def test_ignoreunknown_actually_ignores_unknown(setup):
# Ignore unknown keys
parse_string = setup[-1]
reader = InputReader(comment='//', ignoreunknown=True)
reader.add_boolean_key('red')
reader.add_line_key('path')
inp = reader.read_input(parse_string)
with raises(AttributeError):
inp.blue
def test_unknown_keys_cause_failure(setup):
# Don't ignore unknown keys
parse_string = setup[-1]
reader = InputReader(comment='//', ignoreunknown=False)
reader.add_boolean_key('red')
reader.add_line_key('path')
with raises(ReaderError) as e:
reader.read_input(parse_string)
assert 'Unrecognized key' in str(e.value)
def test_comments_are_handled_correctly(setup):
parse_string = setup[-1]
reader = InputReader(comment='#')
reader.add_boolean_key('red')
reader.add_boolean_key('blue')
reader.add_line_key('path')
with raises(ReaderError) as e:
reader.read_input(parse_string)
regex = r'expected \d+ arguments, got \d+'
assert search(regex, str(e.value))
def test_read_mutex_set_dest_set_required():
r = InputReader()
meg = r.add_mutually_exclusive_group(required=True, dest='color')
meg.add_boolean_key('red')
meg.add_boolean_key('blue')
meg.add_boolean_key('green')
r.add_boolean_key('cyan')
with raises(ReaderError) as e:
inp = r.read_input(['cyan'])
assert search(r'One and only one of .* must be included', str(e.value))
def test_read_mutex_set_dest():
r = InputReader()
# This is the best way to use meg's
meg = r.add_mutually_exclusive_group(dest='color')
meg.add_boolean_key('red', action='red')
meg.add_boolean_key('blue', action='blue')
meg.add_boolean_key('green', action='green')
meg.add_boolean_key('pink', action='pink')
meg.add_boolean_key('gray', action='pink')
meg.add_boolean_key('cyan', action='cyan')
r.add_boolean_key('white')
inp = r.read_input(['cyan', 'white'])
assert inp.color == 'cyan'
assert inp.white
assert 'red' not in inp
assert 'blue' not in inp
assert 'green' not in inp
assert 'pink' not in inp
assert 'gray' not in inp
assert 'cyan' not in inp
def test_string_default_at_class_level():
ir = InputReader(default='roses')
assert ir._default == 'roses'
b = ir.add_boolean_key('RED')
assert b._default == 'roses'
def test_suppress_at_class_level():
ir = InputReader(default=SUPPRESS)
assert ir._default is SUPPRESS
b = ir.add_boolean_key('RED')
assert b._default is SUPPRESS
def read_input(input_file):
'''Defines what to expect from the input file and then
reads it in.'''
# Creates an input reader instance
reader = InputReader(default=SUPPRESS)
# Rate parameter, either rate or lifetime, not both
rate = reader.add_mutually_exclusive_group(required=True)
# The units are s, ns, ps, or fs. The default is ps.
rate.add_line_key('lifetime', type=float,
glob={'len' : '?',
'type' : ('ps', 'fs', 'ns', 's'),
'default' : 'ps'})
rate.add_line_key('rate', type=float,
glob={'len' : '?',
'type' : ('thz', 'phz', 'ghz', 'hz'),
'default' : 'thz'})
# The range of the X-axis
reader.add_line_key('xlim', type=[int, int], default=(1900, 2000))
reader.add_boolean_key('reverse', action=True, default=False)
# Read in the raw data.
reader.add_line_key('raw', type=[], glob={'len':'*', 'join':True, },
default=None, case=True)
# Read in the peak data. The wavenumber and height is required.
# The Lorentzian and Gaussian widths are defaulted to 10 if not given.
floatkw = {'type' : float, 'default' : 10.0}
reader.add_line_key('peak', required=True, repeat=True, type=[float,float],
keywords={'g':floatkw, 'l':floatkw,
'num' : {'type':int,'default':-1}})
# Read the exchange information.
reader.add_line_key('exchange', repeat=True, type=[int, int],
glob={'type' : float,
'default' : 1.0,
'len' : '?'})
reader.add_boolean_key('nosym', action=False, default=True,
dest='symmetric_exchange')
# Actually read the input file
args = reader.read_input(input_file)
# Make sure the filename was given correctly and read in data
if args.raw:
args.add('rawName', args.raw)
args.raw = loadtxt(abs_file_path(args.raw))
# Make the output file path absolute if given
args.data = abs_file_path(args.data) if 'data' in args else ''
if 'save_plot_script' in args:
args.save_plot_script = abs_file_path(args.save_plot_script)
else:
args.save_plot_script = ''
# Adjust the input rate or lifetime to wavenumbers
if 'lifetime' in args:
convert = { 'ps' : 1E-12, 'ns' : 1E-9, 'fs' : 1E-15, 's' : 1 }
args.add('k', 1 / ( convert[args.lifetime[1]] * args.lifetime[0] ))
else:
convert = { 'thz' : 1E12, 'ghz' : 1E9, 'phz' : 1E15, 'hz' : 1 }
args.add('k', convert[args.rate[1]] * args.rate[0])
args.k *= HZ2WAVENUM / ( 2 * pi )
# Parse the vibrational input
num, vib, Gamma_Lorentz, Gamma_Gauss, heights, rel_rates, num_given = (
[], [], [], [], [], [], [])
for peak in args.peak:
# Vibration #
num.append(peak[2]['num'])
num_given.append(False if peak[2]['num'] < 0 else True)
# Angular frequency
vib.append(peak[0])
# Relative peak heights
heights.append(peak[1])
# Default Gaussian or Lorentzian width or relative rate
Gamma_Lorentz.append(peak[2]['l'])
Gamma_Gauss.append(peak[2]['g'])
# Either all or none of the numbers must be given explicitly
if not (all(num_given) or not any(num_given)):
raise ReaderError('All or none of the peaks must '
'be given numbers explicitly')
# If the numbers were give, make sure there are no duplicates
if all(num_given):
if len(num) != len(set(num)):
raise ReaderError('Duplicate peaks cannot be given')
# If none were given, number automatically
else:
num = range(1, len(num)+1, 1)
args.add('num', array(num))
args.add('vib', array(vib))
args.add('heights', array(heights))
args.add('Gamma_Lorentz', array(Gamma_Lorentz))
args.add('Gamma_Gauss', array(Gamma_Gauss))
# Set up the exchanges
# Make sure the each exchange number appears in num.
num = set(num)
ex = []
rates = []
string = 'Requested peak {0} in exchange does not exist'
if 'exchange' in args:
for exchange in args.exchange:
p1 = exchange[0]
if p1 not in num:
raise ReaderError(string.format(p1))
p2 = exchange[1]
if p2 not in num:
raise ReaderError(string.format(p2))
if p1 == p2 and args.symmetric_exchange:
raise ReaderError('Self exchange is not allowed')
rate = exchange[2]
# Offset the peak number by one to match python indicies
ex.append([p1-1, p2-1])
rates.append(rate)
else:
ex = []
rates = []
args.add('exchanges', array(ex, dtype=int))
args.add('exchange_rates', array(rates))
# Make sure the xlimits are ascending
try:
range_check(args.xlim[0], args.xlim[1])
except ValueError:
raise ReaderError('In xrange, the low value must '
'less than the high value')
return args
