[Bioc-devel] Please bump version number when committing changes

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Sat Sep 6 04:06:03 CEST 2014 

Before we go and invent all kinds of stuff, is this a real problem that we
need to spend resources thinking about?

Dan's original post was about 2 people who check out devel from svn may see
the same version number, but have different versions of the code.  I
acknowledge that this is theoretical possible.  In the rare situation where
this might matter, it would be better to compare svn revision numbers.  And
does this really happen with any frequency, I mean, the people who install
packages from devel using svn must be very limited for a given package
(perhaps I am different, but I only do it occasionally, and almost always
for my own packages or if I depend on a package where I have identified an
issue, the other author has fixed it and I need to test now and not
tomorrow).

With the current build policy, as I understand it, two people each
installing not from svn, but from the published tarball throguh biocLite,
is guaranteed to have the same code if they have the same version.

The remaining issue is if one user installs from svn and one user from a
tarball.  But I think everyone who does svn just need to understand that
this can happen.  The affected users must be rather limited.

One version of the problem, which I can see being confusing, is if an
author pushes a bug fix to svn, but does not bump DESCRIPTION.  Then I
could see some unfortunate discussion between the developer and a user, but
that really comes down to lack of understand of the build system for the
developer. While I am sure it happens, the solution in my opinion is better
education for the developers about the build system.

Best,
Kasper



On Fri, Sep 5, 2014 at 9:48 PM, Michael Lawrence <lawrence.michael at gene.com>
wrote:

> As Pete and Ryan have pointed out, it seems that the version control system
> should somehow ease the burden of the developer here.
>
> Let's look at this from the github perspective, since it is likely to be
> the primary hosting mechanism for the foreseeable future. Just thinking out
> loud, if R could somehow dynamically ascertain the version of a package at
> build time, it could query the git checkout for a version. A simple
> algorithm that I have found effective in non-R projects is to consider git
> tags, which on github equate to releases. If the repository state is *at*
> the tag, then use the tag as the version. If the state is ahead of the most
> recent tag, then use the tag + latest commit hash. I wonder if R could
> support this by allowing a path to an R script in the version field?
>
>
>
> On Fri, Sep 5, 2014 at 6:27 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>
> > On Fri, Sep 5, 2014 at 7:50 PM, Peter Haverty <haverty.peter at gene.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > I respectfully disagree.  One should certainly check in each discrete
> > unit
> > > of work.  These will often not result in something that is ready to be
> > used
> > > by someone else.  Bumping the version number constitutes a new release
> > and
> > > carries the implicit promise that the package works again.  This is why
> > >
> >
> > Here I would respectfully disagree.  Code in the devel branch carries no
> > guarantees.
> > I think we have been pretty loose with respect to package version number
> > bumping in devel
> > branch; the svn tracking can be used to deal with isolation of code for
> > rollbacks.
> >
> > In this informal regime the package version number is a simple marker of
> > package state.
> > I think it has served us pretty well in past years but the developer
> > community was smaller
> > and had fairly homogeneous habits.
> >
> > Clearly there is room for more regimentation in this area but at the
> moment
> > I agree with
> > Dan that version numbers are cheap and should be bumped when new code is
> > committed.
> > And the recognition by all that a devel image may not work and may change
> > fairly dramatically
> > while in devel should be general; whether we need to alter that is open
> to
> > question but I would
> > think not.
> >
> >
> > > continuous integration systems do a build when the version number
> > changes.
> > >
> > > One should expect working software when installing a pre-build package
> > (the
> > > tests passed, right?).  Checking out from SVN is for developers of that
> > > package and nothing should be assumed about the current state of the
> > code.
> > >
> > > To keep everyone happy, one could add a commit hook to our SVN setup
> that
> > > would add the SVN revision number to the version string.  This would be
> > for
> > > dev only and hopefully not sufficient to trigger a build.
> > >
> > > That's my two cents.  Happy weekend all.
> > >
> > > Regards,
> > >
> > >
> > >
> > > Pete
> > >
> > > ____________________
> > > Peter M. Haverty, Ph.D.
> > > Genentech, Inc.
> > > phaverty at gene.com
> > >
> > >
> > > On Fri, Sep 5, 2014 at 4:30 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
> > wrote:
> > >
> > > >
> > > >
> > > > ----- Original Message -----
> > > > > From: "Stephanie M. Gogarten" <sdmorris at u.washington.edu>
> > > > > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "bioc-devel" <
> > > > bioc-devel at r-project.org>
> > > > > Sent: Friday, September 5, 2014 4:27:13 PM
> > > > > Subject: Re: [Bioc-devel] Please bump version number when
> committing
> > > > changes
> > > > >
> > > > > I am guilty of doing this today, but I have (I think) a good
> reason.
> > > > > I'm making a bunch of changes that are all related to each other,
> but
> > > > > are being implemented and tested in stages.  I'd like to use svn to
> > > > > commit when I've made a set of changes that works, so I can roll
> back
> > > > > if
> > > > > I break something in the next step, but I'd like the users to see
> > > > > them
> > > > > all at once as a single version update.  Perhaps others are doing
> > > > > something similar?
> > > > >
> > > >
> > > > I understand the motivation but this still results in an ambiguous
> > state
> > > > if two different people check out your package from svn at different
> > > times
> > > > today (before and after your changes).
> > > >
> > > > Version numbers are cheap, so if version 1.2.3 exists for a day
> before
> > > > version 1.2.4 (which contains all the changes you want to push to
> your
> > > > users) then that's ok, IMO.
> > > >
> > > > Including a version bump doesn't impact whether or not you can
> > rollback a
> > > > commit with svn.
> > > >
> > > > Dan
> > > >
> > > >
> > > >
> > > > > Stephanie
> > > > >
> > > > > On 9/4/14, 12:04 PM, Dan Tenenbaum wrote:
> > > > > > Hello,
> > > > > >
> > > > > > Looking through our svn logs, I see that there are many commits
> > > > > > that are not accompanied by version bumps.
> > > > > > All svn commits (or, if you are using the git-svn bridge, every
> > > > > > group of commits included in a push) should include a version
> bump
> > > > > > (that is, incrementing the "z" segment of the x.y.z version
> > > > > > number). This practice is documented at
> > > > > > http://www.bioconductor.org/developers/how-to/version-numbering/
> .
> > > > > >
> > > > > > Failure to bump the version has two consequences:
> > > > > >
> > > > > > 1) Your changes will not propagate to our package repository or
> web
> > > > > > site, so users installing your package via biocLite() will not
> > > > > > receive the latest changes unless you bump the version.
> > > > > >
> > > > > > 2) Users *can* always get the current files of your package using
> > > > > > Subversion, but if you've made changes without bumping the
> version
> > > > > > number, it can be difficult to troubleshoot problems. If two
> > > > > > people are looking at what appears to be the same version of a
> > > > > > package, but it's behaving differently, it can be really
> > > > > > frustrating to realize that the packages actually differ (but not
> > > > > > by version number).
> > > > > >
> > > > > > So if you're not already, please get in the habit of bumping the
> > > > > > version number with each set of changes you commit.
> > > > > >
> > > > > > Let us know on bioc-devel if you have any questions about this.
> > > > > >
> > > > > > Thanks,
> > > > > > Dan
> > > > > >
> > > > > > _______________________________________________
> > > > > > Bioc-devel at r-project.org mailing list
> > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > > >
> > > > >
> > > >
> > > > _______________________________________________
> > > > Bioc-devel at r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >
> > >
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> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
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