Use petab.v1 imports instead of deprecated top-level petab aliases

problems/Blasi_CellSystems2016/resources/petab_select/03_create_petab.py

@@ -1,8 +1,8 @@
 import pandas as pd
-import petab
+import petab.v1 as petab
 import shutil
 
-from petab import (
+from petab.v1 import (
     CONDITION_ID,
     OBSERVABLE_ID,
     MEASUREMENT,

problems/Isensee_JCB2018/resources/README.md

@@ -3,7 +3,7 @@ The paper describes a model selection problem with four hypotheses. Each hypothe
 This benchmark problem is the parameter estimation problem for the H1-only model. The parameters for the other hypotheses are specified in `parameters_Isensee_JCB2018_model_selection.tsv`. For example, this Python code will create the PEtab problem for the H2+H3 model.
 ```python
 import pandas as pd
-import petab
+import petab.v1 as petab
 
 petab_problem = petab.Problem.from_yaml("Isensee_JCB2018.yaml")
 model_selection_parameter_df = petab.get_parameter_df("parameters_Isensee_JCB2018_model_selection.tsv")

problems/Smith_BMCSystBiol2013/resources/generate_petab.py

@@ -1,17 +1,17 @@
 import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
-import petab
+import petab.v1 as petab
 import re
 import os
-import petab.models
+from petab.v1.models import sbml_model  # noqa: F401
 
 
 from amici.petab_import import import_petab_problem
 from amici.petab_simulate import simulate_petab, rdatas_to_measurement_df, RDATAS
 from pathlib import Path
 from urllib.request import urlopen
-from petab.visualize.plot_data_and_simulation import plot_problem
+from petab.v1.visualize.plot_data_and_simulation import plot_problem
 
 
 model_dir = Path(__file__).parent

src/python/benchmark_models_petab/overview.py

@@ -8,7 +8,7 @@
 import numpy as np
 import pandas as pd
 import petab.v1 as petab
-from petab.yaml import load_yaml
+from petab.v1.yaml import load_yaml
 from sbmlmath import sbml_math_to_sympy
 from sbmlmath.csymbol import TimeSymbol
 from . import MODELS, get_problem, get_problem_yaml_path