From a4d554daf0360d16b5b53ba7faddbde25a592079 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Thu, 5 Dec 2024 09:56:12 +0100
Subject: [PATCH] Add `SbmlModel.from_antimony`

Simplify creating a PEtab SbmlModel from antimony files or strings.

Replace simplesbml by antimony in tests.
---
 petab/v1/models/sbml_model.py      | 79 +++++++++++++++++++++++++++++-
 pyproject.toml                     |  8 ++-
 tests/v1/test_combine.py           | 10 ++--
 tests/v1/test_deprecated.py        |  4 +-
 tests/v1/test_lint.py              | 33 +++++++------
 tests/v1/test_observables.py       | 17 ++-----
 tests/v1/test_parameter_mapping.py | 73 ++++++++++++---------------
 tests/v1/test_petab.py             | 38 ++++++--------
 tests/v1/test_sbml.py              | 42 ++++++++++------
 tests/v1/test_simplify.py          |  9 ++--
 10 files changed, 191 insertions(+), 122 deletions(-)

diff --git a/petab/v1/models/sbml_model.py b/petab/v1/models/sbml_model.py
index 5102715d..55cd7b4d 100644
--- a/petab/v1/models/sbml_model.py
+++ b/petab/v1/models/sbml_model.py
@@ -1,4 +1,5 @@
 """Functions for handling SBML models"""
+from __future__ import annotations
 
 import itertools
 from collections.abc import Iterable
@@ -32,8 +33,25 @@ def __init__(
         sbml_document: libsbml.SBMLDocument = None,
         model_id: str = None,
     ):
+        """Constructor.
+
+        :param sbml_model: SBML model. Optional if `sbml_document` is given.
+        :param sbml_reader: SBML reader. Optional.
+        :param sbml_document: SBML document. Optional if `sbml_model` is given.
+        :param model_id: Model ID. Defaults to the SBML model ID."""
         super().__init__()
 
+        if sbml_model is None and sbml_document is None:
+            raise ValueError(
+                "Either sbml_model or sbml_document must be given."
+            )
+
+        if sbml_model is None:
+            sbml_model = sbml_document.getModel()
+
+        if sbml_document is None:
+            sbml_document = sbml_model.getSBMLDocument()
+
         self.sbml_reader: libsbml.SBMLReader | None = sbml_reader
         self.sbml_document: libsbml.SBMLDocument | None = sbml_document
         self.sbml_model: libsbml.Model | None = sbml_model
@@ -70,7 +88,7 @@ def __setstate__(self, state):
         self.__dict__.update(state)
 
     @staticmethod
-    def from_file(filepath_or_buffer, model_id: str = None):
+    def from_file(filepath_or_buffer, model_id: str = None) -> SbmlModel:
         sbml_reader, sbml_document, sbml_model = get_sbml_model(
             filepath_or_buffer
         )
@@ -82,7 +100,12 @@ def from_file(filepath_or_buffer, model_id: str = None):
         )
 
     @staticmethod
-    def from_string(sbml_string, model_id: str = None):
+    def from_string(sbml_string, model_id: str = None) -> SbmlModel:
+        """Create SBML model from an SBML string.
+
+        :param sbml_string: SBML model as string.
+        :param model_id: Model ID. Defaults to the SBML model ID.
+        """
         sbml_reader, sbml_document, sbml_model = load_sbml_from_string(
             sbml_string
         )
@@ -97,6 +120,18 @@ def from_string(sbml_string, model_id: str = None):
             model_id=model_id,
         )
 
+    @staticmethod
+    def from_antimony(ant_model: str | Path) -> SbmlModel:
+        """Create SBML model from an Antimony model.
+
+        Requires the `antimony` package (https://github.com/sys-bio/antimony).
+
+        :param ant_model: Antimony model as string or path to file.
+            Strings are interpreted as Antimony model strings.
+        """
+        sbml_str = antimony2sbml(ant_model)
+        return SbmlModel.from_string(sbml_str)
+
     @property
     def model_id(self):
         return self._model_id
@@ -238,3 +273,43 @@ def sympify_sbml(sbml_obj: libsbml.ASTNode | libsbml.SBase) -> sp.Expr:
     )
 
