This is an automated email from the git hooks/post-receive script. daube-guest pushed a commit to branch master in repository python-skbio.
commit 7ba4eb7483bf3c77700340d72e4813c0debe1a67 Author: Kevin Murray <[email protected]> Date: Tue Nov 15 19:25:59 2016 +1100 Add patch to use libssw in setup.py --- ...02-use-libsww-as-library-not-embedded-src.patch | 48 ++++++++++++++++++++++ debian/patches/mathjax-path | 4 +- debian/patches/series | 1 + 3 files changed, 51 insertions(+), 2 deletions(-) diff --git a/debian/patches/0002-use-libsww-as-library-not-embedded-src.patch b/debian/patches/0002-use-libsww-as-library-not-embedded-src.patch new file mode 100644 index 0000000..01518f5 --- /dev/null +++ b/debian/patches/0002-use-libsww-as-library-not-embedded-src.patch @@ -0,0 +1,48 @@ +From: Kevin Murray <[email protected]> +Date: Tue, 15 Nov 2016 19:21:24 +1100 +Subject: use libsww as library, not embedded src + +--- + setup.py | 22 +++------------------- + 1 file changed, 3 insertions(+), 19 deletions(-) + +diff --git a/setup.py b/setup.py +index 366e058..596323c 100644 +--- a/setup.py ++++ b/setup.py +@@ -58,21 +58,6 @@ with open('README.rst') as f: + USE_CYTHON = os.environ.get('USE_CYTHON', False) + ext = '.pyx' if USE_CYTHON else '.c' + +-# There's a bug in some versions of Python 3.4 that propagates +-# -Werror=declaration-after-statement to extensions, instead of just affecting +-# the compilation of the interpreter. See http://bugs.python.org/issue21121 for +-# details. This acts as a workaround until the next Python 3 release -- thanks +-# Wolfgang Maier (wolma) for the workaround! +-ssw_extra_compile_args = ['-Wno-error=declaration-after-statement'] +-if sys.platform == 'win32': +- ssw_extra_compile_args = [] +- +-# Users with i686 architectures have reported that adding this flag allows +-# SSW to be compiled. See https://github.com/biocore/scikit-bio/issues/409 and +-# http://stackoverflow.com/q/26211814/3776794 for details. +-if platform.machine() == 'i686': +- ssw_extra_compile_args.append('-msse2') +- + extensions = [ + Extension("skbio.metadata._intersection", + ["skbio/metadata/_intersection" + ext]), +@@ -80,10 +65,9 @@ extensions = [ + ["skbio/stats/__subsample" + ext], + include_dirs=[np.get_include()]), + Extension("skbio.alignment._ssw_wrapper", +- ["skbio/alignment/_ssw_wrapper" + ext, +- "skbio/alignment/_lib/ssw.c"], +- extra_compile_args=ssw_extra_compile_args, +- include_dirs=[np.get_include()]), ++ ["skbio/alignment/_ssw_wrapper" + ext], ++ include_dirs=[np.get_include()], ++ libraries=['ssw']), + Extension("skbio.diversity._phylogenetic", + ["skbio/diversity/_phylogenetic" + ext], + include_dirs=[np.get_include()]) diff --git a/debian/patches/mathjax-path b/debian/patches/mathjax-path index 5f57571..eaa9570 100644 --- a/debian/patches/mathjax-path +++ b/debian/patches/mathjax-path @@ -7,10 +7,10 @@ Subject: Set mathjax path to debian's copy 1 file changed, 2 insertions(+) diff --git a/doc/source/conf.py b/doc/source/conf.py -index 3a5d9db..1621c9a 100644 +index 03e7774..a587142 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py -@@ -130,6 +130,8 @@ extensions = [ +@@ -134,6 +134,8 @@ extensions = [ 'sphinx.ext.intersphinx' ] diff --git a/debian/patches/series b/debian/patches/series index 1aaff26..fcc25dc 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ mathjax-path +0002-use-libsww-as-library-not-embedded-src.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
