[Debian-med-packaging] spades_3.6.2+dfsg-1_amd64.changes REJECTED

[Andreas Tille]

Hi folks,

On Sun, Feb 07, 2016 at 01:00:16PM +0000, Thorsten Alteholz wrote:
> please review your debian/copyright. Especially in ext/* I found lots of 
> files with missing licenses (GPL-3, MIT, Apache-2 ...).

I could either decide to work down this or work on the EDAM-DebTags
issue here in my last hours of Debian Med sprint.  I admit I feel my
time better spent with the latter and so I'll leave this for you
(Sascha, Afif?).

I injected a slight change into debian/watch with some new piece of
knowledge I gathered yesterday:

--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,3 @@
 version=3
-opts="downloadurlmangle=s{release([\d.]+)/}{release${1}/SPAdes-${1}.tar.gz},filenamemangle=s{release([\d.]+)/}{SPAdes-${1}.tar.gz},repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+opts="downloadurlmangle=s{release([\d.]+)/}{release${1}/SPAdes-${1}.tar.gz},filenamemangle=s{release([\d.]+)/}{SPAdes-${1}.tar.gz},repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
   http://spades.bioinf.spbau.ru/ release([\d.]+)/

which ensures xz compressed repackaged tarballs which sounds sensible
for larger upstream tarballs.
 
> Maybe you can also take care of:
>  W: spades: script-with-language-extension usr/bin/dipspades.py
>  W: spades: script-with-language-extension usr/bin/spades.py
>  W: spades: script-with-language-extension usr/bin/spades_init.py
>  W: spades: script-with-language-extension usr/bin/truspades.py
> concerns.

Regarding these remarks I would like to discuss something for the
package in general.  When I started in SVN with the spades package
I applied the following concept:

 - The binaries (which now end up in /usr/bin) were *not* installed
   to /usr/bin but rather to /usr/lib/spades/bin since as far as I
   understood upstream users are not supposed to call these directly.
 - Upstream has put the user interface into the *.py files - but
   these do not follow Debian policy - thus the warning.
 - Since you need to make sure the PATH is properly set for the
   Python scripts I used a wrapper anyway which looked like this

#!/bin/sh
PATH="/usr/lib/spades/bin:$PATH"
python /usr/lib/spades/bin/$0.py $@

   and put this script to /usr/bin/spades and link dispades, truspades
   and spades_init to this which should cover calling all the Python
   scripts

I remember that using this wrapper required some patching in the test
suite but it worked to some extend - at least the problem with the test
suite was not finding the executables in the first place.
   
I wonder whether you intend to (re)implement this approach to fulfill
ftpmaster(policy) request or whether you had your reasons to derive from
this and follow upstream more closely.

Kind regards

      Andreas.

-- 
http://fam-tille.de