     return sp.sympify(formula_str, locals=_clash)
+
+
+def antimony2sbml(ant_model: str | Path) -> str:
+    """Convert Antimony model to SBML.
+
+    :param ant_model: Antimony model as string or path to file.
+        Strings are interpreted as Antimony model strings.
+
+    :returns:
+        The SBML model as string.
+    """
+    import antimony as ant
+
+    # Unload everything / free memory
+    ant.clearPreviousLoads()
+    ant.freeAll()
+
+    try:
+        # potentially fails because of too long file name
+        is_file = ant_model and Path(ant_model).exists()
+    except OSError:
+        is_file = False
+
+    if is_file:
+        status = ant.loadAntimonyFile(str(ant_model))
+    else:
+        status = ant.loadAntimonyString(ant_model)
+    if status < 0:
+        raise RuntimeError(
+            f"Antimony model could not be loaded: {ant.getLastError()}"
+        )
+
+    if (main_module_name := ant.getMainModuleName()) is None:
+        raise AssertionError("There is no Antimony module.")
+
+    sbml_str = ant.getSBMLString(main_module_name)
+    if not sbml_str:
+        raise ValueError("Antimony model could not be converted to SBML.")
+
+    return sbml_str
diff --git a/pyproject.toml b/pyproject.toml
index 1758476a..6eeb3480 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,11 +35,11 @@ maintainers = [
 
 [project.optional-dependencies]
 tests = [
+    "antimony>=2.14.0",
+    "pysb",
     "pytest",
     "pytest-cov",
-    "simplesbml",
     "scipy",
-    "pysb",
 ]
 quality = [
     "pre-commit",
@@ -48,6 +48,9 @@ reports = [
     # https://github.com/spatialaudio/nbsphinx/issues/641
     "Jinja2==3.0.3",
 ]
+antimony = [
+    "antimony>=2.14.0",
+]
 combine = [
     "python-libcombine>=0.2.6",
 ]
@@ -61,6 +64,7 @@ doc = [
     # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312
     "ipython>=7.21.0, !=8.7.0",
     "pysb",
+    "antimony>=2.14.0"
 ]
 vis = [
     "matplotlib>=3.6.0",
diff --git a/tests/v1/test_combine.py b/tests/v1/test_combine.py
index 08ad5b77..4fca4105 100644
--- a/tests/v1/test_combine.py
+++ b/tests/v1/test_combine.py
@@ -4,8 +4,9 @@
 
 import pandas as pd
 
-import petab
+import petab.v1 as petab
 from petab.C import *
+from petab.v1.models.sbml_model import SbmlModel
 
 # import fixtures
 pytest_plugins = [
@@ -16,10 +17,7 @@
 def test_combine_archive():
     """Test `create_combine_archive` and `Problem.from_combine`"""
     # Create test files
-    import simplesbml
-
-    ss_model = simplesbml.SbmlModel()
-
+    model = SbmlModel.from_antimony("")
     # Create tables with arbitrary content
     measurement_df = pd.DataFrame(
         data={
@@ -80,7 +78,7 @@ def test_combine_archive():
     ) as tempdir:
         # Write test data
         outdir = Path(tempdir)
-        petab.write_sbml(ss_model.document, outdir / sbml_file_name)
+        model.to_file(outdir / sbml_file_name)
         petab.write_measurement_df(
             measurement_df, outdir / measurement_file_name
         )
diff --git a/tests/v1/test_deprecated.py b/tests/v1/test_deprecated.py
index 4af41fa3..b78e7856 100644
--- a/tests/v1/test_deprecated.py
+++ b/tests/v1/test_deprecated.py
@@ -14,7 +14,7 @@ def test_problem_with_sbml_model():
     """Test that a problem can be correctly created from sbml model."""
     # retrieve test data
     (
-        ss_model,
+        model,
         condition_df,
         observable_df,
         measurement_df,
@@ -23,7 +23,7 @@ def test_problem_with_sbml_model():
 
     with pytest.deprecated_call():
         petab_problem = petab.Problem(  # noqa: F811
-            sbml_model=ss_model.model,
+            model=model,
             condition_df=condition_df,
             measurement_df=measurement_df,
             parameter_df=parameter_df,
diff --git a/tests/v1/test_lint.py b/tests/v1/test_lint.py
index b178a425..d75bdcea 100644
--- a/tests/v1/test_lint.py
+++ b/tests/v1/test_lint.py
@@ -18,7 +18,6 @@
 
 def test_assert_measured_observables_present():
     # create test model
-
     measurement_df = pd.DataFrame(
         data={
             OBSERVABLE_ID: ["non-existing1"],
@@ -255,15 +254,15 @@ def test_assert_no_leading_trailing_whitespace():
 
 
 def test_assert_model_parameters_in_condition_or_parameter_table():
-    import simplesbml
-
     from petab.models.sbml_model import SbmlModel
 
