RMG futurization: Python 3 compatibility and PEP-8 compliance

.conda/meta.yaml

@@ -34,10 +34,10 @@ requirements:
     - cairo
     - cairocffi
     - cantera >=2.3.0
+    - chemprop
     - coolprop
     - coverage
     - cython >=0.25.2
-    - dde
     - ffmpeg
     - gprof2dot
     - graphviz

.travis.yml

@@ -1,5 +1,4 @@
-language: c
-sudo: false
+language: minimal
 
 env:
   global:
@@ -39,17 +38,18 @@ jobs:
       install:
         # Clone RMG-database
         - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
-        # install Q2DTor
-        - git clone https://github.com/mjohnson541/Q2DTor.git RMG-Py/external/Q2DTor --branch arkane
-        # build environment and activate
         - cd RMG-Py
-        - conda env create -q -f environment_linux.yml
+        # Create and activate environment
+        - conda env create -q -f environment.yml
         - source activate rmg_env
         # Install codecov for coverage report
         - conda install -y -c conda-forge codecov
         - conda list
         # Setup MOPAC license key
         - yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
+        # Install Q2DTor
+        - git clone -b arkanepy3 https://github.com/mjohnson541/Q2DTor.git external/Q2DTor
+        # Compile RMG
         - make
       script:
         - make test-unittests
@@ -61,7 +61,7 @@ jobs:
     - stage: documentation
       install:
         - cd RMG-Py
-        - conda env create -q -f environment_linux.yml
+        - conda env create -q -f environment.yml
         - source activate rmg_env
         # Install sphinx for building documentation
         - conda install -y sphinx

Arkane.py

@@ -33,34 +33,35 @@
 reaction rates and other properties used in detailed kinetics models using
 various methodologies and theories. To run Arkane, use the command ::
 
-    $ python arkane.py FILE
+    $ python Arkane.py FILE
 
 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 arkane.py -h
+    $ python Arkane.py -h
 
 for more information.
 """
 
 import os
 import logging
 
-from arkane.main import *
+from arkane.main import Arkane
 
 arkane = Arkane()
 
 # Parse and validate the command-line arguments
-arkane.parseCommandLineArguments()
+arkane.parse_command_line_arguments()
 
 # Execute the job
 arkane.execute()
 
 try:
     import psutil
+
     process = psutil.Process(os.getpid())
     memory_info = process.memory_info()
     logging.info('Memory used: %.2f MB' % (memory_info.rss / 1024.0 / 1024.0))

Makefile

@@ -4,68 +4,42 @@
 #
 ################################################################################
 
-DASPK=$(shell python -c 'import pydas.daspk; print pydas.daspk.__file__')
-DASSL=$(shell python -c 'import pydas.dassl; print pydas.dassl.__file__')
+.PHONY : all minimal main solver check pycheck arkane clean install decython documentation mopac_travis
 
-.PHONY : all minimal main solver check cantherm clean install decython documentation mopac_travis
-
-all: main solver check
+all: pycheck main solver check
 
 minimal:
-	python setup.py build_ext minimal --build-lib . --build-temp build --pyrex-c-in-temp
+	python setup.py build_ext minimal --inplace --build-temp .
 
 main:
-	@ echo "Checking you have PyDQED..."
-	@ python -c 'import pydqed; print pydqed.__file__'
-	python setup.py build_ext main --build-lib . --build-temp build --pyrex-c-in-temp
+	python setup.py build_ext main --inplace --build-temp .
 
 solver:
-
-ifneq ($(DASPK),)
-	@ echo "DASPK solver found. Compiling with DASPK and sensitivity analysis capability..."
-	@ (echo DEF DASPK = 1) > rmgpy/solver/settings.pxi 
-else ifneq ($(DASSL),)
-	@ echo "DASSL solver found. Compiling with DASSL.  Sensitivity analysis capabilities are off..."
-	@ (echo DEF DASPK = 0) > rmgpy/solver/settings.pxi
-else
-	@ echo 'No PyDAS solvers found.  Please check if you have the latest version of PyDAS.'
-	@ python -c 'import pydas.dassl' 
-endif
-	python setup.py build_ext solver --build-lib . --build-temp build --pyrex-c-in-temp
+	@ python utilities.py check-pydas
+	python setup.py build_ext solver --inplace --build-temp .
 
 arkane:
-	python setup.py build_ext arkane --build-lib . --build-temp build --pyrex-c-in-temp
+	python setup.py build_ext arkane --inplace --build-temp .
 
 check:
 	@ python utilities.py check-dependencies
 
+pycheck:
+	@ python utilities.py check-python
+
 documentation:
 	$(MAKE) -C documentation html
 	@ echo "Start at: documentation/build/html/index.html"
 
 clean:
-	@ echo "Removing build directory..."
-	@ python setup.py clean --build-temp build
-	@ echo "Removing compiled files..."
 	@ python utilities.py clean
-	@ echo "Cleanup completed."
 
 clean-solver:
-	@ echo "Removing solver build directories..."
-ifeq ($(OS),Windows_NT)
-	@ -rd /s /q build\pyrex\rmgpy\solver
-	@ -rd /s /q build\build\pyrex\rmgpy\solver
-else
-	@ -rm -r build/pyrex/rmgpy/solver/
-	@ -rm -r build/build/pyrex/rmgpy/solver/
-endif
-	@ echo "Removing compiled files..."
 	@ python utilities.py clean-solver
-	@ echo "Cleanup completed."
 
 install:
 	@ echo "Checking you have PyDQED..."
-	@ python -c 'import pydqed; print pydqed.__file__'
+	@ python -c 'import pydqed; print(pydqed.__file__)'
 ifneq ($(DASPK),)
 	@ echo "DASPK solver found. Compiling with DASPK and sensitivity analysis capability..."
 	@ (echo DEF DASPK = 1) > rmgpy/solver/settings.pxi
@@ -87,7 +61,7 @@ q2dtor:
  and HinderedRotor2D within Arkane please cite:  \n\nD. Ferro-Costas, M. N. D. S.Cordeiro, D. G. Truhlar, A.\
 		  Fernández-Ramos, Comput. Phys. Commun. 232, 190-205, 2018.\n"
 	@ read -p "Press ENTER to continue" dummy
-	@ git clone https://github.com/mjohnson541/Q2DTor.git external/Q2DTor --branch arkane
+	@ git clone https://github.com/mjohnson541/Q2DTor.git external/Q2DTor --branch arkanepy3
 
 decython:
 	# de-cythonize all but the 'minimal'. Helpful for debugging in "pure python" mode.
@@ -113,7 +87,7 @@ ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
 endif
-	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
+	nosetests --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
 
 test-database:
 	nosetests --nocapture --nologcapture --verbose --detailed-errors testing/databaseTest.py

arkane/__init__.py

@@ -1,10 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-"""
-initialize imports
-"""
-
 ###############################################################################
 #                                                                             #
 # RMG - Reaction Mechanism Generator                                          #
@@ -32,9 +28,13 @@
 #                                                                             #
 ###############################################################################
 
+"""
+initialize imports
+"""
+
+from arkane.common import ArkaneSpecies
+from arkane.kinetics import KineticsJob
 from arkane.main import Arkane
+from arkane.pdep import PressureDependenceJob
 from arkane.statmech import StatMechJob
 from arkane.thermo import ThermoJob
-from arkane.kinetics import KineticsJob
-from arkane.pdep import PressureDependenceJob
-from arkane.common import ArkaneSpecies