Merge branch 'develop' into v2_obs_trans

Author: dweindl

petab/v2/core.py

@@ -458,7 +458,7 @@ 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.
     """
@@ -467,20 +467,19 @@ 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] = Field(default_factory=list)
 
     #: :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):
@@ -531,12 +530,20 @@ 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)
@@ -546,10 +553,12 @@ 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
@@ -373,8 +374,10 @@ class CheckValidConditionTargets(ValidationTask):
     """Check that all condition table targets are valid."""
 
     def run(self, problem: Problem) -> ValidationIssue | None:
-        allowed_targets = set(
-            problem.model.get_valid_ids_for_condition_table()
+        allowed_targets = (
+            set(problem.model.get_valid_ids_for_condition_table())
+            if problem.model
+            else set()
         )
         allowed_targets |= set(get_output_parameters(problem))
         allowed_targets |= {
@@ -394,6 +397,28 @@ def run(self, problem: Problem) -> ValidationIssue | None:
                 f"Condition table contains invalid targets: {invalid}"
             )
 
+        # Check that changes of simultaneously applied conditions don't
+        #  intersect
+        for experiment in problem.experiment_table.experiments:
+            for period in experiment.periods:
+                if not period.condition_ids:
+                    continue
+                period_targets = set()
+                for condition_id in period.condition_ids:
+                    condition_targets = {
+                        change.target_id
+                        for cond in problem.condition_table.conditions
+                        if cond.id == condition_id
+                        for change in cond.changes
+                    }
+                    if invalid := (period_targets & condition_targets):
+                        return ValidationError(
+                            "Simultaneously applied conditions for experiment "
+                            f"{experiment.id} have overlapping targets "
+                            f"{invalid} at time {period.time}."
+                        )
+                    period_targets |= condition_targets
+
 
 class CheckUniquePrimaryKeys(ValidationTask):
     """Check that all primary keys are unique."""
@@ -484,11 +509,14 @@ 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 "
@@ -646,12 +674,13 @@ 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
         }

petab/v2/problem.py

@@ -1059,7 +1059,12 @@ def add_experiment(self, id_: str, *args):
             )
 
         periods = [
-            core.ExperimentPeriod(time=args[i], condition_id=args[i + 1])
+            core.ExperimentPeriod(
+                time=args[i],
+                condition_ids=[cond]
+                if isinstance((cond := args[i + 1]), str)
+                else cond,
+            )
             for i in range(0, len(args), 2)
         ]
 

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():

tests/v2/test_lint.py

@@ -3,8 +3,8 @@
 from copy import deepcopy
 
 from petab.v2 import Problem
-from petab.v2.C import *
 from petab.v2.lint import *
+from petab.v2.models.sbml_model import SbmlModel
 
 
 def test_check_experiments():
@@ -21,3 +21,19 @@ def test_check_experiments():
     tmp_problem = deepcopy(problem)
     tmp_problem["e1"].periods[0].time = tmp_problem["e1"].periods[1].time
     assert check.run(tmp_problem) is not None
+
+
+def test_check_incompatible_targets():
+    """Multiple conditions with overlapping targets cannot be applied
+    at the same time."""
+    problem = Problem()
+    problem.model = SbmlModel.from_antimony("p1 = 1; p2 = 2")
+    problem.add_experiment("e1", 0, "c1", 1, "c2")
+    problem.add_condition("c1", p1="1")
+    problem.add_condition("c2", p1="2", p2="2")
+    check = CheckValidConditionTargets()
+    assert check.run(problem) is None
+
+    problem["e1"].periods[0].condition_ids.append("c2")
+    assert (error := check.run(problem)) is not None
+    assert "overlapping targets {'p1'}" in error.message