Merge branch 'main' into fix_dgf

maud/data_model/maud_parameter.py

@@ -1,5 +1,6 @@
 """Provides model MaudParameter, and subclasses for all parameters Maud uses."""
 
+from copy import deepcopy
 from typing import List, Optional, Union
 
 from pydantic import BaseModel, computed_field, field_validator, model_validator
@@ -123,6 +124,29 @@ def split_ids_exist_if_needed(self):
         return self
 
 
+class TrainTestParameter(MaudParameter):
+    """Mark parameter to have different priors between train and test.
+
+    The class must be filled with `shape_names` and `name` for train.
+    The test version is created by calling the `test` method.
+    """
+
+    prior_in_test_model: bool = False
+    prior_in_train_model: bool = True
+
+    def test(self):
+        """Generate the test counterpart."""
+        test_self = deepcopy(self)
+        test_self.shape_names = [
+            shape_name.replace("train", "test")
+            for shape_name in self.shape_names
+        ]
+        test_self.name = self.name.replace("train", "test")
+        test_self.prior_in_test_model = True
+        test_self.prior_in_train_model = False
+        return test_self
+
+
 class Km(MaudParameter):
     """Parameter representing a model's Michaelis constants."""
 
@@ -283,9 +307,11 @@ class KcatPme(MaudParameter):
     prior_in_train_model: bool = True
 
 
-class Drain(MaudParameter):
+class Drain(TrainTestParameter):
     """Stan variable type for drain parameters."""
 
+    name: str = "drain_train"
+    shape_names: List[str] = ["N_experiment_train", "N_drain"]
     id_components: List[List[IdComponent]] = [
         [IdComponent.EXPERIMENT],
         [IdComponent.REACTION],
@@ -295,27 +321,11 @@ class Drain(MaudParameter):
     default_scale: float = 1
 
 
-class DrainTrain(Drain):
-    """Stan variable for drain parameters of training experiments."""
-
-    name: str = "drain_train"
-    shape_names: List[str] = ["N_experiment_train", "N_drain"]
-    prior_in_test_model: bool = False
-    prior_in_train_model: bool = True
-
-
-class DrainTest(Drain):
-    """Stan variable for drain parameters of test experiments."""
-
-    name: str = "drain_test"
-    shape_names: List[str] = ["N_experiment_test", "N_drain"]
-    prior_in_test_model: bool = True
-    prior_in_train_model: bool = False
-
-
-class ConcEnzyme(MaudParameter):
+class ConcEnzyme(TrainTestParameter):
     """Parent class for enzyme concentration parameters."""
 
+    name: str = "conc_enzyme_train"
+    shape_names: List[str] = ["N_experiment_train", "N_enzyme"]
     id_components: List[List[IdComponent]] = [
         [IdComponent.EXPERIMENT],
         [IdComponent.ENZYME],
@@ -327,27 +337,11 @@ class ConcEnzyme(MaudParameter):
     default_scale: float = 1
 
 
-class ConcEnzymeTrain(ConcEnzyme):
-    """Enzyme concentration parameters in training experiments."""
-
-    name: str = "conc_enzyme_train"
-    shape_names: List[str] = ["N_experiment_train", "N_enzyme"]
-    prior_in_test_model: bool = False
-    prior_in_train_model: bool = True
-
-
-class ConcEnzymeTest(ConcEnzyme):
-    """Enzyme concentration parameters in test experiments."""
-
-    name: str = "conc_enzyme_test"
-    shape_names: List[str] = ["N_experiment_test", "N_enzyme"]
-    prior_in_test_model: bool = True
-    prior_in_train_model: bool = False
-
-
-class ConcUnbalanced(MaudParameter):
+class ConcUnbalanced(TrainTestParameter):
     """Parent class for unbalanced mic concentration parameters."""
 
+    name: str = "conc_unbalanced_train"
+    shape_names: List[str] = ["N_experiment_train", "N_unbalanced"]
     id_components: List[List[IdComponent]] = [
         [IdComponent.EXPERIMENT],
         [IdComponent.METABOLITE, IdComponent.COMPARTMENT],
@@ -357,27 +351,11 @@ class ConcUnbalanced(MaudParameter):
     default_scale: float = 2.0
 
 
-class ConcUnbalancedTrain(ConcUnbalanced):
-    """Unbalanced mic concentration parameters in training experiments."""
-
-    name: str = "conc_unbalanced_train"
-    shape_names: List[str] = ["N_experiment_train", "N_unbalanced"]
-    prior_in_test_model: bool = False
-    prior_in_train_model: bool = True
-
-
-class ConcUnbalancedTest(ConcUnbalanced):
-    """Unbalanced mic concentration parameters in test experiments."""
-
-    name: str = "conc_unbalanced_test"
-    shape_names: List[str] = ["N_experiment_test", "N_enzyme"]
-    prior_in_test_model: bool = True
-    prior_in_train_model: bool = False
-
-
-class ConcPme(MaudParameter):
+class ConcPme(TrainTestParameter):
     """Parent class for pme concentration parameters."""
 
+    name: str = "conc_pme_train"
+    shape_names: List[str] = ["N_experiment_train", "N_pme"]
     id_components: List[List[IdComponent]] = [
         [IdComponent.EXPERIMENT],
         [IdComponent.PHOSPHORYLATION_MODIFYING_ENZYME],
@@ -387,46 +365,12 @@ class ConcPme(MaudParameter):
     default_scale: float = 2.0
 
 
-class ConcPmeTrain(ConcPme):
-    """Pme concentration parameters in training experiments."""
-
-    name: str = "conc_pme_train"
-    shape_names: List[str] = ["N_experiment_train", "N_pme"]
-    prior_in_test_model: bool = False
-    prior_in_train_model: bool = True
-
-
-class ConcPmeTest(ConcPme):
-    """Pme concentration parameters in test experiments."""
-
-    name: str = "conc_pme_test"
-    shape_names: List[str] = ["N_experiment_test", "N_pme"]
-    prior_in_test_model: bool = True
-    prior_in_train_model: bool = False
-
-
-class Psi(MaudParameter):
+class Psi(TrainTestParameter):
     """Stan variable representing per-experiment membrane potentials."""
 
+    name: str = "psi_train"
+    shape_names: List[str] = ["N_experiment_train"]
     id_components: List[List[IdComponent]] = [[IdComponent.EXPERIMENT]]
     non_negative: bool = False
     default_loc: float = 0
     default_scale: float = 2
-
-
-class PsiTrain(Psi):
-    """Pme concentration parameters in training experiments."""
-
-    name: str = "psi_train"
-    shape_names: List[str] = ["N_experiment_train"]
-    prior_in_test_model: bool = False
-    prior_in_train_model: bool = True
-
-
-class PsiTest(Psi):
-    """Pme concentration parameters in test experiments."""
-
-    name: str = "psi_test"
-    shape_names: List[str] = ["N_experiment_test"]
-    prior_in_test_model: bool = True
-    prior_in_train_model: bool = False