[Debian-med-packaging] Distribution of MEME source code

[James Johnson]

Hi Debian Med team,

Sorry for the slow reply I thought someone else from the mailing list 
had already replied.

On 18/01/13 01:34, Andreas Tille wrote:
> Hi,
>
> thanks to Faheem Mitha who did some investigation whom to contact about
> wishes of the Debian Med packaging team we've got this e-mail address.
> We are not yet dived very deeply into MEME packaging but there was some
> first effort done by Soon Gweon and we would like to continue from his
> work to finally get MEME packaged for Debian on one hand for the users
> but hopefully also for you as authors to make your life to distribute
> MEME more easy.
>
> We stumbled upon different things but lets split this over different
> e-mails and concentrate on the first issue: obtaining the source.
> Debian has an automatic way to detect and download new upstream versions
> (via a script `uscan` that parses a `watch` file.)  In this `watch`
> file you can basically specify a string with the download URL where
> the version is represented as regular expression.
>
> In the case of MEME this system is spoiled because you are using
> versioned directories on your ftpserver and we can only specify the
> version once for the download tarball.  (Well, we have some dirty
> mangling tricks but to the best of my knowledge none of these will
> really work here.)
>
> We guess the motivation for your directory layout is the other issue
> that is causing problems:  The way you are distributing incremental
> changes to the source via patches.  This is totally out of reach for
> uscan and we do not see any automatic way to handle this.  But finally
> we are somehow bound to get automatic notification about new versions
> (we can not handle 200+x packages by manually visiting all these
> homepages.)
>
> I somehow guess one reason for your versioned directories is the habit
> of using those patches - so lets talk about these patches first and see
> whether everything might come to an easy solution.  IMHO, there is no
> real profit for any user - neither for those who directly build MEME
> from source nor for any distribution be it Debian, other Linux distro or
> BSD - to have this manual step to add a series of patches.  I admit it
> might safe some disk space / band width at your side but these days it
> should be no big deal.  May be dropping some really old versions from
> your ftpsite should solve the disk space issue and we in turn try to
> solve the band width issue by providing MEME from Debian (and thus also
> Ubuntu + derivatives) mirrors.
>
> In short: I would like to suggest to drop the patches approach and
> rather provide fully patched source tarballs by making the patchlevel
> an additional micro version.  For instance the latest MEME version
> would be 4.9.0.2 (with patch_4.9.0_1 and patch_4.9.0_2 applied).
>
> To come back to the directory layout the uniquely versioned source
> tarballs would now enable a flat structure where all MEME source
> tarballs could nicely fit into a single directory.  Uscan can easily
> pick the latest version from such versioned tarball collections.
>
> In case you have some other motivation for this kind of layout there is
> another option with some minimum additional effort from your side: You
> could maintain some HTML page (even automatically created by browsing
> your ftp directory) or some Wiki page which lists either all available
> version or just links to the latest version.  Uscan could be pointed
> to this link collection as well and drain the needed information from
> there (in case the latest version is somehow explicitly specified.
>
> I hope this longish explanation was not to boring for you and that
> you was able to make some sense out of it.  Please let us know what
> you think about this.
The current organization of the tar balls is not ideal. It's mainly that 
way because we moved to the EBI FTP server in a hurry while the 
meme.nbcr.net server was down and they just copyied the directory 
structure I had setup on my pre-release distribution server ( 
http://research.imb.uq.edu.au/~j.johnson/ ) hence while all the folders 
are named rc (release candidate). The original plan was to keep the 
official downloads at NBCR when they recovered their server but they've 
since told us they do not want to host the files as it is not part of 
their "mission statement" (*sigh*).

So now the official server is EBI's FTP site ( 
ftp://ftp.ebi.edu.au/pub/software/MEME/ ). While I'm based in the same 
building as the EBI team I (or anyone else on the MEME Suite team) don't 
have direct access to their servers so unfortunately re-organising the 
folder structure will require some back and forth with them. When I 
manage that I will also be making a HTML listing with links to the 
releases because I want to link it from the updated menu of our next 
full release. If you want I can also make a extra simplified version to 
help with your automated update system.

I'd be happy to create a tar ball release for each patch release but 
we'd still probably release the patches as well because it does make 
updating servers running MEME slightly easier.

~James

>
> Kind regards and thanks for providing MEME
>
>       Andreas.
>