gentoo-overlay/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch

--- a/tests/pysam_data/Makefile
+++ b/tests/pysam_data/Makefile
@@ -3,7 +3,7 @@
 BAI=$(BAM:%.bam=%.bam.bai)
 CRAM=ex1.cram ex2.cram ex3.cram
 CRAI=$(CRAM:%.cram=%.cram.crai)
-NO_PG:=$(findstring --no-PG,$(shell samtools view))
+NO_PG:=--no-PG
 
 # ex2.bam - bam file without index
 
--- a/tests/tabix_test.py
+++ b/tests/tabix_test.py
@@ -14,6 +14,7 @@
 import subprocess
 import glob
 import re
+import pytest
 from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
     load_and_convert, TABIX_DATADIR, get_temp_filename
 
@@ -1014,6 +1015,7 @@
     globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
 
 
+@pytest.mark.skip(reason="requires internet connectivity")
 class TestRemoteFileHTTP(unittest.TestCase):
 
     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
@@ -1053,6 +1055,7 @@
         self.assertEqual(list(self.local_file.header), [])
 
 
+@pytest.mark.skip(reason="requires internet connectivity")
 class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
 
     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"