Fix sympy symbol name clashes during PEtab import (#2069)

Closes #2055

Author: dweindl

python/sdist/amici/petab_import.py

@@ -23,6 +23,7 @@
 import sympy as sp
 from petab.C import *
 from petab.parameters import get_valid_parameters_for_parameter_table
+from sympy.abc import _clash
 
 import amici
 from amici.logging import get_logger, log_execution_time, set_log_level
@@ -595,7 +596,7 @@ def import_model_sbml(
     output_parameters = OrderedDict()
     for formula in formulas:
         # we want reproducible parameter ordering upon repeated import
-        free_syms = sorted(sp.sympify(formula).free_symbols,
+        free_syms = sorted(sp.sympify(formula, locals=_clash).free_symbols,
                            key=lambda symbol: symbol.name)
         for free_sym in free_syms:
             sym = str(free_sym)
@@ -750,11 +751,12 @@ def get_observation_model(
     #  cannot handle states in sigma expressions. Therefore, where possible,
     #  replace species occurring in error model definition by observableIds.
     replacements = {
-        sp.sympify(observable['formula']): sp.Symbol(observable_id)
+        sp.sympify(observable['formula'], locals=_clash):
+            sp.Symbol(observable_id)
         for observable_id, observable in observables.items()
     }
     for observable_id, formula in sigmas.items():
-        repl = sp.sympify(formula).subs(replacements)
+        repl = sp.sympify(formula, locals=_clash).subs(replacements)
         sigmas[observable_id] = str(repl)
 
     noise_distrs = petab_noise_distributions_to_amici(observable_df)

python/sdist/amici/petab_objective.py

@@ -8,20 +8,23 @@
 import copy
 import logging
 import numbers
-from typing import (List, Sequence, Optional, Dict, Tuple, Union, Any,
-                    Collection, Iterator)
+from typing import (Any, Collection, Dict, Iterator, List, Optional, Sequence,
+                    Tuple, Union)
 
-import amici
-from amici.sbml_import import get_species_initial
 import libsbml
 import numpy as np
 import pandas as pd
 import petab
 import sympy as sp
 from petab.C import *  # noqa: F403
+from sympy.abc import _clash
 
-from . import AmiciModel, AmiciExpData
+import amici
+from amici.sbml_import import get_species_initial
+from . import AmiciExpData, AmiciModel
 from .logging import get_logger, log_execution_time
+from .parameter_mapping import (ParameterMapping, ParameterMappingForCondition,
+                                fill_in_parameters)
 from .petab_import import PREEQ_INDICATOR_ID, element_is_state
 from .parameter_mapping import (
     fill_in_parameters,
@@ -568,7 +571,8 @@ def _set_initial_state(condition_id, element_id, init_par_id,
                     .getInitialAssignmentBySymbol(element_id)
                 if initial_assignment:
                     initial_assignment = sp.sympify(
-                        libsbml.formulaToL3String(initial_assignment.getMath())
+                        libsbml.formulaToL3String(initial_assignment.getMath()),
+                        locals=_clash
                     )
                 if type_code == libsbml.SBML_SPECIES:
                     value = get_species_initial(element) \