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 <[email protected]> Uploaders: Andreas Tille <[email protected]> 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}, + ${python3:Depends}, libquicktree-dev Description: compact C/Python library for sequence analysis in bioinformatics SonLib is a small general purpose library for C and Python for sequence ===================================== debian/copyright ===================================== @@ -9,6 +9,28 @@ Files: * Copyright: 2009-2017 by Benedict Paten <[email protected]> License: MIT +Files: externalTools/cutest/* +Copyright: 2002-2003, Asim Jalis <[email protected]> +License: Zlib + This software is provided 'as-is', without any express or implied + warranty. In no event will the authors be held liable for any damages + arising from the use of this software. + . + Permission is granted to anyone to use this software for any purpose, + including commercial applications, and to alter it and redistribute it + freely, subject to the following restrictions: + . + 1. The origin of this software must not be misrepresented; you must not + claim that you wrote the original software. If you use this software in + a product, an acknowledgment in the product documentation would be + appreciated but is not required. + . + 2. Altered source versions must be plainly marked as such, and must not + be misrepresented as being the original software. + . + 3. This notice may not be removed or altered from any source + distribution. + Files: debian/* Copyright: 2020 Andreas Tille <[email protected]> License: MIT ===================================== debian/libsonlib-dev.install ===================================== @@ -0,0 +1,5 @@ +#!/usr/bin/dh-exec + +#include/*.h usr/include/sonlib +lib/* usr/lib/${DEB_HOST_MULTIARCH} +bin/* usr/bin ===================================== debian/patches/2to3.patch ===================================== @@ -1,3 +1,7 @@ +Author: Andreas Tille <[email protected]> +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 <[email protected]> +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} ${cp ===================================== debian/patches/rpath.patch ===================================== @@ -0,0 +1,15 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 16 Jun 2020 08:23:45 +0200 +Description: No rpath + +--- a/include.mk ++++ b/include.mk +@@ -66,7 +66,7 @@ else ifneq ($(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 You're receiving this email because of your account on salsa.debian.org.
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