[med-svn] [Git][med-team/predictprotein][master] 7 commits: New upstream version 1.1.09

Andreas Tille gitlab at salsa.debian.org
Fri Aug 2 22:07:51 BST 2019 


Andreas Tille pushed to branch master at Debian Med / predictprotein


Commits:
863084e3 by Andreas Tille at 2019-08-02T21:05:09Z
New upstream version 1.1.09
- - - - -
42d840cd by Andreas Tille at 2019-08-02T21:05:09Z
Update upstream source from tag 'upstream/1.1.09'

Update to upstream version '1.1.09'
with Debian dir 53142784a0f471a138c2b42a2ab0152ecdf2a092
- - - - -
e83ad658 by Andreas Tille at 2019-08-02T21:05:09Z
New upstream version

- - - - -
cac22162 by Andreas Tille at 2019-08-02T21:05:09Z
debhelper-compat 12

- - - - -
c692abfe by Andreas Tille at 2019-08-02T21:05:19Z
Standards-Version: 4.4.0

- - - - -
1fa5b1d8 by Andreas Tille at 2019-08-02T21:05:20Z
Use secure URI in Homepage field.

Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.

- - - - -
772dbbde by Andreas Tille at 2019-08-02T21:05:47Z
Upload to unstable

- - - - -


8 changed files:

- ChangeLog
- MakefilePP.mk
- configure
- configure.ac
- debian/changelog
- − debian/compat
- debian/control
- predictprotein


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,11 @@
+predictprotein (1.1.09) unstable; urgency=low
+
+  * predbind(1) has been renamed to prona2019(1)
+  * prona2019(1) target and output file have been renamed from 
+    'predbind' to 'prona'
+
+ -- Timothy Karl <karl at rostlab.org>  Mon, 18 Mar 2019 15:57:00 +0100 
+
 predictprotein (1.1.08) unstable; urgency=low
 
   * Added predbind(1) prediction file handling.


=====================================
MakefilePP.mk
=====================================
@@ -59,10 +59,10 @@ PHDFILE:=$(INFILE:%.in=%.phdPred)
 PHDRDBFILE:=$(INFILE:%.in=%.phdRdb)
 # lkajan: never make PHDNOTHTMFILE a target - its creation depends on whether phd found an HTM region or not: it isn't always created
 PHDNOTHTMFILE:=$(INFILE:%.in=%.phdNotHtm)
-PREDBINDFILE:=$(INFILE:%.in=%.predbind)
 PROFFILE:=$(INFILE:%.in=%.profRdb)
 # prof output generated explicitely from one sequence - NO alignment - Chris Schaefer initiated this - B approved
 PROF1FILE:=$(INFILE:%.in=%.prof1Rdb)
+PRONAFILE:=$(INFILE:%.in=%.prona)
 # lkajan: 20120816: profasp is now removed (https://rostlab.org/bugzilla3/show_bug.cgi?id=154)
 ASPFILE:=$(INFILE:%.in=%.asp)
 NORSFILE:=$(INFILE:%.in=%.nors)
@@ -188,7 +188,7 @@ subcell-loc:
 #
 # Optional targets should never appear in other aggregate targets (such as 'interaction').
 .PHONY: optional
-optional: loctree3 metadisorder predbind psic tmhmm tmseg somena consurf
+optional: loctree3 metadisorder prona psic tmhmm tmseg somena consurf
 
 .PHONY: coiledcoils
 coiledcoils: $(COILSFILE)
@@ -395,12 +395,12 @@ $(PROFTEXTFILE): $(PROFFILE)
 	# conv_prof creates query.profAscii.tmp in case query.profAscii already exists - make sure it does not
 	rm -f $(PROFTEXTFILE); $(PROFROOT)scr/conv_prof.pl $< fileOut=$@ ascii nohtml nodet nograph
 
-.PHONY: predbind
-predbind: $(PREDBINDFILE)
+.PHONY: prona
+prona: $(PRONAFILE)
 
-# Predbind needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
-$(PREDBINDFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
-	predbind -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@
+# ProNA needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run
+$(PRONAFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)
+	prona2019 -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@
 
 .PHONY: metastudent
 metastudent: $(METASTUDENTBPO) $(METASTUDENTCCO) $(METASTUDENTMPO)
@@ -505,7 +505,7 @@ install:
 		$(NORSFILE) $(NORSSUMFILE) \
 		$(NORSNETFILE) \
 		$(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \
-        $(PREDBINDFILE) \
+		$(PRONAFILE) \
 		$(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \
 		$(PROFBVALFILE) $(PROFB4SNAPFILE) \
 		$(PROFTMBFILE) $(PROFTMBDATFILE) \


=====================================
configure
=====================================
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for predictprotein 1.1.08.
+# Generated by GNU Autoconf 2.69 for predictprotein 1.1.09.
 #
 # Report bugs to <https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='predictprotein'
 PACKAGE_TARNAME='predictprotein'
-PACKAGE_VERSION='1.1.08'
-PACKAGE_STRING='predictprotein 1.1.08'
+PACKAGE_VERSION='1.1.09'
+PACKAGE_STRING='predictprotein 1.1.09'
 PACKAGE_BUGREPORT='https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein'
 PACKAGE_URL=''
 
@@ -1202,7 +1202,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures predictprotein 1.1.08 to adapt to many kinds of systems.
+\`configure' configures predictprotein 1.1.09 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1268,7 +1268,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of predictprotein 1.1.08:";;
+     short | recursive ) echo "Configuration of predictprotein 1.1.09:";;
    esac
   cat <<\_ACEOF
 
@@ -1342,7 +1342,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-predictprotein configure 1.1.08
+predictprotein configure 1.1.09
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1359,7 +1359,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by predictprotein $as_me 1.1.08, which was
+It was created by predictprotein $as_me 1.1.09, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2223,7 +2223,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='predictprotein'
- VERSION='1.1.08'
+ VERSION='1.1.09'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2876,7 +2876,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by predictprotein $as_me 1.1.08, which was
+This file was extended by predictprotein $as_me 1.1.09, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2929,7 +2929,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-predictprotein config.status 1.1.08
+predictprotein config.status 1.1.09
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 


=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT([predictprotein], [1.1.08], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
+AC_INIT([predictprotein], [1.1.09], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])
 AC_CONFIG_SRCDIR([predictprotein])
 AM_INIT_AUTOMAKE
 AC_CONFIG_FILES([Makefile] [perl/Build.PL] [examples/Makefile] [helper_apps/Makefile] [resources/Makefile])


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+predictprotein (1.1.09-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Use secure URI in Homepage field.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 02 Aug 2019 23:05:22 +0200
+
 predictprotein (1.1.08-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -5,12 +5,12 @@ Uploaders: Guy Yachdav <gyachdav at rostlab.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libmodule-build-perl
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/predictprotein
 Vcs-Git: https://salsa.debian.org/med-team/predictprotein.git
-Homepage: http://www.predictprotein.org
+Homepage: https://www.predictprotein.org
 
 Package: predictprotein
 Architecture: all


=====================================
predictprotein
=====================================
@@ -75,8 +75,8 @@ our %meth_ext_hash = (
   phdNotHtm => 'phd',
   phdPred => 'phd',
   phdRdb => 'phd',
-  predbind => 'predbind',
   profAscii => 'prof',
+  prona => 'prona',
   reprof => 'reprof',
   profbval => 'profbval',
   profb4snap => 'profbval',
@@ -652,7 +652,7 @@ These methods are run by the target 'optional'.
  protein-RNA,           somena            somena                  somena(1)
  protein-DNA
   interaction sites
- DNA- , RNA- and        predbind          predbind                predbind(1)
+ DNA- , RNA- and        prona             prona                   prona2019(1)
   Protein-binding
   protein and binding
   sites



View it on GitLab: https://salsa.debian.org/med-team/predictprotein/compare/d5d9ec0d619867ca811ebd3c013a2c5572f96ddc...772dbbde2af65e812bbd22a5e2bbe96afffab172

-- 
View it on GitLab: https://salsa.debian.org/med-team/predictprotein/compare/d5d9ec0d619867ca811ebd3c013a2c5572f96ddc...772dbbde2af65e812bbd22a5e2bbe96afffab172
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