RMG-Py v1.0.4

• IPython notebooks now found in the ipython folder and contains useful illustrative examples. Requires the installation of jupyter via the command conda install jupyter
• Cantera support in RMG:
  • New module found in rmgpy.tools.canteraModel, which provides functions to help simulate RMG models using Cantera instead of native RMG solvers.
  • Has capability to generate cantera conditions and convert CHEMKIN files to cantera models, or use RMG to directly convert species and reactions objects to Cantera objects.
  • Demonstrative example found in ipython/canteraSimulation.ipynb
• Module for regression testing of models generated by RMG
  • This new module is found at rmgpy.tools.observableRegression and helps identify differences between different versions of models generated by RMG, using the "observables" that the user cares about (i.e. main species mole fractions). Runs simulations via cantera.
• Automatic plotting of simulations and sensitivities when generating models
  • Automatic plotting of simulations in the job's solver folder when saveSimulationProfiles is set to True in the input file.
  • Sensitivities for top 10 most sensitivie reactions and thermo now plotted automatically and stored in the solver folder.
  • New rmgpy.tools.plot module contains plotting classes useful for plotting simulations, sensitivities, and other data
• CHEMKIN files are now read literally: unlisted bath gases are not added when loading a chemkin file
• Functionality to assist in saving training reactions and thermo groups to RMG (see ipython notebook scripts in RMG-database/scripts/ for working examples)
• Improved thermochemistry estimation (mostly for cyclics and polycyclics)
  • Add rank as an additional attribute in thermo database entries to determine trustworthiness
  • Fixes ring group retrieval when multiple rings or polycyclic rings are found in a single molecule
  • Changes to resonance isomer generation to fixes aromatic crashes and print more debugging information
• Bug fixes:
  • Crashes with a useful error message when a Reaction Library and Seed Mechanism contains more than 3 reactants or products
  • Initial mole fractions get handled as floats to prevent integer division errors, and a useful message about renormalization is printed
  • Training reactions now load successfully regardless of generateSpeciesConstraints parameters (#602)
  • Transport data is now saved correctly to CHEMKIN tran.dat file and also imports successfully
  • Fixes appending of reactions to CHEMKIN file when reaction libraries are desired to be appended to output
  • Fixes writing of csv files for simulation and sensitivity results in Windows
  • Reverts the vertex connectivity value algorithm to prevent overflow errors
  • Fixes Reaction.draw() function to draw the entire reaction rather than a single species
• Other fixes
  • Enforces compatible versions of matplotlib and cantera in anaconda build
  • Github pull requests from forked repo's will no longer fail Travis CI builds due to encrypted environment variable issues