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

Martin Morgan mtmorgan at fhcrc.org
Wed Sep 10 22:58:11 CEST 2014

On 09/08/2014 06:15 AM, Gabe Becker wrote:
> Michael,
> Tags could work. Another approach  would be to update the repository and
> then look in the log to see if the version number was changed in the most
> recent commit. In a sense this is the converse of what our GRANBase package
> does when locating historical package versions within the Bioc SVN.
> This has the benefit of not requiring the authors do anything they didn't
> already need to do in order to "flag" a release (i.e., bump the version
> number).
> I should note also to Dan's later point that while the Bioc repository
> always builds whatever is in the latest commit currently, that need not be
> the case. Our internal package repository only builds on  version bumps (of
> a package or any of it's recursive dependencies).

In hopes of closure...

1. The original motivation and primary message is that a version bump is 
required for your commits to propagate to biocLite. Developers often forget to 
bump versions. So please always bump versions.

2. A secondary message is that it is confusing to have two (or more) variants of 
a package represented by the same version number. Since Bioconductor packages do 
not include a reference to the svn revision, this should severely temper any 
system of conditional version bumps. This is reinforced by the nearly unlimited 
availability of version numbers, the build system requirement that the package 
at least build and check successfully before being pushed, diligent application 
of unit tests and test-driven development (;)), and that commits are to the 
'devel' branch where there is some tolerance of broken functionality. So please 
invoke exceptions to 1 only after very careful consideration.

Several valid points came up during the thread. SVN is certainly less flexible 
than git when dealing with branches (and the way our svn repository and 
permissions are structured makes it particularly difficult to commit to a 
non-trunk or release branch). Our build system does have idiosyncratic features 
(e.g., nightly builds of all packages; build from svn regardless of version 
bump; pushing to a public repository on version bump and successful build) that 
conflate version control with software 'release'; these reflect both policy and 
software implementation decisions, both of which could be changed [there are no 
immediate plans to do so]. It is better to understand the current system and 
limitations than to interact with our svn and build system as though they were 
git and implemented CI.

Personally, I have rarely intentionally committed user-visible changes to svn 
without a version bump (hard to say that with an entirely straight face). I'll 
admit to having made temporary strictly local git repositories while I explore 
alternative implementations. The primary scenario that gives me pause is 
committing code that I know to be functional but incorrect; I would not expose 
this as part of the user API (e.g., using a function that is not exported from 
the name space) and recognize that in this case svn and the build system are 
working against rather than with me.


> ~
> G
> On Fri, Sep 5, 2014 at 6:48 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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