[Bioc-devel] All Package Maintainers Please README!

I'm not sure I like this idea, mainly because it is a passive
filtering on the part of the package maintainer, and a pretty big
assumption on my part.

Something active like adding an INTERNAL or as Oleg mentioned, a # at
the beginning of the line signals to me that the maintainer really
wants this stuff filtered out, whereas only taking the first line
requires the assumption that the maintainer really only wanted the
first line to be public.

Also note that a line in this instance is demarcated by a newline
character, so as long as you don't hit the return key, any number of
sentences will be filtered by a single INTERNAL or #, so it shouldn't
be burdensome to filter things out.

Anyway, I'm not sure we should be filtering this stuff out regardless.
As an example here are some recent commit messages:

First from Biobase:

esApply for ExpressionSet

* made esApply(X, MARGIN, FUN, ...) a generic

* method for exprSet same as previous functoin esApply
  (inappropriately modifies FUN environment, breaking lexical scope)

* method for ExpressionSet equivalent to

  with(pData(X), apply(exprs(X), MARGIN, FUN, ...))

* Documentation to follow shortly

Or from AnnotationDBI:

Remove bad constraint from probes table on chip packages

This change only affects packages for rodents and humans.  It drops
the not null constraint from the accessions collumn which is
problematic since lousy platforms will sometimes have probes that are
measuring "who-knows what".  Users ought to have a right to know when
they are using a probe like this...


Do you really want to argue that the first line in these messages is
all that should show up in the changelog? In both cases the first line
is pretty cryptic, but the second line is actually quite useful.

Jim



Martin Morgan wrote:

Jim --

I was actually writing identical sentiment (from across the hall), so
there's a second vote for just the first line (and filtering empty
first lines). Martin

Marc Carlson <mcarlson at fhcrc.org> writes:

James W. MacDonald wrote:

Robert recently suggested that I make a stab at a blog-based
changelog rather than the current monthly postings, sort of similar
to what Duncan Murdoch has done with the R NEWS and windows CHANGELOG.

The biggest difference between what is done for R and what I will
be doing for BioC is this; R-core does a really good job of writing
explanatory notes describing what the change was, and what it means
for the end user.

On the other hand, the commit messages that people use range from
the ridiculous to the sublime. Since I will no longer be parsing
the commit messages by hand, I will not be able to remove the more
useless messages that people tend to use, and these things will go
straight to the changelog for all to see.

So, first thing; if you don't want your section of the changelog to
be populated with things like 'WTF was I thinking?!@!?@!?' or
'Oops', or the venerable 'commit' or better yet, the ever popular '
', you will want to actually use a commit message that means
something with respect to the commit you just made.

Now I know some of the commit messages are not intended for public
consumption, so there is a way out. If you prepend your commit
message with INTERNAL, then it will be scrubbed. Or at least I
think it will ;-D. I'm using Python for the first time to do the
parsing, so I am sure there are bugs aplenty. Note that this
INTERNAL thing is _by line_, so if you do something like:

INTERNAL This is a commit message nobody should ever see.

But they can see this one.

Then the second part of the message _should_ get through. Note that
you need to use INTERNAL exactly, as it is always possible that
someone might use Internal at the beginning of a commit message
that they want published, so I am not doing any case-changing on
the test for this string.

The changelog as it currently exists (with just one day of changes
so far) can be viewed here:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi

Please take a look and send me any suggestions.

Best,

Jim



  

Hmmm,
Here in Seattle, Seth had most of us making commit messages where the
1st  line was a brief title describing the major contents of the change
and then there would be a line break followed by any of the gory
details
that might be needed to carefully describe what the title meant.  I
like
this format because part of a commit message is to say briefly what
changes have taken place, and partly it's also a place to make personal
notes so that later on you can remember what you were thinking at the
time.  So my 1st point is that by habit some of us already separate
these two with a linebreak.

Partly because I adopted this habit already and partly because I don't
want to live in constant fear of what might slip into my commit
messages, it might be nice if you just captured the 1st section and
then
allowed us to tag any lines that fall below that linebreak with a
character if we want them to also be in the public eye (with the rest
remaining private by default)?  Of course I could also tag the lower
stuff, but then I am typing lots of extra characters with each commit.

    Marc