[med-svn] [Git][med-team/libsonlib][master] 4 commits: DEP3
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 22 14:43:59 BST 2020
Andreas Tille pushed to branch master at Debian Med / libsonlib
Commits:
7e5f2baf by Andreas Tille at 2020-06-16T11:44:35+02:00
DEP3
- - - - -
5158a61f by Andreas Tille at 2020-06-16T12:50:49+02:00
Fix imports
- - - - -
7e679d0f by Andreas Tille at 2020-06-16T14:13:35+02:00
Add missing copyright
- - - - -
28ea6666 by Andreas Tille at 2020-06-22T15:43:21+02:00
Fix install
- - - - -
8 changed files:
- debian/control
- debian/copyright
- + debian/libsonlib-dev.install
- debian/patches/2to3.patch
- debian/patches/fix_test.patch
- + debian/patches/rpath.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -4,6 +4,7 @@ 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),
+ dh-exec,
dh-python,
python3,
python3-setuptools,
@@ -21,6 +22,7 @@ Section: libdevel
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
+ ${python3:Depends},
libquicktree-dev
Description: compact C/Python library for sequence analysis in bioinformatics
SonLib is a small general purpose library for C and Python for sequence
=====================================
debian/copyright
=====================================
@@ -9,6 +9,28 @@ Files: *
Copyright: 2009-2017 by Benedict Paten <benedictpaten at gmail.com>
License: MIT
+Files: externalTools/cutest/*
+Copyright: 2002-2003, Asim Jalis <asimjalis at gmail.com>
+License: Zlib
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+ .
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software in
+ a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ .
+ 2. Altered source versions must be plainly marked as such, and must not
+ be misrepresented as being the original software.
+ .
+ 3. This notice may not be removed or altered from any source
+ distribution.
+
Files: debian/*
Copyright: 2020 Andreas Tille <tille at debian.org>
License: MIT
=====================================
debian/libsonlib-dev.install
=====================================
@@ -0,0 +1,5 @@
+#!/usr/bin/dh-exec
+
+#include/*.h usr/include/sonlib
+lib/* usr/lib/${DEB_HOST_MULTIARCH}
+bin/* usr/bin
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Description: Port to Python3
+
--- a/C/Makefile
+++ b/C/Makefile
@@ -65,4 +65,4 @@ ${libPath}/sonLib.a : ${libSources} ${cp
@@ -229,15 +233,6 @@
"""read and write newick trees to and from networkx graphs (as wrapped by nxtree).
"""
-@@ -14,7 +13,7 @@ import math
- import random
- from string import whitespace as ws
- from sonLib.misc import close
--import bioio
-+from . import bioio
- import networkx as NX
- from optparse import OptionParser
- from sonLib.nxtree import NXTree
@@ -187,15 +186,15 @@ def main():
parser.parseFile(args[0])
NX.drawing.nx_agraph.write_dot(parser.nxTree.nxDg, args[1])
@@ -801,24 +796,6 @@
def fn4(newTree):
if newTree.internal:
fn4(newTree.left)
-@@ -596,7 +596,7 @@ def remodelTreeRemovingRoot(root, node):
- """
- Node is mid order number
- """
-- import bioio
-+ from . import bioio
- assert root.traversalID.mid != node
- hash = {}
- def fn(bT):
-@@ -632,7 +632,7 @@ def moveRoot(root, branch):
- """
- Removes the old root and places the new root at the mid point along the given branch
- """
-- import bioio
-+ from . import bioio
- if root.traversalID.mid == branch:
- return bioio.newickTreeParser(bioio.printBinaryTree(root, True))
- def fn2(tree, seq):
@@ -703,7 +703,7 @@ def calculateDupsAndLossesByReconcilingT
if nodes.issubset(a[speciesTree.right.traversalID.mid]):
return fn2(nodes, speciesTree.right)
=====================================
debian/patches/fix_test.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Description: Somehow the test suite was non-functional. Fix some PATHs here
+
--- a/C/Makefile
+++ b/C/Makefile
@@ -65,4 +65,4 @@ ${libPath}/sonLib.a : ${libSources} ${cp
=====================================
debian/patches/rpath.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Description: No rpath
+
+--- a/include.mk
++++ b/include.mk
+@@ -66,7 +66,7 @@ else ifneq ($(wildcard /usr/include/tcbd
+ # /usr install (Ubuntu, and probably most Debain-based systems)
+ tcPrefix = /usr
+ tokyoCabinetIncl = -I${tcPrefix}/include -DHAVE_TOKYO_CABINET=1
+- tokyoCabinetLib = -L${tcPrefix}/lib -Wl,-rpath,${tcPrefix}/lib -ltokyocabinet -lz -lbz2 -lpthread -lm
++ tokyoCabinetLib = -ltokyocabinet -lz -lbz2 -lpthread -lm
+ endif
+ endif
+
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
use_debian_packaged_quicktree.patch
2to3.patch
fix_test.patch
+rpath.patch
=====================================
debian/rules
=====================================
@@ -3,22 +3,10 @@
# DH_VERBOSE := 1
export LC_ALL=C.UTF-8
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@
+ dh $@ --with python3
override_dh_auto_build:
# Somehow Makefile does not deal with this ...
@@ -26,8 +14,7 @@ override_dh_auto_build:
cp -a src/sonLib/test/sonLib_daemonize.py .
dh_auto_build
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
-#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-# do_stuff_for_testing
-#endif
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ dh_auto_test || true
+endif
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/e02ce9f8e568331b7320aaad5855e7fa59c8b051...28ea6666306a261a3160270ab15b82dbd44da03d
--
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/e02ce9f8e568331b7320aaad5855e7fa59c8b051...28ea6666306a261a3160270ab15b82dbd44da03d
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