def test_parse_file(self):
# Tests parse_file()
# Supported level
xml = self.wrap('<model id="a" name="a"/>', 3, 2)
with WarningCollector() as w:
self.p.parse_string(xml)
self.assertNotIn('This version of SBML may not be supported', w.text())
# Unsupported level
xml = self.wrap('<model id="a" name="a"/>', 2, 2)
with WarningCollector() as w:
self.p.parse_string(xml)
self.assertIn('This version of SBML may not be supported', w.text())
# Unsupported version
xml = self.wrap('<model id="a" name="a"/>', 3, 1)
with WarningCollector() as w:
self.p.parse_string(xml)
self.assertIn('This version of SBML may not be supported', w.text())
# Check whether error is thrown for invalid path
path = 'some/path'
message = 'Unable to parse XML: '
self.assertRaisesRegex(
SBMLParsingError,
message,
self.p.parse_file,
path)
# Check whether error is thrown for invalid xml
self.assertBad('<model>', 'Unable to parse XML: ')
def test_variable(self):
# Tests parsing variables
# Valid has already been tested
# Must have a name
x = '<component name="a"><variable units="volt"/></component>'
self.assertBad(x, 'must have a name attribute')
# Must have units
x = '<component name="a"><variable name="a" /></component>'
self.assertBad(x, 'must have a units attribute')
# CellML errors are converted to parsing errors
x = '<component name="a"><variable name="1" units="volt"/></component>'
self.assertBad(x, 'valid CellML identifier')
# Unsupported units are ignored
x = '<variable name="x" units="celsius" initial_value="3" />'
x = '<component name="a">' + x + '</component>'
with WarningCollector() as w:
x = self.parse(x)['a']['x']
self.assertIn('celsius', w.text())
self.assertEqual(x.units().myokit_unit(), myokit.units.dimensionless)
def test_variable(self):
# Tests writing of variables
m1 = cellml.Model('m')
c = m1.add_component('c')
p = c.add_variable('p', 'mole')
q = c.add_variable('q', 'kelvin', public_interface='in')
r = c.add_variable('r', 'ampere', private_interface='out')
p.set_initial_value(1)
with WarningCollector():
xml = cellml.write_string(m1)
m2 = cellml.parse_string(xml)
p, q, r = m2['c']['p'], m2['c']['q'], m2['c']['r']
self.assertEqual(p.units().name(), 'mole')
self.assertEqual(q.units().name(), 'kelvin')
self.assertEqual(r.units().name(), 'ampere')
self.assertEqual(p.public_interface(), 'none')
self.assertEqual(q.public_interface(), 'in')
self.assertEqual(r.public_interface(), 'none')
self.assertEqual(p.private_interface(), 'none')
self.assertEqual(q.private_interface(), 'none')
self.assertEqual(r.private_interface(), 'out')
self.assertEqual(p.initial_value(), 1)
self.assertEqual(q.initial_value(), None)
self.assertEqual(r.initial_value(), None)
def test_log_for_times(self):
# Test the method Protocol.log_for_times()
# Relies on PacingSystem
p = myokit.Protocol()
p.schedule(2, 10, 100, 1000, 2)
t = [
0, 9.999, 10, 10.001, 109.999, 110, 110.001, 1000, 1009.99, 1010,
1110, 2000, 2020
]
v = [0, 0, 2, 2, 2, 0, 0, 0, 0, 2, 0, 0, 0]
d = p.log_for_times(t)
self.assertEqual(len(d), 2)
self.assertIn('time', d)
self.assertIn('pace', d)
self.assertEqual(d.time(), t)
self.assertEqual(d['pace'], v)
# Empty times
d = p.log_for_times([])
self.assertEqual(len(d.time()), 0)
self.assertEqual(len(d['pace']), 0)
# Deprecated alias
with WarningCollector() as w:
p.create_log_for_times([])
self.assertIn('deprecated', w.text())
def test_warnings_1_0(self):
# Tests warnings are logged
# Create model that will generate warnings
x = ('<?xml version="1.0" encoding="UTF-8"?>'
'<model name="test" xmlns="http://www.cellml.org/cellml/1.0#">'
