[med-svn] [Git][med-team/python-pysam][master] 5 commits: Please do not silently ignore changes from unreleased changelog paragraphs
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 12 15:58:50 BST 2018
Andreas Tille pushed to branch master at Debian Med / python-pysam
Commits:
043a6b0c by Andreas Tille at 2018-09-12T12:36:24Z
Please do not silently ignore changes from unreleased changelog paragraphs
- - - - -
cb0b80a6 by Andreas Tille at 2018-09-12T12:37:34Z
Remove ancient fields X-Python*-Version
- - - - -
84eb0baf by Andreas Tille at 2018-09-12T14:53:40Z
Adjust patches for failed tests
- - - - -
fb52fc17 by Andreas Tille at 2018-09-12T14:54:46Z
Adjust versioned Dependencies
- - - - -
0004b93e by Andreas Tille at 2018-09-12T14:57:44Z
Standards-Version: 4.2.1
- - - - -
7 changed files:
- debian/changelog
- debian/control
- − debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
- debian/patches/series
- + debian/patches/skip_test_remote.patch
- − debian/patches/xfail.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,13 +1,18 @@
+python-pysam (0.15.0.1+ds-2) UNRELEASED; urgency=medium
+
+ * Remove ancient fields X-Python*-Version
+ * Adjust patches for build time test suite
+ * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille at debian.org> Wed, 12 Sep 2018 14:37:26 +0200
+
python-pysam (0.15.0.1+ds-1) experimental; urgency=medium
* Team upload.
+ [ Steffen Moeller ]
* New upstream version.
- -- Steffen Moeller <moeller at debian.org> Sun, 29 Jul 2018 00:51:38 +0200
-
-python-pysam (0.14.1+ds-1) UNRELEASED; urgency=medium
-
[ Afif Elghraoui ]
* New upstream version 0.14.1+ds
* Update patches
@@ -17,7 +22,7 @@ python-pysam (0.14.1+ds-1) UNRELEASED; urgency=medium
* Rename d/tests/control to d/tests/control.autodep8
* Standards-Version: 4.1.4
- -- Afif Elghraoui <afif at debian.org> Sun, 22 Apr 2018 19:02:41 -0400
+ -- Steffen Moeller <moeller at debian.org> Sun, 29 Jul 2018 00:51:38 +0200
python-pysam (0.14+ds-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -18,16 +18,14 @@ Build-Depends: debhelper (>= 11~),
python3-setuptools,
cython3 (>= 0.23),
tabix <!nocheck>,
- samtools (>= 1.7) <!nocheck>,
- bcftools (>= 1.7) <!nocheck>,
+ samtools (>= 1.9) <!nocheck>,
+ bcftools (>= 1.9) <!nocheck>,
python-pytest <!nocheck>,
python3-pytest <!nocheck>
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
Homepage: http://pysam.readthedocs.org/en/latest
-X-Python-Version: >= 2.7
-X-Python3-Version: >= 3.2
Package: python-pysam
Architecture: any
=====================================
debian/patches/execute-linking-tests-only-when-explicitely-reque.patch deleted
=====================================
@@ -1,23 +0,0 @@
-From: Andreas Heger <andreas.heger at gmail.com>
-Date: Mon, 18 Sep 2017 11:19:28 +0100
-Bug-Debian: https://bugs.debian.org/871083
-Subject: execute linking tests only when explicitly
- requested via PYSAM_LINKING_TESTS env var. Keep on travis. Fixes #534
-
----
- .travis.yml | 2 ++
- tests/TestUtils.py | 1 +
- tests/linking_test.py | 10 ++++++++++
- 3 files changed, 13 insertions(+)
-
---- a/.travis.yml
-+++ b/.travis.yml
-@@ -11,8 +11,6 @@ env:
- - CONDA_PY=3.4
- - CONDA_PY=3.5
- - CONDA_PY=3.6
-- global:
-- - PYSAM_LINKING_TEST=1
-
- addons:
- apt:
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
-#execute-linking-tests-only-when-explicitely-reque.patch
-#xfail.patch
-#skip_test_needing_missing_data.patch
+skip_test_needing_missing_data.patch
+skip_test_remote.patch
=====================================
debian/patches/skip_test_remote.patch
=====================================
@@ -0,0 +1,72 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
+Description: Skip tests trying to access remote site
+
+--- a/tests/AlignmentFile_test.py
++++ b/tests/AlignmentFile_test.py
+@@ -1596,6 +1596,7 @@ class TestDoubleFetchCRAMWithReference(T
+ reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
+
+
++ at unittest.skip
+ class TestRemoteFileFTP(unittest.TestCase):
+
+ '''test remote access.
