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Transition from Python 2 to 3 #43

Merged
merged 46 commits into from
Oct 22, 2019
Merged

Transition from Python 2 to 3 #43

merged 46 commits into from
Oct 22, 2019

Commits on Sep 9, 2019

  1. Trying to run with RMG-3, we're able to generate guesses, but some wo… 

    …rkflow things need tweaking
    Nate Harms committed Sep 9, 2019
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Commits on Sep 10, 2019

  1. Updated ways of getting information and revised dummy squeue command

    Nate Harms committed Sep 10, 2019
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  2. Revised exec command for py3

    Nate Harms committed Sep 10, 2019
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  3. Changed how ASE atoms are set, how labeled atoms are IDed, and set path

    Nate Harms committed Sep 10, 2019
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  4. Revised how info is obtained from dicts, and how ase atoms are set

    Nate Harms committed Sep 10, 2019
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  5. revised how ase atoms are set

    Nate Harms committed Sep 10, 2019
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  6. Revised assert test, accounted for getLabeledAtom returning lists

    Nate Harms committed Sep 10, 2019
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  7. Made python 3 a dependency, this won't work until rmg3 is released

    Nate Harms committed Sep 10, 2019
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Commits on Sep 25, 2019

  1. Commented out error in job.py

    nateharms committed Sep 25, 2019
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  2. Merge remote-tracking branch 'origin/master' into py3

    Nate Harms committed Sep 25, 2019
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  3. rmg2to3'ed all of the python files in autotst

    Nate Harms committed Sep 25, 2019
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  4. got rid of camelCase in calculator files

    Nate Harms committed Sep 25, 2019
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  5. got rid of camelCase in data files

    Nate Harms committed Sep 25, 2019
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  6. got rid of camelCase in reaction and species

    Nate Harms committed Sep 25, 2019
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  7. removed camelCase from database files

    Nate Harms committed Sep 25, 2019
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  8. updated traning reactions long and short desc

    Nate Harms committed Sep 25, 2019
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  9. removed forgotten camelCase

    Nate Harms committed Sep 25, 2019
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  10. changed SMILES to smiles per RMG update

    Nate Harms committed Sep 25, 2019
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Commits on Sep 26, 2019

  1. Changed SMILES to smiles for RMGMolecule objects

    Nate Harms committed Sep 26, 2019
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  2. Fixed typos and reset some camelCase (for QMData and Arkane)

    Nate Harms committed Sep 26, 2019
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  3. Fixed the setting of rdkit_molecule objects when copying confs

    Nate Harms committed Sep 26, 2019
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  4. Merge remote-tracking branch 'origin/master' into py3

    Nate Harms committed Sep 26, 2019
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  5. Addressed merge conflicts when pulling in master

    Nate Harms committed Sep 26, 2019
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Commits on Sep 30, 2019

  1. fixed a camelCase issue in statmech

    Nate Harms committed Sep 30, 2019
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Commits on Oct 4, 2019

  1. Addressing some of the testing errors that occur on discovery

    nateharms committed Oct 4, 2019
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Commits on Oct 8, 2019

  1. Revised multiprocessing in optimizations to not use objects

    nateharms committed Oct 8, 2019
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  2. Merge branch 'py3' of github.com:ReactionMechanismGenerator/AutoTST i… 

    …nto py3
    nateharms committed Oct 8, 2019
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Commits on Oct 9, 2019

  1. added rmg 3 to the environment file

    Nate Harms committed Oct 9, 2019
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  2. prepull commit

    nateharms committed Oct 9, 2019
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  3. removed unecessary files

    nateharms committed Oct 9, 2019
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  4. updated environment file

    nateharms committed Oct 9, 2019
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  5. Merge branch 'py3' of github.com:ReactionMechanismGenerator/AutoTST i… 

    …nto py3
    nateharms committed Oct 9, 2019
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  6. Updated env again

    nateharms committed Oct 9, 2019
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Commits on Oct 10, 2019

  1. added .symm to gitignore

    Nate Harms committed Oct 10, 2019
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Commits on Oct 22, 2019

  1. removed unecessary .symm files

    Nate Harms committed Oct 22, 2019
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  2. Updated environment file to mirror the new RMG 3 beta. This won't wor… 

    …k when making environemnts on Mac OS but should work for linux.
    Nate Harms committed Oct 22, 2019
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  3. Forgot to add a skip when checking for failed TS opts, added it in

    nateharms committed Oct 22, 2019
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  4. Made some modifications to get scripts running on discovery

    nateharms committed Oct 22, 2019
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  5. Updated travis from py2 to py3

    Nate Harms committed Oct 22, 2019
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  6. Shuffled around imports to import rdkit first. This *might* fix faults

    Nate Harms committed Oct 22, 2019
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  7. Tried to fix segfaults with openbabel, but not sure how to do that...

    Nate Harms committed Oct 22, 2019
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  8. Added krsna's openbabel (let's see if it doesn't segfault)

    Nate Harms committed Oct 22, 2019
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  9. Removed tearDown from inputoutputTest 

    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.
    Nate Harms committed Oct 22, 2019
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  10. Reworked how files are moved / deleted when testing

    Nate Harms committed Oct 22, 2019
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  11. Added .ts and .kinetics files to the gitignore

    Nate Harms committed Oct 22, 2019
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  12. Remove unecessary rm from Make file

    Nate Harms committed Oct 22, 2019
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