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mattwthompsonmattwthompson
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Parametrize tests
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-59
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3 files changed

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-59
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‎.github/workflows/ci.yaml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ jobs:
7878
- name: Test Installed Package
7979
if: always()
8080
run: |
81-
pytest -v -x --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
81+
pytest -nauto -v -x --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
8282
openmmforcefields/tests/test_amber_import.py \
8383
openmmforcefields/tests/test_template_generators.py \
8484
openmmforcefields/tests/test_system_generator.py

‎devtools/conda-envs/test_env.yaml‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,8 @@ dependencies:
1414
# Testing
1515
- pytest
1616
- pytest-cov
17-
- codecov
17+
- pytest-xdist
18+
- pytest-randomly
1819

1920
# Requirements for converted force field installer
2021
- openmm >=7.6.0

‎openmmforcefields/tests/test_template_generators.py‎

Lines changed: 52 additions & 57 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
import os
44
import tempfile
55
import unittest
6+
import pytest
67

78
import numpy as np
89
import openmm
@@ -532,12 +533,6 @@ def test_parameterize(self):
532533
"""Test parameterizing molecules with template generator for all supported force fields"""
533534
# Test all supported small molecule force fields
534535
for small_molecule_forcefield in self.TEMPLATE_GENERATOR.INSTALLED_FORCEFIELDS:
535-
if "ff14sb" in small_molecule_forcefield:
536-
continue
537-
if "tip" in small_molecule_forcefield:
538-
continue
539-
if "opc" in small_molecule_forcefield:
540-
continue
541536

542537
print(f'Testing {small_molecule_forcefield}')
543538
# Create a generator that knows about a few molecules
@@ -712,6 +707,19 @@ def relative_deviation(x, y):
712707
write_xml('openmm-smirnoff.xml', template_generated_system)
713708
raise Exception(f'Relative force deviation for {molecule.to_smiles()} ({relative_force_deviation}) exceeds threshold ({RELATIVE_FORCE_DEVIATION_TOLERANCE})')
714709

710+
def smirnoff_small_molecule_forcefields():
711+
force_fields = list()
712+
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
713+
if 'tip' in small_molecule_forcefield:
714+
continue
715+
if 'opc' in small_molecule_forcefield:
716+
continue
717+
if small_molecule_forcefield.startswith('ff14sb'):
718+
continue
719+
force_fields.append(small_molecule_forcefield)
720+
721+
return force_fields
722+
715723
class TestSMIRNOFFTemplateGenerator(TestGAFFTemplateGenerator):
716724
TEMPLATE_GENERATOR = SMIRNOFFTemplateGenerator
717725

@@ -778,71 +786,55 @@ def test_INSTALLED_FORCEFIELDS(self):
778786
for forbidden in forbidden_force_fields:
779787
assert forbidden not in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
780788

781-
def test_energies(self):
789+
@pytest.mark.parametrize("small_molecule_forcefield", smirnoff_small_molecule_forcefields())
790+
def test_energies(self, small_molecule_forcefield):
782791
"""Test potential energies match between openff-toolkit and OpenMM ForceField"""
783792

784-
# Test all supported SMIRNOFF force fields
785-
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
786-
if "ff14sb" in small_molecule_forcefield:
787-
continue
788-
if "tip" in small_molecule_forcefield:
789-
continue
790-
if "opc" in small_molecule_forcefield:
791-
continue
792-
793-
print(f'Testing energies for {small_molecule_forcefield}...')
794-
# Create a generator that knows about a few molecules
795-
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
796-
generator = SMIRNOFFTemplateGenerator(molecules=self.molecules, forcefield=small_molecule_forcefield)
797-
# Create a ForceField
798-
openmm_forcefield = openmm.app.ForceField()
799-
# Register the template generator
800-
openmm_forcefield.registerTemplateGenerator(generator.generator)
801-
# Parameterize some molecules
802-
for molecule in self.molecules:
803-
# Create OpenMM System using OpenMM app
804-
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
805-
806-
# Retrieve System generated by the SMIRNOFF typing engine
807-
smirnoff_system = generator.get_openmm_system(molecule)
793+
print(f'Testing energies for {small_molecule_forcefield}...')
794+
# Create a generator that knows about a few molecules
795+
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
796+
generator = SMIRNOFFTemplateGenerator(molecules=self.molecules, forcefield=small_molecule_forcefield)
797+
# Create a ForceField
798+
openmm_forcefield = openmm.app.ForceField()
799+
# Register the template generator
800+
openmm_forcefield.registerTemplateGenerator(generator.generator)
801+
# Parameterize some molecules
802+
for molecule in self.molecules:
803+
# Create OpenMM System using OpenMM app
804+
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
808805

