Andreas Tille pushed to branch master at Debian Med / python-pysam
Commits: 089b7cc4 by Andreas Tille at 2018-02-17T16:04:59+01:00 do not depend from non-existing data file in make test target - - - - - 7d981166 by Andreas Tille at 2018-02-17T20:46:41+01:00 Restore old patch since the attempt to exclude tests more easily failed - - - - - 933b6426 by Andreas Tille at 2018-02-17T21:29:46+01:00 Remove test that tries to access missing data file - - - - - 5 changed files: - debian/changelog - debian/patches/exclude_tests_accessing_remote_http.patch - debian/patches/series - + debian/patches/skip_test_needing_missing_data.patch - debian/rules Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -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 <[email protected]> Sat, 17 Feb 2018 15:24:34 +0100 ===================================== debian/patches/exclude_tests_accessing_remote_http.patch ===================================== --- a/debian/patches/exclude_tests_accessing_remote_http.patch +++ b/debian/patches/exclude_tests_accessing_remote_http.patch @@ -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 ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ 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 ===================================== --- /dev/null +++ b/debian/patches/skip_test_needing_missing_data.patch @@ -0,0 +1,32 @@ +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 <[email protected]> +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 ===================================== --- a/debian/rules +++ b/debian/rules @@ -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 %: View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/573a161da5f04049b8f8fb1faf176f4f14b0af83...933b6426545ae28f68fab60490fe3bc1376fdc8e --- View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/573a161da5f04049b8f8fb1faf176f4f14b0af83...933b6426545ae28f68fab60490fe3bc1376fdc8e You're receiving this email because of your account on salsa.debian.org.
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