[EMBOSS] EMBOSS 4.1.0 released

['Fernan Aguero']

+----[ Peter Rice <pmr at ebi.ac.uk> (08.Mar.2007 11:52):
|
| Ryan Golhar wrote:
| >I agree.  I was also expecting the version number on the tarballs to change
| >as well.  At the moment, there is no way to tell they were updated...
| 
| The embassy changes are all minor. We like to use the version numbers of 
| the original code so it is a little difficult to merge in the EMBOSS 
| version ... without making up a very long version number.
|
| Does anyone have strong preferences?
| 
| Peter
|
+----]

My original concern was about distfiles being renamed
without renaming the contained directories. That is a
separate problem from the other, long standing problem of
EMBASSY apps distifiles being re-rolled (with changes in
checksums) without version changes.


1. The problem that appeared with the 4.1.0 release:

MEMENEW-0.1.0.tar.gz was renamed to MEME-0.1.0.tar.gz
but extracting MEME-0.1.0.tar.gz creates a new directory
named MEMENEW-0.1.0 (?)

The same happens with PHYLIP/PHYLIPNEW.

So, what is the correct name of this EMBASSY app?

I'd like to suggest that either 
i) the distfiles are renamed back to MEMENEW and PHYLIPNEW
or
ii) the directory contained within the tarball is renamed to
MEME AND PHYLIP, respectively.

That is to say, keep the same name everywhere. That's what
I'm suggesting for this first point.



2. The long standing problem with EMBASSY app versions:

I agree with Peter in that it is good to have a version
number that is in sync with the upstream sources. 

If the EMBASSY HMMER comes from HMMER-2.3.2 I'd like to see
this reflected in the filename.

But I'd also like to see reflected somewhere that this
particular set of embassy distfiles are in sync with a
particular version of EMBOSS.

Perhaps reorganizing the layout of the FTP directories so as
to have something like the following?

pub/EMBOSS/
  EMBOSS-3.0.0/
    EMBOSS-3.0.0.tar.gz
    EMBASSY/
      DOMAINATRIX-0.1.0.tar.gz
      ...
  EMBOSS-4.0.0/
    EMBOSS-4.0.0.tar.gz
    EMBASSY/
      DOMAINATRIX-0.1.0.tar.gz
      ...
  EMBOSS-4.1.0/
    EMBOSS-4.1.0.tar.gz
    EMBASSY/
      DOMAINATRIX-0.1.0.tar.gz
      ...

or something like

pub/EMBOSS/
  EMBOSS-3.0.0/
    EMBOSS-3.0.0.tar.gz
  EMBASSY-3.0.0/
    DOMAINATRIX-0.1.0.tar.gz
    ...
  EMBOSS-4.0.0/
    EMBOSS-4.0.0.tar.gz
  EMBASSY-4.0.0/
    DOMAINATRIX-0.1.0.tar.gz
    ...
  EMBOSS-4.1.0/
    EMBOSS-4.1.0.tar.gz
  EMBASSY-4.1.0/
    DOMAINATRIX-0.1.0.tar.gz
    ...

either way it's made clear that embassy apps are associated
with a certain emboss version. 


Another alternative is to add some number to the original
(upstream) version number that reflects this. As Peter says,
adding the emboss version number (4.1.0) might make for a
long version number ... but what about using the shared
library (libnucleus) major version number (4 in this case)?

Do the new embassy apps build and work fine against
emboss-4.0.0 (libnucleus is still at v4)?

Fernan