[med-svn] [Git][med-team/gubbins][master] 5 commits: gubbins_drawer was removed upstream so do not link to it any more

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / gubbins


Commits:
7b51c9e5 by Andreas Tille at 2023-08-17T08:23:54+02:00
gubbins_drawer was removed upstream so do not link to it any more

- - - - -
9a839643 by Andreas Tille at 2023-08-17T08:39:50+02:00
Enable building twice in a row

- - - - -
d3ff9795 by Andreas Tille at 2023-08-17T08:40:37+02:00
Set upstream metadata fields: Repository.

Changes-By: lintian-brush

- - - - -
5f682194 by Andreas Tille at 2023-08-17T09:24:15+02:00
Fix lintian-overrides

- - - - -
64d9841b by Andreas Tille at 2023-08-17T09:28:30+02:00
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- + debian/clean
- − debian/gubbins_drawer.1
- debian/links
- debian/lintian-overrides
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+gubbins (3.3.0-3) unstable; urgency=medium
+
+  * gubbins_drawer was removed upstream so do not link to it any more
+    Closes: #986238
+  * Enable building twice in a row
+    Closes: #1044465
+  * Set upstream metadata fields: Repository.
+  * Fix lintian-overrides
+
+ -- Andreas Tille <tille at debian.org>  Thu, 17 Aug 2023 09:25:33 +0200
+
 gubbins (3.3.0-2) unstable; urgency=medium
 
   * Test-Depends: iqtree


=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+tests/run_all_tests-*


=====================================
debian/gubbins_drawer.1 deleted
=====================================
@@ -1,21 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
-.TH GUBBINS_DRAWER "1" "June 2016" "gubbins_drawer 2.0.0" "User Commands"
-.SH NAME
-gubbins_drawer \- draw results for gubbins phylogenetic analysis of genome sequences
-.SH SYNOPSIS
-.B gubbins_drawer
-[\fI\,options\/\fR] \fI\,args\/\fR
-.SH OPTIONS
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.IP
-Output Options:
-.TP
-\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
-output file name [default= test.pdf]
-.TP
-\fB\-t\fR TREE, \fB\-\-tree\fR=\fI\,TREE\/\fR
-tree file to align tab files to
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.


=====================================
debian/links
=====================================
@@ -1,2 +1 @@
 usr/share/gubbins/run_gubbins.py	usr/bin/run_gubbins
-usr/share/gubbins/scripts/gubbins_drawer.py	usr/bin/gubbins_drawer


=====================================
debian/lintian-overrides
=====================================
@@ -1,4 +1,4 @@
 # as per lintian info this warning is overridden
-gubbins: non-dev-pkg-with-shlib-symlink usr/lib/*/libgubbins.so.* usr/lib/*/libgubbins.so
+gubbins: link-to-shared-library-in-wrong-package usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 [usr/lib/x86_64-linux-gnu/libgubbins.so]
 gubbins: package-name-doesnt-match-sonames libgubbins0
 gubbins: no-symbols-control-file usr/lib/*/libgubbins.so.*
\ No newline at end of file


=====================================
debian/rules
=====================================
@@ -30,4 +30,11 @@ override_dh_clean:
 	dh_clean
 	rm -rf python/*.egg-info python/build  python/Makefile
 	find . -name "*.pyc" -delete
-	rm -rf python/output_alignment python/tmp*
+	rm -rf python/output_alignment python/tmp* tests/.deps
+
+override_dh_auto_test:
+	# make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test)
+	cp -a tests/data tests/data.save
+	dh_auto_test
+	rm -rf tests/data
+	mv tests/data.save tests/data


=====================================
debian/upstream/metadata
=====================================
@@ -24,7 +24,7 @@ Registry:
   Entry: NA
 - Name: conda:bioconda
   Entry: gubbins
-Repository: https://github.com/sanger-pathogens/gubbins.git
+Repository: https://github.com/nickjcroucher/gubbins.git
 Repository-Browse: https://github.com/nickjcroucher/gubbins
 Bug-Database: https://github.com/nickjcroucher/gubbins/issues
 Bug-Submit: https://github.com/nickjcroucher/gubbins/issues/new



View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/70f1a835938684a62cd84abfd15d6dc786db02ec...64d9841b2a475f5c7442ff5e5468a64df66097df

-- 
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/70f1a835938684a62cd84abfd15d6dc786db02ec...64d9841b2a475f5c7442ff5e5468a64df66097df
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230817/ef8a8fe9/attachment-0001.htm>