Rename center_dispersion to irf_center_location in result

The name irf_center_location in the results describes more clearly what the variable holds.
Deprecated irf model item center_dispersion  for center_dispersion_coefficients
Deprecated irf model item width_dispersion  for width_dispersion_coefficients

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

@@ -126,9 +126,9 @@ def test_irf(model):
         assert irf.width == want
         want = [3] if i == 1 else [5, 6]
         if i == 2:
-            assert irf.center_dispersion == want
+            assert irf.center_dispersion_coefficients == want
             want = [7, 8]
-            assert irf.width_dispersion == want
+            assert irf.width_dispersion_coefficients == want
             want = [9]
             assert irf.scale == want
         assert irf.normalize == (i == 1)

glotaran/builtin/io/yml/test/test_model_spec.yml

@@ -1,6 +1,5 @@
 default-megacomplex: decay
 
-
 dataset:
   dataset1:
     megacomplex: [cmplx1]
@@ -23,36 +22,36 @@ irf:
   irf2:
     type: spectral-gaussian
     center: [1, 2]
-    width: [3,4]
+    width: [3, 4]
     scale: [9]
     normalize: false
     backsweep: true
     backsweep_period: 55
     dispersion_center: 55
-    center_dispersion: [5,6]
-    width_dispersion: [7,8]
+    center_dispersion_coefficients: [5, 6]
+    width_dispersion_coefficients: [7, 8]
     model_dispersion_with_wavenumber: true
 
 initial_concentration:
   inputD1:
-    compartments: [s1,s2,s3]
-    parameters: [1,2,3]
+    compartments: [s1, s2, s3]
+    parameters: [1, 2, 3]
   inputD2:
-    compartments: [s1,s2,s3]
-    parameters: [1,2,3]
+    compartments: [s1, s2, s3]
+    parameters: [1, 2, 3]
 
 # Convention matrix notation column = source, row = target compartment
 # (2,1) means from 1 to 2
 k_matrix:
   km1:
     matrix:
-      (s1, s1): '1'
-      (s2, s1): '2'
-      (s1, s2): '3'
-      (s3, s1): '4'
-      (s1, s3): '5'
-      (s4, s1): '6'
-      (s1, s4): '7'
+      (s1, s1): "1"
+      (s2, s1): "2"
+      (s1, s2): "3"
+      (s3, s1): "4"
+      (s1, s3): "5"
+      (s4, s1): "6"
+      (s1, s4): "7"
 
 shape:
   shape1:
@@ -63,9 +62,9 @@ shape:
 
 megacomplex:
   cmplx1:
-      k_matrix: [km1] # A megacomplex has one or more k-matrices
+    k_matrix: [km1] # A megacomplex has one or more k-matrices
   cmplx2:
-      k_matrix: [km2]
+    k_matrix: [km2]
   cmplx3:
     type: "spectral"
     shape:
@@ -97,7 +96,7 @@ relations:
   - source: s1
     target: s2
     parameter: 8
-    interval: [[1,100], [2,200]]
+    interval: [[1, 100], [2, 200]]
 
 weights:
   - datasets: [d1, d2]

glotaran/builtin/megacomplexes/decay/irf.py

@@ -47,10 +47,10 @@ class IrfMultiGaussian:
         one or more center of the irf as parameter indices
     width:
         one or more widths of the gaussian as parameter index
-    center_dispersion:
+    center_dispersion_coefficients:
         polynomial coefficients for the dispersion of the
         center as list of parameter indices. None for no dispersion.
-    width_dispersion:
+    width_dispersion_coefficients:
         polynomial coefficients for the dispersion of the
         width as parameter indices. None for no dispersion.
 
@@ -124,8 +124,8 @@ class IrfGaussian(IrfMultiGaussian):
 @model_item(
     properties={
         "dispersion_center": {"type": Parameter, "allow_none": True},
-        "center_dispersion": {"type": List[Parameter], "default": []},
-        "width_dispersion": {"type": List[Parameter], "default": []},
+        "center_dispersion_coefficients": {"type": List[Parameter], "default": []},
+        "width_dispersion_coefficients": {"type": List[Parameter], "default": []},
         "model_dispersion_with_wavenumber": {"type": bool, "default": False},
     },
     has_type=True,
@@ -149,12 +149,12 @@ class IrfSpectralMultiGaussian(IrfMultiGaussian):
         one or more center of the irf as parameter indices
     width:
         one or more widths of the gaussian as parameter index
-    center_dispersion:
-        polynomial coefficients for the dispersion of the
-        center as list of parameter indices. None for no dispersion.
-    width_dispersion:
-        polynomial coefficients for the dispersion of the
-        width as parameter indices. None for no dispersion.
+    center_dispersion_coefficients:
+        list of parameters with polynomial coefficients describing
+        the dispersion of the irf center location. None for no dispersion.
+    width_dispersion_coefficients:
+        list of parameters with polynomial coefficients describing
+        the dispersion of the width of the irf. None for no dispersion.
 
