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debian/changelog
View file @ 933b6426
......@@ -6,6 +6,7 @@ python-pysam (0.14+ds-1) UNRELEASED; urgency=medium
* cme fix dpkg-control
* debhelper 11
* do not remove samtools/tmp_file.h in clean target
* do not depend from non-existing data file in make test target
-- Andreas Tille <tille@debian.org> Sat, 17 Feb 2018 15:24:34 +0100
......
debian/patches/exclude_tests_accessing_remote_http.patch
View file @ 933b6426
......@@ -154,3 +154,72 @@ Description: Exclude tests trying to access remote http sites and thus need
class TestLargeOptValues(unittest.TestCase):
ints = (65536, 214748, 2147484, 2147483647)
--- a/tests/tabix_test.py
+++ b/tests/tabix_test.py
@@ -1039,66 +1039,6 @@ for vcf_file in vcf_files:
globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
-class TestRemoteFileHTTP(unittest.TestCase):
-
- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
- region = "chr1:1-1000"
- local = os.path.join(TABIX_DATADIR, "example.gtf.gz")
-
- def setUp(self):
- if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
- self.remote_file = None
- else:
- self.remote_file = pysam.TabixFile(self.url, "r")
-
- self.local_file = pysam.TabixFile(self.local, "r")
-
- def tearDown(self):
- if self.remote_file is None:
- return
-
- self.remote_file.close()
- self.local_file.close()
-
- def testFetchAll(self):
- if self.remote_file is None:
- return
-
- remote_result = list(self.remote_file.fetch())
- local_result = list(self.local_file.fetch())
-
- self.assertEqual(len(remote_result), len(local_result))
- for x, y in zip(remote_result, local_result):
- self.assertEqual(x, y)
-
- def testHeader(self):
- if self.remote_file is None:
- return
-
- 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 checkURL(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):
filename_src = os.path.join(TABIX_DATADIR, "example.vcf.gz")
debian/patches/series
View file @ 933b6426
execute-linking-tests-only-when-explicitely-reque.patch
xfail.patch
exclude_tests_accessing_remote_http.patch
skip_test_needing_missing_data.patch
debian/patches/skip_test_needing_missing_data.patch 0 → 100644
View file @ 933b6426
Description: do not depend from non-existing data file in make test target
(There is no such file example_reverse_complement.bam)
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 17 Feb 2018 15:24:34 +0100
--- a/tests/pysam_data/Makefile
+++ b/tests/pysam_data/Makefile
@@ -20,8 +20,7 @@ all: ex1.pileup.gz \
explicit_index.bam explicit_index.cram \
faidx_empty_seq.fq.gz \
ex1.fa.gz ex1.fa.gz.csi \
- ex1_csi.bam \
- example_reverse_complement.bam
+ ex1_csi.bam
# ex2.sam - as ex1.sam, but with header
ex2.sam.gz: ex1.bam ex1.bam.bai
--- a/tests/AlignmentFile_test.py
+++ b/tests/AlignmentFile_test.py
@@ -1361,12 +1361,7 @@ class TestEmptyHeader(unittest.TestCase)
'example_empty_header.bam'))
self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]})
- def test_bam_without_seq_in_header(self):
- s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))
- self.assertTrue("SQ" in s.header.to_dict())
- self.assertTrue("@SQ" in str(s.header))
-
class TestHeaderWithProgramOptions(unittest.TestCase):
'''see issue 39.'''
debian/rules
View file @ 933b6426
......@@ -15,8 +15,9 @@ HTSLIBDIR := /usr/lib/$(DEB_HOST_MULTIARCH)
export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
export HTSLIB_INCLUDE_DIR=/usr/include
export PYBUILD_TEST_ARGS_python2=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
# 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
%:
......