v2: handle merged observable.observableTransformation observable.noiseDistribution

Update to changes in PEtab v2 draft, see PEtab-dev/PEtab#619.

Closes #375.

Author: dweindl

petab/v2/C.py

@@ -153,8 +153,6 @@
 OBSERVABLE_FORMULA = "observableFormula"
 #: Noise formula column in the observable table
 NOISE_FORMULA = "noiseFormula"
-#: Observable transformation column in the observable table
-OBSERVABLE_TRANSFORMATION = "observableTransformation"
 #: Noise distribution column in the observable table
 NOISE_DISTRIBUTION = "noiseDistribution"
 
@@ -168,7 +166,6 @@
 #: Optional columns of observable table
 OBSERVABLE_DF_OPTIONAL_COLS = [
     OBSERVABLE_NAME,
-    OBSERVABLE_TRANSFORMATION,
     NOISE_DISTRIBUTION,
 ]
 
@@ -187,8 +184,6 @@
 LOG = "log"
 #: Logarithmic base 10 transformation
 LOG10 = "log10"
-#: Supported observable transformations
-OBSERVABLE_TRANSFORMATIONS = [LIN, LOG, LOG10]
 
 
 # NOISE MODELS
@@ -206,9 +201,9 @@
 #: Laplace distribution on the parameter scale
 PARAMETER_SCALE_LAPLACE = "parameterScaleLaplace"
 #: Log-normal distribution
-LOG_NORMAL = "logNormal"
+LOG_NORMAL = "log-normal"
 #: Log-Laplace distribution
-LOG_LAPLACE = "logLaplace"
+LOG_LAPLACE = "log-laplace"
 
 #: Supported prior types
 PRIOR_TYPES = [
@@ -223,7 +218,7 @@
 ]
 
 #: Supported noise distributions
-NOISE_MODELS = [NORMAL, LAPLACE]
+NOISE_DISTRIBUTIONS = [NORMAL, LAPLACE, LOG_NORMAL, LOG_LAPLACE]
 
 
 # VISUALIZATION

petab/v2/core.py

@@ -32,7 +32,6 @@
 __all__ = [
     "Observable",
     "ObservableTable",
-    "ObservableTransformation",
     "NoiseDistribution",
     "Change",
     "Condition",
@@ -87,20 +86,6 @@ def _valid_petab_id(v: str) -> str:
     return v
 
 
-class ObservableTransformation(str, Enum):
-    """Observable transformation types.
-
-    Observable transformations as used in the PEtab observables table.
-    """
-
-    #: No transformation
-    LIN = C.LIN
-    #: Logarithmic transformation (natural logarithm)
-    LOG = C.LOG
-    #: Logarithmic transformation (base 10)
-    LOG10 = C.LOG10
-
-
 class ParameterScale(str, Enum):
     """Parameter scales.
 
@@ -122,6 +107,10 @@ class NoiseDistribution(str, Enum):
     NORMAL = C.NORMAL
     #: Laplace distribution
     LAPLACE = C.LAPLACE
+    #: Log-normal distribution
+    LOG_NORMAL = C.LOG_NORMAL
+    #: Log-Laplace distribution
+    LOG_LAPLACE = C.LOG_LAPLACE
 
 
 class PriorType(str, Enum):
@@ -167,10 +156,6 @@ class Observable(BaseModel):
     name: str | None = Field(alias=C.OBSERVABLE_NAME, default=None)
     #: Observable formula.
     formula: sp.Basic | None = Field(alias=C.OBSERVABLE_FORMULA, default=None)
-    #: Observable transformation.
-    transformation: ObservableTransformation = Field(
-        alias=C.OBSERVABLE_TRANSFORMATION, default=ObservableTransformation.LIN
-    )
     #: Noise formula.
     noise_formula: sp.Basic | None = Field(alias=C.NOISE_FORMULA, default=None)
     #: Noise distribution.
@@ -187,9 +172,7 @@ class Observable(BaseModel):
         "name",
         "formula",
         "noise_formula",
-        "noise_formula",
         "noise_distribution",
-        "transformation",
         mode="before",
     )
     @classmethod

petab/v2/lint.py

@@ -325,12 +325,12 @@ class CheckPosLogMeasurements(ValidationTask):
     log-transformation are positive."""
 
     def run(self, problem: Problem) -> ValidationIssue | None:
-        from .core import ObservableTransformation as ot
+        from .core import NoiseDistribution as nd
 
         log_observables = {
             o.id
             for o in problem.observable_table.observables
-            if o.transformation in [ot.LOG, ot.LOG10]
+            if o.noise_distribution in [nd.LOG_NORMAL, nd.LOG_LAPLACE]
         }
         if log_observables:
             for m in problem.measurement_table.measurements:

petab/v2/problem.py

@@ -904,7 +904,6 @@ def add_observable(
         formula: str,
         noise_formula: str | float | int = None,
         noise_distribution: str = None,
-        transform: str = None,
         name: str = None,
         **kwargs,
     ):
@@ -915,7 +914,6 @@ def add_observable(
             formula: The observable formula
             noise_formula: The noise formula
             noise_distribution: The noise distribution
-            transform: The observable transformation
             name: The observable name
             kwargs: additional columns/values to add to the observable table
 
@@ -930,8 +928,7 @@ def add_observable(
             record[NOISE_FORMULA] = noise_formula
         if noise_distribution is not None:
             record[NOISE_DISTRIBUTION] = noise_distribution
-        if transform is not None:
-            record[OBSERVABLE_TRANSFORMATION] = transform
+
         record.update(kwargs)
 
         self.observable_table += core.Observable(**record)