diff --git a/pypesto/hierarchical/base_problem.py b/pypesto/hierarchical/base_problem.py index e06b60e4a..af85d05ec 100644 --- a/pypesto/hierarchical/base_problem.py +++ b/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 diff --git a/pypesto/hierarchical/inner_calculator_collector.py b/pypesto/hierarchical/inner_calculator_collector.py index e06f66178..d0cc72e8a 100644 --- a/pypesto/hierarchical/inner_calculator_collector.py +++ b/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 diff --git a/pypesto/hierarchical/ordinal/problem.py b/pypesto/hierarchical/ordinal/problem.py index 8c7e0b73f..0323e4e7b 100644 --- a/pypesto/hierarchical/ordinal/problem.py +++ b/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 diff --git a/pypesto/hierarchical/petab.py b/pypesto/hierarchical/petab.py index 8dfd598ee..278f01116 100644 --- a/pypesto/hierarchical/petab.py +++ b/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, diff --git a/pypesto/hierarchical/relative/problem.py b/pypesto/hierarchical/relative/problem.py index 8c1ddd79c..790fdc099 100644 --- a/pypesto/hierarchical/relative/problem.py +++ b/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, diff --git a/pypesto/hierarchical/semiquantitative/problem.py b/pypesto/hierarchical/semiquantitative/problem.py index fabd7f317..3698a442c 100644 --- a/pypesto/hierarchical/semiquantitative/problem.py +++ b/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, diff --git a/pypesto/objective/roadrunner/petab_importer_roadrunner.py b/pypesto/objective/roadrunner/petab_importer_roadrunner.py index 4d8b4d2ba..3a1f67e1f 100644 --- a/pypesto/objective/roadrunner/petab_importer_roadrunner.py +++ b/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 diff --git a/pypesto/objective/roadrunner/road_runner.py b/pypesto/objective/roadrunner/road_runner.py index 98a9a9e7e..635d2b6e5 100644 --- a/pypesto/objective/roadrunner/road_runner.py +++ b/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 diff --git a/pypesto/objective/roadrunner/roadrunner_calculator.py b/pypesto/objective/roadrunner/roadrunner_calculator.py index 4b6804c76..f6c1cf652 100644 --- a/pypesto/objective/roadrunner/roadrunner_calculator.py +++ b/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, diff --git a/pypesto/objective/roadrunner/utils.py b/pypesto/objective/roadrunner/utils.py index 364ea8776..e29291ef3 100644 --- a/pypesto/objective/roadrunner/utils.py +++ b/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, diff --git a/pypesto/petab/importer.py b/pypesto/petab/importer.py index 23103d673..6160247dd 100644 --- a/pypesto/petab/importer.py +++ b/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, diff --git a/pypesto/select/misc.py b/pypesto/select/misc.py index 62cfad31c..f5af4bf2b 100644 --- a/pypesto/select/misc.py +++ b/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 diff --git a/pypesto/testing/examples.py b/pypesto/testing/examples.py index 32fa0b6d3..10365832c 100644 --- a/pypesto/testing/examples.py +++ b/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 diff --git a/pypesto/visualize/model_fit.py b/pypesto/visualize/model_fit.py index ec8ea466a..7c0c7ec55 100644 --- a/pypesto/visualize/model_fit.py +++ b/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 ( diff --git a/pypesto/visualize/ordinal_categories.py b/pypesto/visualize/ordinal_categories.py index c229d92f6..b93e97f22 100644 --- a/pypesto/visualize/ordinal_categories.py +++ b/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 diff --git a/pypesto/visualize/sampling.py b/pypesto/visualize/sampling.py index 46c6b4d34..cb89d1e58 100644 --- a/pypesto/visualize/sampling.py +++ b/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: diff --git a/setup.cfg b/setup.cfg index 7ee62a957..71971da40 100644 --- a/setup.cfg +++ b/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 = diff --git a/test/base/test_roadrunner.py b/test/base/test_roadrunner.py index bbff88ff7..acffeca09 100644 --- a/test/base/test_roadrunner.py +++ b/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 diff --git a/test/hierarchical/test_censored.py b/test/hierarchical/test_censored.py index c19e2bb14..2538e050f 100644 --- a/test/hierarchical/test_censored.py +++ b/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 diff --git a/test/hierarchical/test_hierarchical.py b/test/hierarchical/test_hierarchical.py index e9bee2709..bb3645df0 100644 --- a/test/hierarchical/test_hierarchical.py +++ b/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 ( diff --git a/test/hierarchical/test_ordinal.py b/test/hierarchical/test_ordinal.py index ed0b1a681..9a316cb30 100644 --- a/test/hierarchical/test_ordinal.py +++ b/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 diff --git a/test/hierarchical/test_spline.py b/test/hierarchical/test_spline.py index 1d99f05e0..dec410df2 100644 --- a/test/hierarchical/test_spline.py +++ b/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 diff --git a/test/petab/test_amici_objective.py b/test/petab/test_amici_objective.py index c6636444b..00c399f6e 100644 --- a/test/petab/test_amici_objective.py +++ b/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 diff --git a/test/petab/test_amici_predictor.py b/test/petab/test_amici_predictor.py index f081a9e18..b610e2b97 100644 --- a/test/petab/test_amici_predictor.py +++ b/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 diff --git a/test/petab/test_petab_import.py b/test/petab/test_petab_import.py index 4c9cd2243..5b9f94a2e 100644 --- a/test/petab/test_petab_import.py +++ b/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 diff --git a/test/petab/test_petab_suite.py b/test/petab/test_petab_suite.py index 29877ea42..87219c6d8 100644 --- a/test/petab/test_petab_suite.py +++ b/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 diff --git a/test/sample/test_sample.py b/test/sample/test_sample.py index 40d246aa4..b2d246111 100644 --- a/test/sample/test_sample.py +++ b/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 diff --git a/test/select/test_select.py b/test/select/test_select.py index 2ff86def3..b471365d6 100644 --- a/test/select/test_select.py +++ b/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, diff --git a/test/visualize/test_visualize.py b/test/visualize/test_visualize.py index cb75c8f4c..149c65719 100644 --- a/test/visualize/test_visualize.py +++ b/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 diff --git a/tox.ini b/tox.ini index 2c860f336..4d4d5225e 100644 --- a/tox.ini +++ b/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 =