+--- a/tests/tabix_test.py
++++ b/tests/tabix_test.py
+@@ -1039,6 +1039,7 @@ for vcf_file in vcf_files:
+ globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
+
+
++ at unittest.skip
+ class TestRemoteFileHTTP(unittest.TestCase):
+
+ url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
+@@ -1078,25 +1079,28 @@ class TestRemoteFileHTTP(unittest.TestCa
+ self.assertEqual(list(self.local_file.header), [])
+
+
+-class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+-
+- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
+- region = "chr1:1-1000"
+- local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
+-
+- def setUp(self):
+- if not pysam.config.HAVE_LIBCURL or not check_url(self.url):
+- self.remote_file = None
+- else:
+- self.remote_file = pysam.TabixFile(self.url, "r")
+- self.local_file = pysam.TabixFile(self.local, "r")
+-
+- def testHeader(self):
+- if self.remote_file is None:
+- return
+-
+- self.assertEqual(list(self.local_file.header), ["# comment at start"])
+- self.assertEqual(list(self.local_file.header), self.remote_file.header)
++#@unittest.skip # this leads to
++ # E TypeError: Error when calling the metaclass bases
++ # E function() argument 1 must be code, not str
++#class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
++#
++# url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
++# region = "chr1:1-1000"
++# local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
++#
++# def setUp(self):
++# if not pysam.config.HAVE_LIBCURL or not check_url(self.url):
++# self.remote_file = None
++# else:
++# self.remote_file = pysam.TabixFile(self.url, "r")
++# self.local_file = pysam.TabixFile(self.local, "r")
++#
++# def testHeader(self):
++# if self.remote_file is None:
++# return
++#
++# self.assertEqual(list(self.local_file.header), ["# comment at start"])
++# self.assertEqual(list(self.local_file.header), self.remote_file.header)
+
+
+ class TestIndexArgument(unittest.TestCase):
=====================================
debian/patches/xfail.patch deleted
=====================================
@@ -1,17 +0,0 @@
-Description: temporarily skip failing test
- See https://github.com/pysam-developers/pysam/issues/542
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2017-10-01
-Index: python-pysam/tests/AlignmentFile_test.py
-===================================================================
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -472,6 +472,7 @@ class TestIO(unittest.TestCase):
- "tmp_ex2.bam",
- "rb", "wb")
-
-+ @unittest.skip
- def testCRAM2CRAM(self):
- # in some systems different reference sequence paths might be
- # embedded in the CRAM files which will result in different headers
=====================================
debian/rules
=====================================
@@ -15,10 +15,6 @@ HTSLIBDIR := /usr/lib/$(DEB_HOST_MULTIARCH)
export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
export HTSLIB_INCLUDE_DIR=/usr/include
-# unfortunately this does not work - any hint to fix this would be really welcome
-#export PYBUILD_TEST_ARGS_python2=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
-#export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
-
clean: clean-tests
%:
dh $@ --with python2,python3 --buildsystem=pybuild
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a
--
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/480bb04a941650ff08250475ad73066a25a691d6...0004b93eb49ac7a146b7f8012fe0d395a31c9a0a
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20180912/6434c65b/attachment-0001.html>
More information about the debian-med-commit
mailing list