diff options
Diffstat (limited to 'sci-libs')
205 files changed, 4580 insertions, 4342 deletions
diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild index ab1a155c3..d1257f0ee 100644 --- a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild +++ b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 2020 Gentoo Authors +# Copyright 2020-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -14,7 +14,7 @@ LICENSE="Apache-2.0" SLOT="0" KEYWORDS="~amd64 ~x86" -DEPEND="app-arch/zstd sci-libs/hdf5" +DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r5" RDEPEND="${DEPEND}" S=${WORKDIR}/${PN}-${COMMIT} @@ -25,9 +25,3 @@ src_configure() { ) cmake_src_configure } - -src_install() { - echo "HDF5_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/hdf5/plugin" >> 99h5zstd || die - doenvd 99h5zstd - cmake_src_install -} diff --git a/sci-libs/HDF5Plugin-Zstandard/metadata.xml b/sci-libs/HDF5Plugin-Zstandard/metadata.xml index 753464ee5..a171606a6 100644 --- a/sci-libs/HDF5Plugin-Zstandard/metadata.xml +++ b/sci-libs/HDF5Plugin-Zstandard/metadata.xml @@ -5,4 +5,7 @@ <email>xgreenlandforwyy@gmail.com</email> <name>Yiyang Wu</name> </maintainer> + <upstream> + <remote-id type="github">aparamon/HDF5Plugin-Zstandard</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/aocl-libm/Manifest b/sci-libs/aocl-libm/Manifest index c27520623..3f320d8be 100644 --- a/sci-libs/aocl-libm/Manifest +++ b/sci-libs/aocl-libm/Manifest @@ -1,2 +1,2 @@ -DIST aocl-libm-linux-aocc-3.6.0-4.tar.gz 855788 BLAKE2B 39874a04bd010382e6b5f14066a7267bc7f999384211c4663ca191dbcc8d2a990597d1b140c6bcd4cb2b945ae8951c430572a9696edef505c6815c5acfad3166 SHA512 6f49cca01eab40ad06b6e3a4166eb83f355245e892171907f1315f5e60372aafd9bca5878dc1480fb102a3de4699369ce5931167ead00165fd1644c988f6c325 -DIST aocl-libm-linux-gcc-3.6.0-4.tar.gz 844698 BLAKE2B 1a72691d9351859f07abdf49663bd1da8932465cfcb0983ba594ad0d09375ca964abd196ab5f26a9eaf0c9f1bd343cbdc0b6b427d7648f148ff880aeb826770b SHA512 fc07d1b45864140cf87410ad3595c681598458a8dd9ef7625a9e520b5d10ab06dccb2551193d4d907b19b188cdb34ef16f587549b94324371ee1e04b612f1ee9 +DIST aocl-libm-linux-aocc-3.1.0.tar.gz 1234123 BLAKE2B d63c5e5a5e5445de59ed5726ae5cc285fa7e9416255b861f337c7f649d460d6f95d4deb2b635166a5ed99f216eefb47054b11f3949c54a2fb06c4fc7bc9098d7 SHA512 0806b50b2f20bfe05a3d3eff16be09c4597f07f1dad15861cb289f1f0850cc9ed53601d4cf41174f6ad1f67963a94f7a6fee66394f787d302bf1a9c7b17e45cc +DIST aocl-libm-linux-gcc-3.1.0.tar.gz 1281295 BLAKE2B 953fbc381182afb7e3b26a93643f4ab18c9fb7b331d686bde75b63f512668a5045fa74209031849a4b3701fd51000c386c96ad7a3d4567913b68b04b9115351a SHA512 3df4700498713c510ff2cc04ad37db12b3b3c174caf6118bfd364f95899a10eeefca566d898c13fb3732f5b7390792f1c786c64dbf928ed9021b11546d5c04c9 diff --git a/sci-libs/aocl-libm/aocl-libm-3.6.0_p4.ebuild b/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild index f7a741abb..890414de2 100644 --- a/sci-libs/aocl-libm/aocl-libm-3.6.0_p4.ebuild +++ b/sci-libs/aocl-libm/aocl-libm-3.1.0.ebuild @@ -1,19 +1,17 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit toolchain-funcs -MY_PV=${PV/_p/-} - DESCRIPTION="Optimized libm replacement from AMD for x86_64 architectures" HOMEPAGE="https://developer.amd.com/amd-aocl/amd-math-library-libm/" SRC_URI=" - aocc? ( aocl-libm-linux-aocc-${MY_PV}.tar.gz ) - !aocc? ( aocl-libm-linux-gcc-${MY_PV}.tar.gz ) + aocc? ( aocl-libm-linux-aocc-${PV}.tar.gz ) + !aocc? ( aocl-libm-linux-gcc-${PV}.tar.gz ) " -S="${WORKDIR}"/amd-libm +S="${WORKDIR}/amd-libm" LICENSE="AMD" SLOT="0" @@ -36,15 +34,15 @@ src_prepare() { sed -e "s/^CC =.*$/CC = $(tc-getCC)/" -i examples/Makefile || die - cat <<- EOF > "${T}"/amdlibm.pc - prefix=${EROOT}/usr + cat <<- EOF > "${T}"/amdlibm.pc || die + prefix=${EPREFIX}/usr exec_prefix=\${prefix} libdir=\${prefix}/$(get_libdir) includedir=\${prefix}/include Name: ${PN} Description: ${DESCRIPTION} - Version: ${MY_PV} + Version: ${PV} Libs: -L\${libdir} -lamdlibm Cflags: -I\${includedir} EOF @@ -61,9 +59,8 @@ src_install() { doheader include/* - dolib.so lib/libamdlibm.so - use static-libs && \ - dolib.a lib/libamdlibm.a + dolib.so lib/*.so + use static-libs && dolib.a lib/*.a if use examples; then dodoc -r examples diff --git a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild index f265da20b..5d2f3c7a4 100644 --- a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild +++ b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit cmake multilib +inherit cmake DESCRIPTION="general purpose GPU library" HOMEPAGE="https://arrayfire.com/" @@ -44,7 +44,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - doc? ( app-doc/doxygen ) + doc? ( app-text/doxygen ) virtual/pkgconfig " diff --git a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild index f265da20b..5d2f3c7a4 100644 --- a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild +++ b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit cmake multilib +inherit cmake DESCRIPTION="general purpose GPU library" HOMEPAGE="https://arrayfire.com/" @@ -44,7 +44,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - doc? ( app-doc/doxygen ) + doc? ( app-text/doxygen ) virtual/pkgconfig " diff --git a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild index f265da20b..5d2f3c7a4 100644 --- a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild +++ b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit cmake multilib +inherit cmake DESCRIPTION="general purpose GPU library" HOMEPAGE="https://arrayfire.com/" @@ -44,7 +44,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - doc? ( app-doc/doxygen ) + doc? ( app-text/doxygen ) virtual/pkgconfig " diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild index 50eaeea5d..cbfbde5c6 100644 --- a/sci-libs/asl/asl-0.1.7.ebuild +++ b/sci-libs/asl/asl-0.1.7.ebuild @@ -26,7 +26,7 @@ RDEPEND=" DEPEND="${RDEPEND} matlab? ( >=sci-libs/matio-1.5.2 ) " -BDEPEND="doc? ( app-doc/doxygen[dot] )" +BDEPEND="doc? ( app-text/doxygen[dot] )" S="${WORKDIR}/${MY_PN}-${PV}" diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild index 82b464f7f..905c8813a 100644 --- a/sci-libs/asl/asl-9999.ebuild +++ b/sci-libs/asl/asl-9999.ebuild @@ -24,7 +24,7 @@ RDEPEND=" DEPEND="${RDEPEND} matlab? ( >=sci-libs/matio-1.5.2 ) " -BDEPEND="doc? ( app-doc/doxygen[dot] )" +BDEPEND="doc? ( app-text/doxygen[dot] )" src_prepare() { cmake_src_prepare diff --git a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild index 00bf81571..a4f7f0340 100644 --- a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild +++ b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-libs/blis-amd/Manifest b/sci-libs/blis-amd/Manifest deleted file mode 100644 index 86192778f..000000000 --- a/sci-libs/blis-amd/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST blis-amd-2.2.tar.gz 9066754 BLAKE2B 9425a927b8dd37cc5a0843a0c5d7958906bcdbdd83b015d2428e2372e0cdc6206ed8ab9c4c0c6e6eccee091498b524061ffed8adcd9b0c857cc9c64446b3a19f SHA512 a7d58bda40c833b5388e0f7b316352cfcb186db535534682b647e2ca7b130518959b3c78043261e9f1f85f99a168bd20b919c6c2c184ee4f4d269da88d41a5d6 diff --git a/sci-libs/blis-amd/blis-amd-2.2.ebuild b/sci-libs/blis-amd/blis-amd-2.2.ebuild deleted file mode 100644 index eb6c16385..000000000 --- a/sci-libs/blis-amd/blis-amd-2.2.ebuild +++ /dev/null @@ -1,128 +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 fortran-2 python-any-r1 - -DESCRIPTION="AMD optimized BLAS-like Library Instantiation Software Framework" -HOMEPAGE="https://developer.amd.com/amd-aocl/" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/amd/blis" -else - SRC_URI="https://github.com/amd/blis/archive/${PV}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/blis-"${PV}" - KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~ppc64 ~x86" -fi - -LICENSE="BSD" -SLOT="0" -IUSE="64bit-index doc eselect-ldso openmp pthread static-libs" -REQUIRED_USE="?? ( openmp pthread ) ?? ( eselect-ldso 64bit-index )" - -RDEPEND+=" - >=app-eselect/eselect-blas-0.2 - !sci-libs/blis -" -DEPEND+="${RDEPEND} - ${PYTHON_DEPS} -" - -PATCHES=( - "${FILESDIR}"/${P}-blas_rpath.patch -) - -pkg_pretend() { - elog "It is very important that you set the BLIS_CONFNAME" - elog "variable when compiling blis as it tunes the" - elog "compilation to the specific CPU architecture." - elog "To look at valid BLIS_CONFNAMEs, look at directories in" - elog "\t https://github.com/amd/blis/tree/master/config" - elog "At the very least, it should be set to the ARCH of" - elog "the machine this will be run on, which gives a" - elog "performance increase of ~4-5x." -} - -src_configure() { - local myconf=( - --prefix="${BROOT}"/usr - --libdir="${BROOT}"/usr/$(get_libdir) - --enable-cblas - --enable-blas - --enable-arg-max-hack - --enable-verbose-make - --without-memkind - --enable-shared - $(use_enable static-libs static) - ) - - use 64bit-index && \ - myconf+=( - --int-size=64 - --blas-int-size=64 - ) - - # threading backend - openmp/pthreads/no - if use openmp; then - myconf+=( --enable-threading=openmp ) - elif use pthread; then - myconf+=( --enable-threading=pthreads ) - else - myconf+=( --enable-threading=no ) - fi - - # not an autotools configure script - ./configure "${myconf[@]}" \ - "${EXTRA_ECONF[@]}" \ - ${BLIS_CONFNAME:-generic} || die -} - -src_compile() { - SET_RPATH=no \ - DEB_LIBBLAS=libblas.so.3 \ - DEB_LIBCBLAS=libcblas.so.3 \ - default -} - -src_test() { - emake check -} - -src_install() { - default - use doc && dodoc README.md docs/*.md - - use eselect-ldso || return - - insinto /usr/$(get_libdir)/blas/blis-amd - doins lib/${BLIS_CONFNAME:-generic}/lib{c,}blas.so.3 - dosym libblas.so.3 usr/$(get_libdir)/blas/blis-amd/libblas.so - dosym libcblas.so.3 usr/$(get_libdir)/blas/blis-amd/libcblas.so -} - -pkg_postinst() { - use eselect-ldso || return - - local libdir=$(get_libdir) me="blis-amd" - - # check blas - elog "adding ${me}" - eselect blas add ${libdir} "${EROOT}"/usr/${libdir}/blas/${me} ${me} - elog "added ${me}" - local current_blas=$(eselect blas show ${libdir} | cut -d' ' -f2) - if [[ ${current_blas} == "${me}" || -z ${current_blas} ]]; then - eselect blas set ${libdir} ${me} - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - else - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - elog "To use blas [${me}] implementation, you have to issue (as root):" - elog "\t eselect blas set ${libdir} ${me}" - fi -} - -pkg_postrm() { - use eselect-ldso && eselect blas validate -} diff --git a/sci-libs/blis-amd/blis-amd-9999.ebuild b/sci-libs/blis-amd/blis-amd-9999.ebuild deleted file mode 100644 index 672277b36..000000000 --- a/sci-libs/blis-amd/blis-amd-9999.ebuild +++ /dev/null @@ -1,128 +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 fortran-2 python-any-r1 - -DESCRIPTION="AMD optimized BLAS-like Library Instantiation Software Framework" -HOMEPAGE="https://developer.amd.com/amd-aocl/" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/amd/blis" -else - SRC_URI="https://github.com/amd/blis/archive/${PV}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/blis-"${PV}" - KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~ppc64 ~x86" -fi - -LICENSE="BSD" -SLOT="0" -IUSE="64bit-index doc eselect-ldso openmp pthread static-libs" -REQUIRED_USE="?? ( openmp pthread ) ?? ( eselect-ldso 64bit-index )" - -RDEPEND+=" - >=app-eselect/eselect-blas-0.2 - !sci-libs/blis -" -DEPEND+="${RDEPEND} - ${PYTHON_DEPS} -" - -PATCHES=( - "${FILESDIR}"/${PN}-2.2-blas_rpath.patch -) - -pkg_pretend() { - elog "It is very important that you set the BLIS_CONFNAME" - elog "variable when compiling blis as it tunes the" - elog "compilation to the specific CPU architecture." - elog "To look at valid BLIS_CONFNAMEs, look at directories in" - elog "\t https://github.com/amd/blis/tree/master/config" - elog "At the very least, it should be set to the ARCH of" - elog "the machine this will be run on, which gives a" - elog "performance increase of ~4-5x." -} - -src_configure() { - local myconf=( - --prefix="${BROOT}"/usr - --libdir="${BROOT}"/usr/$(get_libdir) - --enable-cblas - --enable-blas - --enable-arg-max-hack - --enable-verbose-make - --without-memkind - --enable-shared - $(use_enable static-libs static) - ) - - use 64bit-index && \ - myconf+=( - --int-size=64 - --blas-int-size=64 - ) - - # threading backend - openmp/pthreads/no - if use openmp; then - myconf+=( --enable-threading=openmp ) - elif use pthread; then - myconf+=( --enable-threading=pthreads ) - else - myconf+=( --enable-threading=no ) - fi - - # not an autotools configure script - ./configure "${myconf[@]}" \ - "${EXTRA_ECONF[@]}" \ - ${BLIS_CONFNAME:-generic} || die -} - -src_compile() { - SET_RPATH=no \ - DEB_LIBBLAS=libblas.so.3 \ - DEB_LIBCBLAS=libcblas.so.3 \ - default -} - -src_test() { - emake check -} - -src_install() { - default - use doc && dodoc README.md docs/*.md - - use eselect-ldso || return - - insinto /usr/$(get_libdir)/blas/blis-amd - doins lib/${BLIS_CONFNAME:-generic}/lib{c,}blas.so.3 - dosym libblas.so.3 usr/$(get_libdir)/blas/blis-amd/libblas.so - dosym libcblas.so.3 usr/$(get_libdir)/blas/blis-amd/libcblas.so -} - -pkg_postinst() { - use eselect-ldso || return - - local libdir=$(get_libdir) me="blis-amd" - - # check blas - elog "adding ${me}" - eselect blas add ${libdir} "${EROOT}"/usr/${libdir}/blas/${me} ${me} - elog "added ${me}" - local current_blas=$(eselect blas show ${libdir} | cut -d' ' -f2) - if [[ ${current_blas} == "${me}" || -z ${current_blas} ]]; then - eselect blas set ${libdir} ${me} - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - else - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - elog "To use blas [${me}] implementation, you have to issue (as root):" - elog "\t eselect blas set ${libdir} ${me}" - fi -} - -pkg_postrm() { - use eselect-ldso && eselect blas validate -} diff --git a/sci-libs/blis-amd/files/blis-amd-2.2-blas_rpath.patch b/sci-libs/blis-amd/files/blis-amd-2.2-blas_rpath.patch deleted file mode 100644 index 90ab11d52..000000000 --- a/sci-libs/blis-amd/files/blis-amd-2.2-blas_rpath.patch +++ /dev/null @@ -1,46 +0,0 @@ -diff --git a/Makefile b/Makefile -index ea7a550..1b3a1d2 100644 ---- a/Makefile -+++ b/Makefile -@@ -689,6 +689,9 @@ else - endif - endif - -+ $(LINKER) $(SOFLAGS) -o $(BASE_LIB_PATH)/$(DEB_LIBBLAS) $? $(LDFLAGS) -Wl,--soname,$(DEB_LIBBLAS) -+ $(LINKER) $(SOFLAGS) -o $(BASE_LIB_PATH)/$(DEB_LIBCBLAS) $? $(LDFLAGS) -Wl,--soname,$(DEB_LIBCBLAS) -+ - # Local symlink for shared library. - # NOTE: We use a '.loc' suffix to avoid filename collisions in case this - # rule is executed concurrently with the install-lib-symlinks rule, which -diff --git a/common.mk b/common.mk -index e73a5d1..2aa8a23 100644 ---- a/common.mk -+++ b/common.mk -@@ -565,11 +565,14 @@ ifeq ($(MK_ENABLE_SHARED),yes) - ifeq ($(MK_ENABLE_STATIC),no) - LIBBLIS_L := $(LIBBLIS_SO) - LIBBLIS_LINK := $(LIBBLIS_SO_PATH) -+SET_RPATH ?