[Biopython-dev] Tutorial documentation for Bio.SeqIO

[Peter]

Michiel Jan Laurens de Hoon wrote:
> I've changed the links to the example files to relative paths, and added 
> these files on the server. With the relative paths, links should work 
> both on the web page and from the local documentation as contained in 
> the Biopython distribution.
 >
 > ...
 >
> I put the new Tutorial preview at
> http://biopython.org/DIST/docs/tutorial/Tutorial-new.html

I am the bearer of bad news I'm afraid.

I assume the local file structure looks something like this:

.../Doc/Tutorial.pdf
.../Doc/Tutorial.html
.../Doc/examples/ls_orchid.fasta
.../Doc/examples/ls_orchid.gbk
etc

With the online copies going here:

http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.fasta
http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk

So yes, relative links like "examples/ls_orchids.fasta" and 
"examples/ls_orchids.gbk" should in theory work for both the HTML and 
PDF files, both locally and online.

Sadly it looks like hevea has mangled your relative links.  They looked 
fine in LaTeX, but the HTML file you put online contains things like <A 
HREF="ls_orchid.fasta"> which of course fails.

Also, and this may depend on the version of LaTeX used, but on the 
Tutorial.pdf I just built on windows, using Adobe Reader 6.0, the links 
display with "file:examples/ls_orchid.fasta" as the tool tip, but seem 
to get passed to Internet Explorer as "http://examples/ls_orchid.fasta" 
which fails.

I think it would be simpler and safer to just use an absolute URL to the 
webpage copy, and mention in the text that the files are included in the 
source code.

By the way - am I right in thinking that the Windows installer does not 
come with the documentation directory?  I would assume that some Windows 
users would just download the PDF tutorial and put it anywhere on their 
hard disk (its what I would do!), in which case there is no way the 
relative links idea could work.

Peter