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RMG-Py v2.3.0 release
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mliu49 committed Dec 20, 2018
2 parents 1668d08 + 7ec72c2 commit 071c7dc
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6 changes: 4 additions & 2 deletions meta.yaml → .conda/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ package:
version: {{ environ.get('GIT_DESCRIBE_TAG', '') }}

source:
path: .
path: ../

build:
number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
Expand Down Expand Up @@ -48,6 +48,7 @@ requirements:
- matplotlib >=1.5
- mock
- mopac
- mpmath
- nose
- {{ pin_compatible('numpy') }}
- openbabel >=2.4.1
Expand All @@ -62,11 +63,12 @@ requirements:
- pyzmq
- quantities
- rdkit >=2015.09.2
- rmgdatabase >=2.2.0
- rmgdatabase >=2.3.0
- scipy
- scoop
- symmetry
- xlwt
- dde

test:
source_files:
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1 change: 1 addition & 0 deletions .coveragerc
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Expand Up @@ -17,6 +17,7 @@ exclude_lines =
raise NotImplementedError
if 0:
if __name__ == .__main__.:
omit = *Test.py

[html]
directory = testing/coverage
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/question.md
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Expand Up @@ -11,7 +11,7 @@ General area which your question is related to.
- [ ] Installation of RMG
- [ ] Running an RMG job
- [ ] Using RMG API
- [ ] CanTherm
- [ ] Arkane (formerly CanTherm)
- [ ] Dependencies
- [ ] An error message <!-- consider writing a bug report instead -->

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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -39,6 +39,9 @@ nbproject/*
.pydevproject
.settings/*

# PyCharm project files
.idea/*

# Unit test files
.coverage
testing/*
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26 changes: 23 additions & 3 deletions .travis.yml
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Expand Up @@ -11,8 +11,10 @@ env:

stages:
- test
- name: documentation
if: branch = master AND type = push
- name: deploy
if: branch = stable
if: branch = stable AND type = push

before_install:
- cd ..
Expand All @@ -24,6 +26,9 @@ before_install:
# Update conda
- conda update --yes conda
- conda info -a
# Set git info
- git config --global user.name "Travis Deploy"
- git config --global user.email "[email protected]"

jobs:
include:
Expand All @@ -47,6 +52,21 @@ jobs:
after_success:
- codecov
- bash ./deploy.sh
- stage: documentation
install:
- cd RMG-Py
- conda env create -q -f environment_linux.yml
- source activate rmg_env
# Install sphinx for building documentation
- conda install -y sphinx
- conda list
# Modify setup.py
- sed -i '/embedsignature/s/^#//g' setup.py
- make
- cd documentation
- export COMMITMESSAGE="Automatic documentation rebuild"
script:
- make travis_setup clean html publish
- stage: deploy
install:
# Setup conda build
Expand All @@ -55,7 +75,7 @@ jobs:
- conda config --add channels rmg
- conda config --set anaconda_upload yes
script:
- conda build --token $CONDA_TOKEN --user rmg RMG-Py
- conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda
- os: osx
install:
# Setup conda build
Expand All @@ -64,4 +84,4 @@ jobs:
- conda config --add channels rmg
- conda config --set anaconda_upload yes
script:
- conda build --token $CONDA_TOKEN --user rmg RMG-Py
- conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda
10 changes: 5 additions & 5 deletions Makefile
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Expand Up @@ -33,8 +33,8 @@ else
endif
python setup.py build_ext solver --build-lib . --build-temp build --pyrex-c-in-temp

cantherm:
python setup.py build_ext cantherm --build-lib . --build-temp build --pyrex-c-in-temp
arkane:
python setup.py build_ext arkane --build-lib . --build-temp build --pyrex-c-in-temp

check:
@ python utilities.py check-dependencies
Expand Down Expand Up @@ -88,21 +88,21 @@ ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
endif
nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane

test test-unittests:
ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
endif
nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane

test-functional:
ifneq ($(OS),Windows_NT)
mkdir -p testing/coverage
rm -rf testing/coverage/*
endif
nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane

test-database:
nosetests -v -d testing/databaseTest.py
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22 changes: 11 additions & 11 deletions cantherm.py → arkane.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,35 +29,35 @@
###############################################################################

"""
This is the main executable script for CanTherm, a tool for computing chemical
This is the main executable script for Arkane, a tool for computing chemical
reaction rates and other properties used in detailed kinetics models using
various methodologies and theories. To run CanTherm, use the command ::
various methodologies and theories. To run Arkane, use the command ::
$ python cantherm.py FILE
$ python arkane.py FILE
where ``FILE`` is the path to a CanTherm input file describing the job to
execute. CanTherm will run the specified job, writing the output to
``output.py`` and a log to both the console and to ``cantherm.log``, with both
where ``FILE`` is the path to an Arkane input file describing the job to
execute. Arkane will run the specified job, writing the output to
``output.py`` and a log to both the console and to ``Arkane.log``, with both
files appearing in the same directory as the input file. Some additional
command-line arguments are available; run the command ::
$ python cantherm.py -h
$ python arkane.py -h
for more information.
"""

import os
import logging

from rmgpy.cantherm.main import *
from arkane.main import *

cantherm = CanTherm()
arkane = Arkane()

# Parse and validate the command-line arguments
cantherm.parseCommandLineArguments()
arkane.parseCommandLineArguments()

# Execute the job
cantherm.execute()
arkane.execute()

try:
import psutil
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23 changes: 5 additions & 18 deletions rmgpy/cantherm/common.py → arkane/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -28,21 +28,8 @@
# #
###############################################################################

import numpy
import os.path
import logging
import rmgpy.constants as constants
################################################################################

def checkConformerEnergy(Vlist,path):
"""
Check to see that the starting energy of the species in the potential energy scan calculation
is not 0.5 kcal/mol (or more) higher than any other energies in the scan. If so, print and
log a warning message.
"""
Vlist = numpy.array(Vlist, numpy.float64)
Vdiff = (Vlist[0] - numpy.min(Vlist))*constants.E_h*constants.Na/1000
if Vdiff >= 2: #we choose 2 kJ/mol to be the critical energy
logging.warning('the species corresponding to ' + str(os.path.basename(path)) + ' is different in energy from the lowest energy conformer by ' + "%0.2f" % Vdiff + ' kJ/mol. This can cause significant errors in your computed rate constants. ')


from arkane.main import Arkane
from arkane.statmech import StatMechJob
from arkane.thermo import ThermoJob
from arkane.kinetics import KineticsJob
from arkane.pdep import PressureDependenceJob
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