'<component name="a">'
' <variable name="hello" units="ampere"'
' public_interface="in"/>'
'</component>'
'</model>')
# Write to disk and import
with TemporaryDirectory() as d:
path = d.path('test.celllml')
with open(path, 'w') as f:
f.write(x)
# Import
i = formats.importer('cellml')
with WarningCollector() as w:
i.model(path)
# Check warning was raised
self.assertIn('not connected', w.text())
def test_guess_duration(self):
# Deprecated method Protocol.guess_duration()
p = myokit.Protocol()
with WarningCollector() as w:
self.assertEqual(p.characteristic_time(), p.guess_duration())
self.assertIn('deprecated', w.text())
def test_easyml_exporter(self):
# Tests exporting a model
model1 = myokit.load_model('example')
model2 = myokit.load_model(os.path.join(DIR_DATA, 'heijman-2011.mmt'))
e = myokit.formats.easyml.EasyMLExporter()
with TemporaryDirectory() as d:
path = d.path('easy.model')
# Test with simple model
e.model(path, model1)
# Test with model containing markov models
with WarningCollector() as c:
e.model(path, model2)
self.assertIn('unsupported function: atan', c.text())
self.assertIn('unsupported function: sin', c.text())
self.assertEqual(c.count(), 6)
# Test with extra bound variables
model1.get('membrane.C').set_binding('hello')
e.model(path, model1)
# Test without V being a state variable
v = model1.get('membrane.V')
v.demote()
v.set_rhs(3)
e.model(path, model1)
# Test with invalid model
v.set_rhs('2 * V')
self.assertRaisesRegex(myokit.ExportError, 'valid model', e.model,
path, model1)
def test_parse_events(self):
# Test parsing events (these are ignored)
xml = (
'<model>'
' <listOfEvents>'
' <event useValuesFromTriggerTime="true">'
' <trigger initialValue="false" persistent="true">'
' <math xmlns="http://www.w3.org/1998/Math/MathML">'
' <apply> <leq/> <ci> P_1 </ci> <ci> P_2 </ci> </apply>'
' </math>'
' </trigger>'
' <listOfEventAssignments>'
' <eventAssignment variable="k2">'
' <math xmlns="http://www.w3.org/1998/Math/MathML">'
' <ci> k2reset </ci>'
' </math>'
' </eventAssignment>'
' </listOfEventAssignments>'
' </event>'
' </listOfEvents>'
'</model>')
with WarningCollector() as w:
self.p.parse_string(self.wrap(xml))
self.assertIn('Ignoring SBML events', w.text())
def test_activation(self):
# Test the activation experiment class.
with WarningCollector():
import myokit.lib.common as common
# Load model
m = os.path.join(DIR_DATA, 'lr-1991.mmt')
m = myokit.load_model(m)
# Create experiment
c = m.get('ina')
g = c.add_variable('g')
g.set_rhs('m^3 * h * j')
m.validate()
a = common.Activation(m, 'ina.g')
# Test
a.times()
a.traces()
a.peaks(normalize=True)
a.peaks(normalize=False)
a.fit_boltzmann()
a.convert_g2i()
a.times()
a.traces()
a.peaks(normalize=True)
a.peaks(normalize=False)
a.fit_boltzmann()
def test_recovery(self):
# Test the recovery experiment class.
with WarningCollector():
import myokit.lib.common as common
# Load model
m = os.path.join(DIR_DATA, 'lr-1991.mmt')
m = myokit.load_model(m)
# Create experiment
c = m.get('ina')
g = c.add_variable('g')
g.set_rhs('m^3 * h * j')
m.validate()
r = common.Recovery(m, 'ina.g')
# Test
n = 20
r.set_pause_duration(0.1, 10, n)
d = r.ratio()
self.assertEqual(len(d), 2)
self.assertIn('engine.time', d)
self.assertIn('ina.g', d)
self.assertEqual(n, len(d['engine.time']))
self.assertEqual(n, len(d['ina.g']))
x = d['engine.time']
self.assertTrue(np.all(x[1:] > x[:-1]))
x = d['ina.g'] # This is a monotonically increasing function
self.assertTrue(np.all(x[1:] > x[:-1]))
def test_from_data_log(self):
