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Fix Celcius Behavior #114

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Fix Celcius Behavior #114

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1cee8b9
Correctly read Celsius temperatures
jsantner Jun 14, 2018
cfdbae2
Add test with temperature in Celsius
jsantner Jun 14, 2018
2c0b278
Minor fix in arguments
jsantner Jun 14, 2018
73551ab
Only apply to celsius and fahrenheit
jsantner Jun 14, 2018
3681791
Syntax
jsantner Jun 14, 2018
f759ab1
Fix behavior in chemked.process_quantity
jsantner Jun 14, 2018
2147780
Fixing changes that were requested.
jsantner Jun 25, 2018
5c74873
raise pint.UndefinedUnitError if it can't be fixed by np.nan
jsantner Jun 25, 2018
ae14c43
Remove 'nan' handling
jsantner Jun 26, 2018
befbe89
Add test for changes in chemked.py
jsantner Jul 10, 2018
6eee6df
pint quantities must be in same unit to be compared with np.isclose
jsantner Jul 11, 2018
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11 changes: 10 additions & 1 deletion pyked/chemked.py
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Original file line number Diff line number Diff line change
Expand Up @@ -718,7 +718,16 @@ def __init__(self, properties):
def process_quantity(self, properties):
"""Process the uncertainty information from a given quantity and return it
"""
quant = Q_(properties[0])
if type(properties[0]) is str:
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I think the more simpler way of doing this would be to try to create the Quantity, catch the error, split and create the Quantity again, and let it raise if that still fails. Something like

try:
    quant = Q_(properties[0])
except pint.OffsetUnitCalculusError:
    quant = Q_(*properties[0].split())

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I made those changes, with some slight modifications.
Q_(*properties[0].split()) won't work with an offset unit when the quantity is later converted to the base units, so I have to do the less elegant method where the first value is converted to a float. For example:

test = Q_('50', 'degC')  # This does not raise any error message
test.to('kelvin')  # This raises a TypeError
Q_(50.0, 'degC').to('kelvin')  # This doesn't raise any errors

I also added code to handle nan's. Although it isn't really in the scope of this pull request, it deals with the same section of code. I've found some yaml files where a field is given as

ignition-delay:
      - nan ms

I've added code to handle this case properly by replacing the nan string with np.nan. There may be other errors in yaml files that raise pint.UndefinedUnitError, so I included an if statement to exclude those.

I didn't know if there was a simpler way to import the two errors from pint, so I had to import all of pint. Is there a cleaner way to import the errors?

values = properties[0].split()
if any([temp in values for temp in
['degC', 'degF', 'celsius', 'fahrenheit']]):
value_alt = [float(values[0])] + values[1:]
quant = Q_(*value_alt)
else:
quant = Q_(properties[0])
else:
quant = Q_(properties[0])
if len(properties) > 1:
unc = properties[1]
uncertainty = unc.get('uncertainty', False)
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2 changes: 1 addition & 1 deletion pyked/tests/test_validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -363,7 +363,7 @@ def properties(self, request):

@pytest.mark.parametrize("properties", [
'testfile_st.yaml', 'testfile_st2.yaml', 'testfile_rcm.yaml', 'testfile_required.yaml',
'testfile_uncertainty.yaml', 'testfile_rcm2.yaml',
'testfile_uncertainty.yaml', 'testfile_rcm2.yaml', 'testfile_rcm3.yaml'
], indirect=['properties'])
def test_valid_yaml(self, properties):
"""Ensure ChemKED YAML is validated
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178 changes: 178 additions & 0 deletions pyked/tests/testfile_rcm3.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,178 @@
---
file-authors:
- name: Kyle E Niemeyer
ORCID: 0000-0003-4425-7097
file-version: 0
chemked-version: 0.0.1
reference:
doi: 10.1002/kin.20180
authors:
- name: Gaurav Mittal
- name: Chih-Jen Sung
ORCID: 0000-0003-2046-8076
- name: Richard A Yetter
journal: International Journal of Chemical Kinetics
year: 2006
volume: 38
pages: 516-529
detail: Fig. 6, open circle
experiment-type: ignition delay
apparatus:
kind: rapid compression machine
institution: Case Western Reserve University
facility: CWRU RCM
datapoints:
- temperature:
- 24.25 degC
ignition-delay:
- 1.0 ms
first-stage-ignition-delay:
- 0.5 ms
- uncertainty-type: relative
uncertainty: 0.01
pressure:
- 958.0 torr
rcm-data:
compressed-pressure:
- 7.1 bar
compressed-temperature:
- 765 K
- uncertainty: 0.01
uncertainty-type: relative
compression-time:
- 38.0 ms
stroke:
- 10.0 inch
clearance:
- 2.5 cm
compression-ratio:
- 12.0
composition:
kind: mole fraction
species:
- species-name: H2
InChI: 1S/H2/h1H
amount:
- 0.12500
- species-name: O2
InChI: 1S/O2/c1-2
amount:
- 0.06250
- species-name: N2
InChI: 1S/N2/c1-2
amount:
- 0.18125
- species-name: Ar
InChI: 1S/Ar
amount:
- 0.63125
ignition-type:
target: pressure
type: d/dt max
time-histories:
- type: volume
time:
units: s
column: 0
quantity:
units: cm3
column: 1
values:
- [0.00E+000, 5.47669375000E+002]
- [1.00E-003, 5.46608789894E+002]
- [2.00E-003, 5.43427034574E+002]
- [3.00E-003, 5.38124109043E+002]
- [4.00E-003, 5.30700013298E+002]
- [5.00E-003, 5.21154747340E+002]
- [6.00E-003, 5.09488311170E+002]
- [7.00E-003, 4.95700704787E+002]
- [8.00E-003, 4.79791928191E+002]
- [9.00E-003, 4.61761981383E+002]
- [1.00E-002, 4.41610864362E+002]
- [1.10E-002, 4.20399162234E+002]
- [1.20E-002, 3.99187460106E+002]
- [1.30E-002, 3.77975757979E+002]
- [1.40E-002, 3.56764055851E+002]
- [1.50E-002, 3.35552353723E+002]
- [1.60E-002, 3.14340651596E+002]
- [1.70E-002, 2.93128949468E+002]
- [1.80E-002, 2.71917247340E+002]
- [1.90E-002, 2.50705545213E+002]
- [2.00E-002, 2.29493843085E+002]
- [2.10E-002, 2.08282140957E+002]
- [2.20E-002, 1.87070438830E+002]
- [2.30E-002, 1.65858736702E+002]
- [2.40E-002, 1.44647034574E+002]
- [2.50E-002, 1.23435332447E+002]
- [2.60E-002, 1.02223630319E+002]
- [2.70E-002, 8.10119281915E+001]
- [2.80E-002, 6.33355097518E+001]
- [2.90E-002, 5.27296586879E+001]
- [3.00E-002, 4.91943750000E+001]
- [3.10E-002, 4.97137623933E+001]
- [3.20E-002, 5.02063762048E+001]
- [3.30E-002, 5.06454851923E+001]
- [3.40E-002, 5.10218564529E+001]
- [3.50E-002, 5.13374097598E+001]
- [3.60E-002, 5.16004693977E+001]
- [3.70E-002, 5.18223244382E+001]
- [3.80E-002, 5.20148449242E+001]
- [3.90E-002, 5.21889350372E+001]
- [4.00E-002, 5.23536351113E+001]
- [4.10E-002, 5.25157124459E+001]
- [4.20E-002, 5.26796063730E+001]
- [4.30E-002, 5.28476160610E+001]
- [4.40E-002, 5.30202402028E+001]
- [4.50E-002, 5.31965961563E+001]
- [4.60E-002, 5.33748623839E+001]
- [4.70E-002, 5.35527022996E+001]
- [4.80E-002, 5.37276399831E+001]
- [4.90E-002, 5.38973687732E+001]
- [5.00E-002, 5.40599826225E+001]
- [5.10E-002, 5.42141273988E+001]
- [5.20E-002, 5.43590751578E+001]
- [5.30E-002, 5.44947289126E+001]
- [5.40E-002, 5.46215686913E+001]
- [5.50E-002, 5.47405518236E+001]
- [5.60E-002, 5.48529815402E+001]
- [5.70E-002, 5.49603582190E+001]
- [5.80E-002, 5.50642270863E+001]
- [5.90E-002, 5.51660349836E+001]
- [6.00E-002, 5.52670070646E+001]
- [6.10E-002, 5.53680520985E+001]
- [6.20E-002, 5.54697025392E+001]
- [6.30E-002, 5.55720927915E+001]
- [6.40E-002, 5.56749762728E+001]
- [6.50E-002, 5.57777790517E+001]
- [6.60E-002, 5.58796851466E+001]
- [6.70E-002, 5.59797461155E+001]
- [6.80E-002, 5.60770054561E+001]
- [6.90E-002, 5.61706266985E+001]
- [7.00E-002, 5.62600130036E+001]
- [7.10E-002, 5.63449057053E+001]
- [7.20E-002, 5.64254496625E+001]
- [7.30E-002, 5.65022146282E+001]
- [7.40E-002, 5.65761642150E+001]
- [7.50E-002, 5.66485675508E+001]
- [7.60E-002, 5.67208534842E+001]
- [7.70E-002, 5.67944133373E+001]
- [7.80E-002, 5.68703658198E+001]
- [7.90E-002, 5.69493069272E+001]
- [8.00E-002, 5.70310785669E+001]
- [8.10E-002, 5.71146023893E+001]
- [8.20E-002, 5.71978399741E+001]
- [8.30E-002, 5.72779572372E+001]
- [8.40E-002, 5.73517897984E+001]
- [8.50E-002, 5.74167271960E+001]
- [8.60E-002, 5.74721573687E+001]
- [8.70E-002, 5.75216388520E+001]
- [8.80E-002, 5.75759967785E+001]
- [8.90E-002, 5.76575701358E+001]
- [9.00E-002, 5.78058719368E+001]
- [9.10E-002, 5.80849611077E+001]
- [9.20E-002, 5.85928651155E+001]
- [9.30E-002, 5.94734357453E+001]
- [9.40E-002, 6.09310671165E+001]
- [9.50E-002, 6.32487551103E+001]
- [9.60E-002, 6.68100309742E+001]
...
11 changes: 10 additions & 1 deletion pyked/validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,16 @@ def _validate_isvalid_quantity(self, isvalid_quantity, field, value):
{'isvalid_quantity': {'type': 'bool'}, 'field': {'type': 'str'},
'value': {'type': 'list'}}
"""
quantity = Q_(value[0])
if type(value[0]) is str:
values = value[0].split()
if any([temp in values for temp in
['degC', 'degF', 'celsius', 'fahrenheit']]):
value_alt = [float(values[0])] + values[1:]
quantity = Q_(*value_alt)
else:
quantity = Q_(value[0])
else:
quantity = Q_(value[0])
low_lim = 0.0 * units(property_units[field])

try:
Expand Down