-    ss_model = simplesbml.SbmlModel()
-    ss_model.addParameter("parameter1", 0.0)
-    ss_model.addParameter("noiseParameter1_", 0.0)
-    ss_model.addParameter("observableParameter1_", 0.0)
-    sbml_model = SbmlModel(sbml_model=ss_model.model)
+    ant_model = """
+    parameter1 = 0.0
+    noiseParameter1_ = 0.0
+    observableParameter1_ = 0.0
+    """
+    sbml_model = SbmlModel.from_antimony(ant_model)
+    assert sbml_model.is_valid()
 
     lint.assert_model_parameters_in_condition_or_parameter_table(
         sbml_model, pd.DataFrame(columns=["parameter1"]), pd.DataFrame()
@@ -284,7 +283,10 @@ def test_assert_model_parameters_in_condition_or_parameter_table():
         sbml_model, pd.DataFrame(), pd.DataFrame()
     )
 
-    ss_model.addAssignmentRule("parameter1", "parameter2")
+    sbml_model = SbmlModel.from_antimony(
+        ant_model + "\nparameter2 = 0\nparameter1 := parameter2"
+    )
+    assert sbml_model.is_valid()
     lint.assert_model_parameters_in_condition_or_parameter_table(
         sbml_model, pd.DataFrame(), pd.DataFrame()
     )
@@ -499,12 +501,11 @@ def test_assert_measurement_conditions_present_in_condition_table():
 
 def test_check_condition_df():
     """Check that we correctly detect errors in condition table"""
-    import simplesbml
 
     from petab.models.sbml_model import SbmlModel
 
-    ss_model = simplesbml.SbmlModel()
-    model = SbmlModel(sbml_model=ss_model.model)
+    model = SbmlModel.from_antimony("")
+
     condition_df = pd.DataFrame(
         data={
             CONDITION_ID: ["condition1"],
@@ -527,7 +528,7 @@ def test_check_condition_df():
     lint.check_condition_df(condition_df, model, observable_df)
 
     # fix by adding parameter
-    ss_model.addParameter("p1", 1.0)
+    model = SbmlModel.from_antimony("p1 = 1")
     lint.check_condition_df(condition_df, model)
 
     # species missing in model
@@ -536,7 +537,7 @@ def test_check_condition_df():
         lint.check_condition_df(condition_df, model)
 
     # fix:
-    ss_model.addSpecies("[s1]", 1.0)
+    model = SbmlModel.from_antimony("p1 = 1; species s1 = 1")
     lint.check_condition_df(condition_df, model)
 
     # compartment missing in model
@@ -545,7 +546,9 @@ def test_check_condition_df():
         lint.check_condition_df(condition_df, model)
 
     # fix:
-    ss_model.addCompartment(comp_id="c2", vol=1.0)
+    model = SbmlModel.from_antimony(
+        "p1 = 1; species s1 = 1; compartment c2 = 1"
+    )
     lint.check_condition_df(condition_df, model)
 
 
diff --git a/tests/v1/test_observables.py b/tests/v1/test_observables.py
index f9547fec..e870ac12 100644
--- a/tests/v1/test_observables.py
+++ b/tests/v1/test_observables.py
@@ -69,14 +69,11 @@ def test_write_observable_df():
 
 def test_get_output_parameters():
     """Test measurements.get_output_parameters."""
-    # sbml model
-    import simplesbml
-
     from petab.models.sbml_model import SbmlModel
 
-    ss_model = simplesbml.SbmlModel()
-    ss_model.addParameter("fixedParameter1", 1.0)
-    ss_model.addParameter("observable_1", 1.0)
+    model = SbmlModel.from_antimony(
+        "fixedParameter1 = 1.0; observable_1 = 1.0"
+    )
 
     # observable file
     observable_df = pd.DataFrame(
@@ -88,9 +85,7 @@ def test_get_output_parameters():
         }
     ).set_index(OBSERVABLE_ID)
 
