[med-svn] [Git][med-team/libpal-java][master] 5 commits: Official homepage seems to have vanished, point watch file to Github mirror
Andreas Tille
gitlab at salsa.debian.org
Sun Mar 18 06:32:51 UTC 2018
Andreas Tille pushed to branch master at Debian Med / libpal-java
Commits:
56a51494 by Andreas Tille at 2018-03-18T07:06:22+01:00
Official homepage seems to have vanished, point watch file to Github mirror
- - - - -
89da7aa9 by Andreas Tille at 2018-03-18T07:15:39+01:00
Fix broken encodings in some Java files
- - - - -
be6fca48 by Andreas Tille at 2018-03-18T07:16:34+01:00
Standards-Version: 4.1.3
- - - - -
32332d9e by Andreas Tille at 2018-03-18T07:16:51+01:00
debhelper 11
- - - - -
13d33efc by Andreas Tille at 2018-03-18T07:32:36+01:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- + debian/patches/fix_encoding.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+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 at 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
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at 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
=====================================
--- a/debian/copyright
+++ b/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 at 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
=====================================
--- /dev/null
+++ b/debian/patches/fix_encoding.patch
@@ -0,0 +1,47 @@
+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 at 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
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
TransitionProbability.patch
+fix_encoding.patch
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,4 +1,8 @@
-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 at ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/libpal-java/compare/0cb60e2154e9316aa95b91cdacf37fa20891045d...13d33efc0733a8830ccbee611788c272ff52b386
---
View it on GitLab: https://salsa.debian.org/med-team/libpal-java/compare/0cb60e2154e9316aa95b91cdacf37fa20891045d...13d33efc0733a8830ccbee611788c272ff52b386
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