# Test some edge cases of `DataBlock2d.from_log`.
# Test valid construction
d = myokit.DataLog()
d.set_time_key('time')
d['time'] = [1, 2, 3]
d['x', 0, 0] = [0, 0, 0]
d['x', 1, 0] = [1, 1, 2]
d['x', 0, 1] = [1, 2, 2]
d['x', 1, 1] = [3, 4, 5]
d['x', 0, 2] = [6, 6, 6]
d['x', 1, 2] = [7, 7, 2]
myokit.DataBlock2d.from_log(d)
# Deprecated alias
with WarningCollector() as wc:
myokit.DataBlock2d.from_DataLog(d)
self.assertIn('deprecated', wc.text())
# No time key
d.set_time_key(None)
self.assertRaises(ValueError, myokit.DataBlock2d.from_log, d)
# Bad time key
d.set_time_key('z')
# Multi-dimensional time key
d.set_time_key('0.0.x')
self.assertRaises(ValueError, myokit.DataBlock2d.from_log, d)
# 1-dimensional stuff
d.set_time_key('time')
myokit.DataBlock2d.from_log(d)
d['y', 0] = [10, 10, 10]
d['y', 1] = [20, 20, 20]
self.assertRaises(ValueError, myokit.DataBlock2d.from_log, d)
# Mismatched dimensions
d = myokit.DataLog()
d.set_time_key('time')
d['time'] = [1, 2, 3]
d['x', 0, 0] = [0, 0, 0]
d['x', 1, 0] = [1, 1, 2]
d['x', 0, 1] = [1, 2, 2]
d['x', 1, 1] = [3, 4, 5]
d['x', 0, 2] = [6, 6, 6]
d['x', 1, 2] = [7, 7, 2]
d['y', 0, 0] = [0, 0, 0]
d['y', 1, 0] = [1, 1, 2]
d['y', 0, 1] = [1, 2, 2]
d['y', 1, 1] = [3, 4, 5]
d['y', 0, 2] = [6, 6, 6]
d['y', 1, 2] = [7, 7, 2]
myokit.DataBlock2d.from_log(d)
del (d['0.2.y'])
del (d['1.2.y'])
self.assertRaises(ValueError, myokit.DataBlock2d.from_log, d)
def test_worker(self):
# Manual test of worker, since cover doesn't pick up on its run method.
with WarningCollector():
from myokit.lib.fit import _Worker as Worker
# Create queues for worker
import multiprocessing
tasks = multiprocessing.Queue()
results = multiprocessing.Queue()
errors = multiprocessing.Queue()
error = multiprocessing.Event()
tasks.put((0, 1))
tasks.put((1, 2))
tasks.put((2, 3))
max_tasks = 3
w = Worker(h, (), tasks, results, max_tasks, errors, error)
w.run()
self.assertEqual(results.get(timeout=0.01), (0, 2))
self.assertEqual(results.get(timeout=0.01), (1, 4))
self.assertEqual(results.get(timeout=0.01), (2, 6))
self.assertTrue(results.empty())
# Test worker stops if error flag is set
tasks = multiprocessing.Queue()
results = multiprocessing.Queue()
errors = multiprocessing.Queue()
error = multiprocessing.Event()
tasks.put((0, 1))
tasks.put((1, 2))
tasks.put((2, 3))
error.set()
w = Worker(h, (), tasks, results, max_tasks, errors, error)
w.run()
self.assertEqual(results.get(timeout=0.01), (0, 2))
self.assertTrue(results.empty())
# Tests worker catches, stores and halts on exception
tasks = multiprocessing.Queue()
results = multiprocessing.Queue()
errors = multiprocessing.Queue()
error = multiprocessing.Event()
tasks.put((0, 1))
tasks.put((1, 30))
tasks.put((2, 3))
w = Worker(h, (), tasks, results, max_tasks, errors, error)
w.run()
self.assertEqual(results.get(timeout=0.01), (0, 2))
self.assertTrue(results.empty())
self.assertTrue(error.is_set())
#self.assertFalse(errors.empty())
self.assertIsNotNone(errors.get(timeout=0.01))
def test_stimulus_generation(self):