= yes - ifeq ($(IS_WIN),no) -+ifeq ($(SET_RPATH),yes) - # For Linux and OS X: set rpath property of shared object. - LDFLAGS += -Wl,-rpath,$(BASE_LIB_PATH) - endif - endif -+endif - # On windows, use the shared library even if static is created. - ifeq ($(IS_WIN),yes) - LIBBLIS_L := $(LIBBLIS_SO) -diff --git a/configure b/configure -index 35d4f1d..93c2cd6 100755 ---- a/configure -+++ b/configure -@@ -3055,7 +3055,7 @@ main() - enable_aocl_zen='yes' - enable_aocl_zen_01=1 - else -- enable_aocl_zen = 'no'; -+ enable_aocl_zen='no'; - enable_aocl_zen_01=0; - fi - diff --git a/sci-libs/blis-amd/metadata.xml b/sci-libs/blis-amd/metadata.xml deleted file mode 100644 index 1a481192a..000000000 --- a/sci-libs/blis-amd/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">amd/libflame</remote-id> - </upstream> - <use> - <flag name="64bit-index">Enable 64bit array indexing, incompatible with runtime switching</flag> - <flag name="eselect-ldso">Enable runtime library switching by eselect and ld.so</flag> - <flag name="openmp">Use openmp threadding model</flag> - <flag name="pthread">Use pthread threadding model</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/clfft/clfft-2.12.2.ebuild b/sci-libs/clfft/clfft-2.12.2-r1.ebuild index 9cfbc7f8a..8be3d24d0 100644 --- a/sci-libs/clfft/clfft-2.12.2.ebuild +++ b/sci-libs/clfft/clfft-2.12.2-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 MY_PN="clFFT" @@ -18,7 +18,7 @@ SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${ LICENSE="Apache-2.0" SLOT="0" KEYWORDS="~amd64" -IUSE="callback_client +client test" +IUSE="callback-client +client test" RDEPEND=" virtual/opencl @@ -38,7 +38,7 @@ S="${WORKDIR}/${MY_PN}-${PV}/src" src_configure() { local mycmakeargs=( - -DBUILD_CALLBACK_CLIENT="$(usex callback_client)" + -DBUILD_CALLBACK_CLIENT="$(usex callback-client)" -DBUILD_CLIENT="$(usex client)" -DBUILD_TEST="$(usex test)" -DBoost_USE_STATIC_LIBS=OFF diff --git a/sci-libs/clfft/clfft-9999.ebuild b/sci-libs/clfft/clfft-9999.ebuild index 60e6861e0..10e6ed148 100644 --- a/sci-libs/clfft/clfft-9999.ebuild +++ b/sci-libs/clfft/clfft-9999.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 MY_PN="clFFT" @@ -21,7 +21,7 @@ EGIT_BRANCH="develop" LICENSE="Apache-2.0" SLOT="0" -IUSE="callback_client +client test" +IUSE="callback-client +client test" RDEPEND=" virtual/opencl @@ -40,12 +40,12 @@ S="${WORKDIR}/${P}/src" src_configure() { local mycmakeargs=( - -DBUILD_CALLBACK_CLIENT="$(usex callback_client)" + -DBUILD_CALLBACK_CLIENT="$(usex callback-client)" -DBUILD_CLIENT="$(usex client)" -DBUILD_TEST="$(usex test)" -DBoost_USE_STATIC_LIBS=OFF ) - cmake-utils_src_configure + cmake_src_configure } src_compile() { diff --git a/sci-libs/clfft/metadata.xml b/sci-libs/clfft/metadata.xml index e353d590c..911f5977b 100644 --- a/sci-libs/clfft/metadata.xml +++ b/sci-libs/clfft/metadata.xml @@ -18,7 +18,7 @@ clFFT is part of the clMath sofware library, which is the successor of APPML. </longdescription> <use> - <flag name="callback_client"> + <flag name="callback-client"> Build a command line clFFT client program that tests callback functionality. </flag> <flag name="client"> diff --git a/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild b/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild index cb521f546..ba866df11 100644 --- a/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild +++ b/sci-libs/cs-rosetta-db/cs-rosetta-db-2.01.2019.06.ebuild @@ -3,8 +3,6 @@ EAPI=7 -inherit flag-o-matic toolchain-funcs - MY_PN="${PN%-db}" DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA" diff --git a/sci-libs/daal4py/Manifest b/sci-libs/daal4py/Manifest new file mode 100644 index 000000000..0d9bbdab2 --- /dev/null +++ b/sci-libs/daal4py/Manifest @@ -0,0 +1 @@ +DIST daal4py-2023.0.2.tar.gz 13864043 BLAKE2B dfc082a8b008553e0d20cf7a24417fecd510dd8e6b3286a57a633b1e3b79cecc87fc1189df6f4a3440d7ccb74077c54a9f6eaf58bfbb19181cb4b437b3e06ae6 SHA512 dd8c983365d4f32d2640caab17319970c86bfed5ad6852d15dce35ba66a3584c51b94fa5ef0d8073b917332ea18a8c9af95ef8da125edb47190f27e9b8cab424 diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild new file mode 100644 index 000000000..f23e1c738 --- /dev/null +++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild @@ -0,0 +1,64 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Python API to the oneAPI Data Analytics Library" +HOMEPAGE="https://github.com/intel/scikit-learn-intelex" +SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/scikit-learn-intelex-${PV}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-build/cmake + sys-devel/DPC++ + test? ( + sci-libs/scikit-learn[${PYTHON_USEDEP}] + sci-libs/scikit-learn-intelx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + ) +" + +DEPEND=" + dev-python/jinja[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/dpctl[${PYTHON_USEDEP}] + sci-libs/oneDAL + virtual/mpi +" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +PATCHES=( + "${FILESDIR}/${PN}-2023.0.2-dont-use-entire-include.patch" +) + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl:${ESYSROOT}/usr/lib/llvm/intel/include/sycl/CL/sycl" + export MPIROOT="${ESYSROOT}/usr" + export DALROOT="${ESYSROOT}/usr" + # Parallel build is broken + export MAKEOPTS="-j1" + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch new file mode 100644 index 000000000..d26414105 --- /dev/null +++ b/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch @@ -0,0 +1,104 @@ +diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py +index 203c870..7fdac1e 100755 +--- a/generator/gen_daal4py.py ++++ b/generator/gen_daal4py.py +@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces, + enum_maps, enum_params, wrap_algo, result_to_compute) + from .wrapper_gen import wrapper_gen + from .format import mk_var +-from shutil import copytree, rmtree ++from shutil import copytree, copyfile, rmtree + from subprocess import call + + try: +@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False, + head_path = jp("build", "include") + algo_path = jp(head_path, "algorithms") + rmtree(head_path, ignore_errors=True) +- copytree(orig_path, head_path) ++ copytree(jp(orig_path, 'services'), jp(head_path, 'services')) ++ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal')) ++ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management')) ++ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms')) ++ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h')) ++ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h')) ++ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp')) + for (dirpath, dirnames, filenames) in os.walk(algo_path): + for filename in filenames: + call([shutil.which("clang-format"), "-i", jp(dirpath, filename)]) +diff --git a/scripts/build_backend.py b/scripts/build_backend.py +index dd314e4..ec1ec2c 100755 +--- a/scripts/build_backend.py ++++ b/scripts/build_backend.py +@@ -118,20 +118,12 @@ def custom_build_cmake_clib(iface, cxx=None, onedal_major_binary_version=1): + python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
+ numpy_include = np.get_include()
+
+- if iface == 'dpc':
+- if IS_WIN:
+- cxx = 'icx'
+- else:
+- cxx = 'icpx'
+- elif cxx is None:
+- raise RuntimeError('CXX compiler shall be specified')
+-
+ cmake_args = [
+ "cmake",
+ cmake_generator,
+ "-S" + builder_directory,
+ "-B" + abs_build_temp_path,
+- "-DCMAKE_CXX_COMPILER=" + cxx,
++ "-DCMAKE_CXX_COMPILER=" + os.environ.get('CXX'),
+ "-DCMAKE_INSTALL_PREFIX=" + install_directory,
+ "-DCMAKE_PREFIX_PATH=" + install_directory,
+ "-DIFACE=" + iface,
+@@ -140,7 +132,7 @@ def custom_build_cmake_clib(iface, cxx=None, onedal_major_binary_version=1): + "-DNUMPY_INCLUDE_DIRS=" + numpy_include,
+ "-DPYTHON_LIBRARY_DIR=" + python_library_dir,
+ "-DoneDAL_INCLUDE_DIRS=" + jp(os.environ['DALROOT'], 'include'),
+- "-DoneDAL_LIBRARY_DIR=" + jp(os.environ['DALROOT'], 'lib', 'intel64'),
++ "-DoneDAL_LIBRARY_DIR=" + jp(os.environ['DALROOT'], 'lib', 'lib64'),
+ "-Dpybind11_DIR=" + pybind11.get_cmake_dir(),
+ ]
+
+diff --git a/setup.py b/setup.py +index 8f56b48..36260ea 100644 +--- a/setup.py ++++ b/setup.py +@@ -48,13 +48,13 @@ if dal_root is None: + + if 'linux' in sys.platform: + IS_LIN = True +- lib_dir = jp(dal_root, 'lib', 'intel64') ++ lib_dir = jp(dal_root, 'lib', 'lib64') + elif sys.platform == 'darwin': + IS_MAC = True + lib_dir = jp(dal_root, 'lib') + elif sys.platform in ['win32', 'cygwin']: + IS_WIN = True +- lib_dir = jp(dal_root, 'lib', 'intel64') ++ lib_dir = jp(dal_root, 'lib', 'lib64') + else: + assert False, sys.platform + ' not supported' + +@@ -178,7 +178,8 @@ def get_build_options(): + 'icc', 'icpc', 'icl', 'dpcpp', 'icx', 'icpx'] + eca = ['-DPY_ARRAY_UNIQUE_SYMBOL=daal4py_array_API', + '-DD4P_VERSION="' + d4p_version + '"', '-DNPY_ALLOW_THREADS=1'] +- ela = [] ++ ela = os.environ.get('LDFLAGS').split(" ") ++ eca += os.environ.get('CFLAGS').split(" ") + + if using_intel and IS_WIN: + include_dir_plat.append( +@@ -311,8 +312,8 @@ def build_oneapi_backend(): + ela = ['-fsycl'] + ['-fsycl-device-code-split=per_kernel'] + ela + + return build_backend.build_cpp( +- cc=cc, +- cxx=cxx, ++ cc=os.environ.get('CC'), ++ cxx=os.environ.get('CXX'), + sources=['src/oneapi/oneapi_backend.cpp'], + targetname='oneapi_backend', + targetprefix='' if IS_WIN else 'lib', diff --git a/sci-libs/ipp/metadata.xml b/sci-libs/daal4py/metadata.xml index 7bd17909e..247707c87 100644 --- a/sci-libs/ipp/metadata.xml +++ b/sci-libs/daal4py/metadata.xml @@ -5,9 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> - <longdescription lang="en"> -Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a -library of multi-core-ready, optimized software functions for -multimedia data processing, and communications applications. -</longdescription> + <upstream> + <remote-id type="github">intel/scikit-learn-intelex</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild b/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild index de6c785f8..3961e4951 100644 --- a/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild +++ b/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild @@ -3,11 +3,11 @@ EAPI=7 -inherit fortran-2 multilib +inherit fortran-2 DESCRIPTION="A library of F90 routines to read/write the ETSF file format" HOMEPAGE="https://github.com/ElectronicStructureLibrary/libetsf_io" -SRC_URI="https://launchpad.net/etsf-io/1.0/${PV}/+download/${P}.tar.gz" +SRC_URI="https://launchpad.net/etsf-io/$(ver_cut 1-2)/${PV}/+download/${P}.tar.gz" LICENSE="LGPL-2" SLOT="0" diff --git a/sci-libs/etsf_io/metadata.xml b/sci-libs/etsf_io/metadata.xml index 5c8a3611e..d8e7a0e60 100644 --- a/sci-libs/etsf_io/metadata.xml +++ b/sci-libs/etsf_io/metadata.xml @@ -7,4 +7,8 @@ <use> <flag name="pic">Compile Position Independent Code</flag> </use> + <upstream> + <remote-id type="github">ElectronicStructureLibrary/libetsf_io</remote-id> + <remote-id type="launchpad">etsf-io</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/fast5/Manifest b/sci-libs/fast5/Manifest deleted file mode 100644 index 7ec4bcd49..000000000 --- a/sci-libs/fast5/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST fast5-0.6.5.tar.gz 93639 BLAKE2B 921bf57fa24faf24cfb56a5ee059e12afd8cbccbbb0039205dd27f739abc50f83452dd76726779d700fae93e23bf133aaf5cc42deb80c4ffeae36b89fc68cf9b SHA512 a587e112df36e3d0e151c8c7e01aeffe31294402c2743040c9567ff213f7ae93d6ea7d827a618c7a57fece038b8a53844dbf41fd226416b3fe8c1211bd9311c9 diff --git a/sci-libs/fast5/fast5-0.6.5.ebuild b/sci-libs/fast5/fast5-0.6.5.ebuild deleted file mode 100644 index 38de1b6ff..000000000 --- a/sci-libs/fast5/fast5-0.6.5.