[Bioperl-l] Packaging Bio::Ext::HMM for CPAN, was Re: Problems with Bioperl-ext package on WinVista?

[Yee Man Chan]

I think it is better to keep Bio-Tools-HMM within the Bio-Ext package and then spin this whole Bio-Ext package out to CPAN. I am ok with Robert's arrangement to move the related pm files under Bio/Tools/ to the new Bio-Ext package.

There aren't that many modules in Bio-Ext. Plus, based on Chris and Robert's comments, modules other than my dpAlign and HMM appear to be abandoned. Moving HMM out only makes users less likely to try it out.

If need be, I can also be a co-maintainer of this spinned off Bio-Ext package.

I have a PAUSE already due to my other CPAN contributions. So there is no need to create a new one. My PAUSE account is UMVUE.

Yee Man

--- On Tue, 8/18/09, Chris Fields <cjfields at illinois.edu> wrote:

> From: Chris Fields <cjfields at illinois.edu>
> Subject: Packaging Bio::Ext::HMM for CPAN, was Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?
> To: "Yee Man Chan" <ymc at yahoo.com>
> Cc: "Robert Buels" <rmb32 at cornell.edu>, "BioPerl List" <bioperl-l at lists.open-bio.org>
> Date: Tuesday, August 18, 2009, 8:10 AM
> Yee Man, Robert,
> 
> All tests are passing; there was a small change in the
> expected floating point, but no warning now.
> 
> Re: passing this on to CPAN, I think it needs a distinct
> version from BioPerl (something that should probably happen
> with any spinoffs).  I foresee two options (and a
> possible conflict):
> 
> 1) Use the same versioning scheme, starting with 1.6.1.
> 2) Use a simpler scheme a'la Bio::Graphics, which I
> suggest.  Tripartite versions are a PITA, we'll only
> need to keep that in core.
> 
> Conflict: Bio::Tools::HMM is currently part of the 1.6
> branch (in 1.6.0).  If this stays in 1.6.1 then we have
> two versions of the module floating out there.
> 
> I think we should go ahead and remove Bio::Tools::HMM from
> 1.6.1, and I could attempt to push the initial Bio-Ext-HMM
> release after core 1.6.1 is out.  After that, I could
> then add Yee Man as PAUSE co-maintainer for those modules
> (which means Yee Man needs to sign up for a PAUSE
> account).  Any objections to that?
> 
> chris
> 
> On Aug 17, 2009, at 7:24 PM, Yee Man Chan wrote:
> 
> > I get it now. So it is now spinned off. Anyway, I
> updated the HMM.pm in Bio-Tools-HMM with the latest version.
> I think it should work.
> > 
> > Yee Man
> > 
> > --- On Mon, 8/17/09, Robert Buels <rmb32 at cornell.edu>
> wrote:
> > 
> >> From: Robert Buels <rmb32 at cornell.edu>
> >> Subject: Re: [Bioperl-l] Problems with Bioperl-ext
> package on WinVista?
> >> To: "Yee Man Chan" <ymc at yahoo.com>
> >> Cc: "Chris Fields" <cjfields at illinois.edu>,
> "BioPerl List" <bioperl-l at lists.open-bio.org>
> >> Date: Monday, August 17, 2009, 4:00 PM
> >> Yee Man Chan wrote:
> >>> I noticed that Bio/Tools/HMM.pm was removed
> from the
> >> trunk. So I added it back in. I think you
> shouldn't get the
> >> warnings with this version.
> >> 
> >> Please read my email above with instructions for
> checkout
> >> out the new Bio-Tools-HMM component, where
> Bio::Tools::HMM
> >> has been moved.  Please do not add the
> Bio::Tools::HMM
> >> module back into bioperl-live.
> >> 
> >> I think you might be confused about the functions
> of 'svn
> >> add', 'svn commit', etc, because I don't see any
> actual
> >> addition of the module in the commit logs. 
> Please read
> >> through the SVN manual at http://svnbook.red-bean.com/ if you need
> >> clarification.
> >> 
> >> Rob
> >> 
> >> 
> > 
> > 
> > 
> 
>