-    output_parameters = petab.get_output_parameters(
-        observable_df, SbmlModel(sbml_model=ss_model.model)
-    )
+    output_parameters = petab.get_output_parameters(observable_df, model)
 
     assert output_parameters == ["offset", "scaling"]
 
@@ -105,9 +100,7 @@ def test_get_output_parameters():
         }
     ).set_index(OBSERVABLE_ID)
 
-    output_parameters = petab.get_output_parameters(
-        observable_df, SbmlModel(sbml_model=ss_model.model)
-    )
+    output_parameters = petab.get_output_parameters(observable_df, model)
 
     assert output_parameters == ["N", "beta"]
 
diff --git a/tests/v1/test_parameter_mapping.py b/tests/v1/test_parameter_mapping.py
index e499bd5c..4fe44aa5 100644
--- a/tests/v1/test_parameter_mapping.py
+++ b/tests/v1/test_parameter_mapping.py
@@ -32,16 +32,15 @@ def test_no_condition_specific(condition_df_2_conditions):
             }
         )
 
-        import simplesbml
-
-        ss_model = simplesbml.SbmlModel()
-        ss_model.addParameter("dynamicParameter1", 1.0)
-        ss_model.addParameter("dynamicParameter2", 2.0)
-        ss_model.addParameter("dynamicParameter3", 3.0)
+        model = SbmlModel.from_antimony(
+            "dynamicParameter1 = 1.0; "
+            "dynamicParameter2 = 2.0; "
+            "dynamicParameter3 = 3.0; "
+            # add species, which will have initial concentration in condition
+            #  table but which should not show up in mapping
+            "species someSpecies = 1.0"
+        )
 
-        # add species, which will have initial concentration in condition table
-        #  but which should not show up in mapping
-        ss_model.addSpecies("[someSpecies]", 1.0)
         condition_df["someSpecies"] = [0.0, 0.0]
 
         # Test without parameter table
@@ -80,7 +79,6 @@ def test_no_condition_specific(condition_df_2_conditions):
             ),
         ]
 
-        model = SbmlModel(sbml_model=ss_model.model)
         actual = petab.get_optimization_to_simulation_parameter_mapping(
             model=model,
             measurement_df=measurement_df,
@@ -245,13 +243,9 @@ def test_no_condition_specific(condition_df_2_conditions):
     def test_all_override(condition_df_2_conditions):
         # Condition-specific parameters overriding original parameters
         condition_df = condition_df_2_conditions
-
-        import simplesbml
-
-        ss_model = simplesbml.SbmlModel()
-        ss_model.addParameter("dynamicParameter1", 0.0)
-        ss_model.addParameter("dynamicParameter2", 0.0)
-        model = SbmlModel(sbml_model=ss_model.model)
+        model = SbmlModel.from_antimony(
+            "dynamicParameter1 = 0.0; dynamicParameter2 = 0.0"
+        )
 
         measurement_df = pd.DataFrame(
             data={
@@ -364,15 +358,16 @@ def test_partial_override(condition_df_2_conditions):
         )
         condition_df.set_index("conditionId", inplace=True)
 
-        import simplesbml
-
-        ss_model = simplesbml.SbmlModel()
-        ss_model.addParameter("fixedParameter1", 0.5)
-        ss_model.addParameter("fixedParameter2", 1.0)
-        ss_model.addParameter("dynamicParameter1", 0.0)
-        ss_model.addParameter("observableParameter1_obs1", 0.0)
-        ss_model.addParameter("observableParameter2_obs1", 0.0)
-        ss_model.addParameter("observableParameter1_obs2", 0.0)
+        model = SbmlModel.from_antimony(
+            """
+            fixedParameter1 = 0.5
+            fixedParameter2 = 1.0
+            dynamicParameter1 = 0.0
+            observableParameter1_obs1 = 0.0
+            observableParameter2_obs1 = 0.0
+            observableParameter1_obs2 = 0.0
+            """
+        )
 
         measurement_df = pd.DataFrame(
             data={
@@ -454,7 +449,7 @@ def test_partial_override(condition_df_2_conditions):
         actual = petab.get_optimization_to_simulation_parameter_mapping(
             measurement_df=measurement_df,
             condition_df=condition_df,
-            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            model=model,
             parameter_df=parameter_df,
         )
 
@@ -504,12 +499,9 @@ def test_parameterized_condition_table():
         )
         parameter_df.set_index(PARAMETER_ID, inplace=True)
 
