RMG-Py v2.4.0 release

ReactionMechanismGenerator · Jun 14, 2019 · caebd48 · caebd48
2 parents 756c2f5 + 5e12fd1
commit caebd48
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diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -38,6 +38,7 @@ requirements:
     - coolprop
     - coverage
     - cython >=0.25.2
+    - dde
     - ffmpeg
     - gprof2dot
     - graphviz
@@ -63,13 +64,12 @@ requirements:
     - pyzmq
     - quantities
     - rdkit >=2015.09.2
-    - rmgdatabase >=2.3.0
+    - rmgdatabase >=2.4.0
+    - scikit-learn
     - scipy
     - scoop
     - symmetry
     - xlwt
-    - dde
-
 test:
   source_files:
     - 'examples/rmg/superminimal'

diff --git a/.coveragerc b/.coveragerc
@@ -1,5 +1,6 @@
 # .coveragerc to control coverage.py
 [run]
+plugins = Cython.Coverage
 branch = True
 source =
     rmgpy

diff --git a/Arkane.py b/Arkane.py
@@ -5,7 +5,7 @@
 #                                                                             #
 # RMG - Reaction Mechanism Generator                                          #
 #                                                                             #
-# Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu),           #
+# Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu),           #
 # Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
 #                                                                             #
 # Permission is hereby granted, free of charge, to any person obtaining a     #

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu),
+Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu),
 Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
 
 Permission is hereby granted, free of charge, to any person obtaining a

diff --git a/Makefile b/Makefile
@@ -105,7 +105,8 @@ endif
 	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
 
 test-database:
-	nosetests -v -d testing/databaseTest.py	
+	nosetests --nocapture --nologcapture --verbose --detailed-errors testing/databaseTest.py
+
 eg0: all
 	mkdir -p testing/eg0
 	rm -rf testing/eg0/*

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 [![Build status](https://img.shields.io/travis/ReactionMechanismGenerator/RMG-Py/master.svg)](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py)
 [![Codecov report](https://img.shields.io/codecov/c/github/ReactionMechanismGenerator/RMG-Py/master.svg)](https://codecov.io/gh/ReactionMechanismGenerator/RMG-Py)
-[![Codacy report](https://img.shields.io/codacy/grade/c4b23c89e2e6486e981704d8d973d3e7/master.svg)](https://www.codacy.com/app/ReactionMechanismGenerator/RMG-Py/dashboard)
+[![Codacy report](https://img.shields.io/codacy/grade/5c12cecf3d01400a92ea20e14ca0b880/master.svg)](https://www.codacy.com/app/ReactionMechanismGenerator/RMG-Py/dashboard)
 [![GitHub release](https://img.shields.io/github/release/ReactionMechanismGenerator/RMG-Py.svg)](https://github.com/ReactionMechanismGenerator/RMG-Py/releases)
 [![Anconda](https://img.shields.io/conda/v/rmg/rmg.svg)](https://anaconda.org/rmg/rmg)
 [![Gitter](https://img.shields.io/gitter/room/ReactionMechanismGenerator/RMG-Py.svg)](https://gitter.im/ReactionMechanismGenerator/RMG-Py)
@@ -14,9 +14,9 @@ a tool for automatically generating chemical reaction
 mechanisms for modeling reaction systems including pyrolysis, combustion,
 atmospheric science, and more.
 
-It also includes **CanTherm**, the package for calculating thermodynamics, high-pressure-limit
+It also includes **Arkane**, the package for calculating thermodynamics, high-pressure-limit
 rate coefficients, and pressure dependent rate coefficients from quantum chemical calculations.
-CanTherm is compatible with a variety of ab initio quantum chemistry software programs, including but not limited to
+Arkane is compatible with a variety of ab initio quantum chemistry software programs:
 Gaussian, MOPAC, QChem, and MOLPRO.
 
 ## Source Code Repository
@@ -28,12 +28,10 @@ You can either download the source from GitHub and compile yourself, or download
 Please see the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
 
 ## Documentation
-- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/master/documentation/RMG-Py_and_CanTherm_Documentation.pdf))
-- [CanTherm Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/cantherm/) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/master/documentation/RMG-Py_and_CanTherm_Documentation.pdf))
+- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/master/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [Arkane Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/master/documentation/RMG-Py_and_Arkane_Documentation.pdf))
 - [RMG API Reference](http://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/master/documentation/RMG-Py_API_Reference.pdf))
 
-Alternatively, PDF versions of all the documentation can also be found in the `documentation` folder of the source code.  
-
 ## How to Contribute
 Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/RMG-Contributor-Guidelines)
 for details on how to contribute to RMG-Py or RMG-database.

diff --git a/arkane/__init__.py b/arkane/__init__.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+"""
+initialize imports
+"""
+
 ###############################################################################
 #                                                                             #
 # RMG - Reaction Mechanism Generator                                          #
 #                                                                             #
-# Copyright (c) 2002-2018 Prof. William H. Green (whgreen@mit.edu),           #
+# Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu),           #
 # Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
 #                                                                             #
 # Permission is hereby granted, free of charge, to any person obtaining a     #
@@ -33,3 +37,4 @@
 from arkane.thermo import ThermoJob
 from arkane.kinetics import KineticsJob
 from arkane.pdep import PressureDependenceJob
+from arkane.common import ArkaneSpecies