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WIP -- Migrate to pytest #742

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WIP -- Migrate to pytest #742

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a004815
Using pytest for test_alchemy.py
ijpulidos May 2, 2023
14b009e
test_cache.py using pytest
ijpulidos May 2, 2023
8d4636b
test_forcefactories.py using pytest
ijpulidos May 2, 2023
774c276
WIP. test_forces using pytest
ijpulidos May 22, 2023
81ef958
Running tests with pytest instead
ijpulidos Aug 16, 2024
6f41be1
Merge branch 'main' into move-to-pytest
ijpulidos Aug 16, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,8 @@ jobs:
- name: Run tests
shell: bash -l {0}
run: |
# pytest -v --cov=openmmtools --cov-report=xml --color=yes openmmtools/tests/
nosetests openmmtools/tests --nocapture --cover-tests --with-coverage --cover-package=openmmtools --cover-xml --cover-xml-file=coverage.xml --verbosity=2 --with-timer --with-doctest -a '!slow'
pytest -v --cov=openmmtools --cov-report=xml --color=yes openmmtools/tests/
# nosetests openmmtools/tests --nocapture --cover-tests --with-coverage --cover-package=openmmtools --cover-xml --cover-xml-file=coverage.xml --verbosity=2 --with-timer --with-doctest -a '!slow'

- name: CodeCov
uses: codecov/codecov-action@v3
Expand Down
6 changes: 6 additions & 0 deletions openmmtools/tests/conftest.py
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@@ -0,0 +1,6 @@
import pytest

def pytest_configure(config):
config.addinivalue_line("markers", "slow: mark test as slow to run")
config.addinivalue_line("markers", "gpu_ci: mark test as useful to run on GPU")
config.addinivalue_line("markers", "gpu_needed: mark test as GPU required")
201 changes: 38 additions & 163 deletions openmmtools/tests/test_alchemy.py
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Expand Up @@ -22,13 +22,11 @@
import sys
import zlib
import pickle
import itertools
from functools import partial

import nose
import pytest
import scipy
import numpy as np
from nose.plugins.attrib import attr

import openmm
from openmm import unit
Expand Down Expand Up @@ -1175,104 +1173,6 @@ def overlap_check(reference_system, alchemical_system, positions, nsteps=50, nsa
if dDeltaF > MAX_DEVIATION:
raise Exception(report)


def rstyle(ax):
"""Styles x,y axes to appear like ggplot2

Must be called after all plot and axis manipulation operations have been
carried out (needs to know final tick spacing)

From:
http://nbviewer.ipython.org/github/wrobstory/climatic/blob/master/examples/ggplot_styling_for_matplotlib.ipynb

"""
import pylab
import matplotlib
import matplotlib.pyplot as plt

#Set the style of the major and minor grid lines, filled blocks
ax.grid(True, 'major', color='w', linestyle='-', linewidth=1.4)
ax.grid(True, 'minor', color='0.99', linestyle='-', linewidth=0.7)
ax.patch.set_facecolor('0.90')
ax.set_axisbelow(True)

#Set minor tick spacing to 1/2 of the major ticks
ax.xaxis.set_minor_locator((pylab.MultipleLocator((plt.xticks()[0][1] - plt.xticks()[0][0]) / 2.0)))
ax.yaxis.set_minor_locator((pylab.MultipleLocator((plt.yticks()[0][1] - plt.yticks()[0][0]) / 2.0)))

#Remove axis border
for child in ax.get_children():
if isinstance(child, matplotlib.spines.Spine):
child.set_alpha(0)

#Restyle the tick lines
for line in ax.get_xticklines() + ax.get_yticklines():
line.set_markersize(5)
line.set_color("gray")
line.set_markeredgewidth(1.4)

#Remove the minor tick lines
for line in (ax.xaxis.get_ticklines(minor=True) +
ax.yaxis.get_ticklines(minor=True)):
line.set_markersize(0)

#Only show bottom left ticks, pointing out of axis
plt.rcParams['xtick.direction'] = 'out'
plt.rcParams['ytick.direction'] = 'out'
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')


def lambda_trace(reference_system, alchemical_regions, positions, nsteps=100):
"""
Compute potential energy as a function of lambda.

