test_conversion.py

import logging

import pandas as pd
import pytest

import petab.v1 as v1
import petab.v2 as v2
from petab.v2 import Problem
from petab.v2.petab1to2 import petab1to2, v1v2_observable_df


def test_v1v2_observable_df_noise_distribution():
    """Test that noiseDistribution is correctly merged with
    observableTransformation."""
    observable_df = pd.DataFrame(
        data={
            v1.C.OBSERVABLE_ID: ["obs1", "obs2"],
            v1.C.OBSERVABLE_FORMULA: ["a", "b"],
            v1.C.NOISE_FORMULA: ["1", "1"],
            v1.C.OBSERVABLE_TRANSFORMATION: [v1.C.LIN, v1.C.LOG],
            v1.C.NOISE_DISTRIBUTION: [v1.C.NORMAL, v1.C.NORMAL],
        }
    ).set_index(v1.C.OBSERVABLE_ID)

    new_df = v1v2_observable_df(observable_df)

    assert list(new_df[v2.C.NOISE_DISTRIBUTION]) == [
        v2.C.NORMAL,
        v2.C.LOG_NORMAL,
    ]


def test_petab1to2_remote():
    """Test that we can upgrade a remote PEtab 1.0.0 problem."""
    yaml_url = (
        "https://cdn.jsdelivr.net/gh/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"
)
@pytest.mark.filterwarnings(
    "ignore:.*Initialisation priors in parameter table are not supported.*:"
    "UserWarning"
)
@pytest.mark.filterwarnings(
    "ignore:.*Parameter scales are not supported in PEtab v2.*: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)