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Python3 Script check #1840

Merged
merged 7 commits into from
Dec 9, 2019
Merged

Python3 Script check #1840

merged 7 commits into from
Dec 9, 2019

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yunsiechung
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@yunsiechung yunsiechung commented Dec 3, 2019

Motivation or Problem

I tested all externally-used scripts in python 3 version RMG. This is related to the issue #1726.

  • One thing I could not check is running semi-empirical QM job using thermoEstimator.py in examples/scripts/thermoEstimator/run_QM.sh because I don't have the mopac license. Since it only throws an error that I don't have the mopac license, I don't expect thermoEstimator.py to have any error.

The internally-used scripts like generateTree.py, machineWriteDatabase.py, and rmg2to3.py are not checked in this test.

Description of Changes

  • All the scripts ran fine in python 3, but some were missing examples or had minor error with example files, so I added / fixed the examples.
  • isotopes.py does not have an example because running this example takes too much time. This script seems to run fine when I checked it.
  • convertFAME.py is deleted because it is no longer used.
  • reduction example folder is deleted because it uses the script that is no longer available.
  • One major change is that all the examples relevant to scripts are moved under examples/scripts.

Testing

I ran all the script example bash scripts and everything ran successfully.

Reviewer Tips

You can run bash scripts in examples/scripts to check that everything works fine

@yunsiechung
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travis-ci/push failed on the following:

A general test for a PDep job in Arkane ... FAIL

======================================================================

FAIL: A general test for a PDep job in Arkane

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/travis/build/ReactionMechanismGenerator/RMG-Py/arkane/pdepTest.py", line 107, in test_pdep_job

    self.assertAlmostEquals(rxn.kinetics.get_rate_coefficient(1000.0, 1.0), 88.88253229631246)

AssertionError: 88.9961408998604 != 88.88253229631246 within 7 places (0.11360860354794511 difference)

This does not seem to be related to any of my code changes, and I'm not sure what's causing this

@mliu49
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mliu49 commented Dec 3, 2019

I found the related issue: #1682

It seems like we never figured out the root cause, but it went away on its own in each case.

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codecov bot commented Dec 5, 2019

Codecov Report

Merging #1840 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@          Coverage Diff           @@
##           master   #1840   +/-   ##
======================================
  Coverage    44.2%   44.2%           
======================================
  Files          83      83           
  Lines       21533   21533           
  Branches     5645    5645           
======================================
  Hits         9519    9519           
+ Misses      10961   10947   -14     
- Partials     1053    1067   +14
Impacted Files Coverage Δ
arkane/kinetics.py 12.14% <0%> (ø) ⬆️
rmgpy/data/statmech.py 42.2% <0%> (ø) ⬆️
rmgpy/rmg/pdep.py 12.21% <0%> (ø) ⬆️
rmgpy/data/kinetics/family.py 49.06% <0%> (ø) ⬆️
rmgpy/statmech/ndTorsions.py 59.78% <0%> (ø) ⬆️
rmgpy/yml.py 15.71% <0%> (ø) ⬆️
arkane/sensitivity.py 10% <0%> (ø) ⬆️
rmgpy/data/kinetics/database.py 50.61% <0%> (ø) ⬆️

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@yunsiechung
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I force-pushed this again after rebasing to official/master and got the same error as before with travis-ci/push

Reduction example folder is deleted because /rmgpy/reduction/main.py
no longer exists.
convertFAME.py is also deleted because it is no longer used
All the examples related to scripts are moved under a new folder
example/scripts. Each bash scripts are changed appropriately to have
correct relative paths for each script file.

Also, for the examples file that were throwing error, I made somes
changes to make them work:

1. generateReactions
- This example was origianlly throwing error because surface chemistry
was included in the kinetic_family in the input file. The kinetic family
is changed to 'default', so it no longer throws error

2. simulate/withoutSensitivity
- This example had minor error with default temperature range in
chem.inp file. The temperature range in chem.inp file is changed
appropriately.

3. thermoEstimator
- input.py (run.sh) example had QM on in input file when it was not
supposed to. The QM thermoEstimator has its own example (input_QM.py).
The quantumMechanics portion in the input.py is deleted.
An example for scripts/generateChemkimHTML.py is added
An example for scripts/mergeModels.py is added.
The run.sh file contains two examples: merging 2 models and merging 3
models.
An example for scripts/generateFluxDiagram.py is added
An exmaple for scripts/standardizeModelSpeceisNames.py is added
A few more lines are added in the description
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Thanks!

@mliu49 mliu49 merged commit c46befa into master Dec 9, 2019
@mliu49 mliu49 deleted the python3_script_check branch December 9, 2019 23:36
This was referenced Dec 13, 2019
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2 participants