From 65531d9c170398a321c546ea67946a932842217b Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Tue, 27 Dec 2022 02:09:02 +0000
Subject: gentoo auto-resync : 27:12:2022 - 02:09:02

---
 sci-libs/Manifest.gz                     | Bin 44245 -> 44245 bytes
 sci-libs/cantera/Manifest                |   1 -
 sci-libs/cantera/cantera-2.5.1-r1.ebuild | 144 -------------------------------
 sci-libs/htslib/Manifest                 |   4 +-
 sci-libs/htslib/htslib-1.16.ebuild       |  52 +++++++++++
 sci-libs/htslib/metadata.xml             |  14 +--
 6 files changed, 62 insertions(+), 153 deletions(-)
 delete mode 100644 sci-libs/cantera/cantera-2.5.1-r1.ebuild
 create mode 100644 sci-libs/htslib/htslib-1.16.ebuild

(limited to 'sci-libs')

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 6f9286181477..380196c7dabd 100644
Binary files a/sci-libs/Manifest.gz and b/sci-libs/Manifest.gz differ
diff --git a/sci-libs/cantera/Manifest b/sci-libs/cantera/Manifest
index edf3d352d4f1..1f8b67d8274b 100644
--- a/sci-libs/cantera/Manifest
+++ b/sci-libs/cantera/Manifest
@@ -2,7 +2,6 @@ AUX cantera-2.5.1_env.patch 5928 BLAKE2B d6d0792527a5f50c34d4d6a05c651992a82af7e
 AUX cantera-2.6.0_env.patch 3119 BLAKE2B 16844230d86a292c764da1aa4043b2eff177f2b8a94ed154c3f6a69c1737e85f6ddc9330d5ba6f26936994306381dcb40ab4e70c7b7b44bdbaf7d920ee1ef902 SHA512 12cdabc7cee106ee17050918b483245b39f927b5a5bb8f92bd6177c1d660cc18cd3a91b2710991fa09c44f58aaac464495b15ceb7ae13bf235d34a6caabe7bc4
 DIST cantera-2.5.1.tar.gz 2492422 BLAKE2B b48c5d12fc2b69d309759afd20b55dc2533c23ccba840109cf7a85c4ebb8306eb48d9f007914184a9d409f7bf296814fe09e6e62a29cf8384edd954fdff2af4e SHA512 8cd65f6b86b3009f22ec243cb7cb833e26919c4925fd15fba8fb98aad2180d8c0fe7550e13efeb7cce55abab06d9400230d59c9c43b4d3be6b0575b1164a56bc
 DIST cantera-2.6.0.tar.gz 2586243 BLAKE2B 3562dc3641c70cdbd5e07062ecee56c0658b098c20bb477c3e741731db01e38fccf624e6769377420b01dd4bac72a0608cf226cce40ac12f13e71081090e06bc SHA512 74e12c89af38236bcc064034f74edcc690895151a9e453e728d130b83f5f527e675750c68a3fe36eea3c6aec6969685aa8828ae740a2e27b5df72a8ccc4d2856
-EBUILD cantera-2.5.1-r1.ebuild 3428 BLAKE2B ea9fdf73fe224d9ccc9c589b46e7ea59389e75bfa2eea8f8ea45d08d9c079b926b607c8a5f6edf469cb348803ae20748722227b96c462d39d34b97fb544684e0 SHA512 59383dbd2b324023d0802c179631d4a6edd925449b0d8195d0d7ae34a1b0c46eb695db54659673d1d23756862301b245244c4ce495fd23945541700030ff6127
 EBUILD cantera-2.5.1-r4.ebuild 3470 BLAKE2B 59c9063460a112368419e013a2c5ad8f2f51616ddf5904b461b08a4fe68369a52e8e5ca1bbc8aa27854ff2949921fef87126441bbfa5af2685a5094c86e19a7e SHA512 80f9ce4775d89c068bcea3c322e0af4ca220efb1335e60be31d6ab9f746637d29da22b89aec98572a6fdc22c98efdacdff2072ff2ec4df313aa82f642eb97996
 EBUILD cantera-2.6.0-r1.ebuild 3542 BLAKE2B e64cd0134529dd3f2e4ddeb0d0a4e3c267039249a261e7b2deac1f53bed42cbb4adcaf2a4b67f1722219ad780af12c72441b71c6215bf71cc7cf0439b6bc8f53 SHA512 7df767ac2467f72b37e6cb7b641c5986d486a153eef08c98fca29c92fb21f3de74acc1a0b73cf92d6f3c49962f93ba1b51e98a61dcb4b47865d59c0eb9ec0409
