[med-svn] [Git][med-team/jebl2][master] 8 commits: Rewriting d/watch with version 5

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / jebl2


Commits:
e8416902 by Pierre Gruet at 2026-05-29T12:17:57+02:00
Rewriting d/watch with version 5

- - - - -
e4de1735 by Pierre Gruet at 2026-05-29T12:18:10+02:00
Removing Priority; optional, which is default

- - - - -
905064ca by Pierre Gruet at 2026-05-29T12:18:14+02:00
Removing R-R-R: no, which is default

- - - - -
76f6e026 by Pierre Gruet at 2026-05-29T12:18:24+02:00
Raising Standards version to 4.7.4

- - - - -
664633f1 by Pierre Gruet at 2026-05-29T12:18:35+02:00
New upstream version 0.1+git20231105.51da3b1
- - - - -
5fa1ad77 by Pierre Gruet at 2026-05-29T12:18:36+02:00
Update upstream source from tag 'upstream/0.1+git20231105.51da3b1'

Update to upstream version '0.1+git20231105.51da3b1'
with Debian dir e6cc405320417d1f859b97a7a5f375082224ce63
- - - - -
1841dd0d by Pierre Gruet at 2026-05-29T12:19:25+02:00
Updating changelog

- - - - -
28eb21b0 by Pierre Gruet at 2026-05-29T12:21:44+02:00
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/watch
- src/jebl/evolution/io/NewickImporter.java


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+jebl2 (0.1+git20231105.51da3b1-1) unstable; urgency=medium
+
+  * New upstream version 0.1+git20231105.51da3b1
+  * Raising Standards version to 4.7.4:
+    - Removing Priority; optional, which is default
+    - Removing R-R-R: no, which is default
+  * Rewriting d/watch with version 5
+
+ -- Pierre Gruet <pgt at debian.org>  Fri, 29 May 2026 12:21:37 +0200
+
 jebl2 (0.1+git20230701.b3c0f25-1) unstable; urgency=medium
 
   * New upstream version 0.1+git20230701.b3c0f25


=====================================
debian/control
=====================================
@@ -3,7 +3,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>,
            Pierre Gruet <pgt at debian.org>
 Section: java
-Priority: optional
 Build-Depends: debhelper-compat (= 13),
                javahelper
 Build-Depends-Indep: default-jdk,
@@ -11,8 +10,7 @@ Build-Depends-Indep: default-jdk,
                      libtrove-java,
                      libtrove-java-doc,
                      ant
-Standards-Version: 4.6.2
-Rules-Requires-Root: no
+Standards-Version: 4.7.4
 Vcs-Browser: https://salsa.debian.org/med-team/jebl2
 Vcs-Git: https://salsa.debian.org/med-team/jebl2.git
 Homepage: https://github.com/rambaut/jebl2


=====================================
debian/watch
=====================================
@@ -1,7 +1,9 @@
-version=4
+Version: 5
 
-opts="mode=git,pretty=0.1+git%cd.%h" \
-    https://github.com/rambaut/jebl2.git HEAD
+Source: https://github.com/rambaut/jebl2.git
+Matching-Pattern: HEAD
+Mode: git
+Git-Pretty: 0.1+git%cd.%h
 
 # Issue asking for release tags:
 # https://github.com/rambaut/jebl2/issues/5


=====================================
src/jebl/evolution/io/NewickImporter.java
=====================================
@@ -23,6 +23,8 @@ public class NewickImporter implements TreeImporter {
     private final ImportHelper helper;
     private boolean unquotedLabels;
 
+    private String lastLabel = null;
+
     /**
      * Constructor
      * @param reader  tree text
@@ -154,7 +156,7 @@ public class NewickImporter implements TreeImporter {
      */
     private Node readInternalNode(SimpleRootedTree tree) throws IOException, ImportException
     {
-        List<Node> children = new ArrayList<Node>();
+        List<Node> children = new ArrayList<>();
 
         // read the opening '('
         helper.readCharacter();
@@ -175,7 +177,7 @@ public class NewickImporter implements TreeImporter {
 
         // should have had a closing ')'
         if (helper.getLastDelimiter() != ')') {
-            throw new ImportException.BadFormatException("Missing closing ')' in tree");
+            throw new ImportException.BadFormatException("Missing closing ')' in tree" + (lastLabel != null ? " - after tip " + lastLabel : ""));
         }
 
         final Node node = tree.createInternalNode(children);
@@ -212,6 +214,7 @@ public class NewickImporter implements TreeImporter {
         if ("".equals(label)) {
             throw new ImportException.UnknownTaxonException("Emtpy node names are not allowed.");
         }
+        lastLabel = label;
         try {
             return tree.createExternalNode(Taxon.getTaxon(label));
         } catch (IllegalArgumentException e) {



View it on GitLab: https://salsa.debian.org/med-team/jebl2/-/compare/a223ac0a4555d63ef68eb1b3474464f7516f0ffb...28eb21b0f1a206fdec6114d80eb4919cec39b3c5

-- 
View it on GitLab: https://salsa.debian.org/med-team/jebl2/-/compare/a223ac0a4555d63ef68eb1b3474464f7516f0ffb...28eb21b0f1a206fdec6114d80eb4919cec39b3c5
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