Andreas Tille pushed to branch master at Debian Med / libedlib
Commits: d0a9904c by Andreas Tille at 2018-12-11T10:08:28Z Add Python3 bindings - - - - - 91091344 by Andreas Tille at 2018-12-11T12:12:21Z Try hard to enforce buildsystem=pybuild over cmake but failed - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/cython3.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,8 +1,9 @@ libedlib (1.2.3-4) UNRELEASED; urgency=medium * Make sure the executable is found in test + * Add Python3 bindings - -- Andreas Tille <[email protected]> Sun, 21 Oct 2018 08:05:00 +0200 + -- Andreas Tille <[email protected]> Tue, 11 Dec 2018 09:52:41 +0100 libedlib (1.2.3-3) unstable; urgency=medium ===================================== debian/control ===================================== @@ -5,8 +5,12 @@ Section: science Priority: optional Build-Depends: debhelper (>= 11~), cmake, + dh-python, d-shlibs, - rename + rename, + cython3, + python3-dev, + python3-setuptools Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/libedlib Vcs-Git: https://salsa.debian.org/med-team/libedlib.git @@ -103,3 +107,36 @@ Description: edlib sequence alignment tool using edit distance * It can easily handle small or very large sequences, even when finding alignment path, while consuming very little memory. * Super fast thanks to Myers's bit-vector algorithm. + +Package: python3-edlib +Architecture: any +Section: python +Depends: ${misc:Depends}, + ${shlibs:Depends}, + ${python3:Depends} +Description: library for sequence alignment using edit distance (Python3 module) + A lightweight and super fast C/C++ library for sequence alignment using + edit distance. + . + Calculating edit distance of two strings is as simple as: + . + edlibAlign("hello", 5, "world!", 6, + edlibDefaultAlignConfig()).editDistance; + Features + . + * Calculates edit distance (Levehnstein distance). + * It can find optimal alignment path (instructions how to transform + first sequence into the second sequence). + * It can find just the start and/or end locations of alignment path - + can be useful when speed is more important than having exact + alignment path. + * Supports multiple alignment methods: global(NW), prefix(SHW) and + infix(HW), each of them useful for different scenarios. + * You can extend character equality definition, enabling you to e.g. + have wildcard characters, to have case insensitive alignment or to + work with degenerate nucleotides. + * It can easily handle small or very large sequences, even when finding + alignment path, while consuming very little memory. + * Super fast thanks to Myers's bit-vector algorithm. + . + This package contains the Python3 module. ===================================== debian/patches/cython3.patch ===================================== @@ -0,0 +1,25 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 11 Dec 2018 09:52:41 +0100 +Description: Use Cython3/Python3 + +--- a/bindings/python/Makefile ++++ b/bindings/python/Makefile +@@ -7,15 +7,15 @@ edlib: ../../edlib + cp -R ../../edlib . + + pyedlib.bycython.cpp: edlib.pyx cedlib.pxd +- cython --cplus edlib.pyx -o edlib.bycython.cpp ++ cython3 --cplus edlib.pyx -o edlib.bycython.cpp + ####################################### + + ############## COMMANDS ############### + build: ${FILES} +- python setup.py build_ext -i ++ python3 setup.py build_ext -i + + sdist: ${FILES} +- python setup.py sdist ++ python3 setup.py sdist + + publish: clean sdist + twine upload dist/* ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ soversion.patch do_not_build_hello_example.patch +cython3.patch ===================================== debian/rules ===================================== @@ -2,15 +2,27 @@ # DH_VERBOSE := 1 +export PYBUILD_NAME = edlib + export DEB_BUILD_MAINT_OPTIONS=hardening=+all DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release %: - dh $@ + dh $@ --buildsystem=pybuild override_dh_auto_configure: - dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS) + dh_auto_configure --buildsystem=cmake -- $(DEB_CMAKE_EXTRA_FLAGS) + +override_dh_auto_build: + dh_auto_build --buildsystem=cmake + # $(MAKE) --directory=bindings/python + dh_auto_build -O--buildsystem=pybuild -O--source-directory=bindings/python + +override_dh_auto_install: + dh_auto_install --buildsystem=cmake +# $(MAKE) install --directory=bindings/python + dh_auto_install --buildsystem=pybuild -O--source-directory=bindings/python override_dh_install: dh_install View it on GitLab: https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb -- View it on GitLab: https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb You're receiving this email because of your account on salsa.debian.org.
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