no conditionName, no operationType

Author: dweindl

petab/v2/C.py

@@ -125,28 +125,14 @@
 
 #: Condition ID column in the condition table
 CONDITION_ID = "conditionId"
-# TODO: removed?
-#: Condition name column in the condition table
-CONDITION_NAME = "conditionName"
 #: Column in the condition table with the ID of an entity that is changed
 TARGET_ID = "targetId"
-#: Column in the condition table with the operation type
-OPERATION_TYPE = "operationType"
 #: Column in the condition table with the new value of the target entity
 TARGET_VALUE = "targetValue"
-# operation types:
-OT_CUR_VAL = "setCurrentValue"
-OT_NO_CHANGE = "noChange"
-
-OPERATION_TYPES = [
-    OT_CUR_VAL,
-    OT_NO_CHANGE,
-]
 
 CONDITION_DF_COLS = [
     CONDITION_ID,
     TARGET_ID,
-    OPERATION_TYPE,
     TARGET_VALUE,
 ]
 

petab/v2/core.py

@@ -29,7 +29,6 @@
     "Change",
     "Condition",
     "ConditionsTable",
-    "OperationType",
     "ExperimentPeriod",
     "Experiment",
     "ExperimentsTable",
@@ -248,16 +247,6 @@ def __iadd__(self, other: Observable) -> ObservablesTable:
         return self
 
 
-# TODO remove?!
-class OperationType(str, Enum):
-    """Operation types for model changes in the PEtab conditions table."""
-
-    # TODO update names
-    SET_CURRENT_VALUE = "setCurrentValue"
-    NO_CHANGE = "noChange"
-    ...
-
-
 class Change(BaseModel):
     """A change to the model or model state.
 
@@ -266,17 +255,13 @@ class Change(BaseModel):
 
     >>> Change(
     ...     target_id="k1",
-    ...     operation_type=OperationType.SET_CURRENT_VALUE,
     ...     target_value="10",
     ... )  # doctest: +NORMALIZE_WHITESPACE
-    Change(target_id='k1', operation_type='setCurrentValue',
-    target_value=10.0000000000000)
+    Change(target_id='k1', target_value=10.0000000000000)
     """
 
     #: The ID of the target entity to change.
     target_id: str | None = Field(alias=C.TARGET_ID, default=None)
-    # TODO: remove?!
-    operation_type: OperationType = Field(alias=C.OPERATION_TYPE)
     #: The value to set the target entity to.
     target_value: sp.Basic | None = Field(alias=C.TARGET_VALUE, default=None)
 
@@ -290,14 +275,11 @@ class Change(BaseModel):
     @model_validator(mode="before")
     @classmethod
     def _validate_id(cls, data: dict):
-        if (
-            data.get("operation_type", data.get(C.OPERATION_TYPE))
-            != C.OT_NO_CHANGE
-        ):
-            target_id = data.get("target_id", data.get(C.TARGET_ID))
-
-            if not is_valid_identifier(target_id):
-                raise ValueError(f"Invalid ID: {target_id}")
+        target_id = data.get("target_id", data.get(C.TARGET_ID))
+
+        if not is_valid_identifier(target_id):
+            raise ValueError(f"Invalid ID: {target_id}")
+
         return data
 
     @field_validator("target_value", mode="before")
@@ -323,13 +305,12 @@ class Condition(BaseModel):
     ...     changes=[
     ...         Change(
     ...             target_id="k1",
-    ...             operation_type=OperationType.SET_CURRENT_VALUE,
     ...             target_value="10",
     ...         )
     ...     ],
     ... )  # doctest: +NORMALIZE_WHITESPACE
-    Condition(id='condition1', changes=[Change(target_id='k1',
-    operation_type='setCurrentValue', target_value=10.0000000000000)])
+    Condition(id='condition1',
+    changes=[Change(target_id='k1', target_value=10.0000000000000)])
     """
 
     #: The condition ID.
@@ -633,12 +614,17 @@ def _validate_id(cls, v, info: ValidationInfo):
     )
     @classmethod
     def _sympify_list(cls, v):
+        if v is None:
+            return []
+
         if isinstance(v, float) and np.isnan(v):
             return []
+
         if isinstance(v, str):
             v = v.split(C.PARAMETER_SEPARATOR)
         else:
             v = [v]
+
         return [sympify_petab(x) for x in v]
 