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -DOCS_BUILDER="doxygen" -DOCS_DIR="${WORKDIR}/${P}" - -inherit distutils-r1 docs multilib - -DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files" -HOMEPAGE="https://github.com/mateidavid/fast5" -SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND="sci-libs/hdf5 - dev-python/cython[${PYTHON_USEDEP}]" - -S="${WORKDIR}/${P}/python" - -python_compile() { - HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_compile -} - -python_compile_all(){ - docs_compile -} - -python_install() { - HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_install -} diff --git a/sci-libs/fast5/metadata.xml b/sci-libs/fast5/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-libs/fast5/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/fdlibm/fdlibm-5.3.1.ebuild b/sci-libs/fdlibm/fdlibm-5.3.1.ebuild index a2e6b7a09..d03ecb7fc 100644 --- a/sci-libs/fdlibm/fdlibm-5.3.1.ebuild +++ b/sci-libs/fdlibm/fdlibm-5.3.1.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit cmake multilib +inherit cmake DESCRIPTION="C math library supporting IEEE 754 floating-point arithmetic" HOMEPAGE="https://www.netlib.org/fdlibm" diff --git a/sci-libs/fgsl/fgsl-1.3.0.ebuild b/sci-libs/fgsl/fgsl-1.3.0.ebuild index 58da9c18b..01c415ad2 100644 --- a/sci-libs/fgsl/fgsl-1.3.0.ebuild +++ b/sci-libs/fgsl/fgsl-1.3.0.ebuild @@ -6,7 +6,7 @@ EAPI=7 DOCS_BUILDER="doxygen" DOCS_DEPEND="media-gfx/graphviz" -inherit autotools docs fortran-2 toolchain-funcs +inherit docs fortran-2 DESCRIPTION="A Fortran interface to the GNU Scientific Library" HOMEPAGE="https://doku.lrz.de/display/PUBLIC/FGSL+-+A+Fortran+interface+to+the+GNU+Scientific+Library/" diff --git a/sci-libs/flexiblas/Manifest b/sci-libs/flexiblas/Manifest deleted file mode 100644 index 90c0bcb3d..000000000 --- a/sci-libs/flexiblas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST flexiblas-3.0.4.tar.gz 33597962 BLAKE2B d87190d7fbac70f93a5c4fa23cecd6ce75ef1886eb4f0758b4a9da8e9c3d271304e09c94ae53ad80206886ddc7084ff29e3c27b17d50cbcfa8225bcbe944bd48 SHA512 2f677244d4face8ca5ec8b304da55937e311040cc2bb9278fe28695c74f56e4b29810507a9cda0b30f289058f1f5a2bf0035258c39f69df516ee76c606b9f2a2 diff --git a/sci-libs/flexiblas/flexiblas-3.0.4.ebuild b/sci-libs/flexiblas/flexiblas-3.0.4.ebuild deleted file mode 100644 index 7a7e253d0..000000000 --- a/sci-libs/flexiblas/flexiblas-3.0.4.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit cmake python-any-r1 - -DESCRIPTION="BLAS/LAPACK wrapper library for runtime switching of backends" -HOMEPAGE="https://www.mpi-magdeburg.mpg.de/projects/flexiblas" - -if [[ "${PV}" == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/mpimd-csc/flexiblas" -else - SRC_URI="https://github.com/mpimd-csc/flexiblas/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="GPL-3 MIT" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -BDEPEND=" - test? ( ${PYTHON_DEPS} ) -" - -src_configure() { - local mycmakeargs=( - -DTESTS=$(usex test) - -DEXAMPLES=OFF - -DCBLAS=ON - -DLAPACK=ON - -DBLAS_AUTO_DETECT=OFF - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dosym libflexiblas.so "/usr/$(get_libdir)/libblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/libcblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/liblapack.so" -} diff --git a/sci-libs/flexiblas/flexiblas-9999.ebuild b/sci-libs/flexiblas/flexiblas-9999.ebuild deleted file mode 100644 index 7a7e253d0..000000000 --- a/sci-libs/flexiblas/flexiblas-9999.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit cmake python-any-r1 - -DESCRIPTION="BLAS/LAPACK wrapper library for runtime switching of backends" -HOMEPAGE="https://www.mpi-magdeburg.mpg.de/projects/flexiblas" - -if [[ "${PV}" == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/mpimd-csc/flexiblas" -else - SRC_URI="https://github.com/mpimd-csc/flexiblas/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="GPL-3 MIT" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -BDEPEND=" - test? ( ${PYTHON_DEPS} ) -" - -src_configure() { - local mycmakeargs=( - -DTESTS=$(usex test) - -DEXAMPLES=OFF - -DCBLAS=ON - -DLAPACK=ON - -DBLAS_AUTO_DETECT=OFF - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dosym libflexiblas.so "/usr/$(get_libdir)/libblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/libcblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/liblapack.so" -} diff --git a/sci-libs/flexiblas/metadata.xml b/sci-libs/flexiblas/metadata.xml deleted file mode 100644 index c37e14ea4..000000000 --- a/sci-libs/flexiblas/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> - FlexiBLAS is a wrapper library that enables the - exchange of the BLAS, CBLAS and LAPACK implementations - used in an executable without recompiling or re-linking it. - FlexiBLAS provides a GNU Fortran compatible interface - to all functions and subroutines provided by the Netlib - reference implementations. As backends FlexiBLAS can employ - all BLAS and LAPACK implementations which consist of a - single shared library directly. Other variants like the - Intel MKL or ATLAS that use multiple files are integrated - by FlexiBLAS by wrapping all files into a single surrogate library. - </longdescription> - <upstream> - <remote-id type="github">mpimd-csc/flexiblas</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/gdcm/Manifest b/sci-libs/gdcm/Manifest new file mode 100644 index 000000000..64b9caefd --- /dev/null +++ b/sci-libs/gdcm/Manifest @@ -0,0 +1,2 @@ +DIST gdcm-3.0.14.tar.bz2 2992355 BLAKE2B a97209a8bb6896095bfc59ac974b667386c8711f20118252567cf983f15165d259da7858ccfd6bfdfbb25194d7687c98512953b480913acec4bf6d176af7a005 SHA512 9c7d70723d288bf116a8b594c02dd965a4e80476e1c79a7c3cbd09584a229c83ad67f082c9b286305e3bb64150c8267ced06b5fb963adbeeb36e383f76612220 +DIST gdcmData.tar.gz 121157465 BLAKE2B 19b13efc2094d3e373f0f658f1120b1c83ea6da1be73fb392b815433725b4a6db2debb9ab7d9f2caa665637f152f70694cdf226c934850dfda344107050a14a6 SHA512 ddc67a7a0b41b2d6e1e03defb6fb8a06ceeb2e9dd9bb47dfa4f7283d79df7c1e52577b799c00e930719ae6cdda46bded9497a67b8241359f238f5366085ec9ee diff --git a/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch new file mode 100644 index 000000000..ba99c3547 --- /dev/null +++ b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch @@ -0,0 +1,15 @@ +https://cgit.freebsd.org/ports/plain/devel/gdcm/files/patch-Utilities_VTK_vtkImageMapToWindowLevelColors2.cxx?id=8f5541298099b722e34632ca9ed388bda91064e7 + +- workaround for https://sourceforge.net/p/gdcm/bugs/536/ + +--- a/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx 2022-06-26 20:39:45 UTC ++++ b/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx +@@ -37,6 +37,8 @@ + #include "vtkScalarsToColors.h" + #include "vtkPointData.h" + ++#include <math.h> ++ + //vtkCxxRevisionMacro(vtkImageMapToWindowLevelColors2, "$Revision: 1.3 $") + vtkStandardNewMacro(vtkImageMapToWindowLevelColors2) + diff --git a/sci-libs/gdcm/files/gdcm_support_vtk9.patch b/sci-libs/gdcm/files/gdcm_support_vtk9.patch new file mode 100644 index 000000000..3818a82b5 --- /dev/null +++ b/sci-libs/gdcm/files/gdcm_support_vtk9.patch @@ -0,0 +1,70 @@ +--- a/Utilities/VTK/CMakeLists.txt ++++ b/Utilities/VTK/CMakeLists.txt +@@ -26,6 +26,11 @@ + ) + endif() + ++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 ) ++ set(VTK_INCLUDE_DIRS "${VTK_PREFIX_PATH}/include/vtk-${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}") ++ include_directories(AFTER ${VTK_INCLUDE_DIRS}) ++endif() ++ + include(CheckCXXSourceCompiles) + set(CMAKE_REQUIRED_INCLUDES ${VTK_INCLUDE_DIRS}) + CHECK_CXX_SOURCE_COMPILES( +@@ -94,6 +99,10 @@ + endforeach() + endif() + ++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 ) ++ string(REGEX REPLACE "vtk([^;]+)" "VTK::\\1" vtkgdcm_LIBS "${vtkgdcm_LIBS}") ++endif() ++ + # Use wrapping hints for this project. + #set(VTK_WRAP_HINTS "${PROJECT_SOURCE_DIR}/hints") + +--- a/Utilities/VTK/Applications/CMakeLists.txt ++++ b/Utilities/VTK/Applications/CMakeLists.txt +@@ -25,6 +25,11 @@ + ) + endif() + ++set(vtk_ioxml vtkIOXML) ++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 ) ++ set(vtk_ioxml VTK::IOXML) ++endif() ++ + foreach(app ${GDCM_VTK_APPS}) + add_executable(${app} ${app}.cxx) + if(GDCM_EXECUTABLE_PROPERTIES) +@@ -42,7 +47,7 @@ + endif() + else() + # >= 6.0 +- target_link_libraries(${app} ${VTK_LIBRARIES} vtkIOXML) ++ target_link_libraries(${app} ${VTK_LIBRARIES} ${vtk_ioxml}) + endif() + if(WIN32 AND NOT CYGWIN) + target_link_libraries(${app} gdcmgetopt) +--- a/Utilities/VTK/vtkGDCMPolyDataWriter.cxx ++++ b/Utilities/VTK/vtkGDCMPolyDataWriter.cxx +@@ -496,6 +496,9 @@ + sqi = new SequenceOfItems; + + vtkIdType npts = 0; ++#if VTK_MAJOR_VERSION >= 9 ++ const ++#endif + vtkIdType *indx = 0; + double v[3]; + unsigned int cellnum = 0; +@@ -759,6 +762,9 @@ + vtkPoints *pts; + vtkCellArray *polys; + vtkIdType npts = 0; ++#if VTK_MAJOR_VERSION >= 9 ++ const ++#endif + vtkIdType *indx = 0; + pts = theData->GetPoints(); + polys = theData->GetPolys(); diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild new file mode 100644 index 000000000..467fa623c --- /dev/null +++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild @@ -0,0 +1,121 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) + +inherit cmake python-single-r1 + +DESCRIPTION="Cross-platform DICOM implementation" +HOMEPAGE="http://gdcm.sourceforge.net/" +SRC_URI="https://downloads.sourceforge.net/gdcm/${P}.tar.bz2 + test? ( https://downloads.sourceforge.net/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc python test vtk" +RESTRICT="!test? ( test )" + +DEPEND=" + app-text/poppler:0=[cxx] + dev-libs/expat:0= + dev-libs/json-c:0= + dev-libs/libxml2:2= + dev-libs/openssl:0= + >=media-libs/charls-2.0.0:0= + >=media-libs/openjpeg-2.0.0:2= + sys-apps/util-linux:0= + sys-libs/zlib:0= + python? ( ${PYTHON_DEPS} ) + vtk? ( + sci-libs/vtk[rendering] + python? ( + sci-libs/vtk[python,${PYTHON_SINGLE_USEDEP}] + ) + ) +" +RDEPEND="${DEPEND}" +BDEPEND=" + dev-libs/libxslt + app-text/docbook-xsl-ns-stylesheets + doc? ( app-text/doxygen[dot] ) + python? ( + ${PYTHON_DEPS} + >=dev-lang/swig-3.0.7 + )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +PATCHES=( + "${FILESDIR}/gdcm_support_vtk9.patch" + "${FILESDIR}/gdcm-3.0.14-include-math-h.patch" +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_prepare() { + # drop unbundled libs + local -a DROPS=( gdcmcharls gdcmexpat gdcmopenjpeg gdcmuuid gdcmzlib getopt pvrg KWStyle Release ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x#gdcm}" + rm -r "Utilities/${x}" || die + sed -i "s,^[ \t]*APPEND_COPYRIGHT(\\\${CMAKE_CURRENT_SOURCE_DIR}/${x}/,#&," "Utilities/CMakeLists.txt" || die + eend $? + done + find Utilities -mindepth 1 -maxdepth 1 '!' -name doxygen '!' -name VTK -type d \ + -exec ewarn "Using bundled" {} ';' || die + + # fix charls include case + sed -i 's:CharLS/charls\.h:charls/charls.h:' CMake/FindCharLS.cmake Utilities/gdcm_charls.h || die + sed -i 's:NAMES CharLS:NAMES charls:' CMake/FindCharLS.cmake || die + + # Use prefixed socket++ (to avoid potential conflicts) + sed -i '/target_link_libraries(/s/socketxx/gdcm&/' \ + Source/MessageExchangeDefinition/CMakeLists.txt \ + Applications/Cxx/CMakeLists.txt \ + || die + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DGDCM_BUILD_SHARED_LIBS=ON + -DGDCM_DATA_ROOT="${WORKDIR}/gdcmData" + -DGDCM_INSTALL_LIB_DIR="$(get_libdir)" + -DGDCM_INSTALL_DOC_DIR="share/doc/${P}" + -DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages" + -DGDCM_USE_SYSTEM_ZLIB=ON + -DGDCM_USE_SYSTEM_OPENSSL=ON + -DGDCM_USE_SYSTEM_UUID=ON + -DGDCM_USE_SYSTEM_EXPAT=ON + -DGDCM_USE_SYSTEM_JSON=ON + -DGDCM_USE_SYSTEM_PAPYRUS3=OFF + -DGDCM_USE_SYSTEM_SOCKETXX=OFF + -DSOCKETXX_NAMESPACE=GDCMSOCKETXX + -DGDCM_USE_SYSTEM_LJPEG=OFF + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DGDCM_USE_SYSTEM_CHARLS=ON + -DGDCM_USE_SYSTEM_POPPLER=ON + -DGDCM_USE_SYSTEM_LIBXML2=ON + -DGDCM_BUILD_TESTING=$(usex test) + -DGDCM_WRAP_PYTHON=$(usex python) + $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "") + -DGDCM_WRAP_PERL=OFF + -DGDCM_WRAP_PHP=OFF + -DGDCM_WRAP_JAVA=OFF + -DGDCM_WRAP_CSHARP=OFF + -DGDCM_DOCUMENTATION=$(usex doc) + $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "") + -DGDCM_BUILD_EXAMPLES=OFF + -DGDCM_BUILD_APPLICATIONS=ON + -DGDCM_USE_VTK=$(usex vtk) + ) + cmake_src_configure +} diff --git a/sci-libs/gdcm/metadata.xml b/sci-libs/gdcm/metadata.xml new file mode 100644 index 000000000..1845bf1bd --- /dev/null +++ b/sci-libs/gdcm/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>fx.carton91@gmail.com</email> + <name>François-Xavier Carton</name> + </maintainer> + <use> + <flag name="vtk">Build <pkg>sci-libs/vtk</pkg> bridge</flag> + </use> + <upstream> + <remote-id type="sourceforge">gdcm</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/geom/Manifest b/sci-libs/geom/Manifest deleted file mode 100644 index 008c5d270..000000000 --- a/sci-libs/geom/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST geom-6.3.1.8.tar.gz 754682 BLAKE2B e649ce204b0b77fdf8fb2eb34e579479ccb4ac311933eda261781c1499f6b9732f8471724a563a61e9aa5f6c3b0e822aa40c05066322c62e6698bc61b1fdce13 SHA512 f69b7d8a225ce28226536d4ef890daa423da79c845cdb78e9a008e73b6e3f20f74529de4a9e30551792522a53a4536b1d0ae20d2371a7386e7d17a813ec6718b diff --git a/sci-libs/geom/geom-6.3.1.8.ebuild b/sci-libs/geom/geom-6.3.1.8.ebuild deleted file mode 100644 index 39b097c92..000000000 --- a/sci-libs/geom/geom-6.3.1.8.