[med-svn] [khmer] 04/04: refresh patches

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository khmer.

commit a5add3e694dea46df588763c8ea72a32b473bbee
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
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 <michael.crusoe at gmail.com>
 
 --- khmer.orig/setup.py
 +++ khmer/setup.py
-@@ -5,8 +5,6 @@
+@@ -36,8 +36,6 @@
  # Contact: khmer-project at idyll.org
  """Setup for khmer project."""
  
@@ -12,7 +12,7 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
  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.

-- 
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