WIP ♻️ Rename activation to activations and use dict instead of a list

Co-authored-by: s-weigand <[email protected]>
jsnel · Oct 13, 2024 · a02b1e5 · a02b1e5
1 parent 4598f79
commit a02b1e5
Show file tree

Hide file tree

Showing 14 changed files with 41 additions and 40 deletions.
diff --git a/glotaran/builtin/elements/coherent_artifact/element.py b/glotaran/builtin/elements/coherent_artifact/element.py
@@ -36,11 +36,11 @@ def calculate_matrix(  # type:ignore[override]
         if not 1 <= self.order <= 3:
             raise GlotaranModelError("Coherent artifact order must be between in [1,3]")
 
-        activations = [
-            a
-            for a in model.activation
+        activations = {
+            key: a
+            for key,a in model.activations.items()
             if isinstance(a, MultiGaussianActivation) and self.label in a.compartments
-        ]
+        }
 
         if not len(activations):
             raise GlotaranModelError(
@@ -50,7 +50,7 @@ def calculate_matrix(  # type:ignore[override]
             raise GlotaranModelError(
                 f'Coherent artifact "{self.label}" must be associated with exactly one activation.'
             )
-        activation = activations[0]
+        activation = next(iter(activations.values()))
 
         parameters = activation.parameters(global_axis)
 

diff --git a/glotaran/builtin/elements/damped_oscillation/element.py b/glotaran/builtin/elements/damped_oscillation/element.py
@@ -53,7 +53,7 @@ def calculate_matrix(  # type:ignore[override]
 
         clp_labels = []
         matrices = []
-        for activation in model.activation:
+        for _, activation in model.activations.items():
             oscillation_labels = [
                 label for label in self.oscillations if label in activation.compartments
             ]

diff --git a/glotaran/builtin/elements/kinetic/element.py b/glotaran/builtin/elements/kinetic/element.py
@@ -71,7 +71,7 @@ def calculate_matrix(  # type:ignore[override]
     ) -> tuple[list[str], ArrayLike]:
         compartments = self.compartments
         matrices = []
-        for activation in model.activation:
+        for _,activation in model.activations.items():
             initial_concentrations = np.array(
                 [float(activation.compartments.get(label, 0)) for label in compartments]
             )
@@ -185,7 +185,7 @@ def create_result(
         initial_concentrations = []
         a_matrices = []
         kinetic_amplitudes = []
-        for activation in model.activation:
+        for _,activation in model.activations.items():
             initial_concentration = np.array(
                 [float(activation.compartments.get(label, 0)) for label in self.compartments]
             )

diff --git a/glotaran/builtin/items/activation/data_model.py b/glotaran/builtin/items/activation/data_model.py
@@ -30,7 +30,7 @@ def to_string(self) -> str:
 
 
 def validate_activations(
-    value: list[Activation],
+    value: dict[str,Activation],
     activation: Activation,
     parameters: Parameters | None,
 ) -> list[ItemIssue]:
@@ -41,7 +41,7 @@ def validate_activations(
 
 
 class ActivationDataModel(DataModel):
-    activation: list[Activation.get_annotated_type()] = Attribute(  # type:ignore[valid-type]
+    activations: dict[str,Activation.get_annotated_type()] = Attribute(  # type:ignore[valid-type]
         validator=validate_activations,
         description="The activation(s) of the dataset.",
     )
@@ -54,9 +54,9 @@ def create_result(
         amplitudes: xr.DataArray,
         concentrations: xr.DataArray,
     ) -> dict[str, xr.DataArray]:
-        gaussian_activations = [
-            a for a in model.activation if isinstance(a, MultiGaussianActivation)
-        ]
+        gaussian_activations = {
+            key:a for a in model.activations.items() if isinstance(a, MultiGaussianActivation)
+        }
         if not len(gaussian_activations):
             return {}
 

diff --git a/glotaran/testing/simulated_data/parallel_spectral_decay.py b/glotaran/testing/simulated_data/parallel_spectral_decay.py
@@ -19,7 +19,7 @@
     KineticSpectrumDataModel(
         elements=["parallel"],
         global_elements=["spectral"],
-        activation=[GaussianActivation.model_validate(ACTIVATION)],  # type:ignore[call-arg]
+        activations={"irf":GaussianActivation.model_validate(ACTIVATION)},  # type:ignore[call-arg]
     ),
     ModelLibrary.from_dict(LIBRARY),
     SIMULATION_PARAMETERS,
@@ -35,7 +35,7 @@
             "datasets": {
                 "parallel-decay": {
                     "elements": ["parallel"],
-                    "activation": [ACTIVATION],
+                    "activations": {"irf":ACTIVATION},
                 }
             }
         }

diff --git a/glotaran/testing/simulated_data/sequential_spectral_decay.py b/glotaran/testing/simulated_data/sequential_spectral_decay.py
@@ -19,7 +19,7 @@
     KineticSpectrumDataModel(
         elements=["sequential"],
         global_elements=["spectral"],
-        activation=[GaussianActivation.model_validate(ACTIVATION)],  # type:ignore[call-arg]
+        activations={"irf":GaussianActivation.model_validate(ACTIVATION)},  # type:ignore[call-arg]
     ),
     ModelLibrary.from_dict(LIBRARY),
     SIMULATION_PARAMETERS,
@@ -35,7 +35,7 @@
             "datasets": {
                 "sequential-decay": {
                     "elements": ["sequential"],
-                    "activation": [ACTIVATION],
+                    "activations": {"irf":ACTIVATION},
                 }
             }
         }

diff --git a/tests/builtin/elements/coherent_artifact/test_coherent_artifact_element.py b/tests/builtin/elements/coherent_artifact/test_coherent_artifact_element.py
@@ -72,7 +72,7 @@
     ),
 )
 def test_coherent_artifact(activation: Activation):
-    data_model = ActivationDataModel(elements=["coherent-artifact"], activation=[activation])
+    data_model = ActivationDataModel(elements=["coherent-artifact"], activations={"irf":activation})
     data_model.data = simulate(
         data_model, test_library, test_parameters_simulation, test_axies, clp=test_clp
     )

diff --git a/tests/builtin/elements/damped_oscillation/test_damped_oscillation_element.py b/tests/builtin/elements/damped_oscillation/test_damped_oscillation_element.py
@@ -92,7 +92,7 @@
     ),
 )
 def test_coherent_artifact(activation: Activation):
-    data_model = ActivationDataModel(elements=["doas"], activation=[activation])
+    data_model = ActivationDataModel(elements=["does"], activations={"irf": activation})
     data_model.data = simulate(
         data_model, test_library, test_parameters_simulation, test_axies, clp=test_clp
     )

diff --git a/tests/builtin/elements/kinetic/test_kinetic_element.py b/tests/builtin/elements/kinetic/test_kinetic_element.py
@@ -104,7 +104,7 @@ def test_decay(decay_method: str, activation: Activation):
         activation.compartments = {"s1": 1, "s2": 1}
     else:
         activation.compartments = {"s1": 1}
-    data_model = ActivationDataModel(elements=[decay_method], activation=[activation])
+    data_model = ActivationDataModel(elements=[decay_method], activations={"irf":activation})
     data_model.data = simulate(
         data_model, test_library, test_parameters_simulation, test_axies, clp=test_clp
     )