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DOCS_BUILDER="doxygen" -DOCS_DIR="doc/src" -DOCS_DEPEND="media-gfx/graphviz" - -inherit cmake docs - -DESCRIPTION="A complete OpenCascade - OCAF based CAD framework" -HOMEPAGE="https://sourceforge.net/projects/salomegeometry/" -SRC_URI="mirror://sourceforge/salomegeometry/${P}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -OCC_SLOT="7.4.0" - -RDEPEND="sci-libs/opencascade:${OCC_SLOT}" -DEPEND="${RDEPEND}" - -S="${WORKDIR}" - -src_configure() { - mycmakeargs=( - -DOCC_INCLUDE_PATH="/usr/lib64/opencascade-${OCC_SLOT}/ros/include/opencascade/" - ) - cmake_src_configure -} - -src_compile() { - docs_compile - cmake_src_compile -} diff --git a/sci-libs/gvar/Manifest b/sci-libs/gvar/Manifest new file mode 100644 index 000000000..16bdf1de2 --- /dev/null +++ b/sci-libs/gvar/Manifest @@ -0,0 +1 @@ +DIST gvar-13.0.2.tar.gz 1001282 BLAKE2B 5c4032406e3d514351bac6f21b5353c8db4e2081efd26b758cce126cce4a3df350ac8086e89895c73ffc27367773a43354138e8598490cbe8f7bacdde216f0bd SHA512 541cb5cc44909cf44e9f808a08a959aa5e3e91c49356fb8865879a9dbb5fe6f3c4b46d88bc4f9346d9b83163c938dfd697e73b7b9a00815ed6dc383630795cb4 diff --git a/sci-libs/gvar/gvar-13.0.2.ebuild b/sci-libs/gvar/gvar-13.0.2.ebuild new file mode 100644 index 000000000..b9d9121e4 --- /dev/null +++ b/sci-libs/gvar/gvar-13.0.2.ebuild @@ -0,0 +1,22 @@ +EAPI=8 + +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Gaussian random variables." +HOMEPAGE="https://github.com/gplepage/gvar" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~arm64" + +RDEPEND=" + >=dev-python/cython-0.17[${PYTHON_USEDEP}] + >=dev-python/numpy-1.16[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" +BDEPEND="${RDEPEND}" + +distutils_enable_tests unittest diff --git a/sci-libs/gvar/metadata.xml b/sci-libs/gvar/metadata.xml new file mode 100644 index 000000000..31346f0dd --- /dev/null +++ b/sci-libs/gvar/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + This package facilitates the creation and manipulation of arbitrarily complicated (correlated) multi-dimensional Gaussian random variables. The random variables are represented by a new data type (gvar.GVar) that can be used in arithmetic expressions and pure Python functions. Such expressions/functions create new Gaussian random variables while automatically tracking statistical correlations between the new and old variables. This data type is useful for simple error propagation, but also is heavily used by the Bayesian least-squares fitting module lsqfit.py to define priors and specify fit results, while accounting for correlations between all variables. + </longdescription> + <upstream> + <remote-id type="pypi">gvar</remote-id> + <remote-id type="github">gplepage/gvar</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/handyg/Manifest b/sci-libs/handyg/Manifest new file mode 100644 index 000000000..3487702bd --- /dev/null +++ b/sci-libs/handyg/Manifest @@ -0,0 +1 @@ +DIST handyg-v0.1.5.tar.gz 107946 BLAKE2B 338b0027f51fd8b329c1af4e6a0e76dda7b9a3d29a12cffcf60948c5800ee8e280ff97726359df483b60dc3d76a26c40bf21804113d318d83539828e54c4a1ff SHA512 f6f068e05c80c6dccf1c4c8a284da752d04d4fd3f15a78eee933227c6a93906fe794ef3ada359831a4098c00b0a7684af91e2f9cca2a06dd8d0381c1c20c59be diff --git a/sci-libs/handyg/files/handyg-0.1.5-so.patch b/sci-libs/handyg/files/handyg-0.1.5-so.patch new file mode 100644 index 000000000..48815780e --- /dev/null +++ b/sci-libs/handyg/files/handyg-0.1.5-so.patch @@ -0,0 +1,23 @@ +--- a/configure 2022-09-19 22:54:12.742507414 +0200 ++++ b/configure 2022-09-19 23:00:13.452378883 +0200 +@@ -839,7 +839,7 @@ + objects = \$(addprefix build/,\$(files)) + + +-all: libhandyg.a handyg.mod ${CONF_MPREP:+handyG} geval test ++all: libhandyg.a libhandyg.so handyg.mod ${CONF_MPREP:+handyG} geval test + + EOF + +@@ -868,6 +868,11 @@ + @echo "AR \$@" + @\$(AR) \$@ \$^ + ++libhandyg.so:\$(objects) ++ @echo "\$(FC) \$@" ++ \$(FC) \$(LFLAGS) -Wl,-soname,libhandyg.so -shared -o \$@ \$^ ++ ++ + handyg.mod: build/handyg.mod + cp \$< \$@ + diff --git a/sci-libs/handyg/handyg-0.1.5.ebuild b/sci-libs/handyg/handyg-0.1.5.ebuild new file mode 100644 index 000000000..97a18c08e --- /dev/null +++ b/sci-libs/handyg/handyg-0.1.5.ebuild @@ -0,0 +1,44 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs +MY_P=${PN}-v${PV} + +DESCRIPTION="Rapid numerical evaluation of generalised polylogarithms" +HOMEPAGE="https://gitlab.com/mule-tools/handyg" +SRC_URI="https://gitlab.com/mule-tools/${PN}/-/archive/v${PV}/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND=" + virtual/fortran +" + +PATCHES=( + "${FILESDIR}/${P}-so.patch" +) + +src_configure() { + tc-export CC CXX FC AR + FFLAGS="${FFLAGS} -fPIC" LD="${FC}" ./configure --prefix="${EPREFIX}/usr" LDFLAGS="${LDFLAGS}" +} + +src_compile() { + # single thread force needed since fortan mods depend on each other + export MAKEOPTS=-j1 + emake all +} + +src_install() { + dolib.a libhandyg.a + dolib.so libhandyg.so + doheader handyg.mod + dobin geval +} diff --git a/sci-libs/jhdf5/metadata.xml b/sci-libs/handyg/metadata.xml index 138cb7705..bdee6992b 100644 --- a/sci-libs/jhdf5/metadata.xml +++ b/sci-libs/handyg/metadata.xml @@ -2,11 +2,11 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> </maintainer> <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> </maintainer> </pkgmetadata> diff --git a/sci-libs/iRODS/Manifest b/sci-libs/iRODS/Manifest index 4efc24868..8466e3408 100644 --- a/sci-libs/iRODS/Manifest +++ b/sci-libs/iRODS/Manifest @@ -1 +1,2 @@ -DIST iRODS-4.2.8.tar.gz 1902368 BLAKE2B 7ecbf4da15bb15dba6dbcebb21b66b46f6906daa694c7d9d49fbcfbcc9b9eabffe805f7da411e6d3272c34e605cfed12525130c1cedfd58a6601401ec49a963a SHA512 0a57201f4404e0d023f68591842edd1f750050c16ca2b4fad4dcbdabfce77755540a13140d201bc3fea214dcf3d3c40a43fd079f09f0544e979330f04279a579 +DIST iRODS-4.2.11.tar.gz 2183164 BLAKE2B 8c87938e7c8aa731282bf64ec8e017fe0f9ee70c46f07b4c136973bf0ca50954898d93c045440c79eecab84d8adbda6905f1e8eae434c8094ca50ce9f2c1b5dc SHA512 6f938ecc5b872326a4b59b82f119f1c5526c438e7b5c44248b5bba735445e4bc8b287f3bc0eb53b684b17a247aff31cb48b0211a10fc92870d29bdef978715e5 +DIST iRODS-4.2.11_schema_messaging.tar.gz 454 BLAKE2B 09f1f48e22f05545233017db85b84472d0a84b3926b706af6d81cbaaf5d919f508856572daa6e5c61a5a4830527fb982df2df2eb11540a0c7841513eee206ee2 SHA512 d77b0e9d9f80b1513eacc9a86f14ffb02ff5172df41527c41cd49fea26831f11f2c87dc2ea21ae7ad5fb6e0399f8a72248d9accea65101a08158710c5012184a diff --git a/sci-libs/iRODS/iRODS-4.2.11.ebuild b/sci-libs/iRODS/iRODS-4.2.11.ebuild new file mode 100644 index 000000000..849a7c509 --- /dev/null +++ b/sci-libs/iRODS/iRODS-4.2.11.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit cmake llvm + +MESSAGING_COMMIT="24c73702c88e94c3b159dac97fe7a0640dfc209d" + +DESCRIPTION="Integrated Rule Oriented Data System, a data management software" +HOMEPAGE="https://irods.org" +SRC_URI=" + https://github.com/irods/irods/archive/${PV}.tar.gz -> ${P}.tar.gz + https://github.com/irods/irods_schema_messaging/archive/${MESSAGING_COMMIT}.tar.gz -> ${P}_schema_messaging.tar.gz +" +S="${WORKDIR}/irods-${PV}" + +LICENSE="BSD" +SLOT="0" +# need the c++ version of avro +KEYWORDS="" + +DEPEND=" + app-arch/libarchive + dev-cpp/catch:0 + dev-libs/avro-c + dev-libs/boost:= + dev-libs/jansson + dev-libs/json-c + dev-libs/libfmt + dev-libs/openssl + dev-libs/spdlog + sys-libs/libcxx + sys-libs/pam + net-libs/cppzmq + net-libs/zeromq +" +RDEPEND="${DEPEND}" +BDEPEND=" + sys-devel/clang +" + +src_unpack() { + default + mv "${WORKDIR}/irods_schema_messaging-${MESSAGING_COMMIT}/v1" "${S}/irods_schema_messaging/" || die +} + +src_prepare() { + cmake_src_prepare + # use the correct lib dir + find . -name "CMakeLists.txt" -exec sed -i \ + -e '/${IRODS_EXTERNALS_FULLPATH_.*}/s/\/lib\//\/lib64\//g' \ + {} + || die +} + +src_configure() { + local mycmakeargs=( + -DIRODS_EXTERNALS_FULLPATH_CLANG="$(get_llvm_prefix)" + -DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="$(get_llvm_prefix)" + -DIRODS_EXTERNALS_FULLPATH_ARCHIVE="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_AVRO="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_BOOST="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_CATCH2="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_FMT="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_ZMQ="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_JANSSON="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_SPDLOG="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_CPPZMQ="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_JSON="${EPREFIX}/usr" + -DIRODS_EXTERNALS_FULLPATH_NANODBC="${EPREFIX}/usr" + # pretend we are Arch, otherwise fatal error + -DIRODS_LINUX_DISTRIBUTION_NAME="arch" + -DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR="1" + ) + cmake_src_configure +} diff --git a/sci-libs/iRODS/iRODS-4.2.8.ebuild b/sci-libs/iRODS/iRODS-4.2.8.ebuild deleted file mode 100644 index eba0c76e2..000000000 --- a/sci-libs/iRODS/iRODS-4.2.8.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Integrated Rule Oriented Data System, a data management software" -HOMEPAGE="https://irods.org" -SRC_URI="https://github.com/irods/irods/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" - -DEPEND="" -RDEPEND="${DEPEND}" -BDEPEND="sys-devel/clang" - -S="${WORKDIR}/irods-${PV}" diff --git a/sci-libs/ipp/Manifest b/sci-libs/ipp/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/sci-libs/ipp/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d -DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404 diff --git a/sci-libs/ipp/ipp-18.0.2.199.ebuild b/sci-libs/ipp/ipp-18.0.2.199.ebuild deleted file mode 100644 index 5253840b9..000000000 --- a/sci-libs/ipp/ipp-18.0.2.199.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_SKU=3235 -INTEL_DIST_PV=2018_update2_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel Integrated Performance Primitive library" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="" -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=6500M - -INTEL_DIST_DAT_RPMS=( - "ipp-common-2018.2-199-2018.2-199.noarch.rpm" - "ipp-common-ps-2018.2-199-2018.2-199.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "ipp-mt-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-mt-devel-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-ps-2018.2-199-2018.2-199.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "ipp-mt-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-mt-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-ps-32bit-2018.2-199-2018.2-199.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "ipp-doc-2018-2018.2-199.noarch.rpm") - fi -} diff --git a/sci-libs/ipp/ipp-19.0.4.243.ebuild b/sci-libs/ipp/ipp-19.0.4.243.ebuild deleted file mode 100644 index e42583e20..000000000 --- a/sci-libs/ipp/ipp-19.0.4.243.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel Integrated Performance Primitive library" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="" -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=6500M - -INTEL_DIST_DAT_RPMS=( - "ipp-common-2019.4-243-2019.4-243.noarch.rpm" - "ipp-common-ps-2019.4-243-2019.4-243.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "ipp-mt-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-mt-devel-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-ps-2019.4-243-2019.4-243.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "ipp-mt-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-mt-devel-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-ps-32bit-2019.4-243-2019.4-243.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "ipp-doc-2019-2019.4-243.noarch.rpm") - fi -} diff --git a/sci-libs/ipp/ipp-2020.1.217.ebuild b/sci-libs/ipp/ipp-2020.1.217.ebuild deleted file mode 100644 index 2c0be6abf..000000000 --- a/sci-libs/ipp/ipp-2020.1.217.