gentoo resync : 20.10.2021

8 files changed, 0 insertions, 203 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index fbc00040d679..d128b0b8d2d3 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 359793c2e6bc..572ee9298e8a 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,5 +1,3 @@
-DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
 DIST bcftools-1.13.tar.bz2 6906796 BLAKE2B 4c02d65733d28684f9a976e082913d79dbac4463c9471fc26d8ee0cbe7ad25af429cf7d01b9771bc34309386ccd2d77ebd54fbf64ed4183d1c2ebfbc0e727afb SHA512 aa533233dd2fec2279859204be39430c4fc630137a91d57fe917fd7a220044d5202ddc3d44bcffc3bd5bd5bb64f6ea4c8ec3c31e5e1ec72399998f1e6f23a55a
-EBUILD bcftools-1.10.2.ebuild 864 BLAKE2B b98c493d6e50d982917ecbf32c424a45231c3f512a49a0c9cd675cbb3d5f21a57d62cc53a20556663b6fd1d58a68df01a9ed56185dd5f400b8ee5b5c7b5497fd SHA512 c8c3173376a35824ce10413e7cba172d6a90dae91352a292df5603f1a7e17cd5987fc91b463b030221b577bce5424ae7a219625cb684cb3fa2f6777581bb19bb
 EBUILD bcftools-1.13.ebuild 896 BLAKE2B 74b1387b81ec75926bd76d62033d7cf0708ac3b9a0b0b0573fec1c70efb47b84bd3fa626f3ff3144e380f07822bd3d9e56f4ddb1e09a4a09082cb1d6d3229b39 SHA512 bb0f18c2102fbfa8d5ee636c81308ea8a0ef6de80943423377846ebd2180881ca745e7eddd94be7ad7b34a2313acc43553d8a31ee474542de5d29d4874e935e4
 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1
diff --git a/sci-biology/bcftools/bcftools-1.10.2.ebuild b/sci-biology/bcftools/bcftools-1.10.2.ebuild
deleted file mode 100644
index a484f69133e5..000000000000
--- a/sci-biology/bcftools/bcftools-1.10.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	$(python_gen_cond_dep '
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-	')
-	=sci-libs/htslib-${PV}*:=
-	sys-libs/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--with-htslib=system
-}
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
-}
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 258415bacb57..e81f2187923a 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,8 +1,6 @@
 AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
 DIST samtools-1.13.tar.bz2 7984998 BLAKE2B e46161c43d4ea51c3ef1d9ed74c40c21b70aef80aa903a49b94b3d468f9211e9147281204eb61b9843c071f09ead08c924e3d624d4df76a1d02ba9ceb318399a SHA512 647fbad2935dfc3e4f85da257a6ee59af40078024a3b77f117dada5f55846e381a096db3cf62a63c04ae95dfc9fadb1d515b8d618e6388bc93f0b2ac85eaf6ea
 EBUILD samtools-0.1.20-r4.ebuild 2049 BLAKE2B d377712eaca931258b37645e6a6b3cc379fdb550ef83a0c272a3eb564d7753185fea53416973e4fdf2c25b79475a81ae72b646ce22c570c934e4eabce8a9ded6 SHA512 c0d387f715ebf1f746ea4e4a7eab85a86ef0bff646c9a69639b17ef02e93c39982941d7eb811a6d67b0e635c9c4e05924d2b89a6809c3bd0592db91894dab4aa
-EBUILD samtools-1.10-r1.ebuild 993 BLAKE2B 69080337f15d653be56680f3183c2eab3c1813805e3ffc3be1d6dc0e04264a063ae758b694ccb1ff097e952cad736a387de02905ca4f7d4af779233d9e1fced2 SHA512 15dab01b933e56fc83b71f68b2c52c69b115df19f72599e4b4d9d959f9035a468e3ad825cb2e12a80ba558b953879d1b6f8e9dc50922d099c375312dd7580040
 EBUILD samtools-1.13.ebuild 886 BLAKE2B e96ccbff6d7310e4691118bc191a020525a92aa49dd24478be11185e1767788849bae9d575d59dc139f77b0c977222684c82a45487b4d10d77da20347f5170b5 SHA512 3eb07532ae9d7995279663d8e09602e30a5055b13388ceb83aa369e52bb2291f21014f60dccc5569825f6e7683801b737557539270007bc16a12015d86c17fec
 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24
diff --git a/sci-biology/samtools/samtools-1.10-r1.ebuild b/sci-biology/samtools/samtools-1.10-r1.ebuild
deleted file mode 100644
index 940895616906..000000000000
--- a/sci-biology/samtools/samtools-1.10-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-${PV}*
-	sys-libs/ncurses:=[unicode(+)]
-	sys-libs/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_test() {
-	# the tview test diffs expect 80-columns output
-	unset COLUMNS
-
-	default
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}