This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer.
commit f39ef7bc2de19ed2e76057644cea5604ef01764c Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> --- 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 <[email protected]> --- 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 <[email protected]> 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 <[email protected]> ---- 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 <[email protected]> --- 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 +@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') -- 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