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2020_update1_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel Integrated Performance Primitive library" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="" -RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]" - -CHECKREQS_DISK_BUILD=6500M - -MY_PV="$(ver_rs 2 '-')" # 2020.1-217 - -QA_PREBUILT="*" - -INTEL_DIST_DAT_RPMS=( - "ipp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "ipp-common-ps-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "ipp-mt-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-mt-devel-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-devel-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "ipp-mt-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-mt-devel-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-devel-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "ipp-doc-2020-${MY_PV}.noarch.rpm") - fi -} diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest index 2be705868..87328da27 100644 --- a/sci-libs/itk/Manifest +++ b/sci-libs/itk/Manifest @@ -1,10 +1,12 @@ -DIST ITKGenericLabelInterpolator-5.0.1.tar.gz 136432 BLAKE2B c367d5f29b3b3250f73d3b03b80b50a99607d895ebb83c3613b40ed665bce87b2731b2ecf471a5b77983db1f8894e486404662bb5787056f23de24c8ee897704 SHA512 6044aab4893d6c68c6190c5d81f460ea0dfc4683d33a03a5d56a8a0ae3b767edde530cdc8976e6777237cb1d172f66df044afe11c4cfc9148e5712cf9f3a11fc -DIST ITKGenericLabelInterpolator-5.1.0.tar.gz 140286 BLAKE2B 1c8efa033586368931d78fe4620ddd1449fcd15153b1585c716bce580df74a6fc990b3714677a81cdcedcd0e4626e4f155c522f6e7306e5be399d521213891b4 SHA512 7bf6310e8b0ea2356ae8ce0ddd0bc3a1516aa6bb5e3e8df9ed0114f1bb2b299d2edd046f27dbae364082afc63e225a3691c794c93d347ee564db617ea3fbf489 -DIST ITKGenericLabelInterpolator_test-5.0.1.zip 430662 BLAKE2B f46683bd1b3479ae6fc9ae63752810a1dda7940c67d4be8524edcb8b40ed384b331ac785ab752c3ed1570cce8d79af7de873820fdb76a11f2e4241ad7fd2d2c2 SHA512 435200a70ee8de30cc02b30d805697ebc61fb2792e6e7d8f5da923d2773ccd6adfdcec2ab953a6a043d624ebb01b9f7f30e2aad83a6442272f28104d357a7bde -DIST InsightData-5.0.1.tar.gz 290801718 BLAKE2B dcb7657cb1f8555365b2ec94e7f95c4feab13ba4d585fd70ec240e63e7a55cf48aadf091a63ba2263f1f8c10ce3935812655449bea275af3d2eeff3f2689ef46 SHA512 eb766c115049949937d6527937f1f49ef84304a71dc4924581a53173f45c4e5a0c5a0e180550e75ecd840314609580b9d1fe9b2358c5a87c82a2c6aff8e9f50e -DIST InsightData-5.1.0.tar.gz 292322103 BLAKE2B e55eddf06d72e87e68e7654c634f545923202467b710c75aa929cd040f37a9caa48ee262ca6465631961816af1cd854b9a046ff7e7ffed7731e428e092bc6020 SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa -DIST InsightToolkit-5.0.1.tar.gz 20627889 BLAKE2B 2bd53f64f18746a7d0226d4d97bc02529a1dd2c05fc2294b0c2a5adb3783a8e766b1d20e051a17f20b4e5855e7c5b4a18d5f177f239113bc64f1a0400ce6f04b SHA512 f36613ff72c513ded3d32504f71308a94fe75555cf9fd22b77485d1375601f6e1f1539cc5ac82a9e1e229bcf514a88ccb55122a7dfc74a6ae1b6604aa70bd814 -DIST InsightToolkit-5.1.0.tar.gz 20694338 BLAKE2B 6a14e2e00f6d68a1420cdeebabdef254d23c6ba6610828bb860cf4e27a87f0e1448cd222bf3bc02f6d32b4eb262d7ba032f4459ed05f59f8c95d80907e03571c SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c -DIST itk-5.1.0-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 1014 BLAKE2B e323a0de725e717fddbe70a2e5a20fd5f55af8361caefb1388e3566b80e2496c869e860c9588b2cb579b39bf58a160ce47db454efc656477a40604473780f623 SHA512 aba302ea9921df0af6c9f076850f5923a70ab6c6f6e1450a0dd4bd99f5257641cd8ba9a97c8a84b92f0325295328858785bc6627dab936ac7131de81e1e2d08c -DIST itk-5.1.0-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 1015 BLAKE2B 1c2d888c8fa8ce857c3c02a50fe4fda87d51a5ba1f563a9a0bbe331c1b9656fd3cf510b93d91489ec55785dc0e78d4a6e45c694913e4ab8a7c67db1a27eb786a SHA512 9c34d50f36e569a2b50a8fca21ee271b641a3703aa9465cce5e0e0ac3d24d061be4800b8e800d2634511bbd76dff853a2734df3465c7b62a53b8e6b6fd5f3f77 -DIST itk-5.1.0-testingdata.tar.gz 2409232372 BLAKE2B 7eb1c3ca21558603d3aa915c2a17e9bb656867331dc48e7b514ece50a7eac3d24bdf01c8b0acc703566b598959780d6736b27d1516d932f949e3a5cfe6acd9e0 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f +DIST ITKAdaptiveDenoising-5.2.1.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4 +DIST ITKAdaptiveDenoising-5.3.0.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4 +DIST ITKGenericLabelInterpolator-1.2.0.tar.gz 137697 BLAKE2B f7bb877654e852f56f8eb1086f988ec3b71106b6528d5cf03734a3c3eb4ce5ac875b52081e0a1339ac237e1616b0516b8cc8efb4429ec0e5ef64ac5461a40836 SHA512 bc1fcd3c13cb182420bb4a5d2c9c789553f8b7b581fd7d0b7d687331e22c90d30efdd338bfbc22dfb8c97d3ab7209f761425c4d12755655d86d81ffb231d881c +DIST ITKGenericLabelInterpolator-5.2.1.tar.gz 140427 BLAKE2B b19703872926516d9d07acd4078d343e02f00a162d2cb8b6787d6210223be375a059e767cf9c32dd234e77ff51d1af5e08d9a9844c34e23a531938c7d3ded4a9 SHA512 69e53b281cd3f7c136ad9e7ded2c362e0d9e22dc2bd595f42abcefe2cf9ec4fa0f44192efc3d328290be4adaee1ebd74be3035b18147081cc8b8479a333cdea6 +DIST InsightData-5.2.1.tar.gz 293448802 BLAKE2B fd2bb012c0d96243d3543993a87e73c43be0626b0478959e36633f22c7e8d48a46d0f4d18fa3a8d952d4a705ca20594d92c07044000b8e1bc65390ce981af3e7 SHA512 93eae6bdf62ce29ea6dfb1dddedffe4046400a86074dd4d47e3ddcd7ff9ab10031363275cb7f9741add7c02343f1f3e6a41b0ec6533531f4a3a42607c51aa704 +DIST InsightData-5.3.0.tar.gz 366826437 BLAKE2B ae3cbb3f7a51d6b86717a073c0eb55c528baeff240f44413c25ce11319a7e0ef9ff073d1cb94d2d15d104687fe5b8e95d0d4286832dbb02993da8fe706fecb28 SHA512 3caf7d1d64543312d668ef1a6b8c879161a37deee5c980fbfeb14e299a296a2825ae48463bff915f50c98ec0ccdbef3e1aff7c4f52604a93c6028951f90a4757 +DIST InsightToolkit-5.2.1.tar.gz 20702482 BLAKE2B 06dc73a80b4999baff3fc75e225c8720d00927fd268bd0398bb0eea44679777b777836f307f02a2df3641a300e17c9c2ee9f77d2a87539bf8a6ed49ce341bf23 SHA512 6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7 +DIST InsightToolkit-5.3.0.tar.gz 21577835 BLAKE2B 7538b673cbe17ab23d6b70e2cb2486e6711df6a79d6806c641a10a8b624c4723ca5f562b97be814551c79c42dea772ac64ed7bc8fdf2d28f5a95cb6462e50638 SHA512 29359839c0fb13acd430410e6adadbecb4d9d8cb4871a0aba0ac67b539c235354a591655dd654f43daa5f035a33721671d665eee8a4a129a9d0d3419e2356e97 +DIST itk-5.2.1-testingdata.tar.gz 2411475710 BLAKE2B edb8ba9bea8bf890749aa46ab3fb29f7d3e25e0f8bb7da7d7cca8c6524f75778b823232536602ade763c025b8e0fe134a555e6fcf652b8d42cc08f08cbd0c29b SHA512 89b160dc5f7781e148aad065f539b80b9accb9ec384e424398287e62b42a88cff610afcf41622a6d3e4e12c1938e7403b3dae65fa13bfb40c29a6b2f90a02398 +DIST itk-5.3.0-testingdata.tar.gz 2569680868 BLAKE2B a358bdb3a9f6de883e9fe41129af88d7a476acc4839fd17075d484a441db40d7f1f2f247d07701817464de5c997b18066628921652630a5f110e238d3f2419ec SHA512 5fa0834c25d128c915b5bdaefb13574952e680fe52a5c99ced614737e52f57abce59510be764766ce43769ae5731c35c7d646cdf3e21f495aee14fbb7d1835b4 +DIST itk-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 BLAKE2B cd65212e72cb80eff54ee3f22d05b55036470684c582334fe94826a2d4ed49c840c50a214996f64f2bcd710e5973c2d46201ef31732fe847a43504379df62e25 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a +DIST itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 BLAKE2B 318a6c55ba259a5af1e3e19cf859267caa0a612b05abfd9a83d9943902fd7edc25ec002707ed4ec85f7aebd4c5a82411942b5cfe2dc713c905a5bb5d1aa5ef23 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch deleted file mode 100644 index 094ee3229..000000000 --- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch +++ /dev/null @@ -1,50 +0,0 @@ -From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001 -From: Matt McCormick <matt.mccormick@kitware.com> -Date: Wed, 5 Feb 2014 15:52:34 -0500 -Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter. - -Missing CMakeLists.txt in the wrapping directory. Need to explicitly include -the headers after "Template" was appended to the class name. - -Suggested-by: Sami Koho <sami.koho@gmail.com> - -Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7 ---- - Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++ - Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++ - Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++ - 3 files changed, 7 insertions(+) - create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt - -diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -new file mode 100644 -index 0000000..6072567 ---- /dev/null -+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -@@ -0,0 +1,3 @@ -+itk_wrap_module(ITKIOTransformBase) -+itk_auto_load_submodules() -+itk_end_wrap_module() -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -index 9b52fbc..662df9e 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileReader.h") - itk_wrap_class("itk::TransformFileReaderTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -index 4f1ac4a..356aaf3 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileWriter.h") - itk_wrap_class("itk::TransformFileWriterTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch deleted file mode 100644 index 4c74d5451..000000000 --- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001 -From: Michka Popoff <michkapopoff@gmail.com> -Date: Fri, 7 Feb 2014 19:24:49 +0100 -Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings - -The warning : -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef] -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double > ---- - .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++- - 1 file changed, 7 insertions(+), 1 deletion(-) - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -index 4a43dd4..7eed11c 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkQuasiNewtonOptimizerv4.h") -+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch deleted file mode 100644 index d77345edf..000000000 --- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch +++ /dev/null @@ -1,73 +0,0 @@ -From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001 -From: Michka Popoff <michkapopoff@gmail.com> -Date: Mon, 10 Feb 2014 09:41:42 +0100 -Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping - warnings - -I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping. - -The warnings : -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double > - -Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/) -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored. -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template. - -Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364 ---- - .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++ - .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++--- - .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++ - 3 files changed, 21 insertions(+), 3 deletions(-) - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -new file mode 100644 -index 0000000..74f5a6c ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerBasev4.h") -+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -index d53a176..3236448 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -@@ -1,3 +1,7 @@ --itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerv4.h") -+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -new file mode 100644 -index 0000000..61b2c44 ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkObjectToObjectOptimizerBase.h") -+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch deleted file mode 100644 index 83b395626..000000000 --- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Matt McCormick <matt.mccormick@kitware.com> -Date: Thu Feb 6 10:26:49 2014 -0500 - - COMP: Wrap OptimizerParameterScalesEstimatorTemplate. - - The class name changed and it became templated. Fixes: - - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator - [typedef] - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(4): ITK type not wrapped, or currently not known: - itk::OptimizerParameterScalesEstimatorTemplate< double > - - Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim -index efd6a8c..a647ee4 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkOptimizerParameterScalesEstimator.h") -+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() - diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch deleted file mode 100644 index d760ac7ba..000000000 --- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -index e98077c..70f4286 100644 ---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt -+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -@@ -1,5 +1,5 @@ - if(ITK_USE_SYSTEM_GDCM) -- add_library(ITKGDCM ITK-GDCM.cxx) -+ add_library(ITKGDCM STATIC ITK-GDCM.cxx) - target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF) - itk_module_target(ITKGDCM) - return() diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch deleted file mode 100644 index eb130159a..000000000 --- a/sci-libs/itk/files/ITKModuleRemote.patch +++ /dev/null @@ -1,45 +0,0 @@ -Disable automatic git clone attempt for modules: -https://github.com/InsightSoftwareConsortium/ITK/issues/1157 - ---- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200 -+++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200 -@@ -165,39 +165,4 @@ - set(Module_${_name} ON CACHE FORCE "${_description}") - endif() - -- if(Module_${_name}) -- itk_download_attempt_check(Module_${_name}) -- include(CMakeParseArguments) -- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN}) -- find_package(Git) -- if(NOT GIT_EXECUTABLE) -- message(FATAL_ERROR "error: could not find git for clone of ${_name}") -- endif() -- execute_process( -- COMMAND "${GIT_EXECUTABLE}" --version -- OUTPUT_VARIABLE ov -- OUTPUT_STRIP_TRAILING_WHITESPACE -- ) -- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}") -- if("${_version}" VERSION_LESS 1.6.6) -- message(FATAL_ERROR "Git version 1.6.6 or later is required.") -- endif() -- -- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}") -- -- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}") -- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}") -- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n" -- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n" -- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'") -- endif() -- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}") -- mark_as_advanced(REMOTE_GIT_TAG_${_name}) -- -- _fetch_with_git("${GIT_EXECUTABLE}" -- "${_fetch_options_GIT_REPOSITORY}" -- "${REMOTE_GIT_TAG}" -- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}" -- ) -- endif() - endfunction() diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch deleted file mode 100644 index 34fdb76d1..000000000 --- a/sci-libs/itk/files/itk-5.1.0-downloads.