Merge pull request #935 from ReactionMechanismGenerator/v2.1.0

RMG-Py v2.1.0 release

Author: KEHANG

COPYING.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2002-2016 Prof. William H. Green (whgreen@mit.edu), 
+Copyright (c) 2002-2017 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

README.md

@@ -17,7 +17,7 @@ Gaussian, MOPAC, QChem, and MOLPRO.
 - [RMG-database Github Repository](https://github.com/ReactionMechanismGenerator/RMG-database): contains source code for the latest version of the database
 
 ## Latest Stable Release
-**RMG v2.0.0**
+**RMG v2.1.0**
 [![Anaconda-Server Badge](https://anaconda.org/rmg/rmg/badges/version.svg)](https://anaconda.org/rmg/rmg)
 
 View the [Release Notes](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/releaseNotes.html).

documentation/RMG-Py_API_Reference.pdf

@@ -4,6 +4,60 @@
 Release Notes
 *************
 
+RMG-Py Version 2.1.0
+====================
+Date: March 07, 2017
+
+- Clar structure generation
+    - optimizes the aromatic isomer representations in RMG
+    - lays the foundations for future development of poly-aromatic kinetics reaction families
+
+- Flux pathway analysis
+    - introduces an ipython notebook for post-generatation pathway analysis (``ipython.mechanism_analyzer.ipynb``)
+    - visualizes reactions and provides flux statistics in a more transparent way
+
+- Cantera mechanism
+    - automatically writes cantera version of RMG-generated mechanism at the end of RMG jobs
+
+- Fixes bugs
+    - upgrades ``pruning`` to fix new memory leaks introduced by recent functionalities
+    - fixes the bug of duplicated species creation caused by ``getThermoData`` removing isomers unexpectedly
+    - fixes restart file generation and parsing problems and users can choose restart mode again
+    - upgrades bicyclic decomposition method such that more deterministic behaviors are ensured
+    - change bond order type to float from string to improve RMG's symmetry calculation for species with multiple resonance structures
+
+RMG-database Version 2.1.0
+==========================
+Date: March 07, 2017
+
+- Several new kinetics libraries added
+    - FFCM-1
+    - JetSurF 0.2
+    - Chernov_aromatic_only
+    - Narayanaswamy_aromatic_only
+    - 1989_Stewart_2CH3_to_C2H5_H
+    - 2005_Senosiain_OH_C2H2
+    - 2006_Joshi_OH_CO
+    - C6H5_C4H4_Mebel
+    - c-C5H5_CH3_Sharma
+
+- Several new thermochemistry libraries added
+    - FFCM-1
+    - JetSurF 0.2
+    - Chernov_aromatic_only
+    - Narayanaswamy_aromatic_only
+
+- Improved kinetics tree accessibility
+    - adds database tests ensuring groups in the tree to be accessible
+    - improves definitions of group structures in the kinetics trees to ensure accessibility
+
+- New oxygenates thermo groups are added based Paraskeva et al.
+
+- Improved database tools
+    - ``convertKineticsLibraryToTrainingReactions.ipynb`` now can visualize groups of matched rate rules that training reactions hit 
+    - ``exportKineticsLibrarytoChemkin.py`` and ``importChemkinLibrary.py`` add more logging information on reaction sources
+
+
 RMG-Py Version 2.0.0
 ====================
 Date: September 16, 2016

documentation/RMG-Py_and_CanTherm_Documentation.pdf

@@ -74,7 +74,7 @@ requirements:
     - pyzmq
     - quantities
     - rdkit >=2015.09.2
-    - rmgdatabase >=2.0.0
+    - rmgdatabase >=2.1.0
     - scipy
     - scoop
     - symmetry

documentation/source/users/rmg/releaseNotes.rst

@@ -1,3 +1,3 @@
 # This file describes the version of RMG-Py
 
-__version__ = '2.0.0'
+__version__ = '2.1.0'

meta.yaml

@@ -187,6 +187,8 @@ def getCanthermExtensionModules():
 
 modules = []
 for root, dirs, files in os.walk('rmgpy'):
+    if 'test_data' in root:
+        continue
     for file in files:
         if file.endswith('.py') or file.endswith('.pyx'):
             if 'Test' not in file and '__init__' not in file: