diff options
Diffstat (limited to 'sci-libs')
| -rw-r--r-- | sci-libs/Manifest.gz | bin | 44245 -> 44245 bytes | |||
| -rw-r--r-- | sci-libs/cantera/Manifest | 1 | ||||
| -rw-r--r-- | sci-libs/cantera/cantera-2.5.1-r1.ebuild | 144 | ||||
| -rw-r--r-- | sci-libs/htslib/Manifest | 4 | ||||
| -rw-r--r-- | sci-libs/htslib/htslib-1.16.ebuild | 52 | ||||
| -rw-r--r-- | sci-libs/htslib/metadata.xml | 14 |
6 files changed, 62 insertions, 153 deletions
diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz Binary files differindex 6f9286181477..380196c7dabd 100644 --- a/sci-libs/Manifest.gz +++ b/sci-libs/Manifest.gz 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> |