[med-svn] [Git][med-team/gubbins][master] 5 commits: autoupdate_configure.ac.patch: refresh.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / gubbins


Commits:
4993a189 by Étienne Mollier at 2023-12-16T13:42:38+01:00
autoupdate_configure.ac.patch: refresh.

- - - - -
a1f10408 by Étienne Mollier at 2023-12-16T14:32:03+01:00
d/t/run-example: define HOME directory.

This fixes numba caching issues with the newer test items.

- - - - -
3e6503b4 by Étienne Mollier at 2023-12-16T14:53:52+01:00
d/control: suggest r-core-base.

This is because gubbins ships a couple of R scripts, although they are
not critical to proper gubbins operation.

- - - - -
bd1cbae2 by Étienne Mollier at 2023-12-16T15:22:16+01:00
gubbins_3.1.0_exe_in_usr_lib.patch: delete leftover.

- - - - -
4b2d10cd by Étienne Mollier at 2023-12-16T15:23:05+01:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/autoupdate_configure.ac.patch
- − debian/patches/gubbins_3.1.0_exe_in_usr_lib.patch
- debian/tests/run-example


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,19 @@
-gubbins (3.3.1-1) UNRELEASED; urgency=medium
+gubbins (3.3.1-1) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream version
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Mon, 27 Nov 2023 18:24:30 +0100
+  [ Étienne Mollier ]
+  * autoupdate_configure.ac.patch: refresh.
+  * d/t/run-example: define HOME directory.
+    This fixes numba caching issues with the newer test items.
+  * d/control: suggest r-core-base.
+    This is because gubbins ships a couple of R scripts, although they are
+    not critical to proper gubbins operation.
+  * gubbins_3.1.0_exe_in_usr_lib.patch: delete leftover.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 16 Dec 2023 15:22:50 +0100
 
 gubbins (3.3.0-3) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -38,6 +38,7 @@ Depends: ${shlibs:Depends},
 Recommends: iqtree,
             fasttree,
             python3-numba
+Suggests: r-base-core
 Description: phylogenetic analysis of genome sequences
  Gubbins supports rapid phylogenetic analysis of large samples of
  recombinant bacterial whole genome sequences.


=====================================
debian/patches/autoupdate_configure.ac.patch
=====================================
@@ -2,8 +2,8 @@ Description: autoupdate to avoid warnings from configure.ac
 Author: Andreas Tille <tille at debian.org>
 Last-Update: Wed, 12 Jul 2023 15:32:45 +0200
 
---- a/configure.ac
-+++ b/configure.ac
+--- gubbins.orig/configure.ac
++++ gubbins/configure.ac
 @@ -1,4 +1,5 @@
 -AC_INIT([gubbins], m4_esyscmd([tr -d '\n' < VERSION]), [n.croucher at imperial.ac.uk], [$(PACKAGE_NAME)$(AC_PACKAGE_VERSION)], [https://github.com/nickjcroucher/gubbins])
 +package_version=$(dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/')
@@ -11,12 +11,3 @@ Last-Update: Wed, 12 Jul 2023 15:32:45 +0200
  
  AM_INIT_AUTOMAKE([foreign tar-pax subdir-objects])
  AC_CONFIG_SRCDIR([configure.ac])
-@@ -25,7 +26,7 @@ case $host_os in
- esac
- AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux])
- 
--AC_PROG_LIBTOOL
-+LT_INIT
- AC_PROG_CC
- AC_PROG_CXX
- 


=====================================
debian/patches/gubbins_3.1.0_exe_in_usr_lib.patch deleted
=====================================
@@ -1,21 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 19 Nov 2015 10:45:48 +0100
-Description: gubbins executable prints that it is not intended for direct usage
- While default install procedure installs gubbins executable to /usr/bin
- it prints that it is intended to be called from run_gubbins.  So it makes
- sense to rather install it to /usr/lib/gubbins instead of /usr/bin.
- .
- Attention: This patch applies to gubbins version 3.1.0 which can not be
- packaged yet since it requires raxml-ng
-
---- a/src/main.c
-+++ b/src/main.c
-@@ -38,7 +38,7 @@ const char* program_name;
- 
- void print_usage(FILE* stream, int exit_code)
- {
--  fprintf (stream, "This program is not supposed to be directly run. Use run_gubbins.py instead\n");
-+  fprintf (stream, "This program is not supposed to be directly run. Use run_gubbins instead\n");
-   fprintf (stream, "Usage:  %s [options] alignment_file\n", program_name);
-   fprintf (stream, "Version: %s\n", PACKAGE_VERSION);
-   fprintf (stream,


=====================================
debian/tests/run-example
=====================================
@@ -5,6 +5,8 @@ set -e
 
 TESTDIR=$(pwd)/tests/data
 WORKDIR=$(mktemp -d)
+HOME="$WORKDIR"
+export HOME
 trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
 cd $WORKDIR
 



View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/1bc1c0ec7ebf960cf3d95bc2f9fb1b068de39d23...4b2d10cd8c32cbddd2200bce70d07f536da4625f

-- 
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/1bc1c0ec7ebf960cf3d95bc2f9fb1b068de39d23...4b2d10cd8c32cbddd2200bce70d07f536da4625f
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