[med-svn] [Git][med-team/figtree][master] 7 commits: Fix FTBFS with new jebl2

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / figtree


Commits:
f2c8c875 by Andreas Tille at 2020-08-05T18:59:32+02:00
Fix FTBFS with new jebl2

- - - - -
44800651 by Andreas Tille at 2020-08-05T18:59:44+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
0db783e5 by Andreas Tille at 2020-08-05T18:59:44+02:00
routine-update: debhelper-compat 13

- - - - -
fbd778d1 by Andreas Tille at 2020-08-05T18:59:48+02:00
routine-update: Add salsa-ci file

- - - - -
9839d4c4 by Andreas Tille at 2020-08-05T18:59:48+02:00
routine-update: Rules-Requires-Root: no

- - - - -
0d74461f by Andreas Tille at 2020-08-05T18:59:51+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

- - - - -
d8141b70 by Andreas Tille at 2020-08-05T19:02:07+02:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix_ftbfs.patch
- debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+figtree (1.4.4-5) unstable; urgency=medium
+
+  [ Sudip Mukherjee ]
+  * Fix FTBFS with new jebl2
+    Closes: #966878
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
+
+ -- Andreas Tille <tille at debian.org>  Wed, 05 Aug 2020 18:59:52 +0200
+
 figtree (1.4.4-4) unstable; urgency=medium
 
   * Do not Build-Depend libfreehep-graphics*


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
            Olivier Sallou <osallou at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                javahelper,
                default-jdk,
                ant,
@@ -14,10 +14,11 @@ Build-Depends: debhelper-compat (= 12),
                libjam-java (>= 0.1.20140824),
                libtrove-java,
                libitext5-java
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/figtree
 Vcs-Git: https://salsa.debian.org/med-team/figtree.git
 Homepage: http://tree.bio.ed.ac.uk/software/figtree/
+Rules-Requires-Root: no
 
 Package: figtree
 Architecture: all


=====================================
debian/patches/fix_ftbfs.patch
=====================================
@@ -0,0 +1,45 @@
+Description: Fix FTBFS
+ The recent update of jebl2 removed the 'IOException' and has also added
+ close() which needs to be overriden.
+
+Author: Sudip Mukherjee <sudipm.mukherjee at gmail.com>
+Bug-Debian: https://bugs.debian.org/966878
+Forwarded: no
+
+---
+
+--- figtree-1.4.4.orig/src/figtree/application/JSONTreeExporter.java
++++ figtree-1.4.4/src/figtree/application/JSONTreeExporter.java
+@@ -80,13 +80,13 @@ public class JSONTreeExporter implements
+      * @throws java.io.IOException
+      */
+     @Override
+-    public void exportTree(Tree tree) throws IOException {
++    public void exportTree(Tree tree) {
+         java.util.List<Tree> trees = new ArrayList<Tree>();
+         trees.add(tree);
+         exportTrees(trees);
+     }
+ 
+-    private void writeTrees(Collection<? extends Tree> trees) throws IOException {
++    private void writeTrees(Collection<? extends Tree> trees) {
+         int indent = 0;
+         int treeCount = 0;
+ 
+@@ -178,10 +178,15 @@ public class JSONTreeExporter implements
+     }
+ 
+     @Override
+-    public void exportTrees(Collection<? extends Tree> trees) throws IOException {
++    public void exportTrees(Collection<? extends Tree> trees) {
+         writeTrees(trees);
+     }
+ 
++    @Override
++    public void close() {
++        close();
++    }
++
+     final private String nameRegex = "^(\\w|-)+$";
+ 
+ 


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ fix_classpath_in_build_xml.patch
 fix_itext_api_change.patch
 fix_jebl.patch
 0009-add-batik-all.jar.patch
+fix_ftbfs.patch


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/rambaut/figtree/issues
+Bug-Submit: https://github.com/rambaut/figtree/issues/new
 Registry:
 - Name: SciCrunch
   Entry: SCR_008515
@@ -7,5 +9,5 @@ Registry:
   Entry: OMICS_04268
 - Name: conda:bioconda
   Entry: figtree
-Repository: https://github.com/rambaut/figtree
+Repository: https://github.com/rambaut/figtree.git
 Repository-Browse: https://github.com/rambaut/figtree



View it on GitLab: https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389

-- 
View it on GitLab: https://salsa.debian.org/med-team/figtree/-/compare/a6560d091237e79b1ab394c7d45122f86fceebd5...d8141b70fca82fc6dc84e34303f3fa76d28c7389
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