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400 -+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400 -@@ -11,7 +11,7 @@ - - macro(itk_download_attempt_check _name) - if(ITK_FORBID_DOWNLOADS) -- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON") -+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON") - endif() - endmacro() - ---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400 -+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400 -@@ -44,6 +44,4 @@ - itk_fetch_module(GenericLabelInterpolator - "A generic interpolator for multi-label images." - MODULE_COMPLIANCE_LEVEL 2 -- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git -- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7 - ) diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch new file mode 100644 index 000000000..05c9d5635 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch @@ -0,0 +1,25 @@ +From: François-Xavier Carton <fx.carton91@gmail.com> +Date: Thu, 9 Jun 2022 14:56:22 +0200 +Subject: [PATCH] fix attr malloc error with recent glibc/gcc + +Recent GCC has support for __attribute__((__malloc__)) with arguments, but clang +does not. castxml uses clang internally. And recent glibc/gcc uses the attribute +with arguments. Mix all this, and you get: + +error: '__malloc__' attribute takes no arguments + +when compiling itk with python wrapping. + +To fix this, we add a define to castxml flags to remove the extra arguments. + +--- a/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:53:15.582352715 +0200 ++++ b/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:54:38.182351433 +0200 +@@ -237,7 +237,7 @@ + set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0") + endif() + else() +- set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} )) ++ set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ )) + endif() + set(_target) + if(CMAKE_CROSSCOMPILING) diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch new file mode 100644 index 000000000..ad717f677 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch @@ -0,0 +1,558 @@ +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -1,16 +1,32 @@ + project(ITKOpenJPEG) + set(ITKOpenJPEG_THIRD_PARTY 1) + +-set(ITKOpenJPEG_INCLUDE_DIRS +- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg +- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg +- ) +-set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES}) ++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG) ++ ++if(ITK_USE_SYSTEM_OPENJPEG) ++ find_package(OpenJPEG REQUIRED) ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src ++ ) ++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS ++ ${OPENJPEG_INCLUDE_DIRS} ++ ) ++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}") ++ set(ITKOpenJPEG_NO_SRC 1) ++else() ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg ++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg ++ ) ++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++endif() ++ ++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h) + set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE) +- + itk_module_impl() + +-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h ++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h + DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR} + COMPONENT Development + ) +diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h +rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h ++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +@@ -25,6 +25,12 @@ + #ifndef itk_openjpeg_h + #define itk_openjpeg_h + +-#include <itkopenjpeg/openjpeg.h> ++/* Use the openjpeg library configured for ITK. */ ++#cmakedefine ITK_USE_SYSTEM_OPENJPEG ++#ifdef ITK_USE_SYSTEM_OPENJPEG ++# include <openjpeg.h> ++#else ++# include <itkopenjpeg/openjpeg.h> ++#endif + + #endif +--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx ++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx +@@ -27,8 +27,6 @@ + extern "C" + { + #include "openjpeg.h" +-#include "j2k.h" +-#include "jp2.h" + } + + +@@ -139,11 +137,11 @@ + { + itkDebugMacro(<< "ReadImageInformation()"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- /* decompression parameters */ ++ /* set decoding parameters to default values */ ++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); + +- if (!l_file) ++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); ++ if (!cio) + { + itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl + << "Reason: " +@@ -151,10 +149,5 @@ + } + +- /* set decoding parameters to default values */ +- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); +- +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true); +- + this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */ + + opj_image_t * l_image = nullptr; +@@ -188,9 +181,8 @@ + + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -202,10 +194,9 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -217,10 +208,9 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -230,7 +220,6 @@ + } + default: + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -248,26 +237,8 @@ + } + +- // Image parameters - first tile +- OPJ_INT32 l_tile_x0; +- OPJ_INT32 l_tile_y0; +- +- // Image parameters - tile width, height and number of tiles +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- + itkDebugMacro(<< "Trying to read header now..."); + +- bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- cio); ++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { +@@ -284,13 +255,21 @@ + } + +- this->m_Internal->m_TileStartX = l_tile_x0; +- this->m_Internal->m_TileStartY = l_tile_y0; ++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo); ++ if (!cp) ++ { ++ opj_stream_destroy(cio); ++ opj_image_destroy(l_image); ++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl ++ << "Reason: Error while reading image header"); ++ } ++ this->m_Internal->m_TileStartX = cp->tx0; ++ this->m_Internal->m_TileStartY = cp->ty0; + +- this->m_Internal->m_TileWidth = l_tile_width; +- this->m_Internal->m_TileHeight = l_tile_height; ++ this->m_Internal->m_TileWidth = cp->tdx; ++ this->m_Internal->m_TileHeight = cp->tdy; + +- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x; +- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y; ++ this->m_Internal->m_NumberOfTilesInX = cp->tw; ++ this->m_Internal->m_NumberOfTilesInY = cp->th; + + + itkDebugMacro(<< "Number of Components = " << l_image->numcomps); +@@ -307,6 +286,7 @@ + else + { + opj_stream_destroy(cio); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: " + << "Unknown precision in file: " +@@ -320,6 +300,6 @@ + break; + case 3: +- if (l_image->color_space != CLRSPC_SRGB) ++ if (l_image->color_space != OPJ_CLRSPC_SRGB) + { + itkWarningMacro(<< "file does not specify color space, assuming sRGB"); + } +@@ -349,7 +329,6 @@ + + /* close the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -368,16 +347,7 @@ + { + itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- +- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true); ++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); + if (!l_stream) + { + itkExceptionMacro("JPEG2000ImageIO failed to read file: " +@@ -397,9 +367,10 @@ + { + /* JPEG-2000 codestream */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr"); +@@ -410,9 +381,10 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr"); +@@ -423,9 +395,10 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr"); +@@ -433,7 +406,7 @@ + break; + } + default: +- fclose(l_file); ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -445,32 +418,17 @@ + if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters))) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_decoder returns false"); + } + +- OPJ_INT32 l_tile_x0, l_tile_y0; +- +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- +- bool bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- l_stream); ++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { + opj_destroy_codec(this->m_Internal->m_Dinfo); + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_read_header returns false"); + } +@@ -499,7 +457,7 @@ + itkDebugMacro(<< "p_end_x = " << p_end_x); + itkDebugMacro(<< "p_end_y = " << p_end_y); + +- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y); ++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y); + + itkDebugMacro(<< "opj_set_decode_area() after"); + +@@ -509,6 +467,5 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_set_decode_area returns false"); + } +@@ -525,13 +482,14 @@ + + OPJ_UINT32 l_max_data_size = 1000; + +- bool l_go_on = true; ++ OPJ_BOOL l_go_on = true; + + auto * l_data = (OPJ_BYTE *)malloc(1000); + + while (l_go_on) + { + bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, ++ l_stream, + &l_tile_index, + &l_data_size, + &l_current_tile_x0, +@@ -540,13 +498,11 @@ + &l_current_tile_y1, + &l_nb_comps, +- &l_go_on, +- l_stream); ++ &l_go_on); + + if (!tileHeaderRead) + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -571,7 +527,6 @@ + if (!l_data) + { + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -590,7 +545,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -654,7 +608,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -667,13 +620,11 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: error whle reading image"); + } + + /* close the byte stream */ + opj_stream_destroy(l_stream); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -775,6 +726,6 @@ + } + +- for (int i = 0; i < parameters.numpocs; i++) ++ for (OPJ_UINT32 i = 0; i < parameters.numpocs; i++) + { + if (parameters.POC[i].prg == -1) + { +@@ -840,13 +791,13 @@ + + parameters.numresolution = numberOfResolutions; + +- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY; ++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY; + opj_image_cmptparm_t cmptparms[3]; + + if (this->GetNumberOfComponents() == 3) + { + +- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED; ++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED; + + /* initialize image components */ + memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t)); +@@ -864,7 +815,7 @@ + + if (this->GetNumberOfComponents() == 1) + { +- color_space = CLRSPC_GRAY; ++ color_space = OPJ_CLRSPC_GRAY; + + /* initialize image components */ + memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t)); +@@ -941,8 +892,9 @@ + if (extension == ".j2k") + { +- cinfo = opj_create_compress(CODEC_J2K); ++ cinfo = opj_create_compress(OPJ_CODEC_J2K); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_J2K) returns nullptr"); +@@ -950,9 +902,10 @@ + } + else if (extension == ".jp2") + { +- cinfo = opj_create_compress(CODEC_JP2); ++ cinfo = opj_create_compress(OPJ_CODEC_JP2); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JP2) returns nullptr"); +@@ -960,9 +913,10 @@ + } + else if (extension == ".jpt") + { +- cinfo = opj_create_compress(CODEC_JPT); ++ cinfo = opj_create_compress(OPJ_CODEC_JPT); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JPT) returns nullptr"); +@@ -970,6 +924,7 @@ + } + else + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: unknown encode format: " << extension); + } +@@ -985,23 +940,19 @@ + + if (!opj_setup_encoder(cinfo, ¶meters, l_image)) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_encoder returns false"); + } + +- FILE * l_file = fopen(parameters.outfile, "wb"); +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- + /* open a byte stream for writing */ + /* allocate memory for all tiles */ +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false); ++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false); + if (!cio) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -1017,7 +968,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_start_compress returns false"); + } +@@ -1026,7 +978,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_encode returns false"); + } +@@ -1035,14 +988,14 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_end_compress returns false"); + } + + /* close and free the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + /* free remaining compression structures */ + opj_destroy_codec(cinfo); +--- a/Modules/Nonunit/Review/src/CMakeLists.txt ++++ b/Modules/Nonunit/Review/src/CMakeLists.txt +@@ -5,7 +5,7 @@ + + add_library(ITKReview ${ITKReview_SRC}) + itk_module_link_dependencies() +-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg) ++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES}) + itk_module_target(ITKReview) + + diff --git a/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch new file mode 100644 index 000000000..25c44db2c --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch @@ -0,0 +1,18 @@ +From: François-Xavier Carton <fx.carton91@gmail.com> +Date: Wed, 8 Jun 2022 19:36:48 +0200 +Subject: [PATCH] system