     """
 
@@ -173,16 +173,16 @@ def parameter(self, global_index: int, global_axis: np.ndarray):
                 else (index - self.dispersion_center) / 100
             )
 
-        if len(self.center_dispersion) != 0:
+        if len(self.center_dispersion_coefficients) != 0:
             if self.dispersion_center is None:
                 raise ModelError(f"No dispersion center defined for irf '{self.label}'")
-            for i, disp in enumerate(self.center_dispersion):
+            for i, disp in enumerate(self.center_dispersion_coefficients):
                 centers += disp * np.power(dist, i + 1)
 
-        if len(self.width_dispersion) != 0:
+        if len(self.width_dispersion_coefficients) != 0:
             if self.dispersion_center is None:
                 raise ModelError(f"No dispersion center defined for irf '{self.label}'")
-            for i, disp in enumerate(self.width_dispersion):
+            for i, disp in enumerate(self.width_dispersion_coefficients):
                 widths = widths + disp * np.power(dist, i + 1)
 
         return centers, widths, scale, shift, backsweep, backsweep_period

glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py

@@ -53,7 +53,7 @@
         center: irf.center
         width: irf.width
         dispersion_center: irf.dispersion_center
-        center_dispersion: [irf.center_dispersion]
+        center_dispersion_coefficients: [irf.cdc1]
 """
 MODEL_MULTI_IRF_DISPERSION = f"""\
 {MODEL_BASE}
@@ -63,8 +63,8 @@
         center: [irf.center]
         width: [irf.width]
         dispersion_center: irf.dispersion_center
-        center_dispersion: [irf.center_dispersion1, irf.center_dispersion2]
-        width_dispersion: [irf.width_dispersion]
+        center_dispersion_coefficients: [irf.cdc1, irf.cdc2]
+        width_dispersion_coefficients: [irf.wdc1]
 """
 
 MODEL_MULTIPULSE_IRF_DISPERSION = f"""\
@@ -75,7 +75,7 @@
         center: [irf.center1, irf.center2]
         width: [irf.width]
         dispersion_center: irf.dispersion_center
-        center_dispersion: [irf.center_dispersion1, irf.center_dispersion2, irf.center_dispersion3]
+        center_dispersion_coefficients: [irf.cdc1, irf.cdc2, irf.cdc3]
 """
 
 PARAMETERS_BASE = """\
@@ -98,7 +98,7 @@
     - ['center', 0.3]
     - ['width', 0.1]
     - ['dispersion_center', 400, {{'vary': False}}]
-    - ['center_dispersion', 0.5]
+    - ['cdc1', 0.5]
 """
 
 # What is this?
@@ -108,9 +108,9 @@
     - ["center", 0.3]
     - ["width", 0.1]
     - ["dispersion_center", 400, {{"vary": False}}]
-    - ["center_dispersion1", 0.1]
-    - ["center_dispersion2", 0.01]
-    - ["width_dispersion", 0.025]
+    - ["cdc1", 0.1]
+    - ["cdc2", 0.01]
+    - ["wdc1", 0.025]
 """
 
 PARAMETERS_MULTIPULSE_IRF_DISPERSION = f"""\
@@ -120,9 +120,9 @@
     - ["center2", 0.4]
     - ['width', 0.1]
     - ['dispersion_center', 400, {{'vary': False}}]
-    - ["center_dispersion1", 0.5]
-    - ["center_dispersion2", 0.1]
-    - ["center_dispersion3", -0.01]
+    - ["cdc1", 0.5]
+    - ["cdc2", 0.1]
+    - ["cdc3", -0.01]
 """
 
 
@@ -137,13 +137,15 @@ def _spectral_axis():
     return np.linspace(300, 500, 3)
 
 
-def _calculate_irf_position(index, center, dispersion_center=None, center_dispersion=None):
-    if center_dispersion is None:
-        center_dispersion = []
+def _calculate_irf_position(
+    index, center, dispersion_center=None, center_dispersion_coefficients=None
+):
+    if center_dispersion_coefficients is None:
+        center_dispersion_coefficients = []
     if dispersion_center is not None:
         distance = (index - dispersion_center) / 100
     if dispersion_center is not None:
-        for i, coefficient in enumerate(center_dispersion):
+        for i, coefficient in enumerate(center_dispersion_coefficients):
             center += coefficient * np.power(distance, i + 1)
     return center
 