"""

# Create a factory to produce alchemical intermediates.
factory = AbsoluteAlchemicalFactory()
alchemical_system = factory.create_alchemical_system(reference_system, alchemical_regions)
alchemical_state = AlchemicalState.from_system(alchemical_system)

# Take equally-sized steps.
delta = 1.0 / nsteps

# Compute unmodified energy.
u_original = compute_energy(reference_system, positions)

# Scan through lambda values.
lambda_i = np.zeros([nsteps+1], np.float64) # lambda values for u_i

# u_i[i] is the potential energy for lambda_i[i]
u_i = unit.Quantity(np.zeros([nsteps+1], np.float64), unit.kilocalories_per_mole)
for i in range(nsteps+1):
lambda_i[i] = 1.0-i*delta
alchemical_state.set_alchemical_parameters(lambda_i[i])
alchemical_state.apply_to_system(alchemical_system)
u_i[i] = compute_energy(alchemical_system, positions)
logger.info("{:12.9f} {:24.8f} kcal/mol".format(lambda_i[i], u_i[i] / GLOBAL_ENERGY_UNIT))

# Write figure as PDF.
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.pyplot as plt
with PdfPages('lambda-trace.pdf') as pdf:
fig = plt.figure(figsize=(10, 5))
ax = fig.add_subplot(111)
plt.plot(1, u_original / unit.kilocalories_per_mole, 'ro', label='unmodified')
plt.plot(lambda_i, u_i / unit.kilocalories_per_mole, 'k.', label='alchemical')
plt.title('T4 lysozyme L99A + p-xylene : AMBER96 + OBC GBSA')
plt.ylabel('potential (kcal/mol)')
plt.xlabel('lambda')
ax.legend()
rstyle(ax)
pdf.savefig() # saves the current figure into a pdf page
plt.close()


def generate_trace(test_system):
lambda_trace(test_system['test'].system, test_system['test'].positions, test_system['receptor_atoms'], test_system['ligand_atoms'])


# =============================================================================
# TEST ALCHEMICAL FACTORY SUITE
# =============================================================================
Expand Down Expand Up @@ -1312,12 +1212,12 @@ def test_resolve_alchemical_region():

# An exception is if indices are not part of the system.
alchemical_region = AlchemicalRegion(alchemical_atoms=[10000000])
with nose.tools.assert_raises(ValueError):
with pytest.raises(ValueError):
AbsoluteAlchemicalFactory._resolve_alchemical_region(system, alchemical_region)

# An exception is raised if nothing is defined.
alchemical_region = AlchemicalRegion()
with nose.tools.assert_raises(ValueError):
with pytest.raises(ValueError):
AbsoluteAlchemicalFactory._resolve_alchemical_region(system, alchemical_region)

class TestAbsoluteAlchemicalFactory(object):
Expand Down Expand Up @@ -1469,27 +1369,20 @@ def test_split_force_groups(self):
test_cases.update(self.filter_cases(lambda x: 'Explicit ' in x and 'exact PME' in x, max_number=1))
test_cases.update(self.filter_cases(lambda x: 'Explicit ' in x and 'exact PME' not in x, max_number=1))
for test_name, (test_system, alchemical_system, alchemical_region) in test_cases.items():
f = partial(check_split_force_groups, alchemical_system)
f.description = "Testing force splitting among groups of {}".format(test_name)
yield f
check_split_force_groups(alchemical_system)

def test_fully_interacting_energy(self):
"""Compare the energies of reference and fully interacting alchemical system."""
for test_name, (test_system, alchemical_system, alchemical_region) in self.test_cases.items():
f = partial(compare_system_energies, test_system.system,
alchemical_system, alchemical_region, test_system.positions)
f.description = "Testing fully interacting energy of {}".format(test_name)
yield f
compare_system_energies(test_system.system, alchemical_system, alchemical_region, test_system.positions)

def test_noninteracting_energy_components(self):
"""Check all forces annihilated/decoupled when their lambda variables are zero."""
for test_name, (test_system, alchemical_system, alchemical_region) in self.test_cases.items():
f = partial(check_noninteracting_energy_components, test_system.system, alchemical_system,
alchemical_region, test_system.positions)
f.description = "Testing non-interacting energy of {}".format(test_name)
yield f
check_noninteracting_energy_components(test_system.system, alchemical_system, alchemical_region,
test_system.positions)

@attr('slow')
@pytest.mark.slow
def test_fully_interacting_energy_components(self):
"""Test interacting state energy by force component."""
# This is a very expensive but very informative test. We can
Expand All @@ -1501,7 +1394,7 @@ def test_fully_interacting_energy_components(self):
f.description = "Testing energy components of %s..." % test_name
yield f