libtiff has INT64 + +Enabling this, otherwise using system libtiff leads to errors. In particular +tests fail because there is some IFD8 data but the itkTIFFDataSize function +returns 0 instead of 8, resulting in invalid mem access. + +--- a/Modules/ThirdParty/TIFF/src/itk_tiff.h.in.orig 2022-06-08 19:34:04.412431969 +0200 ++++ b/Modules/ThirdParty/TIFF/src/itk_tiff.h.in 2022-06-08 19:34:26.240431631 +0200 +@@ -34,6 +34,7 @@ + #cmakedefine ITK_TIFF_HAS_TIFFFieldReadCount + #cmakedefine ITK_TIFF_HAS_TIFFField + #ifdef ITK_USE_SYSTEM_TIFF ++# define TIFF_INT64_T int64_t + # include <tiffio.h> + #else + # include "itktiff/tiffio.h" diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch new file mode 100644 index 000000000..2af8c4998 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch @@ -0,0 +1,309 @@ +https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch + +From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001 +From: Niels Dekker <N.Dekker@lumc.nl> +Date: Thu, 24 Jun 2021 18:00:01 +0200 +Subject: [PATCH] COMP: Add missing `#include <iostream>` to Deprecated module + test + +Fixed a Visual C++ 2019 error, saying: + +> Deprecated\test\itkSimpleFastMutexLockTest.cxx(48,12): error C2039: 'cout': is not a member of 'std' +--- + .../Deprecated/test/itkSimpleFastMutexLockTest.cxx | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx +index 11ad0c52700..60aa1c065b4 100644 +--- a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx ++++ b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx +@@ -19,6 +19,8 @@ + + #include "itkSimpleFastMutexLock.h" + ++#include <iostream> // For cout. ++ + + int + itkSimpleFastMutexLockTest(int, char *[]) +From 0c31aa688e82a34e5430873bc6176740fd09ad75 Mon Sep 17 00:00:00 2001 +From: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com> +Date: Tue, 20 Apr 2021 17:21:21 +0200 +Subject: [PATCH] COMP: CastXML, ITKVtkGlue, include only when property exists + +Some targets (VTK libraries) didn't have the property INTERFACE_INCLUDE_DIRECTORIES + +```bash +CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt: + Found relative path while evaluating include directories of + "ITKVtkGluePython": + + "_vtk_lib_include_dirs-NOTFOUND" +``` + +Triggered when compiling Slicer with `Slicer_BUILD_ITKPython:BOOL=ON` +aka `ITK_WRAP_PYTHON:BOOL=ON`. + +Full error log with extra printing: + +```bash + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:3 (message): + ITKVtkGlue_VTK_LIBRARIES: + VTK::IOImage;VTK::ImagingSources;VTK::WrappingPythonCore;VTK::CommonCore;VTK::CommonDataModel;VTK::kwiml;VTK::CommonExecutionModel;VTK::RenderingOpenGL2;VTK::RenderingFreeType;VTK::InteractionStyle;VTK::InteractionWidgets + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: + build/VTK-build/Wrapping/PythonCore;build/VTK/Wrapping/PythonCore + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: + build/VTK-build/Utilities/KWIML;build/VTK/Utilities/KWIML + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +-- ITKVtkGlue: Creating module. +-- ITKVtkGlue: Creating itkImageToVTKImageFilter submodule. +-- ITKVtkGlue: Creating itkVTKImageToImageFilter submodule. +-- ITKVtkGlue: Creating itkViewImage submodule. +-- MGHIO: Creating module. +-- MGHIO: Creating itkMGHImageIO submodule. +-- MorphologicalContourInterpolation: Creating module. +-- MorphologicalContourInterpolation: Creating itkMorphologicalContourInterpolator submodule. +-- ITKPyUtils: Creating module. +-- ITKPyUtils: Creating itkPyCommand submodule. +-- ITKPyUtils: Creating itkPyImageFilter submodule. +-- Configuring done +CMake Error: The following variables are used in this project, but they are set to NOTFOUND. +Please set them or make sure they are set and tested correctly in the CMake files: +_vtk_lib_include_dirs + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + +CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt: + Found relative path while evaluating include directories of + "ITKVtkGluePython": + + "_vtk_lib_include_dirs-NOTFOUND" + +``` +--- + Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt +index 3f3322957e1..2fd6a5af8f6 100644 +--- a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt ++++ b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt +@@ -2,7 +2,9 @@ + if(NOT VTK_RENDERING_BACKEND STREQUAL "None") + foreach(_vtk_lib IN LISTS ITKVtkGlue_VTK_LIBRARIES) + get_target_property(_vtk_lib_include_dirs ${_vtk_lib} INTERFACE_INCLUDE_DIRECTORIES) +- include_directories(${_vtk_lib_include_dirs}) ++ if(_vtk_lib_include_dirs) ++ include_directories(${_vtk_lib_include_dirs}) ++ endif() + endforeach() + endif() + +From 28325d921a9b8793e6aaefd612f53989f951d19c Mon Sep 17 00:00:00 2001 +From: Butui Hu <hot123tea123@gmail.com> +Date: Mon, 1 Aug 2022 14:26:39 +0800 +Subject: [PATCH] COMP: use sysconfig.get_path as PEP 632 deprecate distutils + module + +--- + Wrapping/Generators/Python/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt +index fca3d999b87..3b7a1d37334 100644 +--- a/Wrapping/Generators/Python/CMakeLists.txt ++++ b/Wrapping/Generators/Python/CMakeLists.txt +@@ -36,7 +36,7 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python) + ############################################################################### + # Configure Python wrapping installation + if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH) +- set(python_check "try:\n import distutils.sysconfig\n print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n pass") ++ set(python_check "try:\n import sysconfig\n print(sysconfig.get_path('platlib'))\nexcept:\n pass") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check}) + execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py" + OUTPUT_VARIABLE py_spp +From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001 +From: Hans Johnson <hans-johnson@uiowa.edu> +Date: Wed, 15 Dec 2021 08:10:58 -0600 +Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers + +The ability to include either .h or .hxx files as +header files required recursively reading the +.h files twice. The added complexity is +unnecessary, costly, and can confuse static +analysis tools that monitor header guardes (due +to reaching the maximum depth of recursion +limits for nested #ifdefs in checking). + +Co-authored-by: Simon Rit <simon.rit@creatis.insa-lyon.fr> +--- + CMake/ITKModuleHeaderTest.cmake | 3 +-- + Utilities/Maintenance/BuildHeaderTest.py | 4 ---- + 2 files changed, 1 insertion(+), 6 deletions(-) + +diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake +index eb809d7e93d..82ad192a6f8 100644 +--- a/CMake/ITKModuleHeaderTest.cmake ++++ b/CMake/ITKModuleHeaderTest.cmake +@@ -36,8 +36,7 @@ macro( itk_module_headertest _name ) + # effected. + set( _include ${${_name}_SOURCE_DIR}/include ) + file( GLOB _h_files ${_include}/*.h ) +- file( GLOB _hxx_files ${_include}/*.hxx ) +- set( _header_files ${_h_files} ${_hxx_files} ) ++ set( _header_files ${_h_files} ) + list( LENGTH _h_files _num_headers ) + set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx ) + set( _test_num 1 ) +diff --git a/Utilities/Maintenance/BuildHeaderTest.py b/Utilities/Maintenance/BuildHeaderTest.py +index 26a4b6ccb3f..f8ed9f7901e 100755 +--- a/Utilities/Maintenance/BuildHeaderTest.py ++++ b/Utilities/Maintenance/BuildHeaderTest.py +@@ -130,15 +130,11 @@ def main(): + else: + max_idx = added_header_idx + maximum_number_of_headers + for i in range(added_header_idx, max_idx): +- # Use the .hxx if possible. +- hxx_file = h_files[i][:-1] + "hxx" + # Files that include VTK headers need to link to VTK. + if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") != -1: + to_include = ( + '// #include "' + h_files[i] + '" // Banned in BuildHeaderTest.py\n' + ) +- elif os.path.exists(os.path.join(module_source_path, "include", hxx_file)): +- to_include = '#include "' + hxx_file + '"\n' + else: + to_include = '#include "' + h_files[i] + '"\n' + diff --git a/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch new file mode 100644 index 000000000..27f139553 --- /dev/null +++ b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch @@ -0,0 +1,550 @@ +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -1,16 +1,32 @@ + project(ITKOpenJPEG) + set(ITKOpenJPEG_THIRD_PARTY 1) + +-set(ITKOpenJPEG_INCLUDE_DIRS +- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg +- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg +- ) +-set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES}) ++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG) ++ ++if(ITK_USE_SYSTEM_OPENJPEG) ++ find_package(OpenJPEG REQUIRED) ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src ++ ) ++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS ++ ${OPENJPEG_INCLUDE_DIRS} ++ ) ++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}") ++ set(ITKOpenJPEG_NO_SRC 1) ++else() ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg ++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg ++ ) ++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++endif() ++ ++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h) + set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE) +- + itk_module_impl() + +-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h ++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h + DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR} + COMPONENT Development + ) +diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h +rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h ++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +@@ -25,6 +25,12 @@ + #ifndef itk_openjpeg_h + #define itk_openjpeg_h + +-#include <itkopenjpeg/openjpeg.h> ++/* Use the openjpeg library configured for ITK. */ ++#cmakedefine ITK_USE_SYSTEM_OPENJPEG ++#ifdef ITK_USE_SYSTEM_OPENJPEG ++# include <openjpeg.h> ++#else ++# include <itkopenjpeg/openjpeg.h> ++#endif + + #endif +--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx ++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx +@@ -27,8 +27,6 @@ + extern "C" + { + #include "openjpeg.h" +-#include "j2k.h" +-#include "jp2.h" + } + + +@@ -139,11 +137,11 @@ + { + itkDebugMacro(<< "ReadImageInformation()"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- /* decompression parameters */ ++ /* set decoding parameters to default values */ ++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); + +- if (!l_file) ++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); ++ if (!cio) + { + itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl + << "Reason: " +@@ -151,10 +149,5 @@ + } + +- /* set decoding parameters to default values */ +- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); +- +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true); +- + this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */ + + opj_image_t * l_image = nullptr; +@@ -188,9 +181,8 @@ + + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -202,10 +194,9 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -217,10 +208,9 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -230,7 +220,6 @@ + } + default: + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -248,26 +237,8 @@ + } + +- // Image parameters - first tile +- OPJ_INT32 l_tile_x0; +- OPJ_INT32 l_tile_y0; +- +- // Image parameters - tile width, height and number of tiles +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- + itkDebugMacro(<< "Trying to read header now..."); + +- bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- cio); ++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { +@@ -284,13 +255,21 @@ + } + +- this->m_Internal->m_TileStartX = l_tile_x0; +- this->m_Internal->m_TileStartY = l_tile_y0; ++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo); ++ if (!cp) ++ { ++ opj_stream_destroy(cio); ++ opj_image_destroy(l_image); ++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl ++ << "Reason: Error while reading image header"); ++ } ++ this->m_Internal->m_TileStartX = cp->tx0; ++ this->m_Internal->m_TileStartY = cp->ty0; + +- this->m_Internal->m_TileWidth = l_tile_width; +- this->m_Internal->m_TileHeight = l_tile_height; ++ this->m_Internal->m_TileWidth = cp->tdx; ++ this->m_Internal->m_TileHeight = cp->tdy; + +- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x; +- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y; ++ this->m_Internal->m_NumberOfTilesInX = cp->tw; ++ this->m_Internal->m_NumberOfTilesInY = cp->th; + + + itkDebugMacro(<< "Number of Components = " << l_image->numcomps); +@@ -307,6 +286,7 @@ + else + { + opj_stream_destroy(cio); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: " + << "Unknown precision in file: " +@@ -320,6 +300,6 @@ + break; + case 3: +- if (l_image->color_space != CLRSPC_SRGB) ++ if (l_image->color_space != OPJ_CLRSPC_SRGB) + { + itkWarningMacro(<< "file does not specify color space, assuming sRGB"); + } +@@ -349,7 +329,6 @@ + + /* close the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -368,16 +347,7 @@ + { + itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- +- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true); ++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); + if (!l_stream) + { + itkExceptionMacro("JPEG2000ImageIO