From 9b1e2d6447b2d5c55d06ea46656397ea72c4a751 Mon Sep 17 00:00:00 2001 From: Andreas Tille Date: Wed, 13 Dec 2017 13:29:59 +0100 Subject: [PATCH] Refresh patches --- ...ng-tests-only-when-explicitely-reque.patch | 49 ++----------------- ...vent-it-from-being-picked-up-by-nose.patch | 39 --------------- debian/patches/series | 1 - debian/patches/xfail.patch | 6 +-- 4 files changed, 6 insertions(+), 89 deletions(-) delete mode 100644 debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch diff --git a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch index 185dfbd..fe9bbe4 100644 --- a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch +++ b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch @@ -12,55 +12,12 @@ Subject: execute linking tests only when explicitely --- a/.travis.yml +++ b/.travis.yml -@@ -11,6 +11,8 @@ env: +@@ -11,8 +11,6 @@ env: - CONDA_PY=3.4 - CONDA_PY=3.5 - CONDA_PY=3.6 -+ global: -+ - PYSAM_LINKING_TEST=1 +- global: +- - PYSAM_LINKING_TEST=1 addons: apt: ---- a/tests/TestUtils.py -+++ b/tests/TestUtils.py -@@ -23,6 +23,7 @@ LINKDIR = os.path.abspath(os.path.join(o - - IS_PYTHON3 = sys.version_info[0] >= 3 - -+ - if IS_PYTHON3: - from itertools import zip_longest - from urllib.request import urlopen ---- a/tests/linking_test.py -+++ b/tests/linking_test.py -@@ -31,6 +31,9 @@ def check_tests_pass(statement): - return True - - -+@unittest.skipUnless( -+ os.environ.get("PYSAM_LINKING_TESTS", None), -+ "enable linking tests by setting PYSAM_LINKING_TESTS environment variable") - class TestLinking(unittest.TestCase): - - package_name = "link_with_rpath" -@@ -43,6 +46,10 @@ class TestLinking(unittest.TestCase): - "cd {} && rm -rf build && python setup.py install".format(self.workdir), - shell=True) - -+ -+@unittest.skipUnless( -+ os.environ.get("PYSAM_LINKING_TESTS", None), -+ "enable linking tests by setting PYSAM_LINKING_TESTS environment variable") - class TestLinkWithRpath(TestLinking): - - package_name = "link_with_rpath" -@@ -52,6 +59,9 @@ class TestLinkWithRpath(TestLinking): - "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests")))) - - -+@unittest.skipUnless( -+ os.environ.get("PYSAM_LINKING_TESTS", None), -+ "enable linking tests by setting PYSAM_LINKING_TESTS environment variable") - class TestLinkWithoutRpath(TestLinking): - - package_name = "link_without_rpath" diff --git a/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch b/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch deleted file mode 100644 index d96b801..0000000 --- a/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch +++ /dev/null @@ -1,39 +0,0 @@ -From: Andreas Heger -Date: Mon, 18 Sep 2017 16:48:21 +0100 -Bug-Debian: https://bugs.debian.org/871083 -Subject: rename helper function to prevent it from being picked - up by nose, fixes #541 - ---- - tests/linking_test.py | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - ---- a/tests/linking_test.py -+++ b/tests/linking_test.py -@@ -20,7 +20,7 @@ def check_import(statement): - raise - - --def check_tests_pass(statement): -+def check_pass(statement): - try: - output = subprocess.check_output( - statement, stderr=subprocess.STDOUT, shell=True) -@@ -55,7 +55,7 @@ class TestLinkWithRpath(TestLinking): - package_name = "link_with_rpath" - - def test_package_tests_pass(self): -- self.assertTrue(check_tests_pass( -+ self.assertTrue(check_pass( - "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests")))) - - -@@ -79,7 +79,7 @@ class TestLinkWithoutRpath(TestLinking): - pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries]) - pysam_libdir = pysam_libdirs[0] - -- self.assertTrue(check_tests_pass( -+ self.assertTrue(check_pass( - "export LD_LIBRARY_PATH={}:$PATH && cd {} && python test_module.py".format( - pysam_libdir, - os.path.join(self.workdir, "tests")))) diff --git a/debian/patches/series b/debian/patches/series index 5014bfa..c2c2f28 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,2 @@ execute-linking-tests-only-when-explicitely-reque.patch -rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch xfail.patch diff --git a/debian/patches/xfail.patch b/debian/patches/xfail.patch index 8a214a2..15c77fe 100644 --- a/debian/patches/xfail.patch +++ b/debian/patches/xfail.patch @@ -3,9 +3,9 @@ Description: temporarily skip failing test Author: Afif Elghraoui Forwarded: not-needed Last-Update: 2017-10-01 ---- python-pysam.orig/tests/AlignmentFile_test.py -+++ python-pysam/tests/AlignmentFile_test.py -@@ -521,6 +521,7 @@ +--- a/tests/AlignmentFile_test.py ++++ b/tests/AlignmentFile_test.py +@@ -521,6 +521,7 @@ class TestIO(unittest.TestCase): "tmp_ex2.bam", "rb", "wb") -- 2.30.2