debian/changelog

-primer3 (2.4.0-1) UNRELEASED; urgency=medium
+primer3 (2.4.0-1) unstable; urgency=medium
 
   * New upstream version
   * Secure URI in watch file
+  * Standards-Version: 4.1.3
+  * debhelper 11
 
- -- Andreas Tille <tille@debian.org>  Wed, 21 Feb 2018 09:01:27 +0100
+ -- Andreas Tille <tille@debian.org>  Wed, 21 Feb 2018 09:21:42 +0100
 
 primer3 (2.3.7-5) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -5,8 +5,8 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.0
+Build-Depends: debhelper (>= 11)
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/primer3.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/primer3.git
 Homepage: http://primer3.sourceforge.net

debian/patches/hardening.patch

@@ -15,7 +15,7 @@ Description: Propagate hardening options
  # Note, for profiling, use
  # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
  
-@@ -163,7 +163,7 @@ $(NTTHAL_EXE): thal_main.o thal.o
+@@ -175,7 +175,7 @@ $(NTTHAL_EXE): thal_main.o thal.o
  	$(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
  
  $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)

debian/patches/primer_thermodynamic_parameters_path_2_etc.patch

@@ -8,7 +8,7 @@ Description: Configuration in /etc
 
 --- a/src/primer3_boulder_main.c
 +++ b/src/primer3_boulder_main.c
-@@ -505,18 +505,18 @@ read_thermodynamic_parameters()
+@@ -539,18 +539,18 @@ read_thermodynamic_parameters()
        return;
      }
  #else
@@ -46,7 +46,7 @@ Description: Configuration in /etc
         fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n");
 --- a/src/release_notes.txt
 +++ b/src/release_notes.txt
-@@ -218,9 +218,9 @@ defaults.  The default is --default_vers
+@@ -272,9 +272,9 @@ defaults.  The default is --default_vers
  1.5 IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1,
  PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location.
  This tag specifies the path to the directory that contains all the
@@ -58,26 +58,23 @@ Description: Configuration in /etc
  there is only one default location: .\primer3_config\.  If the the
  parameter files are not in one these locations, be sure to set
  PRIMER_THERMODYNAMIC_PARAMETERS_PATH
---- a/primer3_manual.htm
-+++ b/primer3_manual.htm
-@@ -229,9 +229,9 @@ defaults.  The default is --default_vers
- 2.5. IMPORTANT: because <a href="#PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT">PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT</a>=1,
- <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a> must point to the right location.
+--- a/src/primer3_manual.htm
++++ b/src/primer3_manual.htm
+@@ -222,7 +222,7 @@ defaults.  The default is --default_vers
  This tag specifies the path to the directory that contains all the
--parameter files used by the thermodynamic approach. In Linux, there
-+parameter files used by the thermodynamic approach. In Debian, there
+ parameter files used by the thermodynamic approach. In Linux, there
  are two *default* locations that are tested if this tag is not
 -defined: ./primer3_config/ and /opt/primer3_config/. For Windows,
 +defined: ./primer3_config/ and /etc/primer3_config/. For Windows,
  there is only one default location: .\primer3_config\.  If the the
  parameter files are not in one these locations, be sure to set
  <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a>.<br>
-@@ -2452,7 +2452,7 @@ the propensity of oligos to anneal to un
+@@ -2082,7 +2082,7 @@ the propensity of oligos to anneal to un
  <p>This tag specifies the path to the directory that contains all the
  parameter files used by the thermodynamic approach. In Linux, there are two
- default locations that are tested if this tag is not defined: 
+ default locations that are tested if this tag is not defined:
 -<i>./primer3_config/</i> and <i>/opt/primer3_config/</i>.
 +<i>./primer3_config/</i> and <i>/etc/primer3_config/</i>.
  For Windows, there is only one default location: <i>.\primer3_config\</i>.</p>
- 
- 
+ <h3><a name="PRIMER_MAX_SELF_ANY">PRIMER_MAX_SELF_ANY (decimal, 9999.99; default 8.00)</a></h3>
+ <p>PRIMER_MAX_SELF_ANY describes the tendency of a primer to bind to

debian/primer3.docs

-primer3_manual.htm
+src/primer3_manual.htm
 src/release_notes.txt
 debian/README.test

debian/rules

@@ -23,7 +23,7 @@ override_dh_installexamples:
 	mkdir -p $(sampledir)/src;
 	cp -aR ./test/* $(sampledir)/test;
 	cp -aR ./src/humrep_and_simple.txt $(sampledir)/src;
-	cp primer*.txt $(sampledir)/;
+	cp -a settings_files/primer*.txt $(sampledir)/;
 	chmod -x $(sampledir)/test/thal*;
 	sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(sampledir)/test/long_seq_tm_test.pl ;
 	sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(sampledir)/test/vgrep.pl ;