RMG-Py v2.1.6 release

Author: mliu49

.travis.yml

@@ -2,8 +2,6 @@ language: python
 sudo: false
 python:
   - "2.7"
-virtualenv:
-    system_site_packages: true
 env:
   global:
     - secure: "L2ja+ZnV83w4qG3E8FwTjm0D6IWNOnj5wuFOjYTwbzQP4OAgLAWBzCMtxzWy5sMxFLtRgkswBH1d5f5kg8Ab7GIyAMFgQwe8UFqMJ+N05QNszE1mJkAvJtv2XN7669XXQhTt5EXfHrCcGZaODVnI2CEA8GB5DxiHO2Lcqf/xvgE="
@@ -12,29 +10,24 @@ env:
     - secure: "cfosGf5hvUhIlPoGJu0d/HFddrMwIFU7FfLwd8yRrMGkYv0ePOwAW9kmhFSxUYvuXkxzgD75cIICMFY2fSm6VXBXXzfPQD7vwzoApXf7a8vi0C64XhinXhdEyUYb5/v8fswa0zheUENYhUS1tOqDXT/h8EPNZT5wKizaA3O2Wa8="
     - secure: "QXuqKYuwCocqsTMePBc5OugBbQC4/t+335TYLdkletiateP/rF/eDsVRG792/BVq5gKRZgz3NH9ipTNm5pZoCbAEPt9+eDpfts8WeAbxmjdcEjfBxxwZ69wUTPAVrezTGn2k7W2UBdFrWeUNKPAVCKIkoviXqOHFitqJEC+c6JY="
     - secure: "jIyBEzR10l5SWvY5ouEYzA8YzPHIZNMXMBdcXwuwte8NCU8GBYUqhHA1L67nTaBdLhWbrZ2NireVKPQWJp3ctcI0IB6xZzaYlVpgN/udGPO+1MZd9Xhp9TWuJWrGZ9EoWGB9L5H+O7RYwcDMVH5CUrCIBdsSJuyE8aDpky1/IVE="
-addons:
-  apt:
-    packages:
-    - git
 
 before_install:
-  # Set up anaconda
-  - wget http://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b -p $HOME/miniconda
+  - cd ..
+  # Install miniconda
+  - wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH=$HOME/miniconda/bin:$PATH
-  - export PYTHONPATH=$TRAVIS_BUILD_DIR/RMG-Py:$PYTHONPATH
-  # Update conda itself
   - conda update --yes conda
-  - cd ..
+  - conda info -a
+  # Clone RMG-database
   - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
   - cd RMG-Py
 
 install:
-  - conda env create -f environment_linux.yml
+  - conda env create -q -f environment_linux.yml
   - source activate rmg_env
+  - conda install -y -c conda-forge codecov
   - conda list
-  - pip install codecov
   - yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
   - make
 

documentation/source/users/rmg/database/kinetics.rst

@@ -4,6 +4,47 @@
 Release Notes
 *************
 
+RMG-Py Version 2.1.6
+====================
+Date: December 21, 2017
+
+- Model resurrection:
+    - Automatically attempts to save simulation after encountering a DASPK error
+    - Adds species and reactions in order to modify model dynamics and fix the error
+
+- New features:
+    - Add functionality to read RCCSD(T)-F12 energies from MolPro log files
+    - Add liquidReactor support to flux diagram generation
+
+- Other changes:
+    - Removed rmgpy.rmg.model.Species class and merged functionality into main rmgpy.species.Species class
+    - Refactored parsing of RMG-generated kinetics comments from Chemkin files and fixed related issues
+    - Refactored framework for generating reactions to reduce code duplication
+    - Resonance methods renamed from generateResonanceIsomers to generate_resonance_structures across all modules
+    - Raise CpInf to Cphigh for entropy calculations to prevent invalid results
+
+- Fixes:
+    - Update sensitivity analysis to use ModelSettings and SimulatorSettings classes introduced in v2.1.5
+    - Fixed generate_reactions methods in KineticsDatabase to be directly usable again
+    - Fixed issues with aromaticity perception and generation of aromatic resonance structures
+
+RMG-database Version 2.1.6
+==========================
+Date: December 21, 2017
+
+- Additions:
+    - New training reactions added for [NH2] related H_Abstractions
+    - 14 new kinetics libraries related to aromatics formation (see RMG-database #222 for details)
+
+- Other changes:
+    - Removed some global forbidden groups which are no longer needed
+    - Forbid CO and CS biradicals
+    - Updated lone_electron_pair_bond family and removed from recommended list
+
+- Fixes:
+    - Fixed unit errors in some H_Abstraction and R_Addition_MultipleBond depositories
+
+
 RMG-Py Version 2.1.5
 ====================
 Date: October 18, 2017