conftest.py

import pytest

import sire as sr


def pytest_addoption(parser):
    parser.addoption(
        "--runslow", action="store_true", default=False, help="run slow tests"
    )
    parser.addoption(
        "--runveryslow",
        action="store_true",
        default=False,
        help="run slow and veryslow tests",
    )


def pytest_configure(config):
    config.addinivalue_line(
        "markers",
        "slow: mark tests as slow to run (takes more than a couple of seconds",
    )
    config.addinivalue_line(
        "markers",
        "veryslow: mark tests as veryslow to run (takes more than 5-10 seconds to run",
    )


def pytest_collection_modifyitems(config, items):
    runslow = False
    runveryslow = False

    if config.getoption("--runslow"):
        runslow = True

    if config.getoption("--runveryslow"):
        runslow = True
        runveryslow = True

    if not runslow:
        skip_slow = pytest.mark.skip(reason="need --runslow option to run")
        for item in items:
            if "slow" in item.keywords:
                item.add_marker(skip_slow)

    if not runveryslow:
        skip_veryslow = pytest.mark.skip(reason="need --runveryslow option to run")
        for item in items:
            if "veryslow" in item.keywords:
                item.add_marker(skip_veryslow)


@pytest.fixture(scope="session")
def ala_mols():
    return sr.load_test_files("ala.top", "ala.crd")


@pytest.fixture(scope="session")
def ose_mols():
    return sr.load_test_files("ose.top", "ose.crd")


@pytest.fixture(scope="session")
def zan_mols():
    return sr.load_test_files("zan.top", "zan.rst")


@pytest.fixture(scope="session")
def h7n9_mols():
    return sr.load_test_files("h7n9.pdb", "h7n9.dcd")


@pytest.fixture(scope="session")
def chol_mols():
    return sr.load_test_files("cholesterol.sdf")


@pytest.fixture(scope="session")
def ala_traj():
    return sr.load_test_files("ala.top", "ala.traj")


@pytest.fixture(scope="session")
def ala_trr():
    return sr.load_test_files("ala.top", "ala.trr")


@pytest.fixture(scope="session")
def p38_mols():
    return sr.load_test_files("p38.pdb")


@pytest.fixture(scope="session")
def alanin_mols():
    return sr.load_test_files("alanin.psf")


@pytest.fixture(scope="session")
def kigaki_mols():
    return sr.load_test_files("kigaki.gro", "kigaki.top")


@pytest.fixture(scope="session")
def neura_mols():
    return sr.load_test_files("proteinbox.crd", "proteinbox.top")


@pytest.fixture(scope="session")
def excluded_mols():
    return sr.load_test_files("excluded.rst7", "excluded.prm7")


@pytest.fixture(scope="session")
def wrapped_mols():
    return sr.load_test_files("wrapped.rst7", "wrapped.prm7")


@pytest.fixture(scope="session")
def openmm_interchange_mols():
    return sr.load_test_files("openmm_interchange.rst7", "openmm_interchange.prm7")


@pytest.fixture(scope="session")
def triclinic_protein():
    return sr.load_test_files("triclinic_protein.prm7", "triclinic_protein.crd")


@pytest.fixture(scope="session")
def triclinic_protein_rst7():
    return sr.load_test_files("triclinic_protein.prm7", "triclinic_protein.rst")


@pytest.fixture(scope="session")
def merged_ethane_methanol():
    return sr.load_test_files("merged_molecule.s3")


@pytest.fixture(scope="session")
def merged_ethane_methane():
    return sr.load_test_files("ethane_methane.bss")


@pytest.fixture(scope="session")
def merged_zan_ose():
    return sr.load_test_files("merged_ligand.s3")


@pytest.fixture(scope="session")
def ethane_12dichloroethane():
    return sr.load_test_files("ethane_12dichloroethane.bss")


@pytest.fixture(scope="session")
def cyclopentane_cyclohexane():
    return sr.load_test_files("cyclopentane_cyclohexane.bss")


@pytest.fixture(scope="session")
def propane_cyclopropane():
    return sr.load_test_files("propane_cyclopropane.bss")


@pytest.fixture(scope="session")
def pentane_cyclopentane():
    return sr.load_test_files("pentane_cyclopentane.bss")


@pytest.fixture(scope="session")
def reordered_protein():
    return sr.load_test_files("reordered_protein.top", "reordered_protein.crd")


@pytest.fixture(scope="session")
def pdb_3nss():
    return sr.load_test_files("3NSS.pdb")


@pytest.fixture(scope="session")
def pdbx_3nss():
    if "gemmi" in sr.convert.supported_formats():
        return sr.load_test_files("3NSS.cif")
    else:
        return None


@pytest.fixture(scope="session")
def ejm55_sdf():
    return sr.load_test_files("ejm55.sdf")


@pytest.fixture(scope="session")
def ejm55_gro():
    return sr.load_test_files("ejm55.gro", "ejm55.top")


@pytest.fixture(scope="session")
def testfile_cache_dir():
    import os

    d = os.path.abspath(os.path.curdir)

    if d.endswith("tests"):
        # we are running in the tests directory, so cache downloads here
        cache_dir = os.path.join(d, "cache")
    else:
        d2 = os.path.split(d)[0]
        if d2.endswith("tests"):
            # we are a subdirectory of the parent directory
            cache_dir = os.path.join(d2, "cache")
        else:
            cache_dir = os.path.join(d, "cache")

    return cache_dir


@pytest.fixture(scope="session")
def apo_1264():
    return sr.load_test_files("apo_1264.prm7", "apo_1264.rst7")


@pytest.fixture(scope="session")
def neopentane_methane():
    return sr.load_test_files("neo_meth_scratch.bss")


@pytest.fixture(scope="session")
def solvated_neopentane_methane():
    return sr.load_test_files("neo_meth_solv.bss")


@pytest.fixture(scope="session")
def zero_lj_mols():
    return sr.load_test_files("zero_lj.prm7", "zero_lj.rst7")


@pytest.fixture(scope="session")
def openmm_platform():
    if "openmm" not in sr.convert.supported_formats():
        return None

    mols = sr.load_test_files("ala.top", "ala.crd")

    for platform in ["CUDA", "OpenCL", "CPU"]:
        try:
            mols.dynamics(platform=platform)
            return platform
        except Exception:
            pass

    return "Reference"


@pytest.fixture(scope="session")
def thrombin_complex():
    return sr.load_test_files("thrombin.top", "thrombin.rst7")


@pytest.fixture(scope="session")
def amber_cmap():
    return sr.load_test_files("amber_cmap.prm7")


@pytest.fixture(scope="session")
def multichain_cmap():
    return sr.load_test_files("multichain_cmap.prm7", "multichain_cmap.rst7")


@pytest.fixture(scope="session")
def gromacs_cmap():
    return sr.load_test_files("1aki.gro", "1aki.top")


@pytest.fixture(scope="session")
def tagged_sdf():
    return sr.load_test_files("sdf_tags.sdf")[0]