[med-svn] [khmer] 04/06: refresh patches

Mon Feb 20 13:11:03 UTC 2017

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misterc-guest pushed a commit to branch experimental-2.1
in repository khmer.

commit b1cc8e2c9291fb75e7fe5c8795dbb1f4f61a20a7
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Mon Feb 20 02:00:03 2017 -0800

    refresh patches
---
 debian/patches/cpython-bug-empty-exceptions |  8 ++++----
 debian/patches/disable_google_analytics     |  2 +-
 debian/patches/get_version                  | 23 +++++++++--------------
 debian/patches/local-libs                   |  2 +-
 debian/patches/older-setuptools             |  4 ++--
 debian/patches/pkg-config                   | 12 ------------
 debian/patches/series                       |  1 -
 debian/patches/silence-mt-bug               |  4 ++--
 8 files changed, 19 insertions(+), 37 deletions(-)

diff --git a/debian/patches/cpython-bug-empty-exceptions b/debian/patches/cpython-bug-empty-exceptions
index 5fb9267..dfc9113 100644
--- a/debian/patches/cpython-bug-empty-exceptions
+++ b/debian/patches/cpython-bug-empty-exceptions
@@ -3,8 +3,8 @@ Description: Work around a suspected CPython bug
 Occurs when exception strings are empty. See upstream issues #885, #1190.
 --- khmer.orig/tests/test_read_parsers.py
 +++ khmer/tests/test_read_parsers.py
-@@ -114,7 +114,10 @@
-         for read in rparser:
+@@ -169,7 +169,10 @@
+         for _ in rparser:
              n_reads += 1
      except ValueError as err:
 -        assert "Sequence is empty" in str(err), str(err)
@@ -15,7 +15,7 @@ Occurs when exception 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)
  
-@@ -302,7 +305,10 @@
+@@ -357,7 +360,10 @@
              pass
          assert 0, "No exception raised on a truncated file"
      except ValueError as err:
@@ -27,7 +27,7 @@ Occurs when exception strings are empty. See upstream issues #885, #1190.
  
  
  def test_iterator_identities():
-@@ -361,7 +367,10 @@
+@@ -413,7 +419,10 @@
              pass
          failed = False
      except ValueError as exc:
diff --git a/debian/patches/disable_google_analytics b/debian/patches/disable_google_analytics
index e01f849..6351539 100644
--- a/debian/patches/disable_google_analytics
+++ b/debian/patches/disable_google_analytics
@@ -3,7 +3,7 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 
 --- khmer.orig/doc/conf.py
 +++ khmer/doc/conf.py
-@@ -191,7 +191,7 @@
+@@ -184,7 +184,7 @@
  # Various settings to pass to templates:
  
  html_context = {
diff --git a/debian/patches/get_version b/debian/patches/get_version
index eec7811..93208f2 100644
--- a/debian/patches/get_version
+++ b/debian/patches/get_version
@@ -1,6 +1,6 @@
 Description: Use debian package version instead of git version
---- a/doc/conf.py
-+++ b/doc/conf.py
+--- khmer.orig/doc/conf.py
++++ khmer/doc/conf.py
 @@ -13,6 +13,7 @@
  
  import sys
@@ -9,24 +9,19 @@ Description: Use debian package version instead of git version
  
  # If extensions (or modules to document with autodoc) are in another directory,
  # add these directories to sys.path here. If the directory is relative to the
-@@ -57,16 +58,10 @@
+@@ -57,9 +58,12 @@
  
  # The full version, including alpha/beta/rc tags.
  
--sys.path.insert(0, '../')
--import versioneer
--versioneer.VCS = 'git'
--versioneer.versionfile_source = '../khmer/_version.py'
--versioneer.versionfile_build = '../khmer/_version.py'
--versioneer.tag_prefix = 'v'  # tags are like v1.2.0
--versioneer.parentdir_prefix = '..'
--release = versioneer.get_version()
--del versioneer
--sys.path.remove('../')
+-from khmer._version import get_versions
+-release = get_versions()['version']
+-del get_versions
++#from khmer._version import get_versions
++#release = get_versions()['version']
++#del get_versions
 +release = subprocess.check_output(
 +    ['sh', '-c', 'cd ..; dpkg-parsechangelog --show-field Version'])
 +release = release.decode('utf-8')
-+
  
  # The short X.Y version.
  
diff --git a/debian/patches/local-libs b/debian/patches/local-libs
index 587ecc2..4535584 100644
--- a/debian/patches/local-libs
+++ b/debian/patches/local-libs
@@ -3,7 +3,7 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 
 --- khmer.orig/setup.cfg
 +++ khmer/setup.cfg
-@@ -7,10 +7,10 @@
+@@ -1,10 +1,10 @@
  [build_ext]
  define = SEQAN_HAS_BZIP2,SEQAN_HAS_ZLIB
  undef = NO_UNIQUE_RC
diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools
index c3bad7b..c7ee1b6 100644
--- a/debian/patches/older-setuptools
+++ b/debian/patches/older-setuptools
@@ -18,5 +18,5 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
  import versioneer
 -ez_setup.use_setuptools(version="3.4.1")
  
- versioneer.VCS = 'git'
- versioneer.versionfile_source = 'khmer/_version.py'
+ CMDCLASS = versioneer.get_cmdclass()
+ 
diff --git a/debian/patches/pkg-config b/debian/patches/pkg-config
deleted file mode 100644
index 55b4288..0000000
--- a/debian/patches/pkg-config
+++ /dev/null
@@ -1,12 +0,0 @@
-Description: Enable static compiling with pkg-config
-Author: Sascha Steinbiss <satta at debian.org>
---- a/lib/oxli.pc.in
-+++ b/lib/oxli.pc.in
-@@ -10,5 +10,7 @@
- Version: @VERSION@
- 
- Requires:
-+Requires.private: zlib
- Libs: -L${libdir} -L${sharedlibdir} -loxli
-+Libs.private: -lbz2
- Cflags: -I${includedir}
diff --git a/debian/patches/series b/debian/patches/series
index 5081bda..95db57b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,4 +6,3 @@ get_version
 install-prefix
 cpython-bug-empty-exceptions
 silence-mt-bug
-pkg-config
diff --git a/debian/patches/silence-mt-bug b/debian/patches/silence-mt-bug
index da5d236..98e2006 100644
--- a/debian/patches/silence-mt-bug
+++ b/debian/patches/silence-mt-bug
@@ -2,11 +2,11 @@ Description: silence a known inconsistency with multithreading
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 --- khmer.orig/tests/test_scripts.py
 +++ khmer/tests/test_scripts.py
-@@ -1592,6 +1592,7 @@
+@@ -1375,6 +1375,7 @@
          assert line == '255,2,98,1.0', line
  
  
 + at attr('known_failing')
  def test_abundance_dist_threaded():
-     infile = utils.get_temp_filename('test.fa')
+     infile = utils.copy_test_data('test-abund-read-2.fa')
      outfile = utils.get_temp_filename('test.dist')

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