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Updates for OpenMM 7.6 #50

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Merged
dwhswenson merged 3 commits into from
Sep 3, 2021
Merged

Updates for OpenMM 7.6 #50

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6d3f000
fix dropped simtk in OpenMM URLs
dwhswenson Sep 1, 2021
663a68d
remove other uses of simtk
dwhswenson Sep 2, 2021
70bdc3c
updates after code review
dwhswenson Sep 2, 2021
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22 changes: 20 additions & 2 deletions paths_cli/tests/wizard/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,31 @@
import openpathsampling as paths
import mdtraj as md

# should be able to remove this try block when we drop OpenMM < 7.6
try:
import openmm as mm
from openmm import unit as u
except ImportError:
try:
from simtk import openmm as mm
from simtk import unit as u
except ImportError:
HAS_OPENMM = False
else: # -no-cov-
HAS_OPENMM = True
else:
HAS_OPENMM = True

@pytest.fixture
def ad_openmm(tmpdir):
"""
Provide directory with files to start alanine depeptide sim in OpenMM
"""
mm = pytest.importorskip('simtk.openmm')
u = pytest.importorskip('simtk.unit')
# switch back to importorskip when we drop OpenMM < 7.6
if not HAS_OPENMM:
pytest.skip("could not import openmm")
# mm = pytest.importorskip('simtk.openmm')
# u = pytest.importorskip('simtk.unit')
openmmtools = pytest.importorskip('openmmtools')
md = pytest.importorskip('mdtraj')
testsystem = openmmtools.testsystems.AlanineDipeptideVacuum()
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18 changes: 17 additions & 1 deletion paths_cli/tests/wizard/test_openmm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,28 @@
_load_openmm_xml, _load_topology, openmm, OPENMM_SERIALIZATION_URL
)

# should be able to remove this try block when we drop OpenMM < 7.6
try:
import openmm as mm
except ImportError:
try:
from simtk import openmm as mm
except ImportError:
HAS_OPENMM = False
else:
HAS_OPENMM = True # -no-cov-
else:
HAS_OPENMM = True

def test_helper_url():
assert_url(OPENMM_SERIALIZATION_URL)

@pytest.mark.parametrize('obj_type', ['system', 'integrator', 'foo'])
def test_load_openmm_xml(ad_openmm, obj_type):
mm = pytest.importorskip('simtk.openmm')
# switch back to importorskip when we drop OpenMM < 7.6
if not HAS_OPENMM:
pytest.skip("could not import openmm")
# mm = pytest.importorskip("simtk.openmm")
filename = f"{obj_type}.xml"
inputs = [filename]
expected_count = 1
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14 changes: 10 additions & 4 deletions paths_cli/wizard/openmm.py
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Original file line number Diff line number Diff line change
@@ -1,16 +1,22 @@
from paths_cli.wizard.errors import FILE_LOADING_ERROR_MSG, not_installed
from paths_cli.wizard.core import get_object

# should be able to simplify this try block when we drop OpenMM < 7.6
try:
from simtk import openmm as mm
import mdtraj as md
import openmm as mm
except ImportError:
HAS_OPENMM = False
try:
from simtk import openmm as mm
except ImportError:
HAS_OPENMM = False
else: # -no-cov-
HAS_OPENMM = True
else:
HAS_OPENMM = True

OPENMM_SERIALIZATION_URL=(
"http://docs.openmm.org/latest/api-python/generated/"
"simtk.openmm.openmm.XmlSerializer.html"
"openmm.openmm.XmlSerializer.html"
)

def _openmm_serialization_helper(wizard, user_input): # no-cov
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