failed to read file: " +@@ -397,9 +367,10 @@ + { + /* JPEG-2000 codestream */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr"); +@@ -410,9 +381,10 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr"); +@@ -423,9 +395,10 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr"); +@@ -433,7 +406,7 @@ + break; + } + default: +- fclose(l_file); ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -445,32 +418,17 @@ + if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters))) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_decoder returns false"); + } + +- OPJ_INT32 l_tile_x0, l_tile_y0; +- +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- +- bool bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- l_stream); ++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { + opj_destroy_codec(this->m_Internal->m_Dinfo); + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_read_header returns false"); + } +@@ -499,7 +457,7 @@ + itkDebugMacro(<< "p_end_x = " << p_end_x); + itkDebugMacro(<< "p_end_y = " << p_end_y); + +- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y); ++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y); + + itkDebugMacro(<< "opj_set_decode_area() after"); + +@@ -509,6 +467,5 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_set_decode_area returns false"); + } +@@ -525,13 +482,14 @@ + + OPJ_UINT32 l_max_data_size = 1000; + +- bool l_go_on = true; ++ OPJ_BOOL l_go_on = true; + + auto * l_data = (OPJ_BYTE *)malloc(1000); + + while (l_go_on) + { + bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, ++ l_stream, + &l_tile_index, + &l_data_size, + &l_current_tile_x0, +@@ -540,13 +498,11 @@ + &l_current_tile_y1, + &l_nb_comps, +- &l_go_on, +- l_stream); ++ &l_go_on); + + if (!tileHeaderRead) + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -571,7 +527,6 @@ + if (!l_data) + { + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -590,7 +545,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -654,7 +608,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -667,13 +620,11 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: error whle reading image"); + } + + /* close the byte stream */ + opj_stream_destroy(l_stream); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -840,13 +791,13 @@ + + parameters.numresolution = numberOfResolutions; + +- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY; ++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY; + opj_image_cmptparm_t cmptparms[3]; + + if (this->GetNumberOfComponents() == 3) + { + +- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED; ++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED; + + /* initialize image components */ + memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t)); +@@ -864,7 +815,7 @@ + + if (this->GetNumberOfComponents() == 1) + { +- color_space = CLRSPC_GRAY; ++ color_space = OPJ_CLRSPC_GRAY; + + /* initialize image components */ + memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t)); +@@ -941,8 +892,9 @@ + if (extension == ".j2k") + { +- cinfo = opj_create_compress(CODEC_J2K); ++ cinfo = opj_create_compress(OPJ_CODEC_J2K); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_J2K) returns nullptr"); +@@ -950,9 +902,10 @@ + } + else if (extension == ".jp2") + { +- cinfo = opj_create_compress(CODEC_JP2); ++ cinfo = opj_create_compress(OPJ_CODEC_JP2); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JP2) returns nullptr"); +@@ -960,9 +913,10 @@ + } + else if (extension == ".jpt") + { +- cinfo = opj_create_compress(CODEC_JPT); ++ cinfo = opj_create_compress(OPJ_CODEC_JPT); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JPT) returns nullptr"); +@@ -970,6 +924,7 @@ + } + else + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: unknown encode format: " << extension); + } +@@ -985,23 +940,19 @@ + + if (!opj_setup_encoder(cinfo, ¶meters, l_image)) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_encoder returns false"); + } + +- FILE * l_file = fopen(parameters.outfile, "wb"); +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- + /* open a byte stream for writing */ + /* allocate memory for all tiles */ +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false); ++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false); + if (!cio) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -1017,7 +968,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_start_compress returns false"); + } +@@ -1026,7 +978,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_encode returns false"); + } +@@ -1035,14 +988,14 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_end_compress returns false"); + } + + /* close and free the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + /* free remaining compression structures */ + opj_destroy_codec(cinfo); +--- a/Modules/Nonunit/Review/src/CMakeLists.txt ++++ b/Modules/Nonunit/Review/src/CMakeLists.txt +@@ -5,7 +5,7 @@ + + add_library(ITKReview ${ITKReview_SRC}) + itk_module_link_dependencies() +-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg) ++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES}) + itk_module_target(ITKReview) + + diff --git a/sci-libs/itk/files/itk-5.3.0-uint8.patch b/sci-libs/itk/files/itk-5.3.0-uint8.patch new file mode 100644 index 000000000..724314574 --- /dev/null +++ b/sci-libs/itk/files/itk-5.3.0-uint8.patch @@ -0,0 +1,10 @@ +--- a/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h ++++ b/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h +@@ -20,6 +20,7 @@ + + #include <iostream> + #include "ITKMathematicalMorphologyExport.h" ++#include <cstdint> + + + namespace itk diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch deleted file mode 100644 index a549650d2..000000000 --- a/sci-libs/itk/files/nrrdio-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Description: Link libITKNrrdIO with -lm (needed for sqrt) -Author: Steve Robbins <smr@debian.org> -Forwarded: no - ---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -@@ -64,7 +64,7 @@ - ADD_DEFINITIONS(-DTEEM_ZLIB=1) - - ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} ) --TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES}) -+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm) - - IF(ITK_LIBRARY_PROPERTIES) - SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES}) diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch deleted file mode 100644 index c24714e4d..000000000 --- a/sci-libs/itk/files/tests.patch +++ /dev/null @@ -1,41 +0,0 @@ -Known to fail by upstream: -https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115 - ---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200 -+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200 -@@ -7,8 +7,6 @@ - if(NOT VTK_RENDERING_BACKEND STREQUAL "None") - list(APPEND ITKVtkGlueTests - itkVtkMedianFilterTest.cxx -- itkVtkConnectedComponentImageFilterTest.cxx -- QuickViewTest.cxx - # ### runViewImage ### - # No test generated. Use it for view images (2D or 3D) with: - # ITKVtkGlueTestDriver runViewImage image_file -@@ -40,26 +38,3 @@ - NAME itkVTKImageToImageFilterTest - COMMAND ITKVtkGlueTestDriver - itkVTKImageToImageFilterTest) -- --if(NOT VTK_RENDERING_BACKEND STREQUAL "None") -- itk_add_test( -- NAME itkVtkMedianImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2) -- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) -- -- itk_add_test( -- NAME QuickViewTest -- COMMAND ITKVtkGlueTestDriver -- --compare DATA{Baseline/QuickViewTest.png,:} -- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png -- --compareNumberOfPixelsTolerance 1500 -- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR}) -- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) -- -- itk_add_test( -- NAME itkVtkConnectedComponentImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png}) -- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) --endif() diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild deleted file mode 100644 index 622a7b019..000000000 --- a/sci-libs/itk/itk-5.0.1.ebuild +++ /dev/null @@ -1,178 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit toolchain-funcs cmake python-single-r1 - -MY_PN="InsightToolkit" -MY_P="${MY_PN}-${PV}" -GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1" -GLI_TEST_HASH="57b5d5de8d777f10f269445a" - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI=" - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz - https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz - test? ( - https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz - ) - " - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc examples fftw python review test vtkglue" -RESTRICT="!test? ( test )" -# python will not work, this is a know issue upstream: -# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 -# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/openjpeg:2 - media-libs/libpng:0= - media-libs/tiff:0= - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - virtual/jpeg:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) - python? ( ${PYTHON_DEPS} ) -" -DEPEND="${RDEPEND} - sys-apps/coreutils - python? ( - >=dev-lang/swig-2.0:0 - dev-cpp/castxml - ) - doc? ( app-doc/doxygen ) -" -BDEPEND="app-arch/unzip" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/ITKModuleRemote.patch - "${FILESDIR}"/tests.patch -) - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use of working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_prepare() { - sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ - Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt - ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die - if use test; then - for filename in ../GenericLabelInterpolator/test/*/*mha; do - MD5=$(md5sum $filename) || die - MD5=${MD5% *} || die - cp "$filename" ".ExternalData/MD5/${MD5}" || die - done - fi - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DGDCM_USE_SYSTEM_OPENJPEG=ON - -DITK_FORBID_DOWNLOADS:BOOL=OFF - -DITK_USE_SYSTEM_DCMTK=ON - -DITK_USE_SYSTEM_DOUBLECONVERSION=ON - -DITK_USE_SYSTEM_CASTXML=ON - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_USE_KWSTYLE=OFF - -DITK_BUILD_DEFAULT_MODULES=ON - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" - -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" - -DModule_GenericLabelInterpolator:BOOL=ON - -DModule_ITKReview:BOOL=ON - -DBUILD_TESTING="$(usex test ON OFF)" - -DBUILD_EXAMPLES="$(usex examples ON OFF)" - -DITK_USE_REVIEW="$(usex review ON OFF)" - -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" - -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake_src_configure -} - -src_install() { - cmake_src_install - - if use examples; then - docinto examples - docompress -x /usr/share/doc/${PF}/examples - dodoc -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} - doenvd "${T}"/40${PN} - - if use doc; then - cd "${WORKDIR}"/html || die - rm *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - docinto api-docs - dodoc -r * - fi -} diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild index ad23b6f14..0b1f25860 100644 --- a/sci-libs/itk/itk-5.1.0.ebuild +++ b/sci-libs/itk/itk-5.2.1-r2.ebuild @@ -1,16 +1,18 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) +VIRTUALX_REQUIRED="manual" -inherit toolchain-funcs cmake python-single-r1 +inherit cmake python-single-r1 virtualx MY_PN="InsightToolkit" MY_P="${MY_PN}-${PV}" -GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78" -TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700" +GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6" +IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c" +TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0" declare -a GLI_TEST_HASHES=( "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" @@ -18,14 +20,15 @@ declare -a GLI_TEST_HASHES=( GLI_TEST_SRC="" for i in "${GLI_TEST_HASHES[@]}"; do - GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${P}-test-${i} " + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} " done DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" +HOMEPAGE="https://itk.org" SRC_URI=" https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz + https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz test? ( https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz @@ -37,41 +40,55 @@ LICENSE="Apache-2.0" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + RESTRICT="!test? ( test )" -# python will not work, this is a know issue upstream: -# https://github.com/InsightSoftwareConsortium/ITK/issues/2005 -# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 -# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 RDEPEND=" + dev-cpp/eigen:3 dev-libs/double-conversion:0= + dev-libs/expat:0= media-libs/openjpeg:2 media-libs/libpng:0= media-libs/tiff:0=[jpeg] sci-libs/dcmtk:0= sci-libs/hdf5:0=[cxx] + sci-libs/gdcm:0= sys-libs/zlib:0= - virtual/jpeg:0= + media-libs/libjpeg-turbo:0= fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) + vtkglue? ( + sci-libs/vtk:0=[rendering] + python? ( + sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}] + ) + ) python? ( ${PYTHON_DEPS} ) " DEPEND="${RDEPEND} sys-apps/coreutils python? ( >=dