Pierre Gruet pushed to branch master at Debian Med / htsjdk
Commits: 7a5fc365 by Pierre Gruet at 2022-10-31T22:04:32+01:00 New upstream version 3.0.2+dfsg - - - - - f11d315c by Pierre Gruet at 2022-10-31T22:05:22+01:00 Update upstream source from tag 'upstream/3.0.2+dfsg' Update to upstream version '3.0.2+dfsg' with Debian dir 4cbaa96de4b65c671f27165093a63e0f0592d5e3 - - - - - 38c0a6f4 by Pierre Gruet at 2022-10-31T22:06:05+01:00 Refreshing patches - - - - - 83e969e3 by Pierre Gruet at 2022-10-31T22:06:57+01:00 Installing the javadoc in /usr/share/doc/libhtsjdk-java/ - - - - - b890d4b6 by Pierre Gruet at 2022-10-31T22:07:53+01:00 Updating the Lintian override related to embedded JS after a change in Lintian syntax - - - - - 538406b2 by Pierre Gruet at 2022-10-31T22:09:48+01:00 Updating the POM file and its signature - - - - - c9287029 by Pierre Gruet at 2022-10-31T22:10:42+01:00 Depending on libmjson-java - - - - - 12037018 by Pierre Gruet at 2022-10-31T22:11:38+01:00 Patching for json-simple is not needed anymore - - - - - 5f7d2bf0 by Pierre Gruet at 2022-10-31T22:13:17+01:00 Passing long instead of int in HtsCRAMCodec30And21QueryTest - - - - - b4b82f65 by Pierre Gruet at 2022-10-31T22:15:32+01:00 Excluding new tests requiring the network - - - - - b142879e by Pierre Gruet at 2022-10-31T22:15:43+01:00 Refreshing patches - - - - - 034b9e8e by Pierre Gruet at 2022-10-31T22:17:02+01:00 Refreshing changelog - - - - - 10d705e7 by Pierre Gruet at 2022-11-01T17:17:24+01:00 Deactivating testFlushNotSpammed which seems to be GC-dependent - - - - - b71473c1 by Pierre Gruet at 2022-11-01T17:17:43+01:00 Using rhino instead of nashorn as JS engine, to build against openjdk-17 - - - - - 75a2158d by Pierre Gruet at 2022-11-01T17:18:14+01:00 Updating changelog - - - - - f81d35ef by Pierre Gruet at 2022-11-01T17:19:02+01:00 Raising Standards version to 4.6.1 - - - - - 67b9b998 by Pierre Gruet at 2022-11-01T17:19:50+01:00 Reordering changelog - - - - - 21811dc2 by Pierre Gruet at 2022-11-01T17:38:05+01:00 Upload to experimental - - - - - 91def6a7 by Pierre Gruet at 2022-11-01T21:00:25+01:00 Adding missing DEP-3 headers to patches - - - - - 6790144c by Pierre Gruet at 2022-11-01T21:01:15+01:00 Updating changelog - - - - - 99d0f9e2 by Pierre Gruet at 2022-11-03T20:52:51+01:00 Forwarding patches - - - - - c3c6a7c7 by Pierre Gruet at 2022-11-03T20:55:06+01:00 Upload to unstable - - - - - 30 changed files: - + .github/workflows/tests.yml - .travis.yml - README.md - build.gradle - debian/changelog - debian/control - debian/htsjdk.pom - debian/htsjdk.pom.asc - debian/libhtsjdk-java-doc.javadoc - debian/libhtsjdk-java-doc.lintian-overrides - debian/libhtsjdk-java.classpath - debian/patches/120-fix-build.patch - + debian/patches/130-data-types-in-tests.patch - − debian/patches/130-use-json-simple-instead-of-mjson.patch - + debian/patches/140-skip-testFlushNotSpammed.patch - + debian/patches/150-use-rhino-as-JS-engine.patch - − debian/patches/80-2to3.patch - debian/patches/92-disable-testhttp.patch - debian/patches/series - scripts/explain_sam_flags.py - scripts/htsget-scripts/htsget_config.json - scripts/htsget-scripts/start-htsget-test-server.sh - scripts/install-samtools.sh - + src/main/java/htsjdk/annotations/BetaAPI.java - + src/main/java/htsjdk/annotations/InternalAPI.java - + src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.java - + src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java - + src/main/java/htsjdk/beta/codecs/package-info.java - + src/main/java/htsjdk/beta/codecs/reads/ReadsCodecUtils.java - + src/main/java/htsjdk/beta/codecs/reads/bam/BAMCodec.java The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/9c637b681a18bc9b953179d4447094eb45285b70...c3c6a7c73a8a1fa346070651ff23fe8885aa439b -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/9c637b681a18bc9b953179d4447094eb45285b70...c3c6a7c73a8a1fa346070651ff23fe8885aa439b You're receiving this email because of your account on salsa.debian.org.
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