[med-svn] [Git][med-team/sepp][master] 4 commits: Raising Standards version to 4.7.0 (no change)

[Pierre Gruet (@pgt)]

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

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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 <pgt at debian.org>  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 <pgt at debian.org>
+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

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View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/4ba8cab591159d6b61bf6566ba86d53c11f66b86...33299d5522c2f83598cb20e5ab65f282917efa4e
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