Updates for Sphinx Documentation

[GoogleCodeExporter]

Hi Ray,
I've attached a patch to update some of the sphinx documentation. Most of the 
changes are small, fixing typos/formatting kinds of things, but a couple update 
some examples that were broken. There are 23 patches I've stuck together in 
this one file, but if you want separate patch documents for all the commits I 
did, please let me know. These should be relative to r2616. I hope you find all 
these patches helpful!

Cheers!
Bryan

Original issue reported on code.google.com by bryan.w....@gmail.com on 18 Dec 2013 at 12:00

Attachments:

• docs_patch.patch

[GoogleCodeExporter]

Bryan, thanks for this set of patches. The attention to detail is very much 
appreciated. Most of these patches are incorporated by commits r2620 through 
r2636.

I removed the changes to the variable used for the temperature exponent, as I 
think I would prefer that it be standardized to 'b', which is more consistent 
with what's used in the C++ documentation and source code (see RxnRates.h) and 
the literature that we reference (Kee uses 'beta'). Unfortunately, ctml_writer 
uses 'n' as a keyword argument, which means changing it will be a slight API 
change, though I'm not sure anyone uses the keyword-argument form of the 
constructor for class Arrhenius.

Original comment by yarmond on 18 Dec 2013 at 7:04

• Changed state: Fixed
• Removed labels: OpSys-Linux

[GoogleCodeExporter]

Hi Ray,
My pleasure! Got to do something to procrastinate. 

WRT the temperature exponent: I completely agree, "T to the b" sounds more 
correct to me as well. Maybe you can add a note in the docs about the change in 
notation, if a change in the API would break things. Alternatively, maybe the 
API could be changed transparently - allow either 'n' or 'b' to be used, and 
change the documentation to say 'b'? Something like:

def __init__(self, A=0.0, b=0.0, E=0.0, coverage=[], rate_type='', n=None):
    if n is not None:
        b = n

would allow the docs to be updated to say 'b' everywhere, but allow people 
still using the keyword-argument to keep doing so. It could also print a 
warning if people are using the 'n' keyword-argument that the 'n' will be 
deprecated and removed in a future version, if removal is necessary.

Original comment by bryan.w....@gmail.com on 19 Dec 2013 at 1:29

[GoogleCodeExporter]

Yes, I think that would make for a smooth transition. Feel free to put a patch 
together for that change.

Original comment by yarmond on 19 Dec 2013 at 7:00