[Biopython-dev] Documentation Status

Fri Oct 17 04:01:40 UTC 2014

Pull Request submitted.

-Travis

On Tue, Oct 14, 2014 at 10:10 AM, Travis Wrightsman <twrig002 at ucr.edu>
wrote:

> I finished translating the obviously labeled epytext doc strings to proper
> reStructuredText. Now I'm working through each error/warning that the
> epydoc compiler is spitting out. When I've finished this I'll submit a pull
> request for you all to review before merging.
>
> When it's all merged and done, I can start attempting to compile in
> Sphinx, just to test.
>
> Travis Wrightsman
>
> On Oct 14, 2014, at 6:56 AM, Yanbo Ye <yeyanbo289 at gmail.com> wrote:
>
> Hi Peter and Alexey,
>
> The main documentation can be stored in rst files. I think the way I
> suggest can let potential contributors know where to start the translation,
> although some languages may not have so many contributors. Anyway, this
> make things more complicated with docstrings and transifex. If the main
> tutorial will be continuing in LaTex format, I think a guide to how to
> translate it will be very helpful.
>
> On Tue, Oct 14, 2014 at 9:01 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> Hi Alexey,
>>
>> I would agree there is no need to translate the docstrings (and
>> there is no easy way to do it either at the source code level).
>> [Note we would like to have them all RST formatted to make the
>> API documentation prettier, i.e. using reStructuredText]
>>
>> I would focus any translation efforts on the main Tutorial,
>> which is currently written in LaTeX:
>> https://github.com/biopython/biopython/blob/master/Doc/Tutorial.tex
>>
>> There are also user contributed "Cookbook" examples on our
>> wiki - would people want to translate any of these?
>> http://biopython.org/wiki/Category:Cookbook
>>
>> And various people have written introduction slides for workshops
>> etc over the years, e.g. mine using *.rst on GitHub:
>> https://github.com/peterjc/biopython_workshop
>>
>> Peter
>>
>>
>> On Tue, Oct 14, 2014 at 1:45 PM, Alexey Morozov
>> <alexeymorozov1991 at gmail.com> wrote:
>> > Not really, if the main bulk of documentation is to be stored in
>> docstrings
>> > or made from them automatically for every future release. These things
>> go
>> > untranslated for years for less common languages, cause problems with
>> > non-ASCII characters and so on.
>> >
>> > But I think that there is not much need for translated docstrings. At
>> least
>> > in Russia, everyone in IT/CS and nearly everyone in life sciences knows
>> at
>> > least some English. What I was talking about is multilingual wiki or at
>> > least a few manuals, cookbooks and "Getting started"s, or maybe
>> Biopython
>> > workshop, because it may help bioinformatics teachers.
>> >
>> >
>> > 2014-10-14 19:36 GMT+09:00 Peter Cock <p.j.a.cock at googlemail.com>:
>> >>
>> >> Hi Alexey,
>> >>
>> >> I am not aware of any Russian translation (another interesting language
>> >> in terms of non-ASCII characters and the potential markup
>> implications).
>> >>
>> >> Do you have any thoughts on if and how to track any future translation
>> >> work in the main Biopython repository side by side with the English
>> >> version to help keep things up to date?
>> >>
>> >> Peter
>> >>
>> >> On Tue, Oct 14, 2014 at 11:32 AM, Alexey Morozov
>> >> <alexeymorozov1991 at gmail.com> wrote:
>> >> > Speaking of translations, is Biopython documentation being translated
>> >> > into
>> >> > Russian? I could contribute to such a work, but definitely won't
>> make it
>> >> > all
>> >> > alone.
>> >> >
>> >> > 2014-10-14 18:48 GMT+09:00 Peter Cock <p.j.a.cock at googlemail.com>:
>> >> >>
>> >> >> Hi Yanbo,
>> >> >>
>> >> >> Translations are an interesting case - some of the tutorial was also
>> >> >> translated into Japanese once, but this work often goes out of date
>> :(
>> >> >> Using LaTeX it would be possible to embed alternative versions
>> >> >> into the same file - even at a chapter or section level (you can
>> have
>> >> >> conditional blocks with if statements - so new sections could be in
>> >> >> English only initially while waiting for translation). I don't think
>> >> >> you
>> >> >> can do this with Sphinx - or can you?
>> >> >>
>> >> >> Peter
>> >> >>
>> >> >> P.S. The source files for the Chinese translation is here, plus a
>> port
>> >> >> of the LaTeX tutorial into *.rst:
>> >> >> https://github.com/bigwiv/Biopython-cn
>> >> >>
>> >> >>
>> >> >> On Tue, Oct 14, 2014 at 10:00 AM, Yanbo Ye <yeyanbo289 at gmail.com>
>> >> >> wrote:
>> >> >> > For the Tutorial of Sphinx, here is a Chinese version that we
>> >> >> > translated
>> >> >> > last year. All format seems ok, including  equations, chapter
>> >> >> > hyperlinks,
>> >> >> > references, etc. But it cannot pass the pdf compiling process on
>> >> >> > readthedocs.  I'm not a expert on this. Maybe someone can give it
>> a
>> >> >> > try.
>> >> >> >
>> >> >> > http://biopython-cn.readthedocs.org/zh_CN/latest/index.html
>> >> >> _______________________________________________
>> >> >> Biopython-dev mailing list
>> >> >> Biopython-dev at mailman.open-bio.org
>> >> >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Alexey Morozov,
>> >> > LIN SB RAS, bioinformatics group.
>> >> > Irkutsk, Russia.
>> >
>> >
>> >
>> >
>> > --
>> > Alexey Morozov,
>> > LIN SB RAS, bioinformatics group.
>> > Irkutsk, Russia.
>>
>
>
>
> --
>
> *Yanbo Ye*
> *Guangzhou Institutes of Biomedicine and Health, *
> *Chinese Academy of Sciences*
> *190 Kaiyuan Avenue, Science Park, Guangzhou, China*
>
> *Email: ye_yanbo at gibh.ac.cn <ye_yanbo at gibh.ac.cn>*
> *Web: http://www.yeyanbo.com <http://www.yeyanbo.com>*
> *Phone: (86)-020-32093810*
>
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