@attr('slow')
@pytest.mark.slow
def test_platforms(self):
"""Test interacting and noninteracting energies on all platforms."""
global GLOBAL_ALCHEMY_PLATFORM
Expand All @@ -1519,29 +1412,22 @@ def test_platforms(self):
for platform in platforms:
GLOBAL_ALCHEMY_PLATFORM = platform
for test_name, (test_system, alchemical_system, alchemical_region) in self.test_cases.items():
f = partial(compare_system_energies, test_system.system, alchemical_system,
alchemical_region, test_system.positions)
f.description = "Test fully interacting energy of {} on {}".format(test_name, platform.getName())
yield f
f = partial(check_noninteracting_energy_components, test_system.system, alchemical_system,
alchemical_region, test_system.positions)
f.description = "Test non-interacting energy of {} on {}".format(test_name, platform.getName())
yield f
compare_system_energies(test_system.system, alchemical_system, alchemical_region,
test_system.positions)
check_noninteracting_energy_components(test_system.system, alchemical_system, alchemical_region,
test_system.positions)

# Restore global platform
GLOBAL_ALCHEMY_PLATFORM = old_global_platform

@attr('slow')
@pytest.mark.slow
def test_overlap(self):
"""Tests overlap between reference and alchemical systems."""
for test_name, (test_system, alchemical_system, alchemical_region) in self.test_cases.items():
#cached_trajectory_filename = os.path.join(os.environ['HOME'], '.cache', 'alchemy', 'tests',
# test_name + '.pickle')
cached_trajectory_filename = None
f = partial(overlap_check, test_system.system, alchemical_system, test_system.positions,
cached_trajectory_filename=cached_trajectory_filename, name=test_name)
f.description = "Testing reference/alchemical overlap for {}".format(test_name)
yield f
overlap_check(test_system.system, alchemical_system, test_system.positions)

class TestMultiRegionAbsoluteAlchemicalFactory(TestAbsoluteAlchemicalFactory):
"""Test AbsoluteAlchemicalFactory class using multiple regions."""
Expand Down Expand Up @@ -1691,19 +1577,15 @@ def test_split_force_groups(self):
region_names = []
for region in alchemical_region:
region_names.append(region.name)
f = partial(check_split_force_groups, alchemical_system, region_names)
f.description = "Testing force splitting among groups of {}".format(test_name)
yield f
check_split_force_groups(alchemical_system, region_names)

def test_noninteracting_energy_components(self):
"""Check all forces annihilated/decoupled when their lambda variables are zero."""
for test_name, (test_system, alchemical_system, alchemical_region) in self.test_cases.items():
f = partial(check_multi_noninteracting_energy_components, test_system.system, alchemical_system,
alchemical_region, test_system.positions)
f.description = "Testing non-interacting energy of {}".format(test_name)
yield f
check_multi_noninteracting_energy_components(test_system.system, alchemical_system, alchemical_region,
test_system.positions)

@attr('slow')
@pytest.mark.slow
def test_platforms(self):
"""Test interacting and noninteracting energies on all platforms."""
global GLOBAL_ALCHEMY_PLATFORM
Expand All @@ -1721,19 +1603,14 @@ def test_platforms(self):
for platform in platforms:
GLOBAL_ALCHEMY_PLATFORM = platform
for test_name, (test_system, alchemical_system, alchemical_region) in self.test_cases.items():
f = partial(compare_system_energies, test_system.system, alchemical_system,
alchemical_region, test_system.positions)
f.description = "Test fully interacting energy of {} on {}".format(test_name, platform.getName())
yield f
f = partial(check_multi_noninteracting_energy_components, test_system.system, alchemical_system,
alchemical_region, test_system.positions)
f.description = "Test non-interacting energy of {} on {}".format(test_name, platform.getName())
yield f
compare_system_energies(test_system.system, alchemical_system, alchemical_region, test_system.positions)
check_multi_noninteracting_energy_components(test_system.system, alchemical_system, alchemical_region,
test_system.positions)

# Restore global platform
GLOBAL_ALCHEMY_PLATFORM = old_global_platform

@attr('slow')
@pytest.mark.slow
def test_fully_interacting_energy_components(self):
"""Test interacting state energy by force component."""
# This is a very expensive but very informative test. We can
Expand Down Expand Up @@ -1812,13 +1689,11 @@ def test_overlap(self):
#cached_trajectory_filename = os.path.join(os.environ['HOME'], '.cache', 'alchemy', 'tests',
# test_name + '.pickle')
cached_trajectory_filename = None
f = partial(overlap_check, test_system.system, alchemical_system, test_system.positions,
cached_trajectory_filename=cached_trajectory_filename, name=test_name)
f.description = "Testing reference/alchemical overlap for no alchemical dispersion {}".format(test_name)
yield f
overlap_check(test_system.system, alchemical_system, test_system.positions,
cached_trajectory_filename=cached_trajectory_filename, name=test_name)


@attr('slow')
@pytest.mark.slow
class TestAbsoluteAlchemicalFactorySlow(TestAbsoluteAlchemicalFactory):
"""Test AbsoluteAlchemicalFactory class with a more comprehensive set of systems."""

Expand Down Expand Up @@ -1908,7 +1783,7 @@ def setup_class(cls):
def test_constructor():
"""Test AlchemicalState constructor behave as expected."""
# Raise an exception if parameter is not recognized.
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
AlchemicalState(lambda_electro=1.0)

# Properties are initialized correctly.
Expand All @@ -1926,7 +1801,7 @@ def test_constructor():
def test_from_system_constructor(self):
"""Test AlchemicalState.from_system constructor."""
# A non-alchemical system raises an error.
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
AlchemicalState.from_system(testsystems.AlanineDipeptideVacuum().system)

# Valid parameters are 1.0 by default in AbsoluteAlchemicalFactory,
Expand Down Expand Up @@ -1977,7 +1852,7 @@ def test_apply_to_system(self):
defined_lambdas.pop() # Remove one element.
kwargs = dict.fromkeys(defined_lambdas, 1.0)
alchemical_state = AlchemicalState(**kwargs)
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.apply_to_system(state.system)

# Raise an error if an extra parameter is defined in the state.
Expand All @@ -1988,7 +1863,7 @@ def test_apply_to_system(self):
defined_lambdas.add('lambda_bonds') # Add extra parameter.
kwargs = dict.fromkeys(defined_lambdas, 1.0)
alchemical_state = AlchemicalState(**kwargs)
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.apply_to_system(state.system)

def test_check_system_consistency(self):
Expand All @@ -1998,17 +1873,17 @@ def test_check_system_consistency(self):
alchemical_state.check_system_consistency(self.alanine_state.system)

# Raise error if system has MORE lambda parameters.
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.check_system_consistency(self.full_alanine_state.system)

# Raise error if system has LESS lambda parameters.
alchemical_state = AlchemicalState.from_system(self.full_alanine_state.system)
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.check_system_consistency(self.alanine_state.system)

# Raise error if system has different lambda values.
alchemical_state.lambda_bonds = 0.5
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.check_system_consistency(self.full_alanine_state.system)

def test_apply_to_context(self):
Expand All @@ -2018,14 +1893,14 @@ def test_apply_to_context(self):
# Raise error if Context has more parameters than AlchemicalState.
alchemical_state = AlchemicalState.from_system(self.alanine_state.system)
context = self.full_alanine_state.create_context(copy.deepcopy(integrator))
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.apply_to_context(context)
del context

# Raise error if AlchemicalState is applied to a Context with missing parameters.
alchemical_state = AlchemicalState.from_system(self.full_alanine_state.system)
context = self.alanine_state.create_context(copy.deepcopy(integrator))
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.apply_to_context(context)
del context

Expand Down Expand Up @@ -2109,7 +1984,7 @@ def test_alchemical_functions(self):
assert alchemical_state.get_function_variable('lambda2') == 0.5

# Cannot call an alchemical variable as a supported parameter.
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
alchemical_state.set_function_variable('lambda_sterics', 0.5)

# Assign string alchemical functions to parameters.
Expand Down Expand Up @@ -2192,11 +2067,11 @@ def test_set_system_compound_state(self):
# Setting an inconsistent alchemical system raise an error.
system = compound_state.system
incompatible_state.apply_to_system(system)
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
compound_state.system = system

# Same for set_system when called with default arguments.
with nose.tools.assert_raises(AlchemicalStateError):
with pytest.raises(AlchemicalStateError):
compound_state.set_system(system)

# This doesn't happen if we fix the state.
Expand Down
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