🩹 Fix and re-enable IRF Dispersion Test (#786)

* Fix and re-enable IRF Dispersion Test

Improve the tests in test_spectral_irf
Added NoDispersion test
Re-enable IrfDispersion tests on the CI (de-Volkswagen the tests)
Improve assignment of center_dispersion to result dataset

* 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

.github/workflows/CI_CD_actions.yml

@@ -109,7 +109,7 @@ jobs:
         run: pip freeze
       - name: Run tests
         run: |
-          pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml -k 'not IrfDispersion' glotaran
+          pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml glotaran
 
       - name: Codecov Upload
         uses: codecov/codecov-action@v2

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