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import pytest
from MDAnalysis.analysis.base import AnalysisBase, AnalysisFromFunction
from MDAnalysisTests.analysis.test_base import (
FrameAnalysis,
IncompleteAnalysis,
OldAPIAnalysis,
)
from MDAnalysis.analysis.rms import RMSD, RMSF
from MDAnalysis.analysis.dihedrals import Dihedral, Ramachandran, Janin
from MDAnalysis.analysis.bat import BAT
from MDAnalysis.analysis.gnm import GNMAnalysis
from MDAnalysis.analysis.dssp.dssp import DSSP
from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import (
HydrogenBondAnalysis,
)
from MDAnalysis.analysis.nucleicacids import NucPairDist
from MDAnalysis.analysis.contacts import Contacts
from MDAnalysis.analysis.density import DensityAnalysis
from MDAnalysis.analysis.lineardensity import LinearDensity
from MDAnalysis.analysis.polymer import PersistenceLength
from MDAnalysis.analysis.rdf import InterRDF, InterRDF_s
from MDAnalysis.lib.util import is_installed
def params_for_cls(cls, exclude: list[str] = None):
"""
This part contains fixtures for simultaneous testing
of all available (=installed & supported) backends
for analysis subclasses.
If for some reason you want to limit backends,
simply pass "exclude: list[str]" to the function
that parametrizes fixture.
Parameters
----------
exclude : list[str], optional
list of backends to exclude from parametrization, by default None
Returns
-------
dict
dictionary with all tested keyword combinations for the run
"""
exclude = [] if exclude is None else exclude
possible_backends = cls.get_supported_backends()
installed_backends = [
b for b in possible_backends if is_installed(b) and b not in exclude
]
params = [
pytest.param(
{"backend": backend, "n_workers": nproc},
)
for backend in installed_backends
for nproc in (2,)
if backend != "serial"
]
params.extend([{"backend": "serial"}])
return params
@pytest.fixture(scope="module", params=params_for_cls(FrameAnalysis))
def client_FrameAnalysis(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(AnalysisBase))
def client_AnalysisBase(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(AnalysisFromFunction))
def client_AnalysisFromFunction(request):
return request.param
@pytest.fixture(
scope="module",
params=params_for_cls(AnalysisFromFunction, exclude=["multiprocessing"]),
)
def client_AnalysisFromFunctionAnalysisClass(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(IncompleteAnalysis))
def client_IncompleteAnalysis(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(OldAPIAnalysis))
def client_OldAPIAnalysis(request):
return request.param
# MDAnalysis.analysis.rms
@pytest.fixture(scope="module", params=params_for_cls(RMSD))
def client_RMSD(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(RMSF))
def client_RMSF(request):
return request.param
# MDAnalysis.analysis.dihedrals
@pytest.fixture(scope="module", params=params_for_cls(Dihedral))
def client_Dihedral(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(Ramachandran))
def client_Ramachandran(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(Janin))
def client_Janin(request):
return request.param
# MDAnalysis.analysis.gnm
@pytest.fixture(scope="module", params=params_for_cls(GNMAnalysis))
def client_GNMAnalysis(request):
return request.param
# MDAnalysis.analysis.bat
@pytest.fixture(scope="module", params=params_for_cls(BAT))
def client_BAT(request):
return request.param
# MDAnalysis.analysis.dssp.dssp
@pytest.fixture(scope="module", params=params_for_cls(DSSP))
def client_DSSP(request):
return request.param
# MDAnalysis.analysis.hydrogenbonds
@pytest.fixture(scope="module", params=params_for_cls(HydrogenBondAnalysis))
def client_HydrogenBondAnalysis(request):
return request.param
# MDAnalysis.analysis.nucleicacids
@pytest.fixture(scope="module", params=params_for_cls(NucPairDist))
def client_NucPairDist(request):
return request.param
# MDAnalysis.analysis.contacts
@pytest.fixture(scope="module", params=params_for_cls(Contacts))
def client_Contacts(request):
return request.param
# MDAnalysis.analysis.density
@pytest.fixture(scope="module", params=params_for_cls(DensityAnalysis))
def client_DensityAnalysis(request):
return request.param
# MDAnalysis.analysis.lineardensity
@pytest.fixture(scope="module", params=params_for_cls(LinearDensity))
def client_LinearDensity(request):
return request.param
# MDAnalysis.analysis.polymer
@pytest.fixture(scope="module", params=params_for_cls(PersistenceLength))
def client_PersistenceLength(request):
return request.param
# MDAnalysis.analysis.rdf
@pytest.fixture(scope="module", params=params_for_cls(InterRDF))
def client_InterRDF(request):
return request.param
@pytest.fixture(scope="module", params=params_for_cls(InterRDF_s))
def client_InterRDF_s(request):
return request.param
|
