[med-svn] [Git][med-team/profbval][master] 5 commits: Stop using pp_popcon

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / profbval


Commits:
c7179c68 by Andreas Tille at 2022-01-18T21:21:23+01:00
Stop using pp_popcon

- - - - -
52037d54 by Andreas Tille at 2022-01-18T21:22:02+01:00
Upstream download vanished

- - - - -
b8b175a6 by Andreas Tille at 2022-01-18T21:22:29+01:00
routine-update: Standards-Version: 4.6.0

- - - - -
a879645b by Andreas Tille at 2022-01-18T21:22:34+01:00
Add missing build dependency on dh addon.

Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html

- - - - -
f162ea60 by Andreas Tille at 2022-01-18T21:23:44+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/README.test
- debian/changelog
- debian/control
- + debian/patches/no_pp-popcon.patch
- + debian/patches/series
- debian/watch


Changes:

=====================================
debian/README.test
=====================================
@@ -7,17 +7,6 @@ This package can be tested by executing
 
 in order to confirm its integrity.
 
-This test can write to stderr following message:
-
-    Can't exec "pp_popcon_cnt": No such file or directory at /usr/bin/profbval line 6. 
-    The Rost Lab recommends you install the pp-popularity-contest package that 
-    provides pp_popcon_cnt:
-
-    sudo apt-get install pp-popularity-contest
-
-This appears when associated package named `pp-popularity-contest` is not 
-installed. Other output to stderr must be absent.
-
 To test manually, cd to some dir where you have write permissions and do
  
     cp -a /usr/share/doc/profbval/examples/* .


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+profbval (1.0.22-8) unstable; urgency=medium
+
+  * Stop using pp_popcon
+  * Upstream download vanished
+  * Standards-Version: 4.6.0 (routine-update)
+  * Add missing build dependency on dh addon.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 18 Jan 2022 21:22:48 +0100
+
 profbval (1.0.22-7) unstable; urgency=medium
 
   * Standards-Version: 4.5.1 (routine-update)


=====================================
debian/control
=====================================
@@ -6,8 +6,9 @@ Uploaders: Laszlo Kajan <lkajan at rostlab.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               perl
-Standards-Version: 4.5.1
+               perl,
+               debhelper
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/profbval
 Vcs-Git: https://salsa.debian.org/med-team/profbval.git
 Homepage: https://www.rostlab.org/owiki/index.php/PROFbval
@@ -21,7 +22,6 @@ Depends: ${perl:Depends},
 Recommends: blast2,
             librg-utils-perl,
             profphd
-Suggests: pp-popularity-contest
 Description: predictor of flexible/rigid protein residues from sequence
  PROFbval can be useful for both protein structure and
  function predictions. For instance, a biologist can locate potentially


=====================================
debian/patches/no_pp-popcon.patch
=====================================
@@ -0,0 +1,27 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 18 Jan 2022 19:02:40 +0100
+Description: Stop using pp_popcon
+
+--- a/profbval
++++ b/profbval
+@@ -2,9 +2,6 @@
+ use File::Temp;
+ use Carp qw |croak cluck|;
+ 
+-# popularity contest
+-if( system('pp_popcon_cnt', '-p', 'profbval') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }
+-
+ $mode=1;
+ if (@ARGV<6)  {
+ 	die "\nUsage: $0 [fasta] [prof] [hssp] [output_file] [window] [mode] [debug]\n"; ### target_name will be a random variable Nov 29 2009
+--- a/profbval.spec
++++ b/profbval.spec
+@@ -9,7 +9,7 @@ URL: http://rostlab.org/
+ BuildArch: noarch
+ BuildRoot: %{_tmppath}/%{name}-%{version}-root
+ BuildRequires: perl
+-Requires: librg-utils-perl, pp-popularity-contest, profnet-bval
++Requires: librg-utils-perl, profnet-bval
+ 
+ %description
+  PROFbval is a neural-network based trained on backbone B-value data from X-ray structure. PROFbval 


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+no_pp-popcon.patch


=====================================
debian/watch
=====================================
@@ -1,2 +1,4 @@
 version=4
-opts=pasv ftp://rostlab.org/profbval/profbval-([0-9.]+)\.tar\.gz
+opts=dversionmangle=s/.*/0.No-Site/ \
+https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz
+



View it on GitLab: https://salsa.debian.org/med-team/profbval/-/compare/7e6a9333aa4652a1330dd48cd607d3fdac80ae9a...f162ea60142bb4f02aa553fbda9d02e08edba708

-- 
View it on GitLab: https://salsa.debian.org/med-team/profbval/-/compare/7e6a9333aa4652a1330dd48cd607d3fdac80ae9a...f162ea60142bb4f02aa553fbda9d02e08edba708
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