gentoo resync : 25.08.2020

2 files changed, 37 insertions, 63 deletions

diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
deleted file mode 100644
index 8b323a63fba5..000000000000
--- a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-The build system is not designed with partial out-of-source
-builds in mind. This is evident by using relative includes
-such as '-Isamtools' instead of proper relative or absolute
-paths.
-
-Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
-
---- a/setup.py
-+++ b/setup.py
-@@ -359,6 +359,8 @@
- 
- define_macros = []
- 
-+samtools_include_dirs = [os.path.abspath("samtools")]
-+
- chtslib = Extension(
-     "pysam.libchtslib",
-     [source_pattern % "htslib",
-@@ -385,7 +387,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
-+    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-     extra_compile_args=extra_compile_args,
-@@ -404,7 +406,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
-+    include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-     extra_compile_args=extra_compile_args,
-@@ -423,7 +425,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
-+    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-     extra_compile_args=extra_compile_args,
-@@ -467,7 +469,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=["pysam"] + htslib_library_dirs,
--    include_dirs=["samtools", "pysam", "."] +
-+    include_dirs=["pysam", "."] + samtools_include_dirs +
-     include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-@@ -482,7 +484,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=["pysam"] + htslib_library_dirs,
--    include_dirs=["bcftools", "pysam", "."] +
-+    include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs +
-     include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
new file mode 100644
index 000000000000..9d269878e651
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
@@ -0,0 +1,37 @@
+--- 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"