gentoo resync : 25.08.2020

4 files changed, 65 insertions, 78 deletions

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 7f96ff719811..b61c521c5275 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,4 +1,4 @@
-AUX pysam-0.12-fix-buildsystem.patch 2356 BLAKE2B 95542f99b411a00eeaa24836cb7489bf2bbf690d804669f69f6f1a8c07f66d9c6ef34624eb511036cd36b1268b49959d38db497cb557e9cc40f3a35b2d349f4d SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a
-DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d
-EBUILD pysam-0.12.0.1.ebuild 1182 BLAKE2B 11c3a036ca7c6560a6316963ea6133708d36cce2d0f21a1e327180d303406ae23ad021ba04024191eda1687ef538f41c0bfe34bbed742bc85f9aeb12b38dc6da SHA512 fd71cf196e68f640343e2b43e3bb8b5355462f6816a1eb0e7755d188435c567ce53209f6f2599a84e5052d26b4747038c7a4b5a2e9b916c117f388ca369a3919
+AUX pysam-0.16.0.1-fix-tests.patch 1128 BLAKE2B 8e395496c23186b29622b8e87369f910326724b70b63f3eccfd6d4b6cea86abf8b34a712a931f205711e2c5a6e76c9572a93aa9bd994f915312c55dcc888da52 SHA512 e725143c72d04fc0e2e37e607e6d9b85b4c883bcc5a530ff3c92e3bbd45d7d7fb09c315766a19254bea2a19a2d00a5f64220094a4e9b1090e412b26ea489b530
+DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
+EBUILD pysam-0.16.0.1.ebuild 1393 BLAKE2B a124ddf7b18e31a89d3fe0d47c7f938d5edfe65938bf0360de209cfa7545474f4be780b7a9e8b4c73fa4cd9282ac9176d8289a34805e062176dbacf3405f33d7 SHA512 b24b2c7d9d764a2e451f4f1c00a20ccc203079e17c238f909b5afb5c6d0a26303822ef54920209f22bf9ba08b3a8a27ff7c052d8bf571a14baca511524a28cdc
 MISC metadata.xml 410 BLAKE2B ed86e3ffe38a306e581762625b37cf6596dc2a2ba404406ab12f681d5b48529764e281d40411bedbdf6016bc57d02adb705e8c8703b8120cf89b4961f75bed67 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810
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"
diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.16.0.1.ebuild
index e7567f3501bf..acc0cb99892f 100644
--- a/sci-biology/pysam/pysam-0.12.0.1.ebuild
+++ b/sci-biology/pysam/pysam-0.16.0.1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -11,18 +11,25 @@ DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping for
 HOMEPAGE="
 	https://github.com/pysam-developers/pysam
 	https://pypi.org/project/pysam/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-RDEPEND="=sci-libs/htslib-1.5*:="
+RDEPEND="=sci-libs/htslib-1.10*:="
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		=sci-biology/bcftools-1.10*
+		=sci-biology/samtools-1.10*
+	)"
 
-PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
 
 python_prepare_all() {
 	# unbundle htslib
@@ -31,17 +38,23 @@ python_prepare_all() {
 	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
 	rm -r htslib || die
 
-	# prevent setup.py from adding RPATHs
-	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
-		-i cy_build.py || die
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
 	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
 		-i setup.py || die
 
+	eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
 	distutils-r1_python_prepare_all
 }
 
-src_compile() {
-	# TODO
-	# empty compile, as the build system runs the whole build again in install
-	:
+python_compile() {
+	# breaks with parallel build
+	local MAKEOPTS=-j1
+	distutils-r1_python_compile
 }