Expand model language

.github/workflows/pylint.yml

@@ -27,4 +27,4 @@ jobs:
 
       - name: Lint
         run: |
-          flake8 --max-line-length=120 --ignore=F401,W503,E203 --count --show-source --statistics orsopy
+          flake8 --max-line-length=120 --ignore=F401,W503,E203,E704 --count --show-source --statistics orsopy

examples/sample_model_complex.yml

@@ -0,0 +1,34 @@
+sample:
+  model:
+    origin: ORSO test complex resolution
+    stack: air | 10 ( Si 70 | Fe 70 ) | ss1 | (ss1 in Fe) | ((ss2 | ss3) | 3 (ss1 | ss2) ) | ((((ss4 200))) in air ) | Si
+    sub_stacks:
+      ss1:
+        repetitions: 2
+        stack: ss2 | ss3
+      ss2:
+        repetitions: 1
+        sequence:
+          - {thickness: 2.0, material: Si}
+          - {thickness: 5.0, material: Ti}
+      ss3:
+        repetitions: 1
+        sequence:
+          - {thickness: 3.0, material: copper}
+          - {thickness: 1.0, material: mixin}
+      ss4:
+        sub_stack_class: FunctionTwoElements
+        material1: Ni
+        material2: Ti
+        function: x
+    materials:
+      copper:
+        formula: Cu
+      Fe:
+        formula: Fe[57]
+        mass_density: 7.0
+    composits:
+      mixin:
+        composition:
+          copper: 0.5
+          Si: 0.5

examples/sample_model_example_4.yml

@@ -0,0 +1,23 @@
+sample:
+    model:
+        origin: refnx example leaflet parameters
+        stack: Si  | ( LL | rLL ) in D2O | 2 ( LL | rLL ) |  water
+        sub_stacks:
+            LL:
+                sub_stack_class: LipidLeaflet
+                apm: 56.0
+                b_heads: 6.01e-4
+                vm_heads: 319.0
+                b_tails: -2.92e-4
+                vm_tails: 782.0
+                thickness_heads: 9.0
+                thickness: 23.0
+            rLL:
+                like: LL
+                but:
+                    reverse_monolayer: true
+
+        globals:
+            length_unit: angstrom
+            roughness: {magnitude: 3.0, unit: angstrom}
+            default_solvent: {formula: 'H2O', mass_density: {magnitude: 1.0, unit: g/cm^3}}

examples/sample_model_example_6.yml

@@ -0,0 +1,20 @@
+sample:
+    model:
+        comment: Saw tooth sample model
+        stack: air | gtop 50 | 5 (rgradient 50 | gradient 50) | Si
+        sub_stacks:
+          gradient:
+            sub_stack_class: FunctionTwoElements
+            material1: Ni
+            material2: Ti
+            function: x
+          rgradient:
+            like: gradient
+            but:
+              function: 1-x
+          gtop:
+            like: gradient
+            but:
+              roughness: 15.0
+        globals:
+            slice_resolution: {magnitude: 10.0, unit: nm}

examples/sample_model_example_7.yml

@@ -0,0 +1,10 @@
+sample:
+    model:
+        comment: Sine Wave SLD
+        stack: air | 5 (wave 10) | Si
+        sub_stacks:
+          wave:
+            sub_stack_class: FunctionTwoElements
+            material1: Ni
+            material2: Ti
+            function: 0.5+0.5*sin(x*2*pi)

examples/sample_model_example_8.yml

@@ -0,0 +1,10 @@
+sample:
+    model:
+        comment: Modulated Sine Wave SLD
+        stack: air | wave 200 | Si
+        sub_stacks:
+          wave:
+            sub_stack_class: FunctionTwoElements
+            material1: Ni
+            material2: Ti
+            function: (0.5+0.5*sin(x*20.0*2*pi))*exp(-(x-0.5)**2/0.25**2)

orsopy/__init__.py

@@ -1,3 +1,3 @@
 """Top-level package for orsopy."""
 
