This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer.
commit a5add3e694dea46df588763c8ea72a32b473bbee Author: Michael R. Crusoe <[email protected]> Date: Fri Sep 4 15:49:14 2015 -0700 refresh patches --- debian/patches/cpython-bug-empty-exceptions | 10 +++---- debian/patches/install-prefix | 41 +---------------------------- debian/patches/older-setuptools | 4 +-- debian/patches/setup-py-py3 | 10 +++---- 4 files changed, 13 insertions(+), 52 deletions(-) diff --git a/debian/patches/cpython-bug-empty-exceptions b/debian/patches/cpython-bug-empty-exceptions index d414638..1f46b37 100644 --- a/debian/patches/cpython-bug-empty-exceptions +++ b/debian/patches/cpython-bug-empty-exceptions @@ -1,9 +1,9 @@ Patch unit test asserts to work around a suspected CPython bug where execption strings are empty. See upstream issues #885, #1190. ---- a/tests/test_read_parsers.py -+++ b/tests/test_read_parsers.py -@@ -88,7 +88,10 @@ +--- khmer.orig/tests/test_read_parsers.py ++++ khmer/tests/test_read_parsers.py +@@ -114,7 +114,10 @@ for read in rparser: n_reads += 1 except ValueError as err: @@ -15,7 +15,7 @@ strings are empty. See upstream issues #885, #1190. assert rparser.num_reads == 1, "%d valid reads in file, got %d" % ( n_reads, rparser.num_reads) -@@ -276,7 +279,10 @@ +@@ -302,7 +305,10 @@ pass assert 0, "No exception raised on a truncated file" except ValueError as err: @@ -27,7 +27,7 @@ strings are empty. See upstream issues #885, #1190. def test_iterator_identities(): -@@ -335,7 +341,10 @@ +@@ -361,7 +367,10 @@ pass failed = False except ValueError as exc: diff --git a/debian/patches/install-prefix b/debian/patches/install-prefix index 7909704..5372e73 100644 --- a/debian/patches/install-prefix +++ b/debian/patches/install-prefix @@ -1,7 +1,7 @@ Use correct library version etc. (fixed by upstream #1240, remove for 2.0) --- khmer.orig/lib/Makefile +++ khmer/lib/Makefile -@@ -28,7 +28,7 @@ +@@ -63,7 +63,7 @@ # when optimization is turned on). WANT_DEBUGGING=false @@ -10,42 +10,3 @@ Use correct library version etc. (fixed by upstream #1240, remove for 2.0) ### NOTE: No user-serviceable parts below this line! ### -@@ -118,24 +118,20 @@ - VERSION = $(shell ./get_version.py) - endif - --MAJOR_VERSION = $(shell echo $(VERSION) | sed -e 's/^\([^-\.]*\)\.\([^-\.]*\).*/\1/') --MINOR_VERSION = $(shell echo $(VERSION) | sed -e 's/^\([^-\.]*\)\.\([^-\.]*\).*/\2/') -- --LIB_VERSION = $(MAJOR_VERSION).$(MINOR_VERSION) -+# The ABI version of liboxli -+LIBVERSION = 1 - - ifeq ($(shell uname), Darwin) - SHARED_EXT = dylib --SONAME = liboxli.$(SHARED_EXT).$(MAJOR_VERSION) --SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) -compatibility_version $(MAJOR_VERSION) -current_version $(LIB_VERSION) -+SONAME = liboxli.$(SHARED_EXT).$(LIBVERSION) -+SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) -current_version $(LIBVERSION) - else - SHARED_EXT = so --SONAME = liboxli.$(SHARED_EXT).$(MAJOR_VERSION) -+SONAME = liboxli.$(SHARED_EXT).$(LIBVERSION) - SONAME_FLAGS = -Wl,-soname=$(SONAME) - endif - --# The ABI version of liboxli --LIBVERSION = 1 --LIBKHMERSO=liboxli.$(SHARED_EXT).$(LIB_VERSION) -+LIBKHMERSO=liboxli.$(SHARED_EXT) - - CXXFLAGS += -DVERSION=$(VERSION) - -@@ -270,7 +266,6 @@ - $(LIBKHMERSO): $(LIBKHMER_OBJS) - $(CXX) $(CXXFLAGS) $(LDFLAGS) $(SONAME_FLAGS) -shared -o $@ $^ - ln -sf $(LIBKHMERSO) $(SONAME) -- ln -sf $(SONAME) liboxli.$(SHARED_EXT) - - liboxli.a: $(LIBKHMER_OBJS) - ar rcs $@ $^ diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools index c01be1e..c3bad7b 100644 --- a/debian/patches/older-setuptools +++ b/debian/patches/older-setuptools @@ -3,7 +3,7 @@ Author: Michael R. Crusoe <[email protected]> --- khmer.orig/setup.py +++ khmer/setup.py -@@ -5,8 +5,6 @@ +@@ -36,8 +36,6 @@ # Contact: [email protected] """Setup for khmer project.""" @@ -12,7 +12,7 @@ Author: Michael R. Crusoe <[email protected]> import os import sys from os import listdir as os_listdir -@@ -24,7 +22,6 @@ +@@ -55,7 +53,6 @@ from distutils.errors import DistutilsPlatformError import versioneer diff --git a/debian/patches/setup-py-py3 b/debian/patches/setup-py-py3 index 7a42ee8..05823cd 100644 --- a/debian/patches/setup-py-py3 +++ b/debian/patches/setup-py-py3 @@ -1,9 +1,9 @@ Use /usr/bin/env python3 as the crunchbang interpreter in setup.py ---- a/setup.py -+++ b/setup.py +--- khmer.orig/setup.py ++++ khmer/setup.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python -+#!/usr/bin/env python3 ++#! /usr/bin/env python3 + # vim: set fileencoding=utf-8 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is - # Copyright (C) Michigan State University, 2009-2015. It is licensed under - # the three-clause BSD license; see doc/LICENSE.txt. + # Copyright (C) 2013-2015, Michigan State University. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