 MISC metadata.xml 842 BLAKE2B 85e2a5268aa13a8a92e9f04212c3bcd66252a77c88dd2ddb7d81a34f486754c7faa352998484d4362b16a2bdccb85325337c13cc272a434be463a037eab846a1 SHA512 a9edb0347dc3b1510d3d2b767e7a0e96cd1d6cc50dd4e5c2830d29438dd25a0bdfa41994dbb43bbb7dc70ba3537f783b2d0a143723908dd91d434e1edb11a704
diff --git a/sci-libs/cantera/cantera-2.5.1-r1.ebuild b/sci-libs/cantera/cantera-2.5.1-r1.ebuild
deleted file mode 100644
index ecacad92743b..000000000000
--- a/sci-libs/cantera/cantera-2.5.1-r1.ebuild
+++ /dev/null
@@ -1,144 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8,9} )
-
-FORTRAN_NEEDED=fortran
-FORTRAN_STANDARD="77 90"
-
-inherit fortran-2 python-single-r1 scons-utils toolchain-funcs
-
-DESCRIPTION="Object-oriented tool suite for chemical kinetics, thermodynamics, and transport"
-HOMEPAGE="https://www.cantera.org"
-SRC_URI="https://github.com/Cantera/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="+cti fortran lapack pch +python test"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="
-	python? ( cti )
-	${PYTHON_REQUIRED_USE}
-"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	lapack? ( virtual/lapack )
-	cti? (
-		$(python_gen_cond_dep '
-			dev-python/ruamel-yaml[${PYTHON_USEDEP}]
-		')
-	)
-	python? (
-		$(python_gen_cond_dep '
-			dev-python/numpy[${PYTHON_USEDEP}]
-		')
-	)
-	dev-cpp/yaml-cpp
-	<sci-libs/sundials-5.3.0:0=[lapack?]
-"
-
-DEPEND="
-	${RDEPEND}
-	dev-cpp/eigen:3
-	dev-libs/boost
-	dev-libs/libfmt
-	python? (
-		$(python_gen_cond_dep '
-			dev-python/cython[${PYTHON_USEDEP}]
-		')
-	)
-	test? (
-		>=dev-cpp/gtest-1.8.0
-		python? (
-			$(python_gen_cond_dep '
-				dev-python/h5py[${PYTHON_USEDEP}]
-				dev-python/pandas[${PYTHON_USEDEP}]
-			')
-		)
-	)
-"
-
-PATCHES=( "${FILESDIR}/${P}_env.patch" )
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-## Full list of configuration options of Cantera is presented here:
-## http://cantera.org/docs/sphinx/html/compiling/config-options.html
-src_configure() {
-	scons_vars=(
-		AR="$(tc-getAR)"
-		CC="$(tc-getCC)"
-		CXX="$(tc-getCXX)"
-		cc_flags="${CXXFLAGS}"
-		cxx_flags="-std=c++11"
-		debug="no"
-		FORTRAN="$(tc-getFC)"
-		FORTRANFLAGS="${FCFLAGS}"
-		optimize_flags="-Wno-inline"
-		renamed_shared_libraries="no"
-		use_pch=$(usex pch)
-		## In some cases other order can break the detection of right location of Boost: ##
-		system_fmt="y"
-		system_sundials="y"
-		system_eigen="y"
-		system_yamlcpp="y"
-		env_vars="all"
-		extra_inc_dirs="/usr/include/eigen3"
-	)
-	use lapack && scons_vars+=( blas_lapack_libs="lapack,blas" )
-	use test || scons_vars+=( googletest="none" )
-
-	scons_targets=(
-		f90_interface=$(usex fortran y n)
-	)
-
-	if use cti ; then
-		local scons_python=$(usex python full minimal)
-		scons_targets+=( python_package="${scons_python}" python_cmd="${EPYTHON}" )
-	else
-		scons_targets+=( python_package="none" )
-	fi
-}
-
-src_compile() {
-	escons build "${scons_vars[@]}" "${scons_targets[@]}" prefix="/usr"
-}
-
-src_test() {
-	escons test
-}
-
-src_install() {
-	escons install stage_dir="${D}" libdirname="$(get_libdir)" python_prefix="$(python_get_sitedir)"
-	if ! use cti ; then
-		rm -r "${D}/usr/share/man" || die "Can't remove man files."