809-
# Compare energies and forces
810-
self.compare_energies(molecule, openmm_system, smirnoff_system)
806+
# Retrieve System generated by the SMIRNOFF typing engine
807+
smirnoff_system = generator.get_openmm_system(molecule)
811808

812-
# Run some dynamics
813-
molecule = self.propagate_dynamics(molecule, smirnoff_system)
809+
# Compare energies and forces
810+
self.compare_energies(molecule, openmm_system, smirnoff_system)
814811

815-
# Compare energies again
816-
self.compare_energies(molecule, openmm_system, smirnoff_system)
812+
# Run some dynamics
813+
molecule = self.propagate_dynamics(molecule, smirnoff_system)
817814

815+
# Compare energies again
816+
self.compare_energies(molecule, openmm_system, smirnoff_system)
818817

819-
def test_partial_charges_are_none(self):
818+
@pytest.mark.parametrize("small_molecule_forcefield", smirnoff_small_molecule_forcefields())
819+
def test_partial_charges_are_none(self, small_molecule_forcefield):
820820
"""Test parameterizing a small molecule with `partial_charges=None` instead
821821
of zeros (happens frequently in OFFTK>=0.7.0)"""
822822
molecule = Molecule.from_smiles('C=O')
823823
molecule.generate_conformers(n_conformers=1)
824824
#molecule._partial_charges = None
825825
assert (molecule.partial_charges is None) or np.all(molecule.partial_charges / unit.elementary_charge == 0)
826-
# Test all supported SMIRNOFF force fields
827-
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
828-
if "ff14sb" in small_molecule_forcefield:
829-
continue
830-
if "tip" in small_molecule_forcefield:
831-
continue
832-
if "opc" in small_molecule_forcefield:
833-
continue
834826

835-
print(f'Testing energies for {small_molecule_forcefield}...')
836-
# Create a generator that knows about a few molecules
837-
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
838-
generator = SMIRNOFFTemplateGenerator(molecules=[molecule], forcefield=small_molecule_forcefield)
839-
# Create a ForceField
840-
openmm_forcefield = openmm.app.ForceField()
841-
# Register the template generator
842-
openmm_forcefield.registerTemplateGenerator(generator.generator)
843-
# Create OpenMM System using OpenMM app
844-
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
845-
smirnoff_system = generator.get_openmm_system(molecule)
827+
print(f'Testing energies for {small_molecule_forcefield}...')
828+
# Create a generator that knows about a few molecules
829+
# TODO: Should the generator also load the appropriate force field files into the ForceField object?
830+
generator = SMIRNOFFTemplateGenerator(molecules=[molecule], forcefield=small_molecule_forcefield)
831+
# Create a ForceField
832+
openmm_forcefield = openmm.app.ForceField()
833+
# Register the template generator
834+
openmm_forcefield.registerTemplateGenerator(generator.generator)
835+
# Create OpenMM System using OpenMM app
836+
openmm_system = openmm_forcefield.createSystem(molecule.to_topology().to_openmm(), removeCMMotion=False, nonbondedMethod=NoCutoff)
837+
smirnoff_system = generator.get_openmm_system(molecule)
846838

847839
def test_version(self):
848840
"""Test version"""
@@ -852,6 +844,9 @@ def test_version(self):
852844
assert generator.smirnoff_filename.endswith(forcefield + '.offxml')
853845
assert os.path.exists(generator.smirnoff_filename)
854846

847+
@pytest.mark.skip
848+
def test_parameterize(self, small_molecule_forcefield):
849+
"""Redundant inherited test."""
855850

856851
class TestEspalomaTemplateGenerator(TestGAFFTemplateGenerator):
857852
TEMPLATE_GENERATOR = EspalomaTemplateGenerator

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