Update to libpetab 0.4.0

pypesto/hierarchical/base_problem.py

@@ -11,8 +11,8 @@
 
 try:
     import amici
-    import petab
-    from petab.C import OBSERVABLE_ID, TIME
+    import petab.v1 as petab
+    from petab.v1.C import OBSERVABLE_ID, TIME
 except ImportError:
     pass
 

pypesto/hierarchical/inner_calculator_collector.py

@@ -46,7 +46,7 @@
 
 try:
     import amici
-    import petab
+    import petab.v1 as petab
     from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     petab = None

pypesto/hierarchical/ordinal/problem.py

@@ -43,8 +43,8 @@
 
 try:
     import amici
-    import petab
-    from petab.C import OBSERVABLE_ID, PARAMETER_SEPARATOR
+    import petab.v1 as petab
+    from petab.v1.C import OBSERVABLE_ID, PARAMETER_SEPARATOR
 except ImportError:
     pass
 

pypesto/hierarchical/petab.py

@@ -3,10 +3,10 @@
 from typing import Literal
 
 import pandas as pd
-import petab
+import petab.v1 as petab
 import sympy as sp
 from more_itertools import one
-from petab.C import (
+from petab.v1.C import (
     ESTIMATE,
     LIN,
     NOISE_PARAMETERS,
@@ -15,9 +15,9 @@
     OBSERVABLE_TRANSFORMATION,
     PARAMETER_SEPARATOR,
 )
-from petab.C import LOWER_BOUND as PETAB_LOWER_BOUND
-from petab.C import UPPER_BOUND as PETAB_UPPER_BOUND
-from petab.observables import get_formula_placeholders
+from petab.v1.C import LOWER_BOUND as PETAB_LOWER_BOUND
+from petab.v1.C import UPPER_BOUND as PETAB_UPPER_BOUND
+from petab.v1.observables import get_formula_placeholders
 
 from ..C import (
     CENSORING_BOUNDS,

pypesto/hierarchical/relative/problem.py

@@ -19,8 +19,8 @@
 
 try:
     import amici
-    import petab
-    from petab.C import (
+    import petab.v1 as petab
+    from petab.v1.C import (
         ESTIMATE,
         LOWER_BOUND,
         NOISE_PARAMETERS,

pypesto/hierarchical/semiquantitative/problem.py

@@ -30,8 +30,8 @@
 
 try:
     import amici
-    import petab
-    from petab.C import (
+    import petab.v1 as petab
+    from petab.v1.C import (
         ESTIMATE,
         LOWER_BOUND,
         NOISE_PARAMETERS,

pypesto/objective/roadrunner/petab_importer_roadrunner.py

@@ -14,15 +14,15 @@
 from typing import Any
 
 import libsbml
-import petab
+import petab.v1
 import roadrunner
-from petab.C import (
+from petab.v1.C import (
     OBSERVABLE_FORMULA,
     PREEQUILIBRATION_CONDITION_ID,
     SIMULATION_CONDITION_ID,
 )
-from petab.models.sbml_model import SbmlModel
-from petab.parameter_mapping import ParMappingDictQuadruple
+from petab.v1.models.sbml_model import SbmlModel
+from petab.v1.parameter_mapping import ParMappingDictQuadruple
 
 import pypesto.C
 

pypesto/objective/roadrunner/road_runner.py

@@ -8,8 +8,8 @@
 
 import numpy as np
 import roadrunner
-from petab import Problem as PetabProblem
-from petab.parameter_mapping import ParMappingDictQuadruple
+from petab.v1 import Problem as PetabProblem
+from petab.v1.parameter_mapping import ParMappingDictQuadruple
 
 from ...C import MODE_FUN, MODE_RES, ROADRUNNER_INSTANCE, X_NAMES, ModeType
 from ..base import ObjectiveBase

pypesto/objective/roadrunner/roadrunner_calculator.py

@@ -7,9 +7,9 @@
 from typing import Optional
 
 import numpy as np
-import petab
+import petab.v1 as petab
 import roadrunner
-from petab.parameter_mapping import ParMappingDictQuadruple
+from petab.v1.parameter_mapping import ParMappingDictQuadruple
 
 from ...C import (
     FVAL,

pypesto/objective/roadrunner/utils.py

@@ -11,9 +11,9 @@
 
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 import roadrunner
-from petab.C import (
+from petab.v1.C import (
     LIN,
     MEASUREMENT,
     NOISE_DISTRIBUTION,

pypesto/petab/importer.py

@@ -19,15 +19,15 @@
 
 import numpy as np
 import pandas as pd
-import petab
-from petab.C import (
+import petab.v1 as petab
+from petab.v1.C import (
     ESTIMATE,
     NOISE_PARAMETERS,
     OBSERVABLE_ID,
     PREEQUILIBRATION_CONDITION_ID,
     SIMULATION_CONDITION_ID,
 )
-from petab.models import MODEL_TYPE_SBML
+from petab.v1.models import MODEL_TYPE_SBML
 
 from ..C import (
     CENSORED,

pypesto/select/misc.py

@@ -4,9 +4,9 @@
 from collections.abc import Iterable
 
 import pandas as pd
-import petab
+import petab.v1 as petab
 import petab_select.ui
-from petab.C import ESTIMATE, NOMINAL_VALUE
+from petab.v1.C import ESTIMATE, NOMINAL_VALUE
 from petab_select import Model, parameter_string_to_value
 from petab_select.constants import PETAB_PROBLEM
 

pypesto/testing/examples.py

@@ -14,7 +14,7 @@ def get_Boehm_JProteomeRes2014_hierarchical_petab() -> (
     Creates a modified version of the Boehm_JProteomeRes2014 benchmark problem,
     suitable for hierarchical optimization.
     """
-    import petab
+    import petab.v1 as petab
     from benchmark_models_petab import get_problem
 
     from pypesto.C import PARAMETER_TYPE

pypesto/visualize/model_fit.py

@@ -14,10 +14,10 @@
 import matplotlib.axes
 import matplotlib.pyplot as plt
 import numpy as np
-import petab
+import petab.v1 as petab
 from amici.petab.conditions import fill_in_parameters
 from amici.petab.simulations import rdatas_to_simulation_df
-from petab.visualize import plot_problem
+from petab.v1.visualize import plot_problem
 
 from ..C import CENSORED, ORDINAL, RDATAS, SEMIQUANTITATIVE
 from ..objective import (

pypesto/visualize/ordinal_categories.py

@@ -10,7 +10,7 @@
 try:
     import amici
     from amici.petab.conditions import fill_in_parameters
-    from petab.C import OBSERVABLE_ID
+    from petab.v1.C import OBSERVABLE_ID
 
     from ..hierarchical.ordinal.calculator import OrdinalCalculator
     from ..hierarchical.ordinal.parameter import OrdinalParameter

pypesto/visualize/sampling.py

@@ -816,7 +816,7 @@ def sampling_prediction_trajectories(
     # Handle data
     grouped_measurements = {}
     if measurement_df is not None:
-        import petab
+        import petab.v1 as petab
 
         for condition_id in condition_ids:
             if petab.PARAMETER_SEPARATOR in condition_id:

setup.cfg

@@ -98,7 +98,7 @@ amici =
 roadrunner =
     libroadrunner >= 2.6.0
 petab =
-    petab >= 0.2.0
+    petab >= 0.4.0
 ipopt =
     cyipopt >= 1.3.0
 dlib =

test/base/test_roadrunner.py

@@ -4,7 +4,7 @@
 import os
 
 import benchmark_models_petab as models
-import petab
+import petab.v1 as petab
 import petabtests
 import pytest
 

test/hierarchical/test_censored.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import numpy as np
-import petab
+import petab.v1 as petab
 
 import pypesto
 import pypesto.logging

test/hierarchical/test_hierarchical.py

@@ -6,7 +6,7 @@
 import amici
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 
 import pypesto
 from pypesto.C import (

test/hierarchical/test_ordinal.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import numpy as np
-import petab
+import petab.v1 as petab
 import pytest
 
 import pypesto

test/hierarchical/test_spline.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 import numpy as np
-import petab
+import petab.v1 as petab
 import pytest
 
 import pypesto

test/petab/test_amici_objective.py

@@ -7,7 +7,7 @@
 import amici
 import benchmark_models_petab as models
 import numpy as np
-import petab
+import petab.v1 as petab
 import pytest
 
 import pypesto

test/petab/test_amici_predictor.py

@@ -8,7 +8,7 @@
 import libsbml
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 import pytest
 
 import pypesto

test/petab/test_petab_import.py

@@ -9,7 +9,7 @@
 import amici
 import benchmark_models_petab as models
 import numpy as np
-import petab
+import petab.v1 as petab
 import petabtests
 import pytest
 

test/petab/test_petab_suite.py

@@ -3,7 +3,7 @@
 import logging
 
 import amici.petab.simulations
-import petab
+import petab.v1 as petab
 import petabtests
 import pytest
 

test/sample/test_sample.py

@@ -93,7 +93,7 @@ def rosenbrock_problem():
 
 
 def create_petab_problem():
-    import petab
+    import petab.v1 as petab
 
     import pypesto.petab
 

test/select/test_select.py

@@ -3,11 +3,11 @@
 
 import numpy as np
 import pandas as pd
-import petab
+import petab.v1 as petab
 import petab_select
 import pytest
 from more_itertools import one
-from petab.C import NOMINAL_VALUE
+from petab.v1.C import NOMINAL_VALUE
 from petab_select import (
     ESTIMATE,
     PETAB_PROBLEM,

test/visualize/test_visualize.py

@@ -6,7 +6,7 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-import petab
+import petab.v1 as petab
 import pytest
 import scipy.optimize as so
 

tox.ini

@@ -76,11 +76,12 @@ description =
 extras = test,amici,petab,pyswarm,roadrunner
 deps =
     git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master\#subdirectory=src/python
-    git+https://github.com/PEtab-dev/petab_test_suite@main
-    git+https://github.com/FFroehlich/pysb@fix_pattern_matching
     git+https://github.com/AMICI-dev/amici.git@develop\#egg=amici&subdirectory=python/sdist
 
 commands =
+    python3 -m pip install git+https://github.com/PEtab-dev/petab_test_suite@main
+    python3 -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching
+    python3 -m pip install -U sympy
     pytest --cov=pypesto --cov-report=xml --cov-append \
         test/petab
 description =