-	else
-		# Run the byte-compile of modules
-		python_optimize "${D}/$(python_get_sitedir)/${PN}"
-	fi
-
-	# We install static libs unconditionally here
-	# See https://github.com/gentoo/gentoo/pull/10017#discussion_r229210565
-}
-
-pkg_postinst() {
-	if use cti && ! use python ; then
-		elog "Cantera was build without 'python' use-flag therefore the CTI tools 'ck2cti' and 'ck2yaml"
-		elog "will convert Chemkin files to Cantera format without verification of kinetic mechanism."
-	fi
-
-	local post_msg=$(usex fortran "and Fortran " "")
-	elog "C++ ${post_msg}samples are installed to '/usr/share/${PN}/samples/' directory."
-
-	if use python ; then
-		elog "Python examples are installed to '$(python_get_sitedir)/${PN}/examples/' directories."
-	fi
-}
diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 319557fa6017..839656915080 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,3 +1,5 @@
 DIST htslib-1.15.1.tar.bz2 4141140 BLAKE2B 312f67c8916586199b32b7703b43a9fd365b8af22802bf4d63fc40960c62b956915e7c60bbd777a8b179066608cd3a281929a10b60eef21d6eedb4caf8c147c1 SHA512 69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
+DIST htslib-1.16.tar.bz2 4466776 BLAKE2B 4957dd7a25b3d0b939d4e924db018916a5f8a13a81e55ebd1ce1acc548986e581d017ead9a08245a4af1ebdcd15536f082425ebe05f16eb4faad27d332e48482 SHA512 9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5
 EBUILD htslib-1.15.1.ebuild 1074 BLAKE2B d04ae956ac6d4819704e8342d9679d0c54274c09da155c6d73d0e889b3db75cfbbae80665e750c0d7387cf9eeeac7642ff31bbe301220cef06915d7081c3aa74 SHA512 6c617b18f47e2823077527653dcf2a6976577efde1481087d5188ce151089edc9a98343ef6ad3864117477c60531694287adae5def956f016d6e105445ae1963
-MISC metadata.xml 350 BLAKE2B 6512256a4c692625cb824d90fc8b85942f88db717fd265548b97a5b535158fc65e1f2e74df4ebd3c2a259dfd3a4244a13493fc410b1663b8054b29a14995787d SHA512 926efc676b0619ae901253f2207c8ba948ebe3db560377a55edecd9cd58cd2ec806bcdff875e9c5c9a170921c44818271e8ddd691fe1a84ed651f7aca75265ec
+EBUILD htslib-1.16.ebuild 1074 BLAKE2B d04ae956ac6d4819704e8342d9679d0c54274c09da155c6d73d0e889b3db75cfbbae80665e750c0d7387cf9eeeac7642ff31bbe301220cef06915d7081c3aa74 SHA512 6c617b18f47e2823077527653dcf2a6976577efde1481087d5188ce151089edc9a98343ef6ad3864117477c60531694287adae5def956f016d6e105445ae1963
+MISC metadata.xml 342 BLAKE2B 1c27212ba39cbbd235e2b023af977d5dffbb53dab193e21c989b2da52641fec13317110cfb52fd73cbe7fbdd5aa6b3628ee7cd55ae919551fa82267b05f93e2d SHA512 5b61d1b204a33d6328d3964346c48dc35bc4e29c56dc7920a63caf2fc510be35b10f74f2649a2670239de90cff5ed4652fa99d4ef51a55245b7fc4b31f29674b
diff --git a/sci-libs/htslib/htslib-1.16.ebuild b/sci-libs/htslib/htslib-1.16.ebuild
new file mode 100644
index 000000000000..c4bd910685de
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.16.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+	sys-libs/zlib
+	bzip2? ( app-arch/bzip2 )
+	curl? ( net-misc/curl )
+	lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	default
+
+	# upstream injects LDFLAGS into the .pc file,
+	# which is a big nono for QA
+	sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+		-i htslib.pc.in || die
+}
+
+src_configure() {
+	econf \
+		--disable-gcs \
+		--disable-plugins \
+		--disable-s3 \
+		$(use_enable bzip2 bz2) \
+		$(use_enable curl libcurl) \
+		$(use_enable lzma)
+}
+
+src_compile() {
+	emake AR="$(tc-getAR)"
+}
+
+src_install() {
+	default
+
+	# doesn't use libtool, can't disable static libraries
+	find "${ED}" -name '*.a' -delete || die
+}
diff --git a/sci-libs/htslib/metadata.xml b/sci-libs/htslib/metadata.xml
index 003b4a9e53f3..1950263f31e1 100644
--- a/sci-libs/htslib/metadata.xml
+++ b/sci-libs/htslib/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">samtools</remote-id>
-  </upstream>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">samtools/htslib</remote-id>
+	</upstream>
 </pkgmetadata>
-- 
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