-__version__ = "1.2.1"
+__version__ = "1.3.0"

orsopy/fileio/base.py

@@ -58,6 +58,7 @@ class Header:
     """
 
     _orso_optionals: List[str] = []
+    # _orso_name_export_priority: List[str] # an optional list of attribute names to put first in the yaml export
     _subclass_dict_ = {}
 
     def __init_subclass__(cls, **kwargs):
@@ -271,12 +272,23 @@ def _resolve_type(hint: type, item: Any) -> Any:
                     # check if the item is in the list of allowed
                     # subtypes
                     return item
+                potential_res = []
                 for subt in subtypes:
                     # if it's not, then try to resolve its type.
-                    res = Header._resolve_type(subt, item)
-                    if res is not None:
-                        # This type conversion worked, return the result.
-                        return res
+                    with warnings.catch_warnings(record=True) as w:
+                        res = Header._resolve_type(subt, item)
+                        if res is not None:
+                            # This type conversion worked, return the result.
+                            if len(w) > 0:
+                                potential_res.append((w, res))
+                            else:
+                                return res
+                if len(potential_res) > 0:
+                    # a potential type was found, but it raised a warning
+                    w, res = potential_res[0]
+                    # make sure the warning is displayed
+                    warnings.warn(w[-1].message, w[-1].category, w[-1].lineno)
+                    return res
             elif hbase is Literal:
                 # Special case of a string Literal, which defines a list of valid strings.
                 # TODO: Should we first convert the value to a string?
@@ -375,6 +387,9 @@ def to_yaml(self) -> str:
 
     def _to_object_dict(self):
         output = {}
+        # define dictionary entries for attributes to be exported first
+        for fname in getattr(self, "_orso_name_export_priority", []):
+            output[fname] = None
         for i, value in self.__dict__.items():
             if i.startswith("_") or (value is None and i in self._orso_optionals):
                 continue
@@ -514,6 +529,16 @@ def represent_data(self, data):
 unit_registry = None
 
 
+def get_unit_registry():
+    global unit_registry
+    if unit_registry is None:
+        import pint
+
+        unit_registry = pint.UnitRegistry()
+    # unit_registry.define("Angstrom = angstrom") # optional extra units
+    return unit_registry
+
+
 @dataclass
 class ErrorValue(Header):
     """
@@ -598,11 +623,7 @@ def as_unit(self, output_unit):
         if output_unit == self.unit:
             return self.magnitude
 
-        global unit_registry
-        if unit_registry is None:
-            import pint
-
-            unit_registry = pint.UnitRegistry()
+        unit_registry = get_unit_registry()
 
         val = self.magnitude * unit_registry(self.unit)
         return val.to(output_unit).magnitude
@@ -642,11 +663,7 @@ def as_unit(self, output_unit):
         if output_unit == self.unit:
             return value
 
-        global unit_registry
-        if unit_registry is None:
-            import pint
-
-            unit_registry = pint.UnitRegistry()
+        unit_registry = get_unit_registry()
 
         val = value * unit_registry(self.unit)
         return val.to(output_unit).magnitude
@@ -684,11 +701,7 @@ def as_unit(self, output_unit):
         if output_unit == self.unit:
             return (self.min, self.max)
 
-        global unit_registry
-        if unit_registry is None:
-            import pint
-
-            unit_registry = pint.UnitRegistry()
+        unit_registry = get_unit_registry()
 
         vmin = self.min * unit_registry(self.unit)
         vmax = self.max * unit_registry(self.unit)
@@ -725,11 +738,7 @@ def as_unit(self, output_unit):
         if output_unit == self.unit:
             return (self.x, self.y, self.z)
 
-        global unit_registry
-        if unit_registry is None:
-            import pint
-
-            unit_registry = pint.UnitRegistry()
+        unit_registry = get_unit_registry()
 
         vx = self.x * unit_registry(self.unit)
         vy = self.y * unit_registry(self.unit)