diff --git a/tests/builtin/elements/test_spectral_decay_full_model.py b/tests/builtin/elements/test_spectral_decay_full_model.py
@@ -85,13 +85,13 @@
 test_global_axis = np.arange(0, 50)
 test_model_axis = np.arange(-10, 1500, 1)
 test_axies = {"spectral": test_global_axis, "time": test_model_axis}
-test_activation = [InstantActivation(type="instant", compartments={"s1": 1})]
+test_activation = {"no_irf":InstantActivation(type="instant", compartments={"s1": 1})}
 test_data_model_cls = DataModel.create_class_for_elements((KineticElement, SpectralElement))
 test_data = simulate(
     test_data_model_cls(
         elements=["decay"],
         global_elements=["spectral"],
-        activation=test_activation,
+        activations=test_activation,
     ),
     test_library,
     test_parameters_simulation,
@@ -102,7 +102,7 @@
     ExperimentModel(
         datasets={
             "decay": ActivationDataModel(
-                elements=["decay"], data=test_data, activation=test_activation
+                elements=["decay"], data=test_data, activations=test_activation
             ),
         },
     ),
@@ -117,7 +117,7 @@
                 elements=["decay"],
                 global_elements=["spectral"],
                 data=test_data,
-                activation=test_activation,
+                activations=test_activation,
             ),
         },
     ),
@@ -127,7 +127,7 @@
                 elements=["spectral"],
                 global_elements=["decay"],
                 data=test_data,
-                activation=test_activation,
+                activations=test_activation,
             ),
         },
     ),

diff --git a/tests/builtin/elements/test_spectral_decay_linked_model.py b/tests/builtin/elements/test_spectral_decay_linked_model.py
@@ -74,29 +74,29 @@
     (KineticElement, SpectralElement)
 )
 
-test_activation_1 = [
+test_activation_1 = {"irf":
     GaussianActivation(
         type="gaussian",
         compartments={"s1": 1, "s2": 0.75},
         center="activation.center",
         width="activation.width",
     ),
-]
+}
 
-test_activation_2 = [
+test_activation_2 = {"irf":
     GaussianActivation(
         type="gaussian",
         compartments={"s1": 1, "s2": 0.1},
         center="activation.center",
         width="activation.width",
     ),
-]
+}
 
 test_data_1 = simulate(
     test_data_model_simulation_cls(
         elements=["decay"],
         global_elements=["spectral"],
-        activation=test_activation_1,
+        activations=test_activation_1,
     ),
     test_library,
     test_parameters_simulation,
@@ -110,7 +110,7 @@
     test_data_model_simulation_cls(
         elements=["decay"],
         global_elements=["spectral"],
-        activation=test_activation_2,
+        activations=test_activation_2,
     ),
     test_library,
     test_parameters_simulation,
@@ -126,12 +126,12 @@
             "decay_1": ActivationDataModel(
                 elements=["decay"],
                 data=test_data_1,
-                activation=test_activation_1,
+                activations=test_activation_1,
             ),
             "decay_2": ActivationDataModel(
                 elements=["decay"],
                 data=test_data_2,
-                activation=test_activation_2,
+                activations=test_activation_2,
             ),
         },
     ),

diff --git a/tests/builtin/io/yml/test_load_scheme.py b/tests/builtin/io/yml/test_load_scheme.py
@@ -16,10 +16,11 @@
         datasets:
             kinetic_parallel:
                 elements: [parallel]
-                activation:
-                    - type: instant
-                      compartments:
-                          "s1": 1
+                activations:
+                    irf:
+                        type: instant
+                        compartments:
+                            "s1": 1
 """
 
 

diff --git a/tests/project/test_scheme.py b/tests/project/test_scheme.py
@@ -27,9 +27,9 @@
             "datasets": {
                 "kinetic_parallel": {
                     "elements": ["parallel"],
-                    "activation": [
+                    "activations": {"irf":
                         {"type": "instant", "compartments": {"s1": 1}},
-                    ],
+                    },
                 }
             }
         }

diff --git a/tests/utils/test_json_schema.py b/tests/utils/test_json_schema.py
@@ -17,7 +17,7 @@ def test_create_model_scheme_json_schema(tmp_path: Path):
     blank_schema = create_model_scheme_json_schema()
 
     assert "properties" not in blank_schema["$defs"]["Parameter"]
-    assert "activation" in blank_schema["$defs"]["GlotaranDataModel"]["properties"]
+    assert "activations" in blank_schema["$defs"]["GlotaranDataModel"]["properties"]
     assert create_model_scheme_json_schema() == create_model_scheme_json_schema()
 
     params = Parameters.from_dict({"foo": {"bar": [1]}})