gentoo resync : 20.10.2021

3 files changed, 0 insertions, 100 deletions

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 3647402b6949..c990614486e8 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,6 +1,3 @@
-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
 DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552
-EBUILD pysam-0.16.0.1.ebuild 1393 BLAKE2B 1b68d4d351483c8082905460185395d560a9c3157d10f2cb5b2eee76d8828e7e50252f1eb920b9411761c4081f11b293de2c87cede8e9d5e22b568cee0691cfc SHA512 b8e2b792eefbc12e30e51ae01fa48977dfd904abcaf7fcbbd5b5148da76fb5411d0b412f0f0aae060ddf462eb4b69269f362d00dfa1371bda4a38dcce0a6baca
 EBUILD pysam-0.17.0.ebuild 1586 BLAKE2B 38351a74c0a57348fdc1999f35b10cd8645160175386b94885e49bbd99bc64f577c326d04e09ba56abce0c0c01331276ebef080fbf519dbfbae41960b6ccc61a SHA512 bd0e336603727c67cd363c628daa9aa9b95e6fe2dbcc06425fcbcf03bd8bd4bd79e651b637434cdbbecd85ebc2841647863910e31f94dd9641694fb4c68de8d4
 MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7
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
deleted file mode 100644
index 9d269878e651..000000000000
--- a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- 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-0.16.0.1.ebuild b/sci-biology/pysam/pysam-0.16.0.1.ebuild
deleted file mode 100644
index ec09bbe1f8c9..000000000000
--- a/sci-biology/pysam/pysam-0.16.0.1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.org/project/pysam/"
-SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.10*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
-	test? (
-		=sci-biology/bcftools-1.10*
-		=sci-biology/samtools-1.10*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
-	rm -r htslib || 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
-}
-
-python_compile() {
-	# breaks with parallel build
-	local MAKEOPTS=-j1
-	distutils-r1_python_compile
-}