debian/changelog

 profphd (1.0.42-4) UNRELEASED; urgency=medium
 
   * pp-popularity-contest only suggested
-
- -- Andreas Tille <tille@debian.org>  Thu, 18 Oct 2018 13:06:42 +0200
+  * Do not force users to install pp-popularity-contest
+    Closes: #942064
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Drop useless get-orig-source target
+  * Remove trailing whitespace in debian/changelog
+  * Trim trailing whitespace.
+  * Use secure URI in Homepage field.
+  * Remove obsolete fields Name from debian/upstream/metadata.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 10 Oct 2019 22:23:45 +0200
 
 profphd (1.0.42-3) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -4,13 +4,13 @@ Uploaders: Laszlo Kajan <lkajan@rostlab.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                perl,
                rsync
-Standards-Version: 4.1.5
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/profphd
 Vcs-Git: https://salsa.debian.org/med-team/profphd.git
-Homepage: http://predictprotein.org/
+Homepage: https://predictprotein.org/
 
 Package: profphd
 Architecture: all

debian/patches/6_no_pp_popcon_cnt.patch

+Description: Do not force users to install pp-popularity-contest
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 10 Oct 2019 22:23:45 +0200
+
+--- a/src/prof/prof.pl
++++ b/src/prof/prof.pl
+@@ -12,7 +12,7 @@
+ no warnings 'deprecated';
+ 
+ # popularity contest
+-if( system('pp_popcon_cnt', '-p', 'prof') == -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"); }
++# if( system('pp_popcon_cnt', '-p', 'prof') == -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"); }
+ 
+ # ---------------------------------------------------------------------------- #
+ # change to port (install) program:                                            #
+--- a/src/prof/embl/phd.pl
++++ b/src/prof/embl/phd.pl
+@@ -13,7 +13,7 @@ no warnings 'deprecated';
+ #------------------------------------------------------------------------------#
+ 
+ # popularity contest
+-{ if( system('pp_popcon_cnt', '-p', 'phd.pl') == -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"); } }
++# { if( system('pp_popcon_cnt', '-p', 'phd.pl') == -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"); } }
+ 
+ # ---------------------------------------------------------------------------- #
+ # change to port (install) program:                                            #

debian/patches/series

@@ -3,3 +3,4 @@
 3_fix_indexing.patch
 4_fix_negative_repeat_count.patch
 5_fix_regex_warning.patch
+6_no_pp_popcon_cnt.patch

debian/rules

@@ -9,7 +9,3 @@ include /usr/share/dpkg/default.mk
 
 override_dh_auto_install:
 	make prefix=/usr DESTDIR=$(CURDIR)/debian/$(DEB_SOURCE)/ install
-
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs

debian/upstream/metadata

-Name: profphd
 Reference:
 - Author: Rost, B. and Sander, C.
-   Title: >
-    Combining evolutionary information and neural networks to predict
-    protein secondary structure.
+  Title: "Combining evolutionary information and neural networks to predict protein\
+    \ secondary structure.\n"
   Journal: Proteins
   Volume: 19
   Number: 1
@@ -12,9 +10,7 @@ Reference:
   URL: http://www.ncbi.nlm.nih.gov/pubmed/8066087
   PMID: 8066087
 - Author: Rost, B. and Sander, C.
-   Title: >
-    Conservation and prediction of solvent accessibility in protein
-    families.
+  Title: "Conservation and prediction of solvent accessibility in protein families.\n"
   Journal: Proteins
   Volume: 20
   Number: 3
@@ -23,8 +19,7 @@ Reference:
   URL: http://www.ncbi.nlm.nih.gov/pubmed/7892171
   PMID: 7892171
 - Author: Rost, B. and Casadio, R. and Fariselli, P. and Sander, C.
-   Title: >
-    Transmembrane helices predicted at 95% accuracy.
+  Title: "Transmembrane helices predicted at 95% accuracy.\n"
   Journal: Protein Sci
   Volume: 4
   Number: 3