[Phylobase-devl] release date

Peter D. Cowan pdc at berkeley.edu
Fri Aug 28 01:42:39 CEST 2009

On Thu, Aug 27, 2009 at 09:37:09AM -0700, Jim Regetz wrote:
> I agree the recent progress has been great! I also agree with Peter's 
> sentiment, and am partial to François' second alternative: holding off a 
> little longer on the CRAN release to address these issues and others 
> that arise as we're working (we don't seem to have reached an asymptote 
> yet), but making an immediate announcement on R-sig-phylo to draw more 
> attention to the package on R-Forge. This should expand the user (and 
> thus tester) base, while still limiting it to folks who can be expected 
> to tolerate some ongoing changes and imperfect functionality in places.

Yes, I think an announcement to R-sig is great idea.  My suggestion for the delaying a CRAN release was based on how we've been making sustained steady changes and we have a couple significant bugs remaining.  Should either, our efforts flag, or we fix those bugs we should submit the package to CRAN.


> IMHO François' road map is a good road map to CRAN, coupled with fixing 
> any important bugs that we might come across in the process. The release 
> certainly doesn't have to be totally feature rich and flawless, but 
> making sure the core functionality is rock solid is important. Releasing 
> *tomorrow* seems a bit rushed for my tastes. First impressions can be 
> lasting! There are certainly R packages on CRAN that I've installed 
> once, been unimpressed with, and never tried again...

Agreed.  I think regardless of disclaimers, (and personally I think we should be in beta stage for a while) once a package is released to CRAN there are expectations for basic level of quality.  

To me a 'release' means submitting to CRAN.  That said, I don't feel strongly that we need to have the vignettes and unit tests completed before we submit to CRAN, users are typically more forgiving about poor documentation and unimplemented features than they are for bugs.  So for me the only real release blockers are rerooting and subsetting.  

If we wanted to we could pull rerooting and add it to the feature request list.  But, subsetting feels more like a core function.


> François Michonneau wrote:
> > Hi,
> > 
> >   I think we should still plan of releasing it. My main concern is that
> > if we don't, we won't keep the pace we have been having in the last
> > couple of weeks, and the official release will be delayed. If people do
> > start using it, then they will report bugs (not too many I hope) and
> > keep development going.
> > 
> >   However, I agree there is still some polishing to do before officially
> > releasing it. It would be valuable to identify what are the things that
> > we really need to change before the release. In my opinion, one of main
> > things is that we need to use consistent variable names for
> > phylo4/phylo4d in our functions. They are currently called: x, phy,
> > object, etc. I can imagine that it's confusing for new users reading the
> > documentation. This is important to do before the release because if we
> > harmonize these names in the future, we can break people code if they
> > use explicit variable names in their calls.
> >  
> >   I agree that it would be nice to have our own subsetting and rerooting
> > functions. At this stage, however, it seems to me OK to release
> > phylobase even if these 2 functions don't work. Most other aspects of
> > phylobase are functional and should allow people to start working with
> > it.
> > 
> >   Because these functions don't work and yet are important, we should
> > however probably release phylobase as a beta-1 version. Meanwhile, we
> > should think about a road map with our objectives for the future
> > releases. I propose that we use the 0.4 release series as beta, and have
> > 0.5 series as the first official release.
> > 
> > * beta-2 (0.4.2): non-unique labels, subsetting, rerooting
> > * beta-3 (0.4.3): methods for multiPhylo4 and multiPhylo4d, no
> > dependencies from APE, identify method
> > * rc-1 (0.4.4): all functions have RUnit tests
> > * rc-2 (0.4.5): complete documentation and vignettes
> > 
> >   Alternatively, if we decide to not release quite yet on CRAN, we can
> > just send out announcements to the R-phylo mailing list and ask people
> > to test phylobase (from R-forge) and get their feedback.
> > 
> >   Cheers,
> >   -- François
> > 
> > 
> > On Wed, 2009-08-26 at 23:00 -0700, Peter D. Cowan wrote:
> >> This might be verboten to even suggest, but should we push off the release date?  In the last month we've made a 150 commits to phylobase, that's pretty awesome.  If we can keep up even a portion of this momentum, it may be worth while to hold off on releasing the package until we can finish a few things off.  Or, if we don't see ourselves having time at the moment, we can release as planned on Friday, and address the issues we've identified in a "Known Issues" section, and try to organize a 0.5.1 release down the road.
> >>
> >> Top on my list would be replacing our two ape dependencies.  The rerooting and subsetting are not trivial things to write, but the process of calling out to ape seems not to work the way we had hoped.  Unfortunately, I won't have time to do this until next week sometime.  
> >>
> >> Cheers
> >>
> >> Peter
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