@@ -184,10 +186,10 @@ class MultiCenterIrfDispersion:
 def test_spectral_irf(suite):
 
     model = suite.model
-    assert model.valid()
+    assert model.valid(), model.validate()
 
     parameters = suite.parameters
-    assert model.valid(parameters)
+    assert model.valid(parameters), model.validate(parameters)
 
     sim_model = deepcopy(model)
     sim_model.dataset["dataset1"].global_megacomplex = ["mc2"]
@@ -243,12 +245,14 @@ def test_spectral_irf(suite):
             # calculated irf location
             model_irf_center = suite.model.irf["irf1"].center
             model_dispersion_center = suite.model.irf["irf1"].dispersion_center
-            model_center_dispersion = suite.model.irf["irf1"].center_dispersion
+            model_center_dispersion_coefficients = suite.model.irf[
+                "irf1"
+            ].center_dispersion_coefficients
             calc_irf_location_at_x = _calculate_irf_position(
-                x, model_irf_center, model_dispersion_center, model_center_dispersion
+                x, model_irf_center, model_dispersion_center, model_center_dispersion_coefficients
             )
             # fitted irf location
-            fitted_irf_loc_at_x = resultdata["center_dispersion"].sel(spectral=x)
+            fitted_irf_loc_at_x = resultdata["irf_center_location"].sel(spectral=x)
             assert np.allclose(calc_irf_location_at_x, fitted_irf_loc_at_x)
 
     assert "species_associated_spectra" in resultdata

glotaran/builtin/megacomplexes/decay/util.py

@@ -228,10 +228,9 @@ def retrieve_irf(dataset_model: DatasetModel, dataset: xr.Dataset, global_dimens
     dataset["irf_center"] = ("irf_nr", center) if len(center) > 1 else center[0]
     dataset["irf_width"] = ("irf_nr", width) if len(width) > 1 else width[0]
     if isinstance(irf, IrfSpectralMultiGaussian) and irf.dispersion_center:
-        # TODO: rename center_dispersion to irf_center_location
-        dataset["center_dispersion"] = (
+        dataset["irf_center_location"] = (
             ("irf_nr", global_dimension),
             irf.calculate_dispersion(dataset.coords["spectral"].values),
         )
-        # TODO: deprecate and remove old _n naming for 'center_dispersion'
-        dataset["center_dispersion_1"] = dataset["center_dispersion"].sel(irf_nr=0)
+        # center_dispersion_1 for backwards compatibility (0.3-0.4.1)
+        dataset["center_dispersion_1"] = dataset["irf_center_location"].sel(irf_nr=0)

glotaran/deprecation/modules/builtin_io_yml.py

@@ -85,3 +85,24 @@ def model_spec_deprecations(spec: MutableMapping[Any, Any]) -> None:
         swap_keys=("equal_area_penalties", "clp_area_penalties"),
         stacklevel=load_model_stack_level,
     )
+
+    if "irf" in spec:
+        for _, irf in spec["irf"].items():
+            deprecate_dict_entry(
+                dict_to_check=irf,
+                deprecated_usage="center_dispersion",
+                new_usage="center_dispersion_coefficients",
+                to_be_removed_in_version="0.7.0",
+                swap_keys=("center_dispersion", "center_dispersion_coefficients"),
+                stacklevel=load_model_stack_level,
+            )
+
+        for _, irf in spec["irf"].items():
+            deprecate_dict_entry(
+                dict_to_check=irf,
+                deprecated_usage="width_dispersion",
+                new_usage="width_dispersion_coefficients",
+                to_be_removed_in_version="0.7.0",
+                swap_keys=("width_dispersion", "width_dispersion_coefficients"),
+                stacklevel=load_model_stack_level,
+            )

glotaran/deprecation/modules/test/test_builtin_io_yml.py

@@ -55,13 +55,41 @@
             "clp_area_penalties",
             [{"type": "equal_area"}],
         ),
+        (
+            dedent(
+                """
+                irf:
+                    irf1:
+                        center_dispersion: [cdc1]
+
+                """
+            ),
+            1,
+            "irf",
+            {"irf1": {"center_dispersion_coefficients": ["cdc1"]}},
+        ),
+        (
+            dedent(
+                """
+                irf:
+                    irf1:
+                        "width_dispersion": [wdc1]
+
+                """
+            ),
+            1,
+            "irf",
+            {"irf1": {"width_dispersion_coefficients": ["wdc1"]}},
+        ),
     ),
     ids=(
         "type: kinetic-spectrum",
         "type: spectrum",
         "spectral_relations",
         "spectral_constraints",
         "equal_area_penalties",
+        "center_dispersion",
+        "width_dispersion",
     ),
 )
 def test_model_spec_deprecations(