[med-svn] [Git][med-team/libsonlib][master] 4 commits: Use Debian packaged quicktree

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / libsonlib


Commits:
78ef16a2 by Andreas Tille at 2020-06-16T08:48:43+02:00
Use Debian packaged quicktree

- - - - -
4ec231e4 by Andreas Tille at 2020-06-16T08:51:14+02:00
Remove some cruft

- - - - -
725e96e9 by Andreas Tille at 2020-06-16T08:51:20+02:00
New upstream version 1.1+git20170108.b849f78+dfsg
- - - - -
2fdf58ac by Andreas Tille at 2020-06-16T08:51:21+02:00
Update upstream source from tag 'upstream/1.1+git20170108.b849f78+dfsg'

Update to upstream version '1.1+git20170108.b849f78+dfsg'
with Debian dir 156f9393328f8a1d093bdaf1c1fbee05cf4dfdf4
- - - - -


8 changed files:

- − .gitignore
- − .gitmodules
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/series
- + debian/patches/use_debian_packaged_quicktree.patch
- − src/sonLib/.bioio.py.swp


Changes:

=====================================
.gitignore deleted
=====================================
@@ -1,7 +0,0 @@
-bin/*
-lib/*
-bin/
-lib/
-*.pyc
-*.o
-*.a


=====================================
.gitmodules deleted
=====================================


=====================================
debian/changelog
=====================================
@@ -1,6 +1,5 @@
 libsonlib (1.1+git20170108.b849f78+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
-  TODO: https://github.com/khowe/quicktree
 
  -- Andreas Tille <tille at debian.org>  Tue, 16 Jun 2020 08:23:45 +0200


=====================================
debian/control
=====================================
@@ -3,7 +3,10 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper-compat (= 13)
+Build-Depends: debhelper-compat (= 13),
+               dh-python,
+               python3-all-dev,
+               python3-setuptools,
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/libsonlib
 Vcs-Git: https://salsa.debian.org/med-team/libsonlib.git
@@ -12,7 +15,9 @@ Homepage: https://github.com/ArtRand/sonLib
 Package: libsonlib-dev
 Section: libdevel
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         quicktree
 Description: compact C/Python library for sequence analysis in bioinformatics
  SonLib is a small general purpose library for C and Python for sequence
  analysis with focus on bioinformatics.


=====================================
debian/copyright
=====================================
@@ -2,6 +2,8 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: sonlib
 Source: https://github.com/ArtRand/sonLib
 Files-Excluded: externalTools/quicktree*
+                */*.swp
+                */.git*
 
 Files: *
 Copyright: 2009-2017 by Benedict Paten <benedictpaten at gmail.com>


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+use_debian_packaged_quicktree.patch


=====================================
debian/patches/use_debian_packaged_quicktree.patch
=====================================
@@ -0,0 +1,26 @@
+--- a/externalTools/Makefile
++++ b/externalTools/Makefile
+@@ -1,20 +1,14 @@
+ include ../include.mk
+-.PHONY: all clean cutestM cutestM.clean quicktreeM.clean
++.PHONY: all clean cutestM cutestM.clean
+ 
+ libPath = ../lib
+ 
+-all : cutestM quicktreeM
++all : cutestM
+ 
+-clean : cutestM.clean quicktreeM.clean
++clean : cutestM.clean
+ 
+ cutestM :
+ 	cd cutest && make all
+ 
+ cutestM.clean :
+ 	cd cutest && make clean
+-
+-quicktreeM :
+-	cd quicktree_1.1 && make all
+-
+-quicktreeM.clean :
+-	cd quicktree_1.1 && make clean


=====================================
src/sonLib/.bioio.py.swp deleted
=====================================
Binary files a/src/sonLib/.bioio.py.swp and /dev/null differ



View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/9627fa3e78baceab1b7b54085bdab5e846bc2131...2fdf58ac24255692fccd10b4df734b2ee6304528

-- 
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/9627fa3e78baceab1b7b54085bdab5e846bc2131...2fdf58ac24255692fccd10b4df734b2ee6304528
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