Prettify

[alongd]

Motivation or Problem

As noted in #1726 by @yunsiechung (Thanks!), Arkane's prettify functionality got broken in the Py3 transition.

Description of Changes

Instead of adapting Abstract Syntax Trees to the Py3 changes (which I don't know how to do right now), this PR suggests to use a simple combination of pprint.pformat and RMGObject.as_dict(). This might be advantageous since theoretically the object can be rebuilt using from_dict().

Testing

A test was added, showing how this feature performs for a complex object such as Conformer.

Point for discussion

Arkane's thermo and kinetics blocks we output are not objects, and have no real pythonic form. Here I added a tentative fix for them, we might want to reconsider how to output them better.
I'd like to try removing (not fixing) thermo and kinetic output for output.py, and instead (and finally) save respective RMG library files. We will still output the data in the table form for both in output.py.

---

Here's an example output:

# Conformer for C7H7:
{   'E0': {   'class': 'ScalarQuantity',
              'units': 'kJ/mol',
              'value': 193.74920136178187},
    'class': 'Conformer',
    'coordinates': {   'class': 'ArrayQuantity',
                       'units': 'angstroms',
                       'value': {   'class': 'np_array',
                                    'object': [   [0.0, 0.0, -1.90931],
                                                  [0.0, 1.20973, -1.20462],
                                                  [   0.0,
                                                      1.2163699999999997,
                                                      0.17817],
                                                  [0.0, 0.0, 0.92089],
                                                  [   0.0,
                                                      -1.2163699999999997,
                                                      0.17817],
                                                  [0.0, -1.20973, -1.20462],
                                                  [0.0, 0.0, -2.99302],
                                                  [0.0, 2.14897, -1.74692],
                                                  [0.0, 2.15757, 0.71765],
                                                  [0.0, -2.15757, 0.71765],
                                                  [0.0, -2.14897, -1.74692],
                                                  [0.0, 0.0, 2.32493],
                                                  [0.0, 0.92727, 2.88399],
                                                  [0.0, -0.92727, 2.88399]]}},
    'mass': {   'class': 'ArrayQuantity',
                'units': 'amu',
                'value': {   'class': 'np_array',
                             'object': [   12.000000000000002,
                                           12.000000000000002,
                                           12.000000000000002,
                                           12.000000000000002,
                                           12.000000000000002,
                                           12.000000000000002,
                                           1.00782503224,
                                           1.00782503224,
                                           1.00782503224,
                                           1.00782503224,
                                           1.00782503224,
                                           12.000000000000002,
                                           1.00782503224,
                                           1.00782503224]}},
    'modes': [   {   'class': 'IdealGasTranslation',
                     'mass': {   'class': 'ScalarQuantity',
                                 'units': 'amu',
                                 'value': 91.05478},
                     'quantum': False},
                 {   'class': 'NonlinearRotor',
                     'inertia': {   'class': 'ArrayQuantity',
                                    'units': 'amu*angstrom^2',
                                    'value': {   'class': 'np_array',
                                                 'object': [   91.05665505889641,
                                                               186.6754595575174,
                                                               277.7326559036768]}},
                     'quantum': False,
                     'rotationalConstant': {   'class': 'ArrayQuantity',
                                               'units': 'cm^-1',
                                               'value': {   'class': 'np_array',
                                                            'object': [   0.18513340999012978,
                                                                          0.09030447329984698,
                                                                          0.060697324189327787]}},
                     'symmetry': 2},
                 {   'class': 'HarmonicOscillator',
                     'frequencies': {   'class': 'ArrayQuantity',
                                        'units': 'cm^-1',
                                        'value': {   'class': 'np_array',
                                                     'object': [   199.38075265757388,
                                                                   360.5363271321874,
                                                                   413.7949151525557,
                                                                   480.34741903286914,
                                                                   536.2845084113071,
                                                                   630.7231437836404,
                                                                   687.1180869560582,
                                                                   709.613210214998,
                                                                   776.6617864901739,
                                                                   830.4036310625469,
                                                                   834.386032685694,
                                                                   901.8407934891261,
                                                                   973.4982807999646,
                                                                   975.1481503393776,
                                                                   993.3485157754649,
                                                                   998.6064486942171,
                                                                   1040.1386185625333,
                                                                   1120.6925785487256,
                                                                   1179.2234881852514,
                                                                   1189.0708173043222,
                                                                   1292.8647176431568,
                                                                   1332.909949640503,
                                                                   1357.1753414643513,
                                                                   1479.4620076104507,
                                                                   1495.3606146408765,
                                                                   1507.9144088991889,
                                                                   1583.1430987057158,
                                                                   1604.628263865009,
                                                                   3156.8525679482696,
                                                                   3170.2206892536133,
                                                                   3172.7811150780485,
                                                                   3185.0534994349905,
                                                                   3189.799070842567,
                                                                   3203.232858579444,
                                                                   3253.9889510503353]}},
                     'quantum': True},
                 {   'class': 'HinderedRotor',
                     'fourier': {   'class': 'ArrayQuantity',
                                    'units': 'kJ/mol',
                                    'value': {   'class': 'np_array',
                                                 'object': [   [   -0.31592326520854164,
                                                                   -27.766519216358134,
                                                                   0.177678139795233,
                                                                   3.2437014555229857,
                                                                   0.050951495010736314],
                                                               [   -0.0016495340958863763,
                                                                   -0.0021925030855088038,
                                                                   -0.003863963373036643,
                                                                   -0.0009120676025288776,
                                                                   0.0027420643405067606]]}},
                     'frequency': 0.0,
                     'inertia': {   'class': 'ScalarQuantity',
                                    'units': 'amu*angstrom^2',
                                    'value': 1.7001286526557986},
                     'quantum': True,
                     'rotationalConstant': {   'class': 'ScalarQuantity',
                                               'units': 'cm^-1',
                                               'value': 9.915501998636937},
                     'semiclassical': False,
                     'symmetry': 2}],
    'number': {   'class': 'ArrayQuantity',
                  'value': {   'class': 'np_array',
                               'object': [   6.0,
                                             6.0,
                                             6.0,
                                             6.0,
                                             6.0,
                                             6.0,
                                             1.0,
                                             1.0,
                                             1.0,
                                             1.0,
                                             1.0,
                                             6.0,
                                             1.0,
                                             1.0]}},
    'optical_isomers': 1,
    'spin_multiplicity': 2}

