debian/changelog

+libpal-java (1.5.1+dfsg-4) unstable; urgency=medium
+
+  * Official homepage seems to have vanished, point watch file to Github
+    mirror
+  * Fix broken encodings in some Java files
+    Closes: #893275
+  * Standards-Version: 4.1.3
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Sun, 18 Mar 2018 07:16:54 +0100
+
 libpal-java (1.5.1+dfsg-2) unstable; urgency=medium
 
   * Add Class file that is contained in pal source code copy

debian/compat

-9
+11

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: java
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                javahelper
 Build-Depends-Indep: default-jdk,
                      ant
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libpal-java.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libpal-java.git
 Homepage: http://www.cebl.auckland.ac.nz/pal-project/

debian/copyright

@@ -2,6 +2,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PAL (Phylogenetic Analysis Library)
 Upstream-Contact: Matthew Goode <m.goode@auckland.ac.nz>
 Source: http://www.cebl.auckland.ac.nz/pal-project/
+        Mirror: https://github.com/tamuri/pal/
 Files-Excluded:
     src/org
     doc/COPYRIGHT-org.w3c.dom.html

debian/patches/fix_encoding.patch

+Description: Fix broken encodings in some Java files
+  Strangely enough without this patch grep consideres the files in question
+  as "binary data files"
+Bug-Debian: https://bugs.debian.org/893275
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 18 Mar 2018 07:13:23 +0100
+
+--- a/src/pal/distance/PairwiseDistance.java
++++ b/src/pal/distance/PairwiseDistance.java
+@@ -201,7 +201,7 @@ public class PairwiseDistance implements
+ 			of.setSequences(s1, s2);
+ 			if (start > BranchLimits.MAXARC || start < BranchLimits.MINARC)
+ 			{
+-				// Dont use start value
++				// Don't use start value
+ 				dist = um.findMinimum(of, BranchLimits.FRACDIGITS);
+ 			}
+ 			else
+--- a/src/pal/math/UnivariateMinimum.java
++++ b/src/pal/math/UnivariateMinimum.java
+@@ -298,7 +298,7 @@ public class UnivariateMinimum
+ 			}
+ 			double u = b - ((b - c) * q - (b - a) * r) / 2.0 / (q - r);
+ 			u = constrain(u, searchToMax, min, max);
+-			double fu = 0; // Dont evaluate now
++			double fu = 0; // Don't evaluate now
+ 
+ 			boolean magnify = false;
+ 
+--- a/src/pal/treesearch/UnrootedMLSearcher.java
++++ b/src/pal/treesearch/UnrootedMLSearcher.java
+@@ -15,7 +15,7 @@ package pal.treesearch;
+  * Even given the offsourcing of code this class is rather large!
+  * Includes the algorithm of [1]
+  * </p>
+- * [1]  Guindon, Stphane  Gascuel, Olivier (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology 52:5 pages  696 - 704 / October 2003
++ * [1]  Guindon, Stephane  Gascuel, Olivier (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology 52:5 pages  696 - 704 / October 2003
+  * @author Matthew Goode
+  * @version 1.0
+  */
+@@ -2805,4 +2805,4 @@ public class UnrootedMLSearcher implemen
+ 		public int getNumberOfStates() { return numberOfStates_; }
+ 		public int getNumberOfTransitionCategories() { return numberOfCategories_; }
+ 	}
+-}
+\ No newline at end of file
++}

debian/patches/series

 TransitionProbability.patch
+fix_encoding.patch

debian/watch

-version=3
+version=4
 
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
-  http://www.cebl.auckland.ac.nz/pal-project/download.html bin/pal-([.\d]+)-src\.zip
+#opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+#  http://www.cebl.auckland.ac.nz/pal-project/download.html bin/pal-([.\d]+)-src\.zip
+
+# official homepage above vanished - hope this mirror will stay in sync
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+   https://github.com/tamuri/pal/releases .*/archive/v@ANY_VERSION@@ARCHIVE_EXT@