Update RMG-database scripts and notebooks to Python 3 #364
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
17 tasks
mliu49
reviewed
Nov 19, 2019
scripts/evansPolanyi.py
Outdated
Comment on lines
7
to
12
| from __future__ import division | ||
| from __future__ import print_function | ||
|
|
||
| from builtins import zip | ||
| from builtins import range | ||
| from past.utils import old_div |
There was a problem hiding this comment.
Since we're going for Python 3 compatibility only, we don't need these compatibility measures.
__future__imports are not necessary since we are using Python 3 only- For division, we should use the built-in
/operator instead of importing old_div. - We can use zip and range from the default Python 3 libraries instead of the
builtinsmodule, so these imports are not necessary.
scripts/importChemkinLibrary.py
Outdated
| from rmgpy.chemkin import loadChemkinFile, getSpeciesIdentifier | ||
|
|
||
| from builtins import str | ||
| from builtins import range |
There was a problem hiding this comment.
These imports are also not necessary.
scripts/process_family_images.py
Outdated
| @@ -48,6 +48,7 @@ | |||
| to | |||
| <policy domain="coder" rights="read|write" pattern="EPS" /> | |||
| """ | |||
| from __future__ import print_function | |||
mliu49
reviewed
Dec 3, 2019
| " mydict = dict(zip(index_list, kvals))\n", | ||
| "\n", | ||
| " # Find key and value of max rate coefficient\n", | ||
| " key_max_rate = max(mydict.iteritems(), key=operator.itemgetter(1))[0]\n", | ||
| " key_max_rate = max(iter(mydict.items()), key=operator.itemgetter(1))[0]\n", |
There was a problem hiding this comment.
Could you change this to just max(mydict.items(), ...?
scripts/process_family_images.py
Outdated
| @@ -48,7 +48,6 @@ | |||
| to | |||
| <policy domain="coder" rights="read|write" pattern="EPS" /> | |||
| """ | |||
|
|
|||
There was a problem hiding this comment.
I don't think this change is necessary if there are no other changes to this file.
There was a problem hiding this comment.
This commit is removed.
| "reaction_dict = {}\n", | ||
| "for library_name in libraries:\n", | ||
| " kinetic_library = database.kinetics.libraries[library_name]\n", | ||
| " for index, entry in iter(kinetic_library.entries.items()):\n", |
There was a problem hiding this comment.
This can also be kinetics_library.entries.items() without iter.
| " for index, entry in kineticLibrary.entries.iteritems():\n", | ||
| "for library_name in libraries:\n", | ||
| " kinetic_library = database.kinetics.libraries[library_name]\n", | ||
| " for index, entry in iter(kinetic_library.entries.items()):\n", |
ajocher
force-pushed
the
rmg2to3scripts
branch
from
ca156a7
to
7f5fa5c
Compare
|
Thanks for the comments! I squashed and rebased. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This pull request addresses "Update RMG-database scripts and notebooks" in ReactionMechanismGenerator/RMG-Py#1726.
In addition, RMG-Java related scripts and unnecessary scripts are deleted as discussed in #363.
generateFilterArrheniusFits.ipynb is updated but can only be finalized once from rmgpy/data/kinetics/database.py has 'filter_limit_fits' updated (currently not in master and Python 3).
Errors related to drawing a molecule are fixed in ReactionMechanismGenerator/RMG-Py#1735.
The documentation is updated in ReactionMechanismGenerator/RMG-Py#1767.