[Biopython-dev] Trunk freeze for Biopython 1.54 beta

[Peter]

On Sat, Apr 3, 2010 at 2:21 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> Hi Peter,
>
> On Fri, Apr 2, 2010 at 2:49 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>
>> Eric - do you know any LaTeX? If not, don't worry too
>> much. We can guide you though installing pdflatex
>> and hevea for producing PDF and HTML, and then
>> adding things to the tutorial should be fairly easy.
>> Or, the simpler option (for you) would be to hand
>> over plain text and a kind volunteer (maybe me)
>> can handle the LaTeX markup.
>
> Yes, I can do LaTeX. Would it be better to rework the
> wiki page (or a section of it) into something chapter-like
> first, or just add a draft of the new chapter into the main
> tutorial document right away?

Up to you. Maybe start with polishing the wiki?

The only tricky bit will be images (HTML vs PDF layout),
but there are examples you can copy (e.g. the Graphics
chapter).

> Also, did you have a list of specific topics/subsections
> I should cover?

Well, the basics of reading, writing and converting
trees from different formats. Then something on
using the tree objects...

I was going to suggest re-rooting a tree but as per the
earlier thread, its a bit more complicated than I had
expected.

How about taking a tree, and coloring specific clades
(to save the colors in XML output and/or a graphical
output)?

>> P.S. Note to self or anyone interested: Why did
>> the source code tar ball and zip file jump in size
>> by about 2MB? Was it just the accumulation of
>> more code and more tests - or did I mess up?
>
> The example phyloXML files are kind of hefty,
> especially ncbi_taxonomy_mollusca.xml. If size
> increase is a problem, I can remove that file
> from the unit tests without substantial harm.

That is just a 66K zip file though, so it isn't that.

Peter