[med-svn] [Git][med-team/sumatra][master] 14 commits: sumalibs now available

Andreas Tille gitlab at salsa.debian.org
Thu Apr 9 13:13:08 BST 2020 


Andreas Tille pushed to branch master at Debian Med / sumatra


Commits:
5daa71df by Andreas Tille at 2020-04-09T13:25:39+02:00
sumalibs now available

- - - - -
c1bf3298 by Andreas Tille at 2020-04-09T13:25:58+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
510a2938 by Andreas Tille at 2020-04-09T13:25:58+02:00
routine-update: debhelper-compat 12

- - - - -
0aa7ce70 by Andreas Tille at 2020-04-09T13:26:02+02:00
routine-update: Secure URI in copyright format

- - - - -
9ca6de9c by Andreas Tille at 2020-04-09T13:26:02+02:00
R-U: Trailing whitespace in debian/changelog

- - - - -
32934429 by Andreas Tille at 2020-04-09T13:26:02+02:00
R-U: Trailing whitespace in debian/copyright

- - - - -
1cc7e00e by Andreas Tille at 2020-04-09T13:26:02+02:00
routine-update: Add salsa-ci file

- - - - -
9e623b68 by Andreas Tille at 2020-04-09T13:26:02+02:00
routine-update: Rules-Requires-Root: no

- - - - -
f6f9a27a by Andreas Tille at 2020-04-09T13:26:03+02:00
debian/copyright: use spaces rather than tabs to start continuation lines..

Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html

- - - - -
10010958 by Andreas Tille at 2020-04-09T13:26:17+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
- - - - -
a3d0a389 by Andreas Tille at 2020-04-09T14:08:04+02:00
Cleanup watch file

- - - - -
fe505935 by Andreas Tille at 2020-04-09T14:08:44+02:00
DEP3

- - - - -
42ef2780 by Andreas Tille at 2020-04-09T14:09:40+02:00
Upload to unstable

- - - - -
71edddbf by Andreas Tille at 2020-04-09T14:09:58+02:00
Ending newline

- - - - -


10 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/use_debian_packaged_sumalibs.patch
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,21 @@
-sumatra (1.0.34-1) UNRELEASED; urgency=medium
+sumatra (1.0.34-1) unstable; urgency=medium
 
   * New upstream version
   * debhelper 12
   * Standards-Version: 4.3.0
-  TODO: https://salsa.debian.org/med-team/sumalibs
-
- -- Andreas Tille <tille at debian.org>  Tue, 09 Jul 2019 15:45:27 +0200
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 12 (routine-update)
+  * Secure URI in copyright format (routine-update)
+  * Remove trailing whitespace in debian/changelog (routine-update)
+  * Remove trailing whitespace in debian/copyright (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * debian/copyright: use spaces rather than tabs to start continuation
+    lines.
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+  * Cleanup watch file
+
+ -- Andreas Tille <tille at debian.org>  Thu, 09 Apr 2020 14:08:52 +0200
 
 sumatra (1.0.31-2) unstable; urgency=medium
 
@@ -41,6 +51,6 @@ sumatra (1.0.10-1) unstable; urgency=medium
 
 sumatra (1.0.01-0ubuntu1) trusty; urgency=medium
 
-  * Initial release for QIIME 1.9 
+  * Initial release for QIIME 1.9
 
  -- Tim Booth <tbooth at ceh.ac.uk>  Fri, 13 Feb 2015 16:24:17 +0000


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12


=====================================
debian/control
=====================================
@@ -4,11 +4,14 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~)
-Standards-Version: 4.3.0
+Build-Depends: debhelper-compat (= 12),
+               libsuma-dev,
+               zlib1g-dev
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/sumatra
 Vcs-Git: https://salsa.debian.org/med-team/sumatra.git
 Homepage: http://metabarcoding.org/sumatra
+Rules-Requires-Root: no
 
 Package: sumatra
 Architecture: any


=====================================
debian/copyright
=====================================
@@ -1,11 +1,11 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Contact: Céline Mercier <celine.mercier at metabarcoding.org>
 Source: https://github.com/mesocentrefc/sumatra
 
 Files: *
 Copyright: 2013-2015 Tiayyba Riaz
                      Celine Mercier
-	             Eric Coissac
+                     Eric Coissac
 License: CeCILL-2
 
