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RMG futurization: Python 3 compatibility and PEP-8 compliance #1724
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b54b19f
Update and refactor Travis build configuration
mliu49 9281d86
Add conda environment file for Python 3
mliu49 f83b48c
Adjust Travis build to also test on Python 3
mliu49 c1c74be
Change print syntax in Makefile and setup.py
mliu49 af2e7a1
Import functools.reduce in reaction.py
mliu49 603c87e
Decode bytes returned by subprocess.check_output in utilities.py
mliu49 aba2d5a
Remove external cclib and use cclib conda package
amarkpayne ba25f01
Remove reduction module
mliu49 cc62858
Remove documentation for reduction module
mliu49 ff03112
Remove scoop framework and all usages
mliu49 4c443e7
Various PEP-8 modifications and futurization to Arkane
alongd 3b0a171
BugFix: Nested variable i definition resolved
alongd d9d7f8b
Implement abstract methods in Arkane Logs, raise NotImplementedErrors
alongd 078b9a5
Turned static log methods in Arkane into functions, renamed them
alongd a82e020
Don't shadow `database` from outer scope
alongd b188a17
Create LogError exception class for Arkane
alongd 83a3466
Removed seemingly unnecessary print statements from Arkane input.py
alongd b5a240d
Directly use the correct returned argument (instead of _, markings)
alongd b3fa250
Replace pylab with pyplot for plotting rotor scans
alongd 7e206f3
Upgrade external wip to Python 3
amarkpayne 8423581
Upgrade rmg.py to Python 3
amarkpayne 57edf9a
Upgrade rmgpy/*.py to Python 3
amarkpayne d74b859
Upgrade rmgpy/rmg/*.py to Python 3
amarkpayne 1701e94
Upgrade scripts to Python 3
amarkpayne abe3d06
Correct path issue so that outputTest.py runs from any location
amarkpayne 22af8bb
Prevent file locking for HDF5 files
amarkpayne 2194bf8
Explicitly add h5py dependency
amarkpayne 2913cb7
Bug fix: Import conformer from statmech instead of pdep
amarkpayne 81ed4c6
Merge pull request #1686 from ReactionMechanismGenerator/amp_py3_pr
mliu49 610931a
Various PEP-8 modifications and futurization to the pdep module
alongd 574fb87
Merge pull request #1696 from ReactionMechanismGenerator/pdep_py3
mliu49 0c0467c
Py3 compatibility changes on statmech module
xiaoruiDong 9f5574d
Merge pull request #1689 from ReactionMechanismGenerator/py3_XD
mliu49 396f0b5
Py3 and PEP-8 changes to selected rmgpy/*.py files
mliu49 31efff3
Py3 and PEP-8 changes to pure python part of molecule module
mliu49 3252b00
Py3 and PEP-8 changes to qm module
mliu49 4c7c379
Refactor setup.py and cythonization process
mliu49 0579eca
Refactor make clean
mliu49 069ed2a
Remove old use of rmgpy.rmg.model.Species from thermoengine
mliu49 b09196b
Py3 and PEP-8 changes to thermo and transport modules
mliu49 e70fd60
Py3 and PEP-8 changes to tools module
mliu49 a671e18
Do not warn when setting matplotlib backend in tools.plot
mliu49 46ac799
Replace pylab with pyplot in rmgpy.tools.diff_models
mliu49 ff3a645
Fix import in databaseTest.py
mliu49 3bc2c2c
Merge pull request #1687 from ReactionMechanismGenerator/py3_mliu
amarkpayne 2426437
Py3 and PEP-8 changes to cythonized files in rmgpy
mliu49 52454ae
Fix unreachable code in chemkin module
mliu49 6698aab
Py3 and PEP-8 changes to cythonized files in rmgpy.molecule
mliu49 c363844
Py3 and PEP-8 changes to cythonized files in rmgpy.thermo and rmgpy.k…
mliu49 2998fca
Py3 and PEP-8 changes to cythonized files in rmgpy.statmech
mliu49 448ba9b
Py3 and PEP-8 changes to cythonized files in rmgpy.solver
mliu49 d4974fd
Prevent element-wise comparisons for np arrays when calling as_dict()