 

petab/v2/lint.py

@@ -672,7 +672,7 @@ def get_valid_parameters_for_parameter_table(
         blackset |= placeholders
 
     if condition_df is not None:
-        blackset |= set(condition_df.columns.values) - {CONDITION_NAME}
+        blackset |= set(condition_df.columns.values)
 
     # don't use sets here, to have deterministic ordering,
     #  e.g. for creating parameter tables

petab/v2/petab1to2.py

@@ -226,8 +226,9 @@ def create_experiment_id(sim_cond_id: str, preeq_cond_id: str) -> str:
     validation_issues = v2.lint_problem(new_yaml_file)
 
     if validation_issues:
+        validation_issues = "\n".join(map(str, validation_issues))
         raise ValueError(
-            "Generated PEtab v2 problem did not pass linting: "
+            "The generated PEtab v2 problem did not pass linting: "
             f"{validation_issues}"
         )
 
@@ -287,7 +288,7 @@ def v1v2_condition_df(
     condition_df = condition_df.copy().reset_index()
     with suppress(KeyError):
         # conditionName was dropped in PEtab v2
-        condition_df.drop(columns=[v2.C.CONDITION_NAME], inplace=True)
+        condition_df.drop(columns=[v1.C.CONDITION_NAME], inplace=True)
 
     condition_df = condition_df.melt(
         id_vars=[v1.C.CONDITION_ID],
@@ -301,7 +302,6 @@ def v1v2_condition_df(
             columns=[
                 v2.C.CONDITION_ID,
                 v2.C.TARGET_ID,
-                v2.C.OPERATION_TYPE,
                 v2.C.TARGET_VALUE,
             ]
         )
@@ -320,5 +320,4 @@ def v1v2_condition_df(
                 f"Unable to determine value type {target} in the condition "
                 "table."
             )
-    condition_df[v2.C.OPERATION_TYPE] = v2.C.OT_CUR_VAL
     return condition_df

petab/v2/problem.py

@@ -13,6 +13,7 @@
 from typing import TYPE_CHECKING
 
 import pandas as pd
+import sympy as sp
 from pydantic import AnyUrl, BaseModel, Field
 
 from ..v1 import (
@@ -883,7 +884,7 @@ def validate(
         return validation_results
 
     def add_condition(
-        self, id_: str, name: str = None, **kwargs: tuple[str, Number | str]
+        self, id_: str, name: str = None, **kwargs: Number | str | sp.Expr
     ):
         """Add a simulation condition to the problem.
 
@@ -895,27 +896,20 @@ def add_condition(
         """
         if not kwargs:
             return
-        records = [
-            {
-                CONDITION_ID: id_,
-                TARGET_ID: target_id,
-                OPERATION_TYPE: "setCurrentValue",
-                TARGET_VALUE: target_value
-                if not isinstance(target_value, tuple)
-                else target_value[1],
-            }
+        changes = [
+            core.Change(target_id=target_id, target_value=target_value)
             for target_id, target_value in kwargs.items()
         ]
-        # TODO: is the condition name supported in v2?
-        if name is not None:
-            for record in records:
-                record[CONDITION_NAME] = [name]
-        tmp_df = pd.DataFrame(records)
-        self.condition_df = (
-            pd.concat([self.condition_df, tmp_df], ignore_index=True)
-            if self.condition_df is not None
-            else tmp_df
+        self.conditions_table.conditions.append(
+            core.Condition(id=id_, changes=changes)
         )
+        if name is not None:
+            self.mapping_table.mappings.append(
+                core.Mapping(
+                    petab_id=id_,
+                    model_id=name,
+                )
+            )
 
     def add_observable(
         self,
@@ -1023,8 +1017,8 @@ def add_measurement(
         experiment_id: str,
         time: float,
         measurement: float,
-        observable_parameters: Sequence[str | float] = None,
-        noise_parameters: Sequence[str | float] = None,
+        observable_parameters: Sequence[str | float] | str | float = None,
+        noise_parameters: Sequence[str | float] | str | float = None,
     ):
         """Add a measurement to the problem.
 