 Files: debian/*
@@ -141,7 +141,7 @@ License: CeCILL-2
  The purpose of the Agreement is the grant by the Licensor to the
  Licensee of a non-exclusive, transferable and worldwide license for the
  Software as set forth in Article 5 hereinafter for the whole term of the
- protection granted by the rights over said Software. 
+ protection granted by the rights over said Software.
  .
  .
     Article 3 - ACCEPTANCE
@@ -408,7 +408,7 @@ License: CeCILL-2
  .
  9.3 The Licensee acknowledges that the Software is supplied "as is" by
  the Licensor without any other express or tacit warranty, other than
- that provided for in Article 9.2 and, in particular, without any warranty 
+ that provided for in Article 9.2 and, in particular, without any warranty
  as to its commercial value, its secured, safe, innovative or relevant
  nature.
  .


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 hardening.patch
+use_debian_packaged_sumalibs.patch


=====================================
debian/patches/use_debian_packaged_sumalibs.patch
=====================================
@@ -0,0 +1,49 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 09 Apr 2020 14:06:08 +0200
+Description: Build using Debian packaged libsuma
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,4 +1,4 @@
+-PREFIX=/usr/local
++PREFIX=/usr
+ 
+ CFLAGS=-I$(PREFIX)/include
+ 
+@@ -38,7 +38,6 @@ sumatra: $(SUMATRA_OBJ)
+ clean:
+ 	rm -f $(SUMATRA_OBJ)	
+ 	rm -f $(EXEC)
+-	$(MAKE) -C ./sumalibs clean
+ 
+ install: all
+ 	install -d $(DESTDIR)$(PREFIX)/bin/
+--- a/global.mk
++++ b/global.mk
+@@ -1,16 +1,16 @@
+ 
+-LIBSUMAPATH = -L./sumalibs
++LIBSUMAPATH = 
+ 
+-LIBSUMA = ./sumalibs/libsuma.a
++LIBSUMA = 
+ 
+ CC=gcc
+ LDFLAGS:=$(LDFLAGS)
+ 
+ 
+ ifeq ($(CC),gcc)
+-        CFLAGS = -O3 -s -DOMP_SUPPORT -w
++        CFLAGS += -O3 -s -DOMP_SUPPORT -w
+ else
+-        CFLAGS = -O3 -w
++        CFLAGS += -O3 -w
+ endif
+ 
+ 
+@@ -26,5 +26,3 @@ default: all
+ #
+ ########
+ 
+-./sumalibs/libsuma.a:
+-	$(MAKE) -C ./sumalibs


=====================================
debian/rules
=====================================
@@ -9,12 +9,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 %:
 	dh $@
 
-override_dh_clean:
-	dh_clean
-	#Upstream is very messy.  Scrub out all the .svn stuff
-	#and .o files.
-	find sumalibs -name '*.[oa]' -delete
-
 override_dh_compress:
 	dh_compress --exclude=.pdf
 
@@ -22,4 +16,4 @@ override_dh_compress:
 # source for the manpage - currently the result is not really
 # the usual manpage structure
 #override_dh_installman:
-#	go-md2man -in=sumatra_user_manual.md -out=sumatra.1
\ No newline at end of file
+#	go-md2man -in=sumatra_user_manual.md -out=sumatra.1


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/mesocentrefc/sumatra/issues
+Bug-Submit: https://github.com/mesocentrefc/sumatra/issues/new
 Registry:
  - Name: OMICtools
    Entry: OMICS_01498


=====================================
debian/watch
=====================================
@@ -1,12 +1,3 @@
-version=3
+version=4
 
 https://git.metabarcoding.org/obitools/sumatra/wikis/home .*/sumatra/uploads/.*/sumatra_v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-
-# sumatra is maintained in a Gitlab repository
-#    https://wiki.debian.org/debian/watch#Gitlab
-# recommends something like this but it does not work
-# opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/<project>-$1\.tar\.gz/g \
-#  https://git.metabarcoding.org/obitools/sumatra/tags .*archive\.tar\.gz\?ref=v?(\d\S*)
-
-# Tags on Github are not up to date
-# https://github.com/mesocentrefc/sumatra/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)



View it on GitLab: https://salsa.debian.org/med-team/sumatra/-/compare/5e690fd5d5a6ac2cc830ee6d2045353a491020a0...71edddbf0175461a92c6d1286b3c46d7ed60a104

-- 
View it on GitLab: https://salsa.debian.org/med-team/sumatra/-/compare/5e690fd5d5a6ac2cc830ee6d2045353a491020a0...71edddbf0175461a92c6d1286b3c46d7ed60a104
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