This causes problems to be caught early, where they can at least sometimes be
handled as recoverable intergrator errors, rather than letting NaN values
propagate through the solution.
For binary (or higher order) reactions, multiple negative (but small, i.e. with
respect to integration tolerances) species concentrations should not produce
positive reaction rates that would drive those concentrations to even more
negative values.
Throwing an exception when a state variable is being set to NaN transforms some
reactor network integration errors from unrecoverable errors into recoverable
errors.
In Cygwin, some versions of SCons append a 'cyg' prefix to DLL names, which
breaks the Python extension module that is supposed to be named just
'_cantera.dll'.
The constructor with the signature (inputFile, [id]) just calls initThermoFile.
The constructor with the signature (phase XML node, [id]) just calls importPhase
(note that the id argument is unused, since the correct XML node must already be
given).
In Python 3, 'map' returns an object which evalutes the function as it is
consumed, not when 'map' is called. Therefore, the correct comparison to
pool.map(...) is list(map(...)).
Replace distutils with setuptools in the Cython and python_minimal
interfaces. Add console_scripts option to generate OS specific scripts to run
ck2cti, mixmaster, and ctml_writer
Remove script files that are obsoleted by console_scripts from
setuptools. Remove installation of the script modules from SConstruct.
Fix Python installers so that when a prefix directory is specified on the
command line, setuptools doesn't throw an error. The setuptools documentation at
[1] prefers setting PYTHONUSERBASE rather than PYTHONPATH. Use normpath to avoid
bugs in setuptools on Windows [2]. Specify an empty "--prefix" if the compiler
is clang to fix a bug with Homebrew Python on Mac OSX [3].
[1]: https://pythonhosted.org/setuptools/easy_install.html#custom-installation-locations
[2]: http://stackoverflow.com/q/31629398
[3]: https://github.com/Homebrew/homebrew-python/issues/187
