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

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

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

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