v2: Allow applying multiple conditions simultaneously

Author: dweindl

petab/v2/core.py

@@ -475,7 +475,7 @@ def free_symbols(self) -> set[sp.Symbol]:
 
 class ExperimentPeriod(BaseModel):
     """A period of a timecourse or experiment defined by a start time
-    and a condition ID.
+    and a list of condition IDs.
 
     This corresponds to a row of the PEtab experiments table.
     """
@@ -484,20 +484,19 @@ class ExperimentPeriod(BaseModel):
     time: Annotated[float, AfterValidator(_is_finite_or_neg_inf)] = Field(
         alias=C.TIME
     )
-    #: The ID of the condition to be applied at the start time.
-    condition_id: str | None = Field(alias=C.CONDITION_ID, default=None)
+    #: The IDs of the conditions to be applied at the start time.
+    condition_ids: list[str] = []
 
     #: :meta private:
     model_config = ConfigDict(populate_by_name=True, extra="allow")
 
-    @field_validator("condition_id", mode="before")
+    @field_validator("condition_ids", mode="before")
     @classmethod
-    def _validate_id(cls, condition_id):
-        if pd.isna(condition_id) or not condition_id:
-            return None
-        if not is_valid_identifier(condition_id):
-            raise ValueError(f"Invalid ID: {condition_id}")
-        return condition_id
+    def _validate_ids(cls, condition_ids):
+        for condition_id in condition_ids:
+            if not is_valid_identifier(condition_id):
+                raise ValueError(f"Invalid ID: {condition_id}")
+        return condition_ids
 
 
 class Experiment(BaseModel):
@@ -548,12 +547,20 @@ def from_df(cls, df: pd.DataFrame) -> ExperimentTable:
 
         experiments = []
         for experiment_id, cur_exp_df in df.groupby(C.EXPERIMENT_ID):
-            periods = [
-                ExperimentPeriod(
-                    time=row[C.TIME], condition_id=row[C.CONDITION_ID]
+            periods = []
+            for timepoint in cur_exp_df[C.TIME].unique():
+                condition_ids = [
+                    cid
+                    for cid in cur_exp_df.loc[
+                        cur_exp_df[C.TIME] == timepoint, C.CONDITION_ID
+                    ]
+                    if not pd.isna(cid)
+                ]
+                periods.append(
+                    ExperimentPeriod(
+                        time=timepoint, condition_ids=condition_ids
+                    )
                 )
-                for _, row in cur_exp_df.iterrows()
-            ]
             experiments.append(Experiment(id=experiment_id, periods=periods))
 
         return cls(experiments=experiments)
@@ -563,10 +570,12 @@ def to_df(self) -> pd.DataFrame:
         records = [
             {
                 C.EXPERIMENT_ID: experiment.id,
-                **period.model_dump(by_alias=True),
+                C.TIME: period.time,
+                C.CONDITION_ID: condition_id,
             }
             for experiment in self.experiments
             for period in experiment.periods
+            for condition_id in period.condition_ids or [""]
         ]
         return (
             pd.DataFrame(records)

petab/v2/lint.py

@@ -8,6 +8,7 @@
 from collections.abc import Set
 from dataclasses import dataclass, field
 from enum import IntEnum
+from itertools import chain
 from pathlib import Path
 
 import pandas as pd
@@ -484,11 +485,14 @@ def run(self, problem: Problem) -> ValidationIssue | None:
             c.id for c in problem.condition_table.conditions
         }
         for experiment in problem.experiment_table.experiments:
-            missing_conditions = {
-                period.condition_id
-                for period in experiment.periods
-                if period.condition_id is not None
-            } - available_conditions
+            missing_conditions = (
+                set(
+                    chain.from_iterable(
+                        period.condition_ids for period in experiment.periods
+                    )
+                )
+                - available_conditions
+            )
             if missing_conditions:
                 messages.append(
                     f"Experiment {experiment.id} requires conditions that are "
@@ -499,6 +503,9 @@ def run(self, problem: Problem) -> ValidationIssue | None:
             return ValidationError("\n".join(messages))
 
 
+# TODO: Check that changes of simultaneously applied conditions don't intersect
+
+
 class CheckAllParametersPresentInParameterTable(ValidationTask):
     """Ensure all required parameters are contained in the parameter table
     with no additional ones."""
@@ -646,12 +653,13 @@ class CheckUnusedConditions(ValidationTask):
     table."""
 
     def run(self, problem: Problem) -> ValidationIssue | None:
-        used_conditions = {
-            p.condition_id
-            for e in problem.experiment_table.experiments
-            for p in e.periods
-            if p.condition_id is not None
-        }
+        used_conditions = set(
+            chain.from_iterable(
+                p.condition_ids
+                for e in problem.experiment_table.experiments
+                for p in e.periods
+            )
+        )
         available_conditions = {
             c.id for c in problem.condition_table.conditions
         }

tests/v2/test_core.py

@@ -39,9 +39,9 @@ def test_experiment_add_periods():
     exp = Experiment(id="exp1")
     assert exp.periods == []
 
-    p1 = ExperimentPeriod(time=0, condition_id="p1")
-    p2 = ExperimentPeriod(time=1, condition_id="p2")
-    p3 = ExperimentPeriod(time=2, condition_id="p3")
+    p1 = ExperimentPeriod(time=0, condition_ids=["p1"])
+    p2 = ExperimentPeriod(time=1, condition_ids=["p2"])
+    p3 = ExperimentPeriod(time=2, condition_ids=["p3"])
     exp += p1
     exp += p2
 
@@ -201,22 +201,22 @@ def test_change():
 
 def test_period():
     ExperimentPeriod(time=0)
-    ExperimentPeriod(time=1, condition_id="p1")
-    ExperimentPeriod(time="-inf", condition_id="p1")
+    ExperimentPeriod(time=1, condition_ids=["p1"])
+    ExperimentPeriod(time="-inf", condition_ids=["p1"])
 
     assert (
         ExperimentPeriod(time="1", condition_id="p1", non_petab=1).non_petab
         == 1
     )
 
     with pytest.raises(ValidationError, match="got inf"):
-        ExperimentPeriod(time="inf", condition_id="p1")
+        ExperimentPeriod(time="inf", condition_ids=["p1"])
 
     with pytest.raises(ValidationError, match="Invalid ID"):
-        ExperimentPeriod(time=1, condition_id="1_condition")
+        ExperimentPeriod(time=1, condition_ids=["1_condition"])
 
     with pytest.raises(ValidationError, match="type=missing"):
-        ExperimentPeriod(condition_id="condition")
+        ExperimentPeriod(condition_ids=["condition"])
 
 
 def test_parameter():