[cctbxbb] Documentation .... again

[Richard Gildea]

Hi Graeme,

I agree that the documentation of much of the cctbx code is somewhat
lacking, although I am not sure what is the best solution (especially for
the huge volumes of code that is already written). Perhaps some combination
of people adding documentation when asking or answering questions on here
about specifics would go some way to helping future users of the code.

As to your specific question:

Setting cos_sin_table=True uses interpolation of values from
a pre-calculated lookup table for trigonometric function calls in the
structure factor calculations in preference to calling the system
libraries. Ralf makes some comment on the speed (and variation in speed) of
the trigonometric functions in system math libraries in his FABLE paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448510/

However, without digging into the source, I am not sure of the meaning of
some of the other keywords to that function (e.g. wing_cutoff), which makes
it hard for me to write comprehensive documentation for this class.

Cheers,

Richard


On 7 December 2012 01:59, <Graeme.Winter at diamond.ac.uk> wrote:

>  Hi Folks,****
>
> ** **
>
> Been thinking some more about the old chestnut of documentation. The lack
> thereof is a well understood issue, and to be honest one which is not going
> to change any time soon as no one has the time to maintain a manual – this
> is fine and well understood. ****
>
> ** **
>
> As a kind of “patch” for this I was wondering if it would be possible to
> have a forum where someone could ask for e.g. documentation for a currently
> undocumented function, which could then be added to the subversion in the
> code itself. For example:****
>
> ** **
>
> cctbx_project/cctbx/xray/structure.py****
>
> ** **
>
> …****
>
> ** **
>
>   def structure_factors(self, anomalous_flag=None, d_min=None,****
>
>                               algorithm=None,****
>
>                               cos_sin_table=False,****
>
>                               quality_factor=None,****
>
>                               u_base=None,****
>
>                               b_base=None,****
>
>                               wing_cutoff=None):****
>
> ** **
>
> what is cos_sin_table for? with things like this there is the attitude
> that it is safe to ignore, however if we’re writing code to guide people’s
> experiments it would be good to be sure of this. Some simple documentation
> explaining this would be very useful.****
>
> ** **
>
> I’m definitely not suggesting (i) that anyone writes a manual or (ii) that
> all undocumented functions are suddenly documented, only that there is a
> mechanism set up that someone could ask about this and that someone who
> knows the answer could commit the changes to cctbx and then reply with the
> diffs – perhaps the way that stackoverflow works, or an email, or something
> really lightweight. Even this mailing list could be used I guess?****
>
> ** **
>
> I would be happy to help with this, though the above example is not one
> where I know the answer!****
>
> ** **
>
> Thoughts?****
>
> ** **
>
> Best wishes,****
>
> ** **
>
> Graeme****
>
> ** **
>
> Dr. Graeme Winter****
>
> Senior Software Scientist****
>
> Diamond Light Source****
>
>  ****
>
> +44 1235 778091 (work)****
>
> +44 7786 662784 (work mobile)****
>
>  ****
>
> ** **
>
>
>
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