cond. free syms

Author: dweindl

petab/v2/conditions.py

@@ -2,15 +2,11 @@
 
 from __future__ import annotations
 
-from itertools import chain
 from pathlib import Path
 
 import pandas as pd
-import sympy as sp
 
-from .. import v2
 from ..v1.lint import assert_no_leading_trailing_whitespace
-from .C import *
 
 __all__ = [
     "get_condition_df",
@@ -50,20 +46,3 @@ def write_condition_df(df: pd.DataFrame, filename: str | Path) -> None:
     """
     df = get_condition_df(df)
     df.to_csv(filename, sep="\t", index=False)
-
-
-def get_condition_table_free_symbols(problem: v2.Problem) -> set[sp.Basic]:
-    """Free symbols from condition table assignments.
-
-    Collects all free symbols from the condition table `targetValue` column.
-
-    :returns: Set of free symbols.
-    """
-    return set(
-        chain.from_iterable(
-            change.target_value.free_symbols
-            for condition in problem.conditions_table.conditions
-            for change in condition.changes
-            if change.target_value is not None
-        )
-    )

petab/v2/core.py

@@ -5,6 +5,7 @@
 import re
 from collections.abc import Sequence
 from enum import Enum
+from itertools import chain
 from pathlib import Path
 from typing import Annotated, Literal
 
@@ -468,6 +469,23 @@ def __iadd__(self, other: Condition) -> ConditionsTable:
         self.conditions.append(other)
         return self
 
+    @property
+    def free_symbols(self) -> set[sp.Symbol]:
+        """Get all free symbols in the conditions table.
+
+        This includes all free symbols in the target values of the changes,
+        independently of whether it is referenced by any experiment, or
+        (indirectly) by any measurement.
+        """
+        return set(
+            chain.from_iterable(
+                change.target_value.free_symbols
+                for condition in self.conditions
+                for change in condition.changes
+                if change.target_value is not None
+            )
+        )
+
 
 class ExperimentPeriod(BaseModel):
     """A period of a timecourse or experiment defined by a start time

petab/v2/lint.py

@@ -13,7 +13,6 @@
 import pandas as pd
 import sympy as sp
 
-from .. import v2
 from .problem import Problem
 
 logger = logging.getLogger(__name__)
@@ -743,7 +742,7 @@ def append_overrides(overrides):
         append_overrides(measurement.noise_parameters)
 
     # Append parameter overrides from condition table
-    for p in v2.conditions.get_condition_table_free_symbols(problem):
+    for p in problem.conditions_table.free_symbols:
         parameter_ids[str(p)] = None
 
     return set(parameter_ids.keys())
@@ -822,7 +821,7 @@ def append_overrides(overrides):
     #  model
     parameter_ids.update(
         str(p)
-        for p in v2.conditions.get_condition_table_free_symbols(problem)
+        for p in problem.conditions_table.free_symbols
         if not problem.model.has_entity_with_id(str(p))
     )
 

tests/v2/test_core.py

@@ -251,3 +251,28 @@ def test_experiment():
 
     with pytest.raises(ValidationError, match="Invalid ID"):
         Experiment(id="experiment 1")
+
+
+def test_conditions_table():
+    assert ConditionsTable().free_symbols == set()
+
+    assert (
+        ConditionsTable(
+            conditions=[
+                Condition(
+                    id="condition1",
+                    changes=[Change(target_id="k1", target_value="true")],
+                )
+            ]
+        ).free_symbols
+        == set()
+    )
+
+    assert ConditionsTable(
+        conditions=[
+            Condition(
+                id="condition1",
+                changes=[Change(target_id="k1", target_value=x / y)],
+            )
+        ]
+    ).free_symbols == {x, y}