Moving of symbols and molecular calculation (#61)

* Reorganize import and lists * Update to break on Travis * Create help text string from helpTextPython39 * Reorganize test Update to replace \r in travis specific string * Update all cmd help tests * Add print statement for temporary debugging * Update help texts * Update test to (hopefully) remove error for windows 10 + pyhton3.9 * Catch typo * Add print for debut... * Update help string * Restrict matplotlib to version <3.4 Add python 3.9 to classifiers * Update version
MJOLNIRPackage · Apr 13, 2021 · 199caa8 · 199caa8
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diff --git a/MJOLNIR/__init__.py b/MJOLNIR/__init__.py
@@ -8,7 +8,7 @@
 import sys,os
 sys.path.append('.')
 
-__version__ = '1.1.17'
+__version__ = '1.1.18'
 __author__ = 'Jakob Lass'
 
 __multiFLEXXNormalization__ = os.path.join(os.path.dirname(__file__),'CalibrationMultiFLEXX.csv') 

diff --git a/MJOLNIR/_tools.py b/MJOLNIR/_tools.py
@@ -9,6 +9,7 @@
 import os
 import inspect
 import matplotlib
+import regex as re
 
 # E = hbar^2k^2/(2m)
 m = 1.67492749804e-27 # kg
@@ -827,6 +828,45 @@ def generateLabelDirection(vec,labels=['H','K','L']):
     returnLabel = ''.join(['(',', '.join([x for x in label]),')'])
     return returnLabel
 
+
+symbols = (
+    'H', 'D', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al',
+    'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe',
+    'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr',
+    'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
+    'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm',
+    'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',
+    'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',
+    'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf',
+    'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds',
+    'Rg', 'Cn', 'Uut', 'Fl', 'Uup', 'Lv', 'Uus', 'Uuo'
+)
+
+
+
+# Molar mass of natural compund
+_relative_atomic_masses = (
+    "1.008 2.0(1) 4.002602(2) 6.94 9.0121831(5) 10.81 12.011 14.007 15.999"
+    " 18.998403163(6) 20.1797(6) 22.98976928(2) 24.305 26.9815385(7) 28.085"
+    " 30.973761998(5) 32.06 35.45 39.948(1) 39.0983(1) 40.078(4)"
+    " 44.955908(5) 47.867(1) 50.9415(1) 51.9961(6) 54.938044(3) 55.845(2)"
+    " 58.933194(4) 58.6934(4) 63.546(3) 65.38(2) 69.723(1) 72.630(8)"
+    " 74.921595(6) 78.971(8) 79.904 83.798(2) 85.4678(3) 87.62(1)"
+    " 88.90584(2) 91.224(2) 92.90637(2) 95.95(1) [98] 101.07(2) 102.90550(2)"
+    " 106.42(1) 107.8682(2) 112.414(4) 114.818(1) 118.710(7) 121.760(1)"
+    " 127.60(3) 126.90447(3) 131.293(6) 132.90545196(6) 137.327(7)"
+    " 138.90547(7) 140.116(1) 140.90766(2) 144.242(3) [145] 150.36(2)"
+    " 151.964(1) 157.25(3) 158.92535(2) 162.500(1) 164.93033(2) 167.259(3)"
+    " 168.93422(2) 173.045(10) 174.9668(1) 178.49(2) 180.94788(2) 183.84(1)"
+    " 186.207(1) 190.23(3) 192.217(3) 195.084(9) 196.966569(5) 200.592(3)"
+    " 204.38 207.2(1) 208.98040(1) [209] [210] [222] [223] [226] [227]"
+    " 232.0377(4) 231.03588(2) 238.02891(3) [237] [244] [243] [247] [247]"
+    " [251] [252] [257] [258] [259] [266] [267] [268] [269] [270] [269]"
+    " [278] [281] [282] [285] [286] [289] [289] [293] [294] [294]"
+)
+
+
+
 def calculateMolarMass(sampleChemicalFormula,formulaUnitsPerUnitCell=1,returnElements=False):
     """Calculate Molar mass given chemical formula and number of formula units per cell
     
