Re: How to deal with tools used by BioPython and PyCogent
Hi,
thanks to Eric and Peter for their insights. These are really welcome.
On Tue, May 06, 2014 at 04:13:52PM +0100, Peter Cock wrote:
> I would agree with Eric, "suggests" seems like a better match than
> "recommends" for the command line tools which Biopython has
> wrapper code for. Perhaps the only exception where I might suggest
> a full "recommends" would be the NCBI BLAST+ binaries,
> https://packages.debian.org/sid/ncbi-blast+ but even these will
> not be used by everyone using Biopython.
Since I think that having ncbi-blast+ installed on a machine featuring
Biopython I think I'll keep this and move all other packages to
Suggests.
> The related question of should they be included as Build-Depends
> just because there is a unit test which would exercise them is again
> more policy driven.
Definitely.
> Andreas has uncovered a couple of gotchas where we'd not yet
> noticed a behaviour change in a recent tool release (e.g. EMBOSS),
> so there is certainly merit in including these at build time (thank
> you again for flagging these issues!).
I'm quite opinionated about testing as much as possible - so I would
really keep these Build-Depends.
> However, for anyone doing "apt-get build-deps python-biopython"
> as a precursor to building the latest Biopython from source, having
> things like EMBOSS and NCBI BLAST+ installed is not required.
If people are installing build-deps they have usually a machine which is
able to bear some packages. I expect people who are doing this to know
what they are doing.
> Does that help?
Definitely.
> (So that's two votes for "suggests" from Biopython developers,
> but this is of course up to you guys as the Debian packaging
> experts.)
These are quite serious votes and beeing a packaging expert does not
necessary mean that you know your users needs as good as you should. So
I finally noticed that the package fits actually your suggestions -
probably Philipp Benner has reverted my initial change to Recommends
and so his changes scores another point for Suggests. So I'll leave
the package as it is now and I'm happy that we have talked about this
issue anyway.
Thanks for your opinions
Andreas.
--
http://fam-tille.de
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