test_conversion.py

import logging

import pytest

from petab.v2 import Problem
from petab.v2.petab1to2 import petab1to2


def test_petab1to2_remote():
    """Test that we can upgrade a remote PEtab 1.0.0 problem."""
    yaml_url = (
        "https://raw.githubusercontent.com/PEtab-dev/petab_test_suite"
        "/main/petabtests/cases/v1.0.0/sbml/0001/_0001.yaml"
    )

    problem = petab1to2(yaml_url)
    assert isinstance(problem, Problem)
    assert len(problem.measurements)


try:
    import benchmark_models_petab

    parametrize_or_skip = pytest.mark.parametrize(
        "problem_id", benchmark_models_petab.MODELS
    )
except ImportError:
    parametrize_or_skip = pytest.mark.skip(
        reason="benchmark_models_petab not installed"
    )


@pytest.mark.filterwarnings(
    "ignore:.*Using `log-normal` instead.*:UserWarning"
)
@parametrize_or_skip
def test_benchmark_collection(problem_id):
    """Test that we can upgrade all benchmark collection models."""
    logging.basicConfig(level=logging.DEBUG)

    if problem_id == "Froehlich_CellSystems2018":
        # this is mostly about 6M sympifications in the condition table
        pytest.skip("Too slow. Re-enable once we are faster.")

    yaml_path = benchmark_models_petab.get_problem_yaml_path(problem_id)
    try:
        problem = petab1to2(yaml_path)
    except NotImplementedError as e:
        pytest.skip(str(e))
    assert isinstance(problem, Problem)
    assert len(problem.measurements)