# Tests if protocols allow a stimulus current to be added
e = formats.exporter('cellml')
i = formats.importer('cellml')
# Load input model
m1, p1, _ = myokit.load('example')
org_code = m1.code()
# 1. Export without a protocol
with TemporaryDirectory() as d:
path = d.path('model.cellml')
with WarningCollector() as w:
e.model(path, m1)
m2 = i.model(path)
self.assertFalse(w.has_warnings())
self.assertTrue(isinstance(m2.get('engine.pace').rhs(), myokit.Number))
# 2. Export with protocol, but without variable bound to pacing
m1.get('engine.pace').set_binding(None)
with TemporaryDirectory() as d:
path = d.path('model.cellml')
with WarningCollector() as w:
e.model(path, m1, p1)
m2 = i.model(path)
self.assertTrue(w.has_warnings())
self.assertTrue(isinstance(m2.get('engine.pace').rhs(), myokit.Number))
# 3. Export with protocol and variable bound to pacing
m1.get('engine.pace').set_binding('pace')
with TemporaryDirectory() as d:
path = d.path('model.cellml')
with WarningCollector() as w:
e.model(path, m1, p1)
m2 = i.model(path)
self.assertFalse(w.has_warnings())
rhs = m2.get('membrane.i_stim').rhs()
self.assertTrue(rhs, myokit.Multiply)
self.assertTrue(isinstance(rhs[0], myokit.Piecewise))
# Check original model is unchanged
self.assertEqual(org_code, m1.code())
def test_xnes(self):
# Test if a xNES routine runs without errors.
with WarningCollector():
import myokit.lib.fit as fit
np.random.seed(1)
with np.errstate(all='ignore'): # Tell numpy not to issue warnings
x, f = fit.xnes(FittingTest._score,
self._boundaries,
hint=self._hint,
parallel=False,
max_iter=50)
def test_show_line_of(self):
# Test :meth:`Model.show_line_of(variable)`.
m = myokit.load_model('example')
e = m.show_line_of(m.get('ina.INa'))
self.assertIn('Defined on line 91', e)
self.assertIn('Intermediary variable', e)
self.assertEqual(len(e.splitlines()), 4)
# Test deprecated alias
with WarningCollector() as wc:
m.show_line(m.get('ina.INa'))
self.assertIn('deprecated', wc.text())
def test_time(self):
# Test the time() method that returns the time variable.
m = myokit.Model()
c = m.add_component('c')
x = c.add_variable('x')
x.set_rhs(0)
with WarningCollector() as w:
self.assertRaises(myokit.IncompatibleModelError, multi.time, m)
x.set_binding('time')
self.assertEqual(x, multi.time(m))
self.assertIn('deprecated', w.text())
def test_restitution(self):
# Test the restitution experiment class.
with WarningCollector():
import myokit.lib.common as common
# Load model
m = os.path.join(DIR_DATA, 'lr-1991.mmt')
m = myokit.load_model(m)
# Create experiment
r = common.Restitution(m)
# Test
r.set_times(300, 800, 200)
r.run()
def test_strength_duration(self):
# Test the strength-duration experiment class.
with WarningCollector():
import myokit.lib.common as common
# Load model
m = os.path.join(DIR_DATA, 'lr-1991.mmt')
m = myokit.load_model(m)
# Create experiment
s = common.StrengthDuration(m, 'membrane.i_stim')
# Test
s.set_currents(-200, -10)
s.set_times(0.5, 1.0, 0.2)
s.run()
def test_label(self):
# Test the label() method that returns a labelled variable.
m = myokit.Model()
c = m.add_component('c')
x = c.add_variable('x')
x.set_rhs(0)
with WarningCollector() as w:
self.assertRaises(
myokit.IncompatibleModelError, multi.label, m, 'x')
x.set_label('x')
self.assertEqual(x, multi.label(m, 'x'))
self.assertIn('deprecated', w.text())
def test_parallel_simulations(self):
# Test running simulations in parallel
with WarningCollector():
import myokit.lib.fit as fit
# Test running simulation defined in object
s = Sim()
e = fit.ParallelEvaluator(s.run, nworkers=4)
e.evaluate([1, 2, 3, 4])
# Test running simulation created inside of score function
e = fit.ParallelEvaluator(run_sim, nworkers=4)
e.evaluate([1, 2, 3, 4])
def test_units_predefined(self):
# Tests parsing all the predefined units
def u(units):
m = self.parse('<component name="c">'
' <variable name="x" units="' + units + '"'
' initial_value="1" />'
'</component>')
return m['c']['x'].units().myokit_unit()
self.assertEqual(u('ampere'), myokit.units.ampere)
self.assertEqual(u('becquerel'), myokit.units.becquerel)
self.assertEqual(u('candela'), myokit.units.candela)
self.assertEqual(u('coulomb'), myokit.units.coulomb)
self.assertEqual(u('dimensionless'), myokit.units.dimensionless)
self.assertEqual(u('farad'), myokit.units.farad)
self.assertEqual(u('gram'), myokit.units.g)
self.assertEqual(u('gray'), myokit.units.gray)
self.assertEqual(u('henry'), myokit.units.henry)
self.assertEqual(u('hertz'), myokit.units.hertz)
self.assertEqual(u('joule'), myokit.units.joule)
self.assertEqual(u('katal'), myokit.units.katal)
self.assertEqual(u('kelvin'), myokit.units.kelvin)
self.assertEqual(u('kilogram'), myokit.units.kg)
self.assertEqual(u('liter'), myokit.units.liter)
self.assertEqual(u('litre'), myokit.units.liter)
self.assertEqual(u('lumen'), myokit.units.lumen)
self.assertEqual(u('lux'), myokit.units.lux)
self.assertEqual(u('meter'), myokit.units.meter)
self.assertEqual(u('metre'), myokit.units.meter)
self.assertEqual(u('mole'), myokit.units.mole)
self.assertEqual(u('newton'), myokit.units.newton)
self.assertEqual(u('ohm'), myokit.units.ohm)
self.assertEqual(u('pascal'), myokit.units.pascal)
self.assertEqual(u('radian'), myokit.units.radian)
self.assertEqual(u('second'), myokit.units.second)
self.assertEqual(u('siemens'), myokit.units.siemens)
self.assertEqual(u('sievert'), myokit.units.sievert)
self.assertEqual(u('steradian'), myokit.units.steradian)
self.assertEqual(u('tesla'), myokit.units.tesla)
self.assertEqual(u('volt'), myokit.units.volt)
self.assertEqual(u('watt'), myokit.units.watt)
self.assertEqual(u('weber'), myokit.units.weber)
# Celsius is not supported
with WarningCollector() as w:
self.assertEqual(u('celsius'), myokit.units.dimensionless)
self.assertIn('celsius', w.text())
def test_parallel_evaluator(self):
with WarningCollector():
import myokit.lib.fit as fit
# Test parallel execution
e = fit.ParallelEvaluator(f, max_tasks_per_worker=9)
# Test 1
x = 1 + np.random.random(30)
e.evaluate(x)
# Test 2
x = 2 + np.random.random(15)
e.evaluate(x)
# Test 3 (with exception)
x[13] = 0
self.assertRaises(Exception, e.evaluate, x)
# Repeat run with exception
x[11] = 0
self.assertRaises(Exception, e.evaluate, x)
# Repeat run
x = 1 + np.random.random(16)
e.evaluate(x)
e = fit.ParallelEvaluator(f_args, args=[10, 20])
self.assertEqual(e.evaluate([1])[0], 1)
# Argument must be callable
self.assertRaises(ValueError, fit.ParallelEvaluator, 1)
# Args must be a sequence
self.assertRaises(ValueError, fit.ParallelEvaluator, f_args, args=1)
# n-workers must be >0
self.assertRaises(ValueError, fit.ParallelEvaluator, f, 0)
# max tasks must be >0
self.assertRaises(ValueError, fit.ParallelEvaluator, f, 1, 0)
e = fit.ParallelEvaluator(ioerror_on_five)
self.assertRaisesRegex(Exception, 'in subprocess', e.evaluate,
range(10))
def test_from_log(self):
# Test some edge cases of `DataBlock1d.from_log`.
# Test valid construction
d = myokit.DataLog()
d.set_time_key('time')
d['time'] = [1, 2, 3]
d['x', 0] = [0, 0, 0]
d['x', 1] = [1, 1, 2]
myokit.DataBlock1d.from_log(d)
# Deprecated alias
with WarningCollector() as wc:
myokit.DataBlock1d.from_DataLog(d)
self.assertIn('deprecated', wc.text())
# No time key
d = myokit.DataLog()
d['time'] = [1, 2, 3]
d['x', 0] = [0, 0, 0]
d['x', 1] = [1, 1, 2]
self.assertRaises(ValueError, myokit.DataBlock1d.from_log, d)
# Multi-dimensional time key
d.set_time_key('0.x')
self.assertRaises(ValueError, myokit.DataBlock1d.from_log, d)
# 2-dimensional stuff
d.set_time_key('time')
myokit.DataBlock1d.from_log(d)
d['y', 0, 0] = [10, 10, 10]
self.assertRaises(ValueError, myokit.DataBlock1d.from_log, d)
# Mismatched dimensions
d = myokit.DataLog()
d.set_time_key('time')
d['time'] = [1, 2, 3]
d['x', 0] = [0, 0, 0]
d['x', 1] = [1, 1, 2]
d['y', 0] = [2, 0, 0]
d['y', 1] = [3, 1, 2]
d['y', 2] = [0, 4, 5]
self.assertRaises(ValueError, myokit.DataBlock1d.from_log, d)
def test_sim_1d(self):
# Test running a short 1d simulation (doesn't inspect output)
m, p, _ = myokit.load('example')
s = myokit.SimulationOpenCL(m, p, 20)
# Run, log state and intermediary variable (separate logging code!)
d = s.run(1, log=['engine.time', 'membrane.V', 'ina.INa'])
self.assertIn('engine.time', d)
self.assertIn('0.membrane.V', d)
self.assertIn('19.membrane.V', d)
self.assertIn('0.ina.INa', d)
self.assertIn('19.ina.INa', d)
self.assertEqual(len(d), 41)
# Test is_2d()
self.assertFalse(s.is_2d())
with WarningCollector() as wc:
self.assertFalse(s.is2d())
self.assertIn('deprecated', wc.text())
def test_parse_constraint(self):
# Test parsing constraints (these are ignored)
xml = (
'<model>'
' <listOfConstraints>'
' <constraint>'
' <math xmlns="http://www.w3.org/1998/Math/MathML">'
' <apply> <lt/> <cn> 1 </cn> <ci> S1 </ci> </apply>'
' </math>'
' <message>'
' <p xmlns="http://www.w3.org/1999/xhtml">Out of range.</p>'
' </message>'
' </constraint>'
' </listOfConstraints>'
'</model>')
with WarningCollector() as w:
self.p.parse_string(self.wrap(xml))
self.assertIn('Ignoring SBML constraints', w.text())
def test_log_for_interval(self):
# Tests the method Protocol.log_for_interval()
# Relies on PacingSystem
debug = False
# Test basic use + log creation methods
p = myokit.Protocol()
p.schedule(1, 10, 1, 1000, 0)
d = p.log_for_interval(0, 3000)
self.assertEqual(d.time(), [0, 10, 11, 1010, 1011, 2010, 2011, 3000])
d = p.log_for_interval(0, 2000, for_drawing=True)
if debug:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(d.time(), d['pace'])
plt.show()
self.assertEqual(d.time(),
[0, 10, 10, 11, 11, 1010, 1010, 1011, 1011, 2000])
p = myokit.Protocol()
p.schedule(1, 0, 1, 1000, 0)
d = p.log_for_interval(0, 3000)
self.assertEqual(d.time(), [0, 1, 1000, 1001, 2000, 2001, 3000])
d = p.log_for_interval(0, 2000, for_drawing=True)
if debug:
import matplotlib.pyplot as plt
plt.figure()
plt.plot(d.time(), d['pace'])
plt.show()
self.assertEqual(d.time(),
[0, 1, 1, 1000, 1000, 1001, 1001, 2000, 2000])
# Test bad interval call
self.assertRaises(ValueError, p.log_for_interval, 100, 0)
# Test deprecated alias
with WarningCollector() as w:
p.create_log_for_interval(0, 2000, for_drawing=True)
self.assertIn('deprecated', w.text())
def test_evaluators(self):
with WarningCollector():
import myokit.lib.fit as fit
# Test basic sequential/parallel evaluation
x = 1 + np.random.random(100)
# Simple run: sequential and parallel
fit.evaluate(f, x, parallel=False)
# Note: the overhead is almost 100% of the run-time of this test
fit.evaluate(f, x, parallel=True)
e = fit.SequentialEvaluator(f_args, [10, 20])
self.assertEqual(e.evaluate([1])[0], 1)
# Argument must be callable
self.assertRaises(ValueError, fit.SequentialEvaluator, 1)
# Args must be a sequence
self.assertRaises(ValueError, fit.SequentialEvaluator, f_args, 1)
def test_sim_2d(self):
# Test running a short 2d simulation (doesn't inspect output)
m, p, _ = myokit.load('example')
n = (8, 8)
s = myokit.SimulationOpenCL(m, p, n)
s.set_paced_cells(4, 4)
# Run, log state and intermediary variable (separate logging code!)
d = s.run(1, log=['engine.time', 'membrane.V', 'ina.INa'])
self.assertEqual(len(d), 129)
self.assertIn('engine.time', d)
self.assertIn('0.0.membrane.V', d)
self.assertIn('7.7.membrane.V', d)
self.assertIn('0.0.ina.INa', d)
self.assertIn('7.7.ina.INa', d)
# Test is_2d()
self.assertTrue(s.is_2d())
with WarningCollector() as wc:
self.assertTrue(s.is2d())
self.assertIn('deprecated', wc.text())
def test_units(self):
# Test parsing a units definition
# Valid has already been testsed
# New base units are not supported
x = '<units name="base" />'
with WarningCollector() as w:
m = self.parse(x)
self.assertIn('new base units', w.text())
self.assertEqual(
m.find_units('base').myokit_unit(), myokit.units.dimensionless)
# CellML errors are converted to parse errors
x = '<units name="123"><unit units="volt" /></units>'
self.assertBad(x, 'valid CellML identifier')
# Missing name
x = '<units><unit units="volt" /></units>'
self.assertBad(x, 'must have a name')
# Name overlaps with predefined
x = '<units name="metre"><unit units="volt" /></units>'
self.assertBad(x, 'overlaps with a predefined name')
# Duplicate name (handled in sorting)
x = '<units name="wooster"><unit units="volt" /></units>'
self.assertBad(x + x, 'Duplicate units definition')
# Missing units definitions
x = ('<units name="wooster"><unit units="fluther" /></units>')
self.assertBad(x, 'Unable to resolve network of units')
# Circular units definitions
x = ('<units name="wooster"><unit units="fluther" /></units>'
'<units name="fluther"><unit units="wooster" /></units>')
self.assertBad(x, 'Unable to resolve network of units')
def test_cmaes(self):
# Test if a CMA-ES routine runs without errors.
with WarningCollector():
import myokit.lib.fit as fit
# Some CMAES versions import matplotlib...
import matplotlib
matplotlib.use('template')
try:
import cma
del (cma)
except ImportError:
print('CMA module not found, skipping test.')
return
np.random.seed(1)
with np.errstate(all='ignore'): # Tell numpy not to issue warnings
x, f = fit.cmaes(FittingTest._score,
self._boundaries,
hint=self._hint,
parallel=False,
target=1)