[med-svn] [Git][med-team/libslow5lib][master] 15 commits: s/inclue/include

Nilesh Patra (@nilesh) gitlab at salsa.debian.org
Sat Jul 2 09:27:49 BST 2022 


Nilesh Patra pushed to branch master at Debian Med / libslow5lib


Commits:
c08625f9 by Nilesh Patra at 2022-07-02T05:49:56+00:00
s/inclue/include

- - - - -
ea7e62e8 by Nilesh Patra at 2022-07-02T06:19:01+00:00
d/clean: more files to clean

- - - - -
a0af5bd3 by Nilesh Patra at 2022-07-02T06:19:01+00:00
Install py so properly

- - - - -
a7d32d3e by Nilesh Patra at 2022-07-02T06:22:38+00:00
d/rules: substvars for python3 binding properly

- - - - -
fa12772d by Nilesh Patra at 2022-07-02T06:32:55+00:00
Build-dep on python3-all

- - - - -
2f4ced62 by Nilesh Patra at 2022-07-02T12:13:58+05:30
Add upstream/metadata

- - - - -
641b9b42 by Nilesh Patra at 2022-07-02T12:20:39+05:30
Uncomment test, remove redundant lines

- - - - -
c74d49a4 by Nilesh Patra at 2022-07-02T12:40:32+05:30
Fix copyr

- - - - -
0afc2369 by Nilesh Patra at 2022-07-02T12:53:15+05:30
Install examples for python binding

- - - - -
974c7eb3 by Nilesh Patra at 2022-07-02T07:44:30+00:00
Run python unitest rather than example as build time test

- - - - -
e788f19f by Nilesh Patra at 2022-07-02T07:45:49+00:00
Install more files in header lib

- - - - -
77da6d3b by Nilesh Patra at 2022-07-02T08:03:39+00:00
Use DEB_HOST_MULTIARCH instead of DEB_HOST_GNU_TYPE

- - - - -
c08d729e by Nilesh Patra at 2022-07-02T08:03:55+00:00
Add patch to avoid baseline violation

- - - - -
a76a31fa by Nilesh Patra at 2022-07-02T13:36:37+05:30
Add autopkgtests

- - - - -
a8339849 by Nilesh Patra at 2022-07-02T13:42:30+05:30
Upload to unstable

- - - - -


12 changed files:

- debian/changelog
- debian/clean
- debian/control
- debian/copyright
- debian/patches/enable_shared_and_static.patch
- + debian/patches/fix-baseline.patch
- debian/patches/series
- debian/rules
- + debian/tests/control
- + debian/tests/run-pkg-test
- + debian/tests/run-pybinding-test
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-libslow5lib (0.5.1+dfsg-1) UNRELEASED; urgency=medium
+libslow5lib (0.5.1+dfsg-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #1014210)
 
- -- Andreas Tille <tille at debian.org>  Wed, 29 Jun 2022 20:34:40 +0200
+ -- Andreas Tille <tille at debian.org>  Sat, 02 Jul 2022 13:39:22 +0530


=====================================
debian/clean
=====================================
@@ -2,3 +2,5 @@
 build/
 lib/
 python/pyslow5.c
+examples/*.idx
+examples/*.blow5


=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 13),
                cmake,
                d-shlibs,
                dh-python,
+               python3-all,
                python3-all-dev,
                libstreamvbyte-dev,
                libzstd-dev,


=====================================
debian/copyright
=====================================
@@ -22,6 +22,7 @@ Copyright: 2020-2022 Hasindu Gamaarachchi, Sasha Jenner, Hiruna Samarakoon
 License: MIT
 
 Files: include/slow5/klib/*
+       src/klib/ksort.h
 Copyright: 2008 Attractive Chaos <attractor at live.co.uk>
 License: MIT
 


=====================================
debian/patches/enable_shared_and_static.patch
=====================================
@@ -4,7 +4,7 @@ Description: Enable static and shared library
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -42,18 +42,31 @@ set(slow5_press src/slow5_press.c)
+@@ -42,18 +42,31 @@
  # add_executable(slow5exmp ${openmp_get_reads})
  
  
@@ -38,13 +38,13 @@ Description: Enable static and shared library
 +target_compile_definitions(slow5_static PUBLIC _GLIBCXX_DEBUG) # PUBLIC to maintain ABI compatibility
 +target_compile_definitions(slow5 PUBLIC _GLIBCXX_DEBUG) # PUBLIC to maintain ABI compatibility
 +
-+target_include_directories(slow5_static PUBLIC inclue)
++target_include_directories(slow5_static PUBLIC include)
 +target_include_directories(slow5 PUBLIC include)
 +
  # Build a static lib
  #add_library(slow5 STATIC ${slow5_} ${slow5_idx} ${slow5_misc} ${slow5_press})
  #
-@@ -72,3 +85,10 @@ target_link_libraries(slow5)
+@@ -72,3 +85,10 @@
  #     target_link_libraries(slow5test slow5 streamvbyte_slow5 -lz -ldl -lm)
  #     target_link_libraries(slow5exmp slow5 streamvbyte_slow5 -lz -ldl -lm)
  # ENDIF()


=====================================
debian/patches/fix-baseline.patch
=====================================
@@ -0,0 +1,21 @@
+Description: remove fpu flags that are not present on ancient CPUs
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2022-07-02
+--- a/setup.py
++++ b/setup.py
+@@ -49,15 +49,6 @@
+ # extra_compile_args = []
+ # os.environ["CFLAGS"] = '-g -Wall -O2 -std=c99'
+ 
+-arch=platform.machine()
+-if arch in ["aarch64", "arm64"]:
+-    extra_compile_args.append('-D__ARM_NEON__')
+-elif arch in ["aarch64"]:
+-	extra_compile_args.append('-mfpu=neon')
+-elif arch in ["x86_64"]:
+-    extra_compile_args.extend(['-DSTREAMVBYTE_SSSE3=1', '-mssse3'])   # WARNING: ancient x86_64 CPUs don't have SSSE3
+-
+-
+ # include_dirs = ['include/', np.get_include() ]
+ libraries = ['m', 'z', 'streamvbyte']
+ library_dirs = ['.']


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 use_debian_packaged_streamvbyte.patch
 enable_shared_and_static.patch
+fix-baseline.patch


=====================================
debian/rules
=====================================
@@ -24,22 +24,31 @@ override_dh_auto_build:
 	for py in `py3versions -s`; do \
 		$$py setup.py build; \
 	done
-#FIXME	cp build/lib.*/*.so  ./
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	mkdir -p lib
-	#cp -a obj-$(DEB_HOST_GNU_TYPE)/libslow5_static.a lib/libslow5.a
-	#$(MAKE) -C test zstd=1
-	PYTHONPATH=$(CURDIR)/build/lib.$(PY_PLATFORM)-$(DEFPY3) python3 < python/example.py
+	cp -a obj-$(DEB_HOST_GNU_TYPE)/libslow5_static.a lib/libslow5.a
+	$(MAKE) -C test zstd=1
+	PYTHONPATH=$(CURDIR)/build/lib.$(PY_PLATFORM)-$(DEFPY3) python3 -m unittest -v python/test.py
 endif
 
 override_dh_install:
-	mv debian/tmp/usr/lib/$(DEB_HOST_GNU_TYPE)/libslow5_static.a debian/tmp/usr/lib/$(DEB_HOST_GNU_TYPE)/libslow5.a
+	mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libslow5_static.a debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libslow5.a
 	d-shlibmove --commit \
 		    --multiarch \
 		    --devunversioned \
 		    --exclude-la \
 		    --movedev include usr \
-		    debian/tmp/usr/lib/$(DEB_HOST_GNU_TYPE)/libslow5.so
+		    debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libslow5.so
 	dh_install
+	dh_install -plibslow5-dev src/*.h usr/include/slow5/
+	dh_install -ppython3-slow5 build/lib.*-*/* usr/lib/python3/dist-packages/
+
+execute_after_dh_install:
+	dh_numpy3
+
+override_dh_installexamples:
+	dh_installexamples
+	dh_installexamples -ppython3-slow5 python/example.py
+	dh_installexamples -ppython3-slow5 examples/*.slow5


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,7 @@
+Tests: run-pybinding-test
+Depends: @, python3-all
+Restrictions: allow-stderr
+
+Tests: run-pkg-test
+Depends: @, build-essential, zlib1g-dev, libstreamvbyte-dev
+Restrictions: allow-stderr


=====================================
debian/tests/run-pkg-test
=====================================
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+CUR_DIR=`pwd`
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a ${CUR_DIR}/test/unit_test* "${AUTOPKGTEST_TMP}"
+cd "${AUTOPKGTEST_TMP}"
+
+for f in unit_test*.c
+do
+	echo "Checking $f"
+	gcc -I/usr/include/slow5/ $f -lslow5 -lm -lz -lstreamvbyte -o test.out
+	rm -f test.out
+	echo "Done!"
+done


=====================================
debian/tests/run-pybinding-test
=====================================
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/python3-slow5/examples/ "${AUTOPKGTEST_TMP}"
+cd "${AUTOPKGTEST_TMP}"
+
+mv examples/example.py .
+
+set -e
+for py in $(py3versions -s 2> /dev/null)
+do echo "Testing with $py in $(pwd):"
+    $py example.py
+done


=====================================
debian/upstream/metadata
=====================================
@@ -1,19 +1,7 @@
-Reference:
- - Author: 
-   Title: 
-   Journal: 
-   Year: 
-   Volume: 
-   Number: 
-   Pages: 
-   DOI: 
-   PMID:
-   URL: 
-   eprint: 
-Registry:
- - Name: conda:bioconda
-   Entry:
- - Name: SciCrunch
-   Entry:
- - Name: bio.tools
-   Entry:
+---
+Archive: GitHub
+Bug-Database: https://github.com/hasindu2008/slow5lib/issues
+Bug-Submit: https://github.com/hasindu2008/slow5lib/issues/new
+Changelog: https://github.com/hasindu2008/slow5lib/tags
+Repository: https://github.com/hasindu2008/slow5lib.git
+Repository-Browse: https://github.com/hasindu2008/slow5lib



View it on GitLab: https://salsa.debian.org/med-team/libslow5lib/-/compare/1cb1272072f8fc913be1e61b817eb278632d7505...a8339849786e5feb751c3ba7917cfae51695802f

-- 
View it on GitLab: https://salsa.debian.org/med-team/libslow5lib/-/compare/1cb1272072f8fc913be1e61b817eb278632d7505...a8339849786e5feb751c3ba7917cfae51695802f
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