amarkpayne 7b5ddd7
Refactor and simplify Reaction.generatePairs
mliu49 065c8dd
Merge pull request #1694 from ReactionMechanismGenerator/py3_mliu_2
alongd ef139e8
databaseTest futurization
mjohnson541 6811038
rmgpy.pdep py3 changes
mjohnson541 6655729
rmgpy.kinetics py3 changes
mjohnson541 ef1e174
rmgpy.solver py3 changes
mjohnson541 53a2476
ndTorsions py3 changes
mjohnson541 670aa7e
rmgpy.data py3 changes
mjohnson541 221a8e1
Remove disfunctional PDepNetwork property label
mjohnson541 427e8bf
Additional Py3 and PEP-8 fixes to rmgpy.data
mliu49 47a142d
Format ndTorsions and refactor paths
mliu49 200e84e
Py3 and PEP-8 changes to databaseTest.py
mliu49 3a607a9
Additional Py3 and PEP-8 fixes to rmgpy.solver
mliu49 3769a09
Additional Py3 and PEP-8 fixes to rmgpy.pdep
mliu49 106fc50
Additional Py3 and PEP-8 fixes to rmgpy.kinetics
mliu49 2d9cfa5
Update environment file
mliu49 50e6ae4
Merge pull request #1707 from ReactionMechanismGenerator/py_matt
amarkpayne fdf0a48
Modified the ArkaneSpecies.update_xyz_string() method
alongd af9dc41
Merge pull request #1714 from ReactionMechanismGenerator/arkane_speci…
mliu49 72b92a0
Switch ML estimator to chemprop
3b7cb4c
Update documentation and ML example
1522599
Update meta.yaml
d0e5ca3
Revert Fix Travis builds by adding in missing miniconda dependencies
amarkpayne 0b48cb7
Update Python 3 environment
86f4bf9
Adjust directory structure for N4H6 in arkane examples
mliu49 2c158ad
Move PyDQED check to check_dependencies function
mliu49 8d4d526
Refactor check_dependencies to be more modular
mliu49 86156b6
Move PyDAS solver check from Makefile to utilities.py
mliu49 f59814c
Remove `u` tag for unicode string from testing databases
mliu49 4e78f1d
Change travis to only run py3 build, since py2 will always fail now
mliu49 73d2d65
Change cython language level to 3
mliu49 fc523e1
Refactor and standardize short/long description writing
mliu49 0abf56b
Fix `exec` usage
mliu49 6657f61
Change molecule fingerprint to enable better sorting
mliu49 c90c407
Add sorting_key attribute to Atom, Bond, Molecule, Species
mliu49 0c0c7ed
Add/update comparison methods for Atom, Bond, Molecule, Species
mliu49 fea1ac5
Fix unit tests affected by changes to sorting
mliu49 b8acca0
Fix I/O related string issues
mliu49 a22b616
Fix other string formatting issues
mliu49 256de03
Fix exception message handling
mliu49 0b3884f
Fix dictionary item retrieval/iteration issues
mliu49 92c584f
Fix usage of str.translate
mliu49 715b6bf
Fix issue with calling lpsolve
mliu49 190fe9a
Fix family loading to account for __pycache__
mliu49 90c6803
Miscellaneous fixes to unit tests
mliu49 f487687
Fix sorting when using machine learning thermo
mliu49 4589119
Fix type comparison
mliu49 df19793
Fix sorting in generateReactionKey
mliu49 403b44c
Fix file opening using `file`
mliu49 aba04e0
Fix interesting symmetry bug
mliu49 cca187f
Remove work_in_progress decorator from a test
mliu49 bcac42d
Capture standard output when running functional tests
mliu49 195f49b
Mark InChI pickle test as work_in_progress
mliu49 2dd0a79
Fix sorting of Quantity objects in main.execute
mliu49 34b3bc0
Decode dot output when generating flux diagram
mliu49 6c8004e
Refactor removeVanDerWaalsBonds to not modify dict while iterating
mliu49 bfb51b1
Switch to Py3 compatible version of Q2DTor
mliu49 aa6243f
Remove uses of six.string_types
mliu49 4baba99
Make Entry.shortDesc and Entry.longDesc standard attributes
mliu49 aaaa9b1
Fix min usage with Entry objects
mliu49 7b4f66e
Make the python 3 environment file the only environment file
