From 0fcffbdac0c069eeb437382ad5edaef2f18ebf09 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 12 Oct 2026 11:02:09 +0200 Subject: [PATCH] Use `petab.v1` imports instead of deprecated top-level `petab` aliases libpetab-python will remove the deprecated top-level `petab.*` aliases, leaving only `petab.v1`, `petab.v2`, `petab.ENV_NUM_THREADS` and `petab.__version__`. `from petab.yaml import load_yaml` in `overview.py` would then break `import benchmark_models_petab`. Switch to `petab.v1` there and in the problem-specific generator scripts and README snippets under `problems/*/resources/` (Smith_BMCSystBiol2013, Blasi_CellSystems2016, Isensee_JCB2018). In Smith_BMCSystBiol2013's `generate_petab.py`, `import petab.v1.models` would rebind `petab` to the top-level package and shadow the `petab.v1` alias, so use `from petab.v1.models import sbml_model` instead. `petab.v1` exists since petab 0.4.0, so the `petab>=0.4.0` requirement is unchanged. Drafted with AI assistance. Co-Authored-By: Claude Opus 5.5 --- .../resources/petab_select/03_create_petab.py | 4 ++-- problems/Isensee_JCB2018/resources/README.md | 2 +- problems/Smith_BMCSystBiol2013/resources/generate_petab.py | 6 +++--- src/python/benchmark_models_petab/overview.py | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/problems/Blasi_CellSystems2016/resources/petab_select/03_create_petab.py b/problems/Blasi_CellSystems2016/resources/petab_select/03_create_petab.py index 02051089..074cd7de 100644 --- a/problems/Blasi_CellSystems2016/resources/petab_select/03_create_petab.py +++ b/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, diff --git a/problems/Isensee_JCB2018/resources/README.md b/problems/Isensee_JCB2018/resources/README.md index 8bc5aeca..bb205311 100644 --- a/problems/Isensee_JCB2018/resources/README.md +++ b/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") diff --git a/problems/Smith_BMCSystBiol2013/resources/generate_petab.py b/problems/Smith_BMCSystBiol2013/resources/generate_petab.py index 4b78efeb..74d402a2 100644 --- a/problems/Smith_BMCSystBiol2013/resources/generate_petab.py +++ b/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 diff --git a/src/python/benchmark_models_petab/overview.py b/src/python/benchmark_models_petab/overview.py index 8ff3706f..35759c9a 100644 --- a/src/python/benchmark_models_petab/overview.py +++ b/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