-        import simplesbml
-
-        ss_model = simplesbml.SbmlModel()
-        ss_model.addParameter("dynamicParameter1", 1.0)
+        model = SbmlModel.from_antimony("dynamicParameter1 = 1.0")
 
-        assert petab.get_model_parameters(ss_model.model) == [
+        assert petab.get_model_parameters(model.sbml_model) == [
             "dynamicParameter1"
         ]
 
@@ -517,7 +509,7 @@ def test_parameterized_condition_table():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            model=model,
         )
 
         expected = [
@@ -550,13 +542,10 @@ def test_parameterized_condition_table_changed_scale():
         overridee_id = "overridee"
 
         # set up model
-        import simplesbml
-
-        ss_model = simplesbml.SbmlModel()
-        ss_model.addParameter(overridee_id, 2.0)
-        assert petab.get_model_parameters(ss_model.model) == [overridee_id]
+        model = SbmlModel.from_antimony(f"{overridee_id} = 2.0")
+        assert petab.get_model_parameters(model.sbml_model) == [overridee_id]
         assert petab.get_model_parameters(
-            ss_model.model, with_values=True
+            model.sbml_model, with_values=True
         ) == {overridee_id: 2.0}
 
         # set up condition table
@@ -614,7 +603,7 @@ def test_parameterized_condition_table_changed_scale():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            model=model,
         )
 
         expected = [
@@ -638,7 +627,7 @@ def test_parameterized_condition_table_changed_scale():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            model=model,
             scaled_parameters=True,
         )
 
@@ -669,7 +658,7 @@ def test_parameterized_condition_table_changed_scale():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            model=model,
         )
 
         expected = [
diff --git a/tests/v1/test_petab.py b/tests/v1/test_petab.py
index eac237d2..ff9621fa 100644
--- a/tests/v1/test_petab.py
+++ b/tests/v1/test_petab.py
@@ -6,7 +6,6 @@
 from math import nan
 from pathlib import Path
 
-import libsbml
 import numpy as np
 import pandas as pd
 import pytest
@@ -39,11 +38,8 @@ def condition_df_2_conditions():
 def petab_problem():
     """Test petab problem."""
     # create test model
-    import simplesbml
-
-    model = simplesbml.SbmlModel()
-    model.addParameter("fixedParameter1", 0.0)
-    model.addParameter("observable_1", 0.0)
+    ant_model = "fixedParameter1=0.0; observable_1=0.0"
+    model = SbmlModel.from_antimony(ant_model)
 
     petab_problem = petab.Problem()
     petab_problem.add_measurement(
@@ -79,7 +75,7 @@ def petab_problem():
 
     with tempfile.TemporaryDirectory() as temp_dir:
         sbml_file_name = Path(temp_dir, "model.xml")
-        libsbml.writeSBMLToFile(model.document, str(sbml_file_name))
+        model.to_file(sbml_file_name)
 
         measurement_file_name = Path(temp_dir, "measurements.tsv")
         petab.write_measurement_df(
@@ -285,13 +281,15 @@ def test_create_parameter_df(
     condition_df_2_conditions,
 ):  # pylint: disable=W0621
     """Test petab.create_parameter_df."""
-    import simplesbml
-
-    ss_model = simplesbml.SbmlModel()
-    ss_model.addSpecies("[x1]", 1.0)
-    ss_model.addParameter("fixedParameter1", 2.0)
-    ss_model.addParameter("p0", 3.0)
-    model = SbmlModel(sbml_model=ss_model.model)
+    ant_model = """
+    species x1 = 1.0
+    fixedParameter1 = 2.0
+    p0 = 3.0
+    # Add assignment rule target which should be ignored
+    assignment_target = 0.0
+    assignment_target := 1.0
+    """
+    model = SbmlModel.from_antimony(ant_model)
 
     observable_df = pd.DataFrame(
         data={
@@ -300,10 +298,6 @@ def test_create_parameter_df(
         }
     ).set_index(OBSERVABLE_ID)
 