@@ -857,46 +897,7 @@ def calculateMolarMass(sampleChemicalFormula,formulaUnitsPerUnitCell=1,returnEle
     stop = sampleChemicalFormula.count(')')
     if not start==stop:
         raise AttributeError('The number of starting and closing parenthesis do not match. Got {} "(" and {} ")"'.format(start,stop))
-
-    # Definition of chemical symbols
-    symbols = (
-        'H', 'D', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al',
-        'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe',
-        'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr',
-        'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
-        'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm',
-        'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',
-        'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',
-        'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf',
-        'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds',
-        'Rg', 'Cn', 'Uut', 'Fl', 'Uup', 'Lv', 'Uus', 'Uuo'
-    )
-
-
-
-    # Molar mass of natural compund
-    _relative_atomic_masses = (
-        "1.008 2.0(1) 4.002602(2) 6.94 9.0121831(5) 10.81 12.011 14.007 15.999"
-        " 18.998403163(6) 20.1797(6) 22.98976928(2) 24.305 26.9815385(7) 28.085"
-        " 30.973761998(5) 32.06 35.45 39.948(1) 39.0983(1) 40.078(4)"
-        " 44.955908(5) 47.867(1) 50.9415(1) 51.9961(6) 54.938044(3) 55.845(2)"
-        " 58.933194(4) 58.6934(4) 63.546(3) 65.38(2) 69.723(1) 72.630(8)"
-        " 74.921595(6) 78.971(8) 79.904 83.798(2) 85.4678(3) 87.62(1)"
-        " 88.90584(2) 91.224(2) 92.90637(2) 95.95(1) [98] 101.07(2) 102.90550(2)"
-        " 106.42(1) 107.8682(2) 112.414(4) 114.818(1) 118.710(7) 121.760(1)"
-        " 127.60(3) 126.90447(3) 131.293(6) 132.90545196(6) 137.327(7)"
-        " 138.90547(7) 140.116(1) 140.90766(2) 144.242(3) [145] 150.36(2)"
-        " 151.964(1) 157.25(3) 158.92535(2) 162.500(1) 164.93033(2) 167.259(3)"
-        " 168.93422(2) 173.045(10) 174.9668(1) 178.49(2) 180.94788(2) 183.84(1)"
-        " 186.207(1) 190.23(3) 192.217(3) 195.084(9) 196.966569(5) 200.592(3)"
-        " 204.38 207.2(1) 208.98040(1) [209] [210] [222] [223] [226] [227]"
-        " 232.0377(4) 231.03588(2) 238.02891(3) [237] [244] [243] [247] [247]"
-        " [251] [252] [257] [258] [259] [266] [267] [268] [269] [270] [269]"
-        " [278] [281] [282] [285] [286] [289] [289] [293] [294] [294]"
-    )
-
-
-    import regex as re
+
 
 
     # Combination of https://stackoverflow.com/questions/26385984/recursive-pattern-in-regex

diff --git a/docs/Tutorials/Advanced/ConstantEnergy3D.png b/docs/Tutorials/Advanced/ConstantEnergy3D.png
diff --git a/docs/Tutorials/Advanced/FittedQEPlot.png b/docs/Tutorials/Advanced/FittedQEPlot.png
diff --git a/docs/Tutorials/Advanced/RawQEPlot.png b/docs/Tutorials/Advanced/RawQEPlot.png
diff --git a/docs/Tutorials/Advanced/ViewerAnimationEPlane.gif b/docs/Tutorials/Advanced/ViewerAnimationEPlane.gif
diff --git a/docs/Tutorials/Advanced/ViewerAnimationEPlane.png b/docs/Tutorials/Advanced/ViewerAnimationEPlane.png
diff --git a/docs/Tutorials/Advanced/plotCutQELineMnF2.png b/docs/Tutorials/Advanced/plotCutQELineMnF2.png
diff --git a/docs/Tutorials/Advanced/plotCutQELineMnF21D.png b/docs/Tutorials/Advanced/plotCutQELineMnF21D.png
diff --git a/docs/Tutorials/Instrument/SimpleInstrument.png b/docs/Tutorials/Instrument/SimpleInstrument.png
diff --git a/docs/Tutorials/Instrument/SimpleInstrument2.png b/docs/Tutorials/Instrument/SimpleInstrument2.png
diff --git a/docs/Tutorials/Instrument/SimpleInstrument2_A4.png b/docs/Tutorials/Instrument/SimpleInstrument2_A4.png
diff --git a/docs/Tutorials/Instrument/SimpleInstrument2_Ef.png b/docs/Tutorials/Instrument/SimpleInstrument2_Ef.png
diff --git a/docs/Tutorials/Quick/ConstantEnergy3DPolar.png b/docs/Tutorials/Quick/ConstantEnergy3DPolar.png
diff --git a/docs/Tutorials/Quick/ConstantEnergy3DXY.png b/docs/Tutorials/Quick/ConstantEnergy3DXY.png
diff --git a/docs/Tutorials/Quick/EnergyPlaneViewer.png b/docs/Tutorials/Quick/EnergyPlaneViewer.png
diff --git a/docs/Tutorials/Quick/HPlaneViewer.png b/docs/Tutorials/Quick/HPlaneViewer.png
diff --git a/docs/Tutorials/Quick/OrthogonalPlaneViewer.png b/docs/Tutorials/Quick/OrthogonalPlaneViewer.png
diff --git a/docs/Tutorials/Quick/masking_10.png b/docs/Tutorials/Quick/masking_10.png
diff --git a/docs/Tutorials/Quick/masking_40.png b/docs/Tutorials/Quick/masking_40.png
diff --git a/docs/Tutorials/Quick/masking_QELine.png b/docs/Tutorials/Quick/masking_QELine.png
diff --git a/docs/Tutorials/Quick/plotCutQELineMnF2.png b/docs/Tutorials/Quick/plotCutQELineMnF2.png
diff --git a/docs/Tutorials/Tools/Binning.png b/docs/Tutorials/Tools/Binning.png
diff --git a/docs/Tutorials/Tools/Here.png b/docs/Tutorials/Tools/Here.png
diff --git a/docs/Tutorials/Tools/RLUAxis.png b/docs/Tutorials/Tools/RLUAxis.png
diff --git a/docs/Tutorials/Tools/RLUAxis2.png b/docs/Tutorials/Tools/RLUAxis2.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -31,9 +31,9 @@
 author = u'Jakob Lass'
 
 # The short X.Y version
-version = u'1.1.17'
+version = u'1.1.18'
 # The full version, including alpha/beta/rc tags
-release = u'1.1.17'
+release = u'1.1.18'
 
 
 

diff --git a/setup.py b/setup.py
@@ -20,7 +20,7 @@
 setup(
     name='MJOLNIR',
 
-    version='1.1.17',
+    version='1.1.18',
     description=('Neutron Scattering software suite.'),
     long_description=long_description,
     author='Jakob Lass',
@@ -39,7 +39,7 @@
                             'MJOLNIR3DView = MJOLNIR.CommandLineScripts.MJOLNIR3DView:main']
         },
     python_requires='>=3.5' if not operatingSystem == 'darwin' else '>=3.6',
-    install_requires=['matplotlib>=3','numpy>=1.14','h5py>=2.5','scipy','datetime','pytest>=4.6','pyperclip','decorator','pandas','future',
+    install_requires=['matplotlib>=3,<3.4','numpy>=1.14','h5py>=2.5','scipy','datetime','pytest>=4.6','pyperclip','decorator','pandas','future',
                     'pip>=20','ufit>=1.4.0','pyqtgraph','regex'], # ,'ufit','sip','PyQt5-sip','PyQt5<=5.12'
     classifiers=[
         'Development Status :: 3 - Alpha',
@@ -52,5 +52,6 @@
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8'],
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9'],
     )