def test_version(self):
# Test the version() method.
# Raw version
raw = myokit.version(raw=True)
self.assertIsInstance(raw, basestring)
parts = raw.split('.')
self.assertTrue(len(parts) in [3, 4])
# Formatted version
v = myokit.version()
v = v.splitlines()
self.assertEqual(len(v), 3)
def system(live_printing=False):
"""
Returns a (long) string with system information.
If ``live_printing`` is set to ``True``, no string is returned but the
results are printed to screen as they come in.
"""
# Print directly to screen or store in array
if not live_printing:
out = []
else:
# Create fake list interface that just prints
class Out(object):
def append(self, x):
print(x)
def extend(self, xs):
print('\n'.join(xs))
out = Out()
# Basic system information
out.append('== System information ==')
out.append('Myokit: ' + myokit.version(raw=True))
ver = iter(sys.version.splitlines())
out.append('Python: ' + next(ver))
out.extend([' ' * 8 + v for v in ver])
out.append(
'OS: ' + platform.system()
+ ' (' + sys.platform + ', ' + os.name + ')')
out.append('')
# Python requirements
out.append('== Python requirements ==')
out.append('NumPy: ' + _module_version('numpy'))
out.append('SciPy: ' + _module_version('scipy'))
out.append('Matplotlib: ' + _module_version('matplotlib'))
out.append('ConfigParser: ' + _module_version('configparser'))
out.append('Setuptools: ' + _module_version('setuptools'))
out.append('')
# Python extras
out.append('== Python extras ==')
out.append('SymPy: ' + _module_version('sympy'))
ver = _module_version('cma')
try:
ver = ver[:ver.index('$')].strip()
except ValueError: # pragma: no cover
pass
out.append('CMAES: ' + ver)
out.append('MoviePy: ' + _module_version('moviepy'))
out.append('')
# GUI toolkits
out.append('== GUI ==')
try: # pragma: no cover
from PyQt5.QtCore import QT_VERSION_STR
out.append('PyQt5: ' + QT_VERSION_STR)
out.append(' Sip: ' + _module_version('sip'))
del(QT_VERSION_STR)
except ImportError:
out.append('PyQt5: Not found')
try: # pragma: no cover
from PyQt4.QtCore import QT_VERSION_STR
out.append('PyQt4: ' + QT_VERSION_STR)
out.append(' Sip: ' + _module_version('sip'))
del(QT_VERSION_STR)
except ImportError:
out.append('PyQt4: Not found')
except RuntimeError: # pragma: no cover
# Happens if PyQt5 was also found
out.append('PyQt4: OK')
out.append('PySide: ' + _module_version('PySide'))
out.append('PySide2: ' + _module_version('PySide2'))
out.append('')
# Development tools
out.append('== Development tools ==')
out.append('Sphinx: ' + _module_version('sphinx'))
out.append('Flake8: ' + _module_version('flake8'))
out.append('')
# Simulation tools / compilation
out.append('== Simulation tools ==')
compiler = myokit.Compiler.info()
if compiler is None: # pragma: no cover
out.append('Compiler: NOT FOUND')
out.append('Sundials: Compiler not found')
out.append('OpenCL: Compiler not found')
else:
out.append('Compiler: ' + compiler)
out.append('Sundials: ' + (myokit.Sundials.version() or 'Not found'))
opencl = myokit.OpenCL()
if not opencl.supported(): # pragma: no cover
out.append('OpenCL: No OpenCL support detected.')
else: # pragma: no cover
devices = []
for p in opencl.info().platforms:
for d in p.devices:
devices.append(d.name + ' on ' + p.name)
out.append('OpenCL: ' + str(len(devices)) + ' device(s) found')
for d in devices:
out.append(' ' + d)
out.append(' Use `python -m myokit opencl` for more information.')
if not live_printing:
return '\n'.join(out)
def save_atf(log, filename, fields=None):
"""
Saves the :class:`myokit.DataLog` ``log`` to ``filename`` in ATF format.
ATF requires that the times in the log be regularly spaced.
The first column in an ATF file should always be time. Remaining fields
will be written in a random order. To indicate an order or make a selection
of fields, pass in a sequence ``fields`` containing the field names.
"""
log.validate()
import myokit
# Check filename
filename = os.path.expanduser(filename)
# Delimiters
# Dos-style EOL: Open file in 'wb' mode to stop windows writing \r\r\n
eol = '\r\n'
delim = '\t'
# Create data and keys lists
data = [iter(log.time())]
time = log.time_key()
keys = [time]
# Check fields
if fields:
for field in fields:
field = str(field)
if field == time:
continue
keys.append(field)
try:
data.append(iter(log[field]))
except KeyError:
raise ValueError('Variable <' + field + '> not found in log.')
else:
for k, v in log.items():
if k != time:
keys.append(k)
data.append(iter(v))
for k in keys:
if '"' in k:
raise ValueError('Column names must not contain double quotes.')
if '\r' in k or '\n' in k:
raise ValueError(
'Column names must not contain newlines or carriage returns.')
# Check if time is equally spaced
t = np.asarray(log.time())
dt = t[1:] - t[:-1]
dt_ref = dt[0]
dt_err = dt_ref * 1e-6
if np.any(np.abs(dt - dt_ref) > dt_err):
raise ValueError('The time variable must be regularly spaced.')
# Create header
header = []
header.append(('myokit-version', 'Myokit ' + myokit.version(raw=True)))
header.append(('date-created', myokit.date()))
header.append(('sampling-interval', dt_ref))
# Get sizes
nh = len(header)
nf = len(keys)
nd = log.length()
# Write file
with open(filename, 'wb') as f:
# Write version number
f.write(('ATF 1.0' + eol).encode(_ENC))
# Write number of header lines, number of fields
f.write((str(nh) + delim + str(nf) + eol).encode(_ENC))
for k, v in header:
f.write(('"' + str(k) + '=' + str(v) + '"' + eol).encode(_ENC))
# Write field names
f.write((delim.join(['"' + k + '"' for k in keys]) + eol).encode(_ENC))
# Write data
for i in range(nd):
f.write((
delim.join([myokit.strfloat(next(d)) for d in data]) + eol
).encode(_ENC))
def version(raw=False):
import myokit
print(myokit.version(raw))