[Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl

Brian Osborne osborne1 at optonline.net
Thu Jun 1 15:44:13 EDT 2006


You asked about the doc/ directory. The only directory I see in my
bioperl-live/doc directory is examples/, the reason this remains is that it
contains scripts and images related to the Graphics HOWTO, in theory these
could be moved to the Wiki and the examples/ directory deleted. One
explanation for why you see doc/html and all those other dirs is that you
aren't using the 'cvs -d' option (there are other explanations) when you

If examples/ is removed then presumably the README can be removed and
makedoc.pl moved elsewhere.

Brian O.

On 5/31/06 9:54 PM, "Jay Hannah" <jay at jays.net> wrote:

> Brian Osborne wrote:
>> - Do we remove the file bptutorial.pl from the package now? I'd say yes, we
>> don't want to have to maintain two bptutorials.
> We certainly wouldn't want to try to maintain two copies, one POD one in wiki.
> That would be the worst of all options. One option that hasn't been mentioned
> yet is to keep maintenance of that in POD in the distro (leaving the cool
> runability alone), and then flag that document as unchangeable in the wiki
> with a note on top "Maintenance of this document is done in POD in the distro.
> Submit POD patches to bioperl-l and we'll re-post an updated copy to this
> wiki."
> Just a thought.
>> - What do we do with the script part of bptutorial.pl? It certainly could be
>> excised and put into the examples/ directory, for example, but this would
>> break a few of the paths that are being used.
> /README says this:
>  scripts/    - Useful production-quality scripts with POD documentation
>  examples/   - Scripts demonstrating the many uses of Bioperl
> I'm personally not clear on the difference. Little stuff should start in
> examples/ and graduate to scripts/ once they've matured?
> Is the doc/ tree being abandoned?
> doc/faq        (empty?)
> doc/howto      
> doc/howto/examples
> doc/howto/figs (empty?)
> doc/howto/html (empty?)
> doc/howto/pdf  (empty?)
> doc/howto/sgml (empty?)
> doc/howto/txt  (empty?)
> doc/howto/xml  (empty?)
> Does all that stuff officially live in and is being changed in the wiki, never
> to return to the distro?
> Any reason those empty dirs aren't nuked out of CVS?
> Chris Fields wrote:
>> Jay, looks like there are still some weird formatting issues with the
>> bptutorial wiki page, something which I ran into before when getting the
>> Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
>> spaces preceding a line denotes code for some reason).  Not much you can do
>> in these cases except remove the extra spaces in those spots.  Looking good
>> though!  
> Sorry, I spent zero time on the whole conversion. I'm not sure what parts
> didn't convert well. I've never done that conversion before, and know nothing
> about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran
> off to work. :)
> Mauricio Herrera Cuadra wrote:
>> I've added a link in the left menu of the wiki. If you think it should
>> point to the Tutorials page instead of the Bptutorial.pl page please let
>> me know.
> Instead of all these competing links on the left, maybe we should have a
> master "documentation" page linked on the left cascading like so?
> Documentation  (linked on the left menu)
> - Quick start
> - FAQ
> - HOWTOs
> - Tutorials
> (What's the conceptual difference between a HOWTO and a tutorial?)
> It's hard for me to dive into a wiki lifestyle for the huge documentation
> pillars since it can't ever get back into the distro... (can it?)  Small,
> throw away stuff is great for the wiki, but huge, established, thoughtful,
> long documents should be left in the distro? Present (and searchable) on the
> wiki but static?
> Why isn't the short "Current events" just listed on the top of the "News"
> page?
> Sick of my endless questions yet? -grin-
> j
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