Michael R. Crusoe pushed to branch debian/unstable at Debian Med / iqtree
Commits: 62495702 by Michael R. Crusoe at 2026-04-11T14:53:10+02:00 New upstream location for legacy IQ-TREE version 2.x. Updated primary citation as well. - - - - - d6ed65af by Michael R. Crusoe at 2026-04-11T14:55:51+02:00 New upstream version - - - - - 84d2d54e by Michael R. Crusoe at 2026-04-11T14:55:52+02:00 New upstream version 2.4.0+dfsg - - - - - b13ded15 by Michael R. Crusoe at 2026-04-11T14:56:04+02:00 Update upstream source from tag 'upstream/2.4.0+dfsg' Update to upstream version '2.4.0+dfsg' with Debian dir 48178738441d6fc9eafe90ccc01f85d5faf6de3b - - - - - 71396415 by Michael R. Crusoe at 2026-04-11T14:56:05+02:00 Standards-Version: 4.7.4 (routine-update) - - - - - 7ce0a9fd by Michael R. Crusoe at 2026-04-11T14:56:11+02:00 Remove trailing whitespace in debian/changelog (routine-update) - - - - - 48ce76d6 by Michael R. Crusoe at 2026-04-11T14:56:20+02:00 debputy lint --auto-fix (routine-update) - - - - - b6670245 by Michael R. Crusoe at 2026-04-11T15:00:21+02:00 d/patches: refreshed, dropped 2 no-longer needed: boost1.90 & gcc- 15. - - - - - e871ad21 by Michael R. Crusoe at 2026-04-11T15:32:43+02:00 d/watch: download using git, due to submodules. - - - - - 29cc275f by Michael R. Crusoe at 2026-04-11T15:33:43+02:00 New upstream version 2.4.0+dfsg - - - - - 421f9fe8 by Michael R. Crusoe at 2026-04-11T15:33:55+02:00 Update upstream source from tag 'upstream/2.4.0+dfsg' Update to upstream version '2.4.0+dfsg' with Debian dir f8f2ec89cb9558a4b02e454699d6845a0f250ebe - - - - - 2437648c by Michael R. Crusoe at 2026-04-11T15:39:42+02:00 refresh cmake patch - - - - - 0c071cb5 by Michael R. Crusoe at 2026-04-11T16:35:23+02:00 Added patch to use googletest, yaml-cpp, & SIMDe packages. - - - - - e951cb72 by Michael R. Crusoe at 2026-04-11T17:02:40+02:00 d/rules: add openmpi include path - - - - - 512 changed files: - CMakeLists.txt - + CMakeSettings.json - + CODE_OF_CONDUCT.md - README.md - alignment/CMakeLists.txt - alignment/alignment.cpp - alignment/alignment.h - alignment/alignmentpairwise.cpp - alignment/alignmentpairwise.h - + alignment/alignmentsummary.cpp - + alignment/alignmentsummary.h - alignment/maalignment.cpp - alignment/pattern.cpp - alignment/pattern.h - + alignment/sequence.cpp - + alignment/sequence.h - + alignment/sequencechunkstr.cpp - + alignment/sequencechunkstr.h - + alignment/substitution.cpp - + alignment/substitution.h - alignment/superalignment.cpp - alignment/superalignment.h - alignment/superalignmentpairwise.cpp - alignment/superalignmentpairwise.h - alignment/superalignmentpairwiseplen.cpp - alignment/superalignmentunlinked.cpp - booster/booster.c - booster/tree.c - booster/tree.h - booster/version.h - + cmaple/.github/workflows/ci.yaml - + cmaple/.gitignore - + cmaple/CMakeLists.txt - + cmaple/CMakeSettings.json - + cmaple/CMapleLib.md - + cmaple/CODE_OF_CONDUCT.md - + cmaple/CONTRIBUTING.md - + cmaple/LICENSE - + cmaple/README.md - + cmaple/alignment/CMakeLists.txt - + cmaple/alignment/alignment.cpp - + cmaple/alignment/alignment.h - + cmaple/alignment/mutation.cpp - + cmaple/alignment/mutation.h - + cmaple/alignment/seqregion.cpp - + cmaple/alignment/seqregion.h - + cmaple/alignment/seqregions.cpp - + cmaple/alignment/seqregions.h - + cmaple/alignment/sequence.cpp - + cmaple/alignment/sequence.h - + cmaple/cmaple.doxy - + cmaple/cmaple_config.h.in - + cmaple/example/example.maple - + cmaple/example/input.fa - + cmaple/example/input.phy - + cmaple/example/ref.fa - + cmaple/example/test_100.maple - + cmaple/example/test_5K.maple - + cmaple/example/tree.nwk - + cmaple/layout.xml - + cmaple/layout.xml.bak - + cmaple/libraries/ncl/CMakeLists.txt - + cmaple/libraries/ncl/ncl.h - + cmaple/libraries/ncl/nxsblock.cpp - + cmaple/libraries/ncl/nxsblock.h - + cmaple/libraries/ncl/nxsdefs.h - + cmaple/libraries/ncl/nxsexception.cpp - + cmaple/libraries/ncl/nxsexception.h - + cmaple/libraries/ncl/nxsindent.h - + cmaple/libraries/ncl/nxsreader.cpp - + cmaple/libraries/ncl/nxsreader.h - + cmaple/libraries/ncl/nxsstring.cpp - + cmaple/libraries/ncl/nxsstring.h - + cmaple/libraries/ncl/nxstoken.cpp - + cmaple/libraries/ncl/nxstoken.h - + cmaple/libraries/nclextra/CMakeLists.txt - + cmaple/libraries/nclextra/modelsblock.cpp - + cmaple/libraries/nclextra/modelsblock.h - + cmaple/libraries/nclextra/myreader.h - + cmaple/main/CMakeLists.txt - + cmaple/main/main.cpp - + cmaple/maple/CMakeLists.txt - + cmaple/maple/cmaple.cpp - + cmaple/maple/cmaple.h - + cmaple/model/CMakeLists.txt - + cmaple/model/model.cpp - + cmaple/model/model.h - + cmaple/model/model_aa.cpp - + cmaple/model/model_aa.h - + cmaple/model/model_aa.nexus - + cmaple/model/model_dna.cpp - + cmaple/model/model_dna.h - + cmaple/model/modelbase.cpp - + cmaple/model/modelbase.h - + cmaple/tree/CMakeLists.txt - + cmaple/tree/altbranch.h - + cmaple/tree/internal.h - + cmaple/tree/leaf.h - + cmaple/tree/phylonode.cpp - + cmaple/tree/phylonode.h - + cmaple/tree/rootcandidate.h - + cmaple/tree/traversingnode.cpp - + cmaple/tree/traversingnode.h - + cmaple/tree/tree.cpp - + cmaple/tree/tree.h - + cmaple/tree/updatingnode.cpp - + cmaple/tree/updatingnode.h - + cmaple/unittest/CMakeLists.txt - + cmaple/unittest/alignment_test.cpp - + cmaple/unittest/cmaple_test.cpp - + cmaple/unittest/matrix_test.cpp - + cmaple/unittest/model_test.cpp - + cmaple/unittest/mutation_test.cpp - + cmaple/unittest/phylonode_test.cpp - + cmaple/unittest/seqregion_test.cpp - + cmaple/unittest/seqregions_test.cpp - + cmaple/unittest/sequence_test.cpp - + cmaple/utils/CMakeLists.txt - + cmaple/utils/gzstream.cpp - + cmaple/utils/gzstream.h - + cmaple/utils/logstream.cpp - + cmaple/utils/logstream.h - + cmaple/utils/matrix.h - + cmaple/utils/operatingsystem.cpp - + cmaple/utils/operatingsystem.h - + cmaple/utils/timeutil.h - + cmaple/utils/tools.cpp - + cmaple/utils/tools.h - debian/changelog - debian/control - debian/copyright - − debian/patches/boost1.90.patch - debian/patches/cmake-4.patch - + debian/patches/find-libs - − debian/patches/gcc-15.patch - debian/patches/series - debian/rules - debian/upstream/metadata - debian/watch - + example/custom_distributions.txt - + example/tree.nwk - + flake.lock - + flake.nix - + iqtree.doxy - + lsd2/CMakeLists.txt - + lsd2/LICENSE - + lsd2/NEWS - + lsd2/README.md - + lsd2/examples/fig/ex.png - + lsd2/examples/rooted_tree/h1n1.date - + lsd2/examples/rooted_tree/h1n1_flexible.date - + lsd2/examples/rooted_tree/h1n1_partition - + lsd2/examples/rooted_tree/h1n1_phyml.tree - + lsd2/examples/rooted_tree/h1n1_phyml.tree.result - + lsd2/examples/unrooted_tree_with_outgroups/h1n1.date - + lsd2/examples/unrooted_tree_with_outgroups/h1n1_outgroup.txt - + lsd2/examples/unrooted_tree_with_outgroups/h1n1_phyml.tree - + lsd2/examples/unrooted_tree_without_outgroups/Dengue.date - + lsd2/examples/unrooted_tree_without_outgroups/Dengue.phy_phyml_tree.txt - + lsd2/src/confidence_interval.cpp - + lsd2/src/confidence_interval.h - + lsd2/src/date.h - + lsd2/src/dating.cpp - + lsd2/src/dating.h - + lsd2/src/estimate_root.cpp - + lsd2/src/estimate_root.h - + lsd2/src/lsd.cpp - + lsd2/src/lsd.h - + lsd2/src/makefile - + lsd2/src/node.h - + lsd2/src/options.cpp - + lsd2/src/options.h - + lsd2/src/outliers.cpp - + lsd2/src/outliers.h - + lsd2/src/pair.h - + lsd2/src/part.h - + lsd2/src/pr.h - + lsd2/src/readData.cpp - + lsd2/src/readData.h - + lsd2/src/subtree.h - + lsd2/src/utils.cpp - + lsd2/src/utils.h - main/CMakeLists.txt - + main/alisim.cpp - + main/alisim.h - main/main.cpp - main/phyloanalysis.cpp - main/phyloanalysis.h - main/phylotesting.cpp - main/phylotesting.h - + main/terraceanalysis.cpp - + main/terraceanalysis.h - main/timetree.cpp - main/treetesting.cpp - main/treetesting.h - model/CMakeLists.txt - model/modelbin.cpp - model/modelbin.h - model/modelcodon.cpp - model/modelcodon.h - model/modeldna.cpp - model/modeldna.h - + model/modeldnaerror.cpp - + model/modeldnaerror.h - model/modelfactory.cpp - model/modelfactory.h - model/modelfactorymixlen.cpp - + model/modelhmm.cpp - + model/modelhmm.h - + model/modelhmmgm.cpp - + model/modelhmmgm.h - + model/modelhmmtm.cpp - + model/modelhmmtm.h - model/modelliemarkov.cpp - model/modelliemarkov.h - model/modelmarkov.cpp - model/modelmarkov.h - model/modelmixture.cpp - model/modelmixture.h - model/modelmorphology.cpp - model/modelmorphology.h - model/modelpomo.cpp - model/modelpomo.h - model/modelpomomixture.cpp - model/modelpomomixture.h - model/modelprotein.cpp - model/modelprotein.h - model/modelset.cpp - model/modelset.h - model/modelsubst.cpp - model/modelsubst.h - model/modelunrest.cpp - model/modelunrest.h - model/partitionmodel.cpp - model/partitionmodel.h - model/partitionmodelplen.cpp - + model/ratecontinuousgamma.cpp - + model/ratecontinuousgamma.h - + model/ratecontinuousgammainvar.cpp - + model/ratecontinuousgammainvar.h - model/ratefree.cpp - model/ratefree.h - model/ratefreeinvar.cpp - model/ratefreeinvar.h - model/rategamma.cpp - model/rategammainvar.cpp - model/rateheterogeneity.h - model/rateheterotachy.cpp - model/rateinvar.cpp - model/rateinvar.h - model/ratekategory.cpp - model/ratemeyerdiscrete.cpp - model/ratemeyerhaeseler.cpp - ncl/ncl.h - ncl/nxsblock.h - ncl/nxscharactersblock.cpp - ncl/nxscharactersblock.h - ncl/nxsdefs.h - ncl/nxsexception.cpp - ncl/nxsexception.h - ncl/nxsindent.h - ncl/nxsstring.cpp - ncl/nxsstring.h - ncl/nxstaxablock.h - ncl/nxstoken.h - nclextra/msetsblock.h - nclextra/myreader.h - pda/ecopd.cpp - pda/pdnetwork.cpp - pda/splitgraph.h - phylo-yaml/statespace.cpp - phylo-yaml/statespace.h - pll/avxLikelihood.c - pll/bipartitionList.c - pll/cycle.h - pll/evaluateGenericSpecial.c - pll/evaluatePartialGenericSpecial.c - pll/fastDNAparsimony.c - pll/genericParallelization.c - pll/genericParallelization.h - pll/hardware.c - pll/makenewzGenericSpecial.c - pll/mem_alloc.h - pll/mic_native_aa.c - pll/mic_native_dna.c - pll/models.c - pll/newviewGenericSpecial.c - pll/optimizeModel.c - pll/parsimony.c - pll/pll.h - pll/pllInternal.h - pll/recom.c - pll/restartHashTable.c - pll/searchAlgo.c - + pll/systypes.h - pll/topologies.c - pll/trash.c - pll/treeIO.c - pll/utils.c - + simulator/CMakeLists.txt - + simulator/alisimulator.cpp - + simulator/alisimulator.h - + simulator/alisimulatorheterogeneity.cpp - + simulator/alisimulatorheterogeneity.h - + simulator/alisimulatorheterogeneityinvar.cpp - + simulator/alisimulatorheterogeneityinvar.h - + simulator/alisimulatorinvar.cpp - + simulator/alisimulatorinvar.h - sprng/lcg64.c - terrace/CMakeLists.txt - + terrace/README.md - + terrace/presenceabsencematrix.cpp - + terrace/presenceabsencematrix.hpp - terrace/terrace.cpp - + terrace/terrace.hpp - + terrace/terracenode.cpp - + terrace/terracenode.hpp - + terrace/terracetree.cpp - + terrace/terracetree.hpp - + terracetphast/CMakeLists.txt - + terracetphast/terracetphast.cpp - terrace/terrace.h → terracetphast/terracetphast.h - + terraphast/.gitattributes - + terraphast/.gitignore - terraphast/CMakeLists.txt - terraphast/appveyor.yml - terraphast/include/terraces/constraints.hpp - terraphast/include/terraces/definitions.hpp - terraphast/lib/multitree_iterator.cpp - terraphast/lib/multitree_iterator.hpp - + test_scripts/iqtree2.h - + test_scripts/unify-static-libs.sh - tree/CMakeLists.txt - tree/candidateset.cpp - tree/discordance.cpp - + tree/genomenode.cpp - + tree/genomenode.h - + tree/genometree.cpp - + tree/genometree.h - tree/iqtree.cpp - tree/iqtree.h - + tree/iqtreemix.cpp - + tree/iqtreemix.h - + tree/iqtreemixhmm.cpp - + tree/iqtreemixhmm.h - tree/mexttree.cpp - tree/mexttree.h - tree/mtree.cpp - tree/mtree.h - tree/mtreeset.cpp - tree/node.cpp - tree/node.h - + tree/phylohmm.cpp - + tree/phylohmm.h - tree/phylokernel.h - tree/phylokernelfma.cpp - tree/phylokernelnew.h - tree/phylokernelnonrev.h - tree/phylokernelsse.cpp - tree/phylonode.cpp - tree/phylosupertree.cpp - tree/phylosupertree.h - tree/phylosupertreeplen.cpp - tree/phylosupertreeplen.h - tree/phylotree.cpp - tree/phylotree.h - tree/phylotreeavx.cpp - tree/phylotreemixlen.cpp - tree/phylotreemixlen.h - tree/phylotreepars.cpp - tree/phylotreesse.cpp - tree/quartet.cpp - tree/tinatree.cpp - utils/CMakeLists.txt - utils/MPIHelper.cpp - utils/MPIHelper.h - utils/bionj.h → utils/bionj.cpp - + utils/bionj2.cpp - + utils/bionj2.h - utils/checkpoint.cpp - utils/checkpoint.h - + utils/decenttree.cpp - utils/eigendecomposition.cpp - utils/gzstream.cpp - utils/gzstream.h - + utils/hammingdistance.h - + utils/heapsort.h - + utils/operatingsystem.cpp - + utils/operatingsystem.h - utils/optimization.cpp - utils/pllnni.cpp - + utils/progress.cpp - + utils/progress.h - + utils/sse2neon.h - + utils/starttree.cpp - + utils/starttree.h - utils/stoprule.cpp - utils/timeutil.h - utils/tools.cpp - utils/tools.h - vectorclass/instrset.h - vectorclass/instrset_detect.cpp - vectorclass/vectorf128.h - vectorclass/vectori128.h - whtest/eigen.c - whtest/weisslambda_sub.h - whtest/whtest.c - whtest/whtest_wrapper.cpp - − yaml-cpp/CMakeLists.txt - − yaml-cpp/CONTRIBUTING.md - − yaml-cpp/LICENSE - − yaml-cpp/README.md - − yaml-cpp/include/yaml-cpp/anchor.h - − yaml-cpp/include/yaml-cpp/binary.h - − yaml-cpp/include/yaml-cpp/contrib/anchordict.h - − yaml-cpp/include/yaml-cpp/contrib/graphbuilder.h - − yaml-cpp/include/yaml-cpp/dll.h - − yaml-cpp/include/yaml-cpp/emitfromevents.h - − yaml-cpp/include/yaml-cpp/emitter.h - − yaml-cpp/include/yaml-cpp/emitterdef.h - − yaml-cpp/include/yaml-cpp/emittermanip.h - − yaml-cpp/include/yaml-cpp/emitterstyle.h - − yaml-cpp/include/yaml-cpp/eventhandler.h - − yaml-cpp/include/yaml-cpp/exceptions.h - − yaml-cpp/include/yaml-cpp/mark.h - − yaml-cpp/include/yaml-cpp/node/convert.h - − yaml-cpp/include/yaml-cpp/node/detail/bool_type.h - − yaml-cpp/include/yaml-cpp/node/detail/impl.h - − yaml-cpp/include/yaml-cpp/node/detail/iterator.h - − yaml-cpp/include/yaml-cpp/node/detail/iterator_fwd.h - − yaml-cpp/include/yaml-cpp/node/detail/memory.h - − yaml-cpp/include/yaml-cpp/node/detail/node.h - − yaml-cpp/include/yaml-cpp/node/detail/node_data.h - − yaml-cpp/include/yaml-cpp/node/detail/node_iterator.h - − yaml-cpp/include/yaml-cpp/node/detail/node_ref.h - − yaml-cpp/include/yaml-cpp/node/emit.h - − yaml-cpp/include/yaml-cpp/node/impl.h - − yaml-cpp/include/yaml-cpp/node/iterator.h - − yaml-cpp/include/yaml-cpp/node/node.h - − yaml-cpp/include/yaml-cpp/node/parse.h - − yaml-cpp/include/yaml-cpp/node/ptr.h - − yaml-cpp/include/yaml-cpp/node/type.h - − yaml-cpp/include/yaml-cpp/noncopyable.h - − yaml-cpp/include/yaml-cpp/null.h - − yaml-cpp/include/yaml-cpp/ostream_wrapper.h - − yaml-cpp/include/yaml-cpp/parser.h - − yaml-cpp/include/yaml-cpp/stlemitter.h - − yaml-cpp/include/yaml-cpp/traits.h - − yaml-cpp/include/yaml-cpp/yaml.h - − yaml-cpp/install.txt - − yaml-cpp/src/binary.cpp - − yaml-cpp/src/collectionstack.h - − yaml-cpp/src/contrib/graphbuilder.cpp - − yaml-cpp/src/contrib/graphbuilderadapter.cpp - − yaml-cpp/src/contrib/graphbuilderadapter.h - − yaml-cpp/src/contrib/yaml-cpp.natvis - − yaml-cpp/src/contrib/yaml-cpp.natvis.md - − yaml-cpp/src/convert.cpp - − yaml-cpp/src/directives.cpp - − yaml-cpp/src/directives.h - − yaml-cpp/src/emit.cpp - − yaml-cpp/src/emitfromevents.cpp - − yaml-cpp/src/emitter.cpp - − yaml-cpp/src/emitterstate.cpp - − yaml-cpp/src/emitterstate.h - − yaml-cpp/src/emitterutils.cpp - − yaml-cpp/src/emitterutils.h - − yaml-cpp/src/exceptions.cpp - − yaml-cpp/src/exp.cpp - − yaml-cpp/src/exp.h - − yaml-cpp/src/indentation.h - − yaml-cpp/src/memory.cpp - − yaml-cpp/src/node.cpp - − yaml-cpp/src/node_data.cpp - − yaml-cpp/src/nodebuilder.cpp - − yaml-cpp/src/nodebuilder.h - − yaml-cpp/src/nodeevents.cpp - − yaml-cpp/src/nodeevents.h - − yaml-cpp/src/null.cpp - − yaml-cpp/src/ostream_wrapper.cpp - − yaml-cpp/src/parse.cpp - − yaml-cpp/src/parser.cpp - − yaml-cpp/src/ptr_vector.h - − yaml-cpp/src/regex_yaml.cpp - − yaml-cpp/src/regex_yaml.h - − yaml-cpp/src/regeximpl.h - − yaml-cpp/src/scanner.cpp - − yaml-cpp/src/scanner.h - − yaml-cpp/src/scanscalar.cpp - − yaml-cpp/src/scanscalar.h - − yaml-cpp/src/scantag.cpp - − yaml-cpp/src/scantag.h - − yaml-cpp/src/scantoken.cpp - − yaml-cpp/src/setting.h - − yaml-cpp/src/simplekey.cpp - − yaml-cpp/src/singledocparser.cpp - − yaml-cpp/src/singledocparser.h - − yaml-cpp/src/stream.cpp - − yaml-cpp/src/stream.h - − yaml-cpp/src/streamcharsource.h - − yaml-cpp/src/stringsource.h - − yaml-cpp/src/tag.cpp - − yaml-cpp/src/tag.h - − yaml-cpp/src/token.h - − yaml-cpp/util/CMakeLists.txt - − yaml-cpp/util/api.cpp - − yaml-cpp/util/parse.cpp - − yaml-cpp/util/read.cpp - − yaml-cpp/util/sandbox.cpp - − yaml-cpp/yaml-cpp-config-version.cmake.in - − yaml-cpp/yaml-cpp-config.cmake.in - − yaml-cpp/yaml-cpp.pc.cmake The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/iqtree/-/compare/07dc39a888e8cab024bfa59555009cb83c4603a1...e951cb727403b5909d816ef8fd1cbfe8f7407773 -- View it on GitLab: https://salsa.debian.org/med-team/iqtree/-/compare/07dc39a888e8cab024bfa59555009cb83c4603a1...e951cb727403b5909d816ef8fd1cbfe8f7407773 You're receiving this email because of your account on salsa.debian.org.
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