[med-svn] [Git][med-team/libedlib][master] 2 commits: Add Python3 bindings

[Andreas Tille]

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 <tille at debian.org>  Sun, 21 Oct 2018 08:05:00 +0200
+ -- Andreas Tille <tille at debian.org>  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 <tille at debian.org>
+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
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