@@ -1036,27 +1030,25 @@ def add_measurement(
             observable_parameters: The observable parameters
             noise_parameters: The noise parameters
         """
-        record = {
-            OBSERVABLE_ID: [obs_id],
-            EXPERIMENT_ID: [experiment_id],
-            TIME: [time],
-            MEASUREMENT: [measurement],
-        }
-        if observable_parameters is not None:
-            record[OBSERVABLE_PARAMETERS] = [
-                PARAMETER_SEPARATOR.join(map(str, observable_parameters))
-            ]
-        if noise_parameters is not None:
-            record[NOISE_PARAMETERS] = [
-                PARAMETER_SEPARATOR.join(map(str, noise_parameters))
-            ]
-
-        tmp_df = pd.DataFrame(record)
-        self.measurement_df = (
-            pd.concat([self.measurement_df, tmp_df])
-            if self.measurement_df is not None
-            else tmp_df
-        ).reset_index(drop=True)
+        if observable_parameters is not None and not isinstance(
+            observable_parameters, Sequence
+        ):
+            observable_parameters = [observable_parameters]
+        if noise_parameters is not None and not isinstance(
+            noise_parameters, Sequence
+        ):
+            noise_parameters = [noise_parameters]
+
+        self.measurement_table.measurements.append(
+            core.Measurement(
+                observable_id=obs_id,
+                experiment_id=experiment_id,
+                time=time,
+                measurement=measurement,
+                observable_parameters=observable_parameters,
+                noise_parameters=noise_parameters,
+            )
+        )
 
     def add_mapping(self, petab_id: str, model_id: str):
         """Add a mapping table entry to the problem.

tests/v2/test_core.py

@@ -1,14 +1,15 @@
 import tempfile
 from pathlib import Path
 
+import sympy as sp
+
 from petab.v2.core import (
     Change,
     Condition,
     ConditionsTable,
     Experiment,
     ExperimentPeriod,
     ObservablesTable,
-    OperationType,
 )
 from petab.v2.petab1to2 import petab1to2
 
@@ -55,17 +56,17 @@ def test_experiment_add_periods():
     assert exp.periods == [p1, p2]
 
 
-def test_conditions_table_add_changeset():
+def test_conditions_table_add_changes():
     conditions_table = ConditionsTable()
     assert conditions_table.conditions == []
 
     c1 = Condition(
         id="condition1",
-        changes=[Change(operation_type=OperationType.NO_CHANGE)],
+        changes=[Change(target_id="k1", target_value=1)],
     )
     c2 = Condition(
         id="condition2",
-        changes=[Change(operation_type=OperationType.NO_CHANGE)],
+        changes=[Change(target_id="k2", target_value=sp.sympify("2 * x"))],
     )
 
     conditions_table += c1

tests/v2/test_problem.py

@@ -16,8 +16,6 @@
     NOMINAL_VALUE,
     OBSERVABLE_FORMULA,
     OBSERVABLE_ID,
-    OPERATION_TYPE,
-    OT_CUR_VAL,
     PARAMETER_ID,
     PETAB_ENTITY_ID,
     TARGET_ID,
@@ -73,7 +71,7 @@ def test_problem_from_yaml_multiple_files():
 
         for i in (1, 2):
             problem = Problem()
-            problem.add_condition(f"condition{i}", parameter1=(OT_CUR_VAL, i))
+            problem.add_condition(f"condition{i}", parameter1=i)
             petab.write_condition_df(
                 problem.condition_df, Path(tmpdir, f"conditions{i}.tsv")
             )
@@ -109,14 +107,13 @@ def test_problem_from_yaml_multiple_files():
 def test_modify_problem():
     """Test modifying a problem via the API."""
     problem = Problem()
-    problem.add_condition("condition1", parameter1=(OT_CUR_VAL, 1))
-    problem.add_condition("condition2", parameter2=(OT_CUR_VAL, 2))
+    problem.add_condition("condition1", parameter1=1)
+    problem.add_condition("condition2", parameter2=2)
 
     exp_condition_df = pd.DataFrame(
         data={
             CONDITION_ID: ["condition1", "condition2"],
             TARGET_ID: ["parameter1", "parameter2"],
-            OPERATION_TYPE: [OT_CUR_VAL, OT_CUR_VAL],
             TARGET_VALUE: [1.0, 2.0],
         }
     )