory=lambda: Value(0.3, "nm"))
+    length_unit: str = "nm"
+    mass_density_unit: str = "g/cm^3"
+    number_density_unit: str = "1/nm^3"
+    sld_unit: str = "1/angstrom^2"
+    magnetic_moment_unit: str = "muB"
 
 
 @orsodataclass
@@ -152,6 +153,8 @@ def get_sld(self, xray_energy=None) -> complex:
 class Composit(Header):
     composition: Dict[str, float]
 
+    original_name = None
+
     def resolve_names(self, resolvable_items):
         self._composition_materials = {}
         for key, value in self.composition.items():
@@ -288,6 +291,8 @@ class SubStack(Header):
     arguments: Optional[List[Any]] = None
     keywords: Optional[Dict[str, Any]] = None
 
+    original_name = None
+
     def resolve_names(self, resolvable_items):
         if self.stack is None and self.sequence is None:
             raise ValueError("SubStack has to either define stack or sequence")
@@ -319,6 +324,7 @@ def resolve_names(self, resolvable_items):
                             obj.thickness = thickness
                     else:
                         obj = Layer(material=item, thickness=thickness)
+                        obj.original_name = item
                 if hasattr(obj, "resolve_names"):
                     obj.resolve_names(resolvable_items)
                 output.append(obj)
@@ -375,6 +381,8 @@ def __post_init__(self):
     def resolvable_items(self):
         output = {}
         if self.sub_stacks:
+            for key, ssi in self.sub_stacks.items():
+                ssi.original_name = key
             output.update(self.sub_stacks)
         if self.layers:
             for key, li in self.layers.items():
@@ -385,6 +393,8 @@ def resolvable_items(self):
                 mi.original_name = key
             output.update(self.materials)
         if self.composits:
+            for key, ci in self.composits.items():
+                ci.original_name = key
             output.update(self.composits)
         return output
 
@@ -421,6 +431,7 @@ def resolve_stack(self):
                         obj.thickness = thickness
                 else:
                     obj = Layer(material=item, thickness=thickness)
+                    obj.original_name = item
             if hasattr(obj, "resolve_names"):
                 obj.resolve_names(ri)
             if hasattr(obj, "resolve_defaults"):