Pierre Gruet pushed to branch master at Debian Med / sepp
Commits: 2c8626f1 by Pierre Gruet at 2024-05-25T22:58:46+02:00 Raising Standards version to 4.7.0 (no change) - - - - - 649aaee4 by Pierre Gruet at 2024-05-25T23:00:33+02:00 Fixing wrong import from dendropy - - - - - 5873c564 by Pierre Gruet at 2024-05-25T23:01:03+02:00 Updating changelog - - - - - 33299d55 by Pierre Gruet at 2024-05-25T23:02:33+02:00 Upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/series - + debian/patches/wrong_import_from_dendropy.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +sepp (4.5.1+really4.5.1+dfsg-6) unstable; urgency=medium + + * Fixing wrong import from dendropy (Closes: #1071780) + * Raising Standards version to 4.7.0 (no change) + + -- Pierre Gruet <[email protected]> Sat, 25 May 2024 23:02:26 +0200 + sepp (4.5.1+really4.5.1+dfsg-5) unstable; urgency=medium * Dropping "U" mode from open() invocations, thanks to Steve Langasek! ===================================== debian/control ===================================== @@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13), ncbi-blast+ <!nocheck>, pplacer <!nocheck>, hmmer <!nocheck> -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/sepp Vcs-Git: https://salsa.debian.org/med-team/sepp.git Homepage: https://github.com/smirarab/sepp/ ===================================== debian/patches/series ===================================== @@ -8,3 +8,4 @@ using_python3_interpreter.patch hmmbuild_path_for_testUPP.patch py310_collections_import.patch open-U-obsolete.patch +wrong_import_from_dendropy.patch ===================================== debian/patches/wrong_import_from_dendropy.patch ===================================== @@ -0,0 +1,26 @@ +Description: reworking syntax of call to convert_node_to_root_polytomy +Author: Pierre Gruet <[email protected]> +Bug-Debian: https://bugs.debian.org/1071780 +Forwarded: no +Last-Update: 2024-05-25 + +--- a/sepp/tree.py ++++ b/sepp/tree.py +@@ -22,8 +22,6 @@ + + from dendropy import Tree, Taxon, treecalc + from dendropy import DataSet as Dataset +-from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ +- convert_node_to_root_polytomy + from sepp import get_logger, sort_by_value + from sepp.alignment import get_pdistance + from sepp.decompose_tree import decompose_by_diameter +@@ -258,7 +256,7 @@ + + nr.edge.length = None + nr.parent_node = None +- convert_node_to_root_polytomy(nr) ++ nr._convert_node_to_root_polytomy() + t1 = PhylogeneticTree(Tree(seed_node=nr)) + # temp we could speed this up, + # by telling the Phylogenetic tree how many leaves it has View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/4ba8cab591159d6b61bf6566ba86d53c11f66b86...33299d5522c2f83598cb20e5ab65f282917efa4e -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/4ba8cab591159d6b61bf6566ba86d53c11f66b86...33299d5522c2f83598cb20e5ab65f282917efa4e You're receiving this email because of your account on salsa.debian.org.
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