-    # Add assignment rule target which should be ignored
-    ss_model.addParameter("assignment_target", 0.0)
-    ss_model.addAssignmentRule("assignment_target", "1.0")
-
     measurement_df = pd.DataFrame(
         data={
             OBSERVABLE_ID: ["obs1", "obs2"],
@@ -319,10 +313,10 @@ def test_create_parameter_df(
     with warnings.catch_warnings(record=True) as w:
         warnings.simplefilter("always")
         parameter_df = petab.v1.create_parameter_df(
-            ss_model.model,
-            condition_df_2_conditions,
-            observable_df,
-            measurement_df,
+            sbml_model=model.sbml_model,
+            condition_df=condition_df_2_conditions,
+            observable_df=observable_df,
+            measurement_df=measurement_df,
         )
         assert len(w) == 1
         assert issubclass(w[-1].category, DeprecationWarning)
diff --git a/tests/v1/test_sbml.py b/tests/v1/test_sbml.py
index 350a2f0d..5c262d43 100644
--- a/tests/v1/test_sbml.py
+++ b/tests/v1/test_sbml.py
@@ -13,17 +13,16 @@
 
 def create_test_data():
     # Create test model and data files
-    import simplesbml
-
-    ss_model = simplesbml.SbmlModel()
-    ss_model.addCompartment(comp_id="compartment_1", vol=1)
-    for i in range(1, 4):
-        ss_model.addParameter(f"parameter_{i}", i)
-
-    for i in range(1, 5):
-        ss_model.addSpecies(f"[species_{i}]", 10 * i)
-
-    ss_model.addAssignmentRule("species_2", "25")
+    model = SbmlModel.from_antimony(
+        "\n".join(
+            [
+                "compartment compartment_1 = 1",
+                *(f"species species_{i} = 10 * {i}" for i in range(1, 5)),
+                *(f"parameter_{i} = {i}" for i in range(1, 4)),
+                "species_2 := 25",
+            ]
+        )
+    )
 
     condition_df = pd.DataFrame(
         {
@@ -68,7 +67,7 @@ def create_test_data():
     )
     parameter_df.set_index([petab.PARAMETER_ID], inplace=True)
 
-    return ss_model, condition_df, observable_df, measurement_df, parameter_df
+    return model, condition_df, observable_df, measurement_df, parameter_df
 
 
 def check_model(condition_model):
@@ -99,7 +98,7 @@ def test_get_condition_specific_models():
     """Test for petab.sbml.get_condition_specific_models"""
     # retrieve test data
     (
-        ss_model,
+        model,
         condition_df,
         observable_df,
         measurement_df,
@@ -107,7 +106,7 @@ def test_get_condition_specific_models():
     ) = create_test_data()
 
     petab_problem = petab.Problem(
-        model=petab.models.sbml_model.SbmlModel(ss_model.model),
+        model=model,
         condition_df=condition_df,
         observable_df=observable_df,
         measurement_df=measurement_df,
@@ -133,3 +132,18 @@ def test_sbml_model_repr():
     sbml_model.setId("test")
     petab_model = SbmlModel(sbml_model)
     assert repr(petab_model) == "<SbmlModel 'test'>"
+
+
+def test_sbml_from_ant():
+    ant_model = """
+    model test
+        R1: S1 -> S2; k1*S1
+        k1 = 1
+    end
+    """
+    petab_model = SbmlModel.from_antimony(ant_model)
+    assert petab_model.model_id == "test"
+    assert petab_model.get_parameter_value("k1") == 1.0
+    assert set(petab_model.get_valid_parameters_for_parameter_table()) == {
+        "k1"
+    }
diff --git a/tests/v1/test_simplify.py b/tests/v1/test_simplify.py
index 3d9a8909..9aa25f8f 100644
--- a/tests/v1/test_simplify.py
+++ b/tests/v1/test_simplify.py
@@ -3,7 +3,6 @@
 
 import pandas as pd
 import pytest
-import simplesbml
 from pandas.testing import *
 
 from petab import Problem
@@ -14,9 +13,9 @@
 
 @pytest.fixture
 def problem() -> Problem:
-    ss_model = simplesbml.SbmlModel()
-    ss_model.addParameter("some_parameter", val=1.0)
-    ss_model.addParameter("same_value_for_all_conditions", val=1.0)
+    model = SbmlModel.from_antimony(
+        "some_parameter = 1.0; same_value_for_all_conditions = 1.0"
+    )
 
     observable_df = pd.DataFrame(
         {
@@ -53,7 +52,7 @@ def problem() -> Problem:
         }
     )
     yield Problem(
-        model=SbmlModel(sbml_model=ss_model.getModel()),
+        model=model,
         condition_df=conditions_df,
         observable_df=observable_df,
         measurement_df=measurement_df,