amarkpayne 3d9fbdb
Remove xrange calls in chemkin.pyx
mliu49 6cfa689
Close all matplotlib.pyplot figures
alongd 28931a0
Merge pull request #1713 from ReactionMechanismGenerator/py3_only
amarkpayne 90aa855
PEP-8 renaming in rmgpy.data
mliu49 92d627e
PEP-8 renaming in rmgpy.kinetics
mliu49 14bfbbe
PEP-8 renaming in rmgpy.molecule
mliu49 0ee066a
PEP-8 renaming in rmgpy.pdep and rmgpy.statmech
mliu49 952e526
PEP-8 renaming fixes
mliu49 feb62df
PEP-8 renaming in rmgpy.thermo and rmgpy.transport
mliu49 fdcd194
PEP-8 renaming in rmgpy.qm
mliu49 5a04472
PEP-8 renaming in top level modules
mliu49 e9a65fc
PEP-8 renaming in rmgpy.solver
mliu49 4a41739
PEP-8 renaming in rmgpy.rmg
mliu49 a55ab9d
PEP-8 renaming in rmgpy.tools and scripts
mliu49 2e5afaa
PEP-8 renaming fixes
mliu49 e527706
Make Arkane unit tests PEP-8 compliant
amarkpayne 8f47f47
Remove unused unit test in solvationTest.py
amarkpayne 038aede
Make rmgpy/data/* unit tests PEP-8 compliant
amarkpayne e08f2fa
Make rmgpy/kinetics/* unit tests PEP-8 compliant
amarkpayne e41116f
Make select rmgpy/molecule/* unit tests PEP-8 compliant
amarkpayne e205547
Make test_lone_pair_retention error when exceptions are encountered
amarkpayne 7732682
Make rmgpy/pdep/* unit tests PEP-8 compliant
amarkpayne 3770769
Make rmgpy/qm/* unit tests PEP-8 compliant
amarkpayne 42a2623
Make rmgpy/rmg/* unit tests PEP-8 compliant
amarkpayne 3324ee3
Make rmgpy/solver/* unit tests PEP-8 compliant
amarkpayne d26da0c
Make rmgpy/statmech/* unit tests PEP-8 compliant
amarkpayne 4089edd
Make rmgpy/thermo/* unit tests PEP-8 compliant
amarkpayne 601d52e
Make rmgpy/tools/* unit tests PEP-8 compliant
amarkpayne 0f82030
Make rmgpy/* unit tests PEP-8 compliant
amarkpayne 1a90a74
Fix doctring in tests for debye units
amarkpayne f94e417
Make testing/databaseTest.py unit tests PEP-8 compliant
amarkpayne 59d8060
Make Arkane PEP8 compliant
alongd e2fa0d7
Renamed argument `format` to `file_format`
alongd 66795f7
Added generate_high_p_limit_kinetics() to Reaction
alongd e8369f2
Arkane PEP8 compliant changes in the RMG code
alongd 7c12457
Preserve backward compatibility with Arkane YAML files
alongd 51994ed
Tests: Load Arkane YAML files both from v 2.4.1 and a recent version
alongd 8ad5293
Implement parent methods in HinderedRotorClassicalND()
alongd 2e317a3
Create rmgpy.util.as_list function
mliu49 13a225c
Fix database loading in arkane.input
mliu49 02af7dd
Fix bath gas loading for arkane explorer tool
mliu49 999beb2
Refactor database loading in rmgpy.rmg.input
mliu49 61ad9ba
PEP-8 renaming in rmgpy.rmg.input
mliu49 82e12f4
Additional renaming in rmgpy.data
mliu49 8565041
Additional renaming in rmgpy.species
mliu49 f5e4ee0
Additional renaming of missed functions
mliu49 8cac287
Refactor properties in rmgpy.quantity to be more pythonic
mliu49 6069719
Fix bug when generating profile graph
mliu49 c09504d
Add rmg2to3.py script to facilitate user transition
mliu49 5b85619
Merge pull request #1719 from ReactionMechanismGenerator/py3_pep8
mliu49 f73cb57
Add check for Python version to Makefile and rmg.py
mliu49 File filter
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(Outside the scope of this PR) Are our .PHONY targets up to date? Should things like
test
andeg0
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I was also wondering about this. I looked it up, and it seems like phony targets are most important if you have files with the same name as the target. In that case, putting the target in the phony list tells make to execute the target rather than compile the file.