debian/changelog

+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@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@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@debian.org>  Sun, 22 Apr 2018 19:02:41 -0400
+ -- Steffen Moeller <moeller@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

-From: Andreas Heger <andreas.heger@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

-#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

+Author: Andreas Tille <tille@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')
+ 
+ 
++@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,))
+ 
+ 
++@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

-Description: temporarily skip failing test
- See https://github.com/pysam-developers/pysam/issues/542
-Author: Afif Elghraoui <afif@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