Transition from Python 2 to 3 #43
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…rkflow things need tweaking
autotst/calculator/statmech.py
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| "", | ||
| "externalSymmetry = {}".format(external_symmetry), | ||
| "", | ||
| "spinMultiplicity = {}".format(conformer.rmg_molecule.multiplicity), | ||
| "", | ||
| "opticalIsomers = 1", | ||
| "optical_isomers = 1", |
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I think this is part of arkane input file and should remain camelCase
autotst/calculator/statmech.py
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| @@ -402,7 +402,7 @@ def write_ts_input(self, transitionstate): | |||
| "spinMultiplicity = {}".format( | |||
| transitionstate.rmg_molecule.multiplicity), | |||
| "", | |||
| "opticalIsomers = 1", | |||
| "optical_isomers = 1", | |||
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Arkane input should be camelCase? (I won't comment on any others - do a full search)
| resultFile.write('method = "{0!s}"\n'.format(self.method)) | ||
| resultFile.write("qmData = {0!r}\n".format(self.qmdata)) | ||
| with open(file_path, 'w') as results_file: | ||
| results_file.write('rxn_label = "{0!s}"\n'.format(self.reaction.label)) |
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If we've changed the syntax of our TS results file, do we have a "load" method that can read both old and new syntaxes? or plans to convert all your old data?
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We should probably make it backward compatible, good comment, this will be true for the .kinetics files too
| @@ -2,8 +2,8 @@ | |||
| # encoding: utf-8 | |||
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| name = "intra_H_migration/TS_groups" | |||
| shortDesc = u"" | |||
| longDesc = u""" | |||
| short_desc = u"" | |||
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Did they change the syntax of RMG-database??
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They have not, but we changed the syntax of ours. Should we change it back?
…k when making environemnts on Mac OS but should work for linux.
Codecov Report
@@ Coverage Diff @@
## master #43 +/- ##
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- Coverage 64.32% 63.21% -1.11%
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Files 27 27
Lines 4647 4654 +7
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- Hits 2989 2942 -47
- Misses 1658 1712 +54
Continue to review full report at Codecov.
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There is an error when running this on travis, I'm guessing what's happening is that the tearDown is running (removing a directory) while another directory is being created.
This PR address recent changes in RMG to move from Python 2 to 3. This transition was needed for a while, but RMG (one of the dependencies) needed to be moved to Python 3 before we were able to make this transition ourself.
Summary of changes:
TSandConformerobjects was refactored for python 3ToDo:
environment.ymlfile to use the new RMG 3 (when the binary gets released)krsna's openbabel to the environment file