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 <[email protected]> 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 <[email protected]. Uploaders: Andreas Tille <[email protected]>, Pierre Gruet <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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