[codecov]

Codecov Report

Merging #1744 into master will not change coverage.
The diff coverage is n/a.

@@          Coverage Diff           @@
##           master   #1744   +/-   ##
======================================
  Coverage    32.6%   32.6%           
======================================
  Files          87      87           
  Lines       26115   26115           
  Branches     6875    6875           
======================================
  Hits         8516    8516           
+ Misses      16641   16629   -12     
- Partials      958     970   +12

Impacted Files	Coverage Δ
rmgpy/data/statmech.py	42.2% <0%> (ø)	⬆️
rmgpy/rmg/pdep.py	12.21% <0%> (ø)	⬆️
rmgpy/reaction.py	0% <0%> (ø)	⬆️
rmgpy/data/kinetics/family.py	48.28% <0%> (ø)	⬆️
rmgpy/yml.py	15.71% <0%> (ø)	⬆️
rmgpy/data/kinetics/database.py	50.61% <0%> (ø)	⬆️
rmgpy/molecule/molecule.py	0% <0%> (ø)	⬆️
rmgpy/statmech/ndTorsions.py	59.78% <0%> (ø)	⬆️

---

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[mliu49]

Prettify was broken because of changes to method names in PrettifyVisitor in 59d8060. It subclasses ast.NodeVisitor, which relies on having special methods named visit_classname, where classname may be Call, Str, Num, etc.

For now, I think we should revert the method renaming in this class to restore the original behavior. However, I do agree that we should reconsider our output formats in the near future.

[alongd]

OK, I reverted the PEP8 prettify changes, and added a test.
We'll find time to discuss a new format for Arkane's output.
Thanks for the guidance, @mliu49!

[mliu49]

I added two more fixes and a unit test. Turns out that Python 3 handles negative numbers differently than Python 2...

[alongd]

Looking good! I added one comment/question

[alongd]

@mliu49, thanks for your excellent additions to this PR!
I rebased and squashed, should be ready to merge after the tests pass.

[mliu49]

Sorry, I merged another PR so I went ahead and rebased this again. I will merge after tests pass, unless you think we need a third reviewer.

[alongd]

@mliu49, I think this is ready to be merged. Thanks again