[med-svn] [python-pybedtools] 05/08: Adapt patches
Andreas Tille
tille at debian.org
Wed Jul 19 19:35:40 UTC 2017
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tille pushed a commit to branch master
in repository python-pybedtools.
commit 5bd42efea85e9f2244b1c944e37cf9635a662441
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 19 21:19:59 2017 +0200
Adapt patches
---
debian/patches/disable-test-156 | 68 +++++++++---------------------------
debian/patches/disable-write-version | 16 ++++-----
debian/patches/enable-package-data | 6 ++--
debian/patches/rename-scripts | 6 ++--
4 files changed, 30 insertions(+), 66 deletions(-)
diff --git a/debian/patches/disable-test-156 b/debian/patches/disable-test-156
index 1d79038..6ff75e8 100644
--- a/debian/patches/disable-test-156
+++ b/debian/patches/disable-test-156
@@ -1,60 +1,24 @@
Description: skip a known failing test
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
---- python-pybedtools.orig/pybedtools/test/test1.py
-+++ python-pybedtools/pybedtools/test/test1.py
-@@ -1952,28 +1952,33 @@
- # that lists of filenames works.
+--- a/pybedtools/test/test1.py
++++ b/pybedtools/test/test1.py
+@@ -1956,7 +1956,8 @@ def test_issue_156():
a = pybedtools.example_bedtool('a.bed')
b = [pybedtools.example_filename('b.bed'), pybedtools.example_filename('c.gff')]
-- assert str(a.intersect(b)) == fix(
-- """
-- chr1 60 100 feature1 0 +
-- chr1 155 200 feature2 0 +
-- chr1 174 200 feature2 0 +
-- chr1 174 200 feature2 0 +
-- chr1 100 200 feature2 0 +
-- chr1 155 200 feature3 0 -
-- chr1 465 500 feature3 0 -
-- chr1 486 500 feature3 0 -
-- chr1 174 326 feature3 0 -
-- chr1 439 500 feature3 0 -
-- chr1 496 500 feature3 0 -
-- chr1 486 500 feature3 0 -
-- chr1 174 326 feature3 0 -
-- chr1 439 500 feature3 0 -
-- chr1 150 269 feature3 0 -
-- chr1 900 901 feature4 0 +
-- chr1 900 913 feature4 0 +
-- chr1 900 913 feature4 0 +
-- chr1 900 950 feature4 0 +
-- """)
+ res = str(a.intersect(b))
+- assert res == fix(
+ try:
-+ assert str(a.intersect(b)) == fix(
-+ """
-+ chr1 60 100 feature1 0 +
-+ chr1 155 200 feature2 0 +
-+ chr1 174 200 feature2 0 +
-+ chr1 174 200 feature2 0 +
-+ chr1 100 200 feature2 0 +
-+ chr1 155 200 feature3 0 -
-+ chr1 465 500 feature3 0 -
-+ chr1 486 500 feature3 0 -
-+ chr1 174 326 feature3 0 -
-+ chr1 439 500 feature3 0 -
-+ chr1 496 500 feature3 0 -
-+ chr1 486 500 feature3 0 -
-+ chr1 174 326 feature3 0 -
-+ chr1 439 500 feature3 0 -
-+ chr1 150 269 feature3 0 -
-+ chr1 900 901 feature4 0 +
-+ chr1 900 913 feature4 0 +
-+ chr1 900 913 feature4 0 +
-+ chr1 900 950 feature4 0 +
-+ """)
++ assert res == fix(
+ """
+ chr1 59 100 feature1 0 +
+ chr1 155 200 feature2 0 +
+@@ -1978,6 +1979,9 @@ def test_issue_156():
+ chr1 900 913 feature4 0 +
+ chr1 900 950 feature4 0 +
+ """), res
+ except AssertionError:
+ raise SkipTest('Known failure on Debian Unstable. '
+ 'https://github.com/daler/pybedtools/issues/193')
-+
- assert str(a.intersect(b, wb=True, names=['B', 'C'])) == fix(
- """
- chr1 60 100 feature1 0 + C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
+
+ res = str(a.intersect(b, wb=True, names=['B', 'C']))
+ assert res == fix(
diff --git a/debian/patches/disable-write-version b/debian/patches/disable-write-version
index 391ec7f..67a7aec 100644
--- a/debian/patches/disable-write-version
+++ b/debian/patches/disable-write-version
@@ -1,13 +1,13 @@
Description: don't rewrite the version
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
---- python-pybedtools.orig/setup.py
-+++ python-pybedtools/setup.py
-@@ -323,7 +323,7 @@
- if _have_setuptools:
- setuptools_kwargs['setup_requires'] = setup_requires
- setuptools_kwargs['install_requires'] = install_requires
-- write_version_py()
-+ #write_version_py()
+--- a/setup.py
++++ b/setup.py
+@@ -328,7 +328,7 @@ if __name__ == "__main__":
+ install_requires) = check_dependency_versions(min_versions)
+ setuptools_kwargs['setup_requires'] = setup_requires
+ setuptools_kwargs['install_requires'] = install_requires
+- write_version_py()
++ #write_version_py()
cwd = os.path.abspath(os.path.dirname(__file__))
if not os.path.exists(os.path.join(cwd, 'PKG-INFO')) and not no_frills:
diff --git a/debian/patches/enable-package-data b/debian/patches/enable-package-data
index 991a970..3dccf57 100644
--- a/debian/patches/enable-package-data
+++ b/debian/patches/enable-package-data
@@ -1,8 +1,8 @@
Description: ship test data
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
---- python-pybedtools.orig/setup.py
-+++ python-pybedtools/setup.py
-@@ -368,7 +368,7 @@
+--- a/setup.py
++++ b/setup.py
+@@ -373,7 +373,7 @@ if __name__ == "__main__":
"*.c",
"*.cpp"]
},
diff --git a/debian/patches/rename-scripts b/debian/patches/rename-scripts
index 17f0683..2a67ca2 100644
--- a/debian/patches/rename-scripts
+++ b/debian/patches/rename-scripts
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: rename the scripts to follow policy
---- python-pybedtools.orig/setup.py
-+++ python-pybedtools/setup.py
-@@ -368,13 +368,15 @@
+--- a/setup.py
++++ b/setup.py
+@@ -373,13 +373,15 @@ if __name__ == "__main__":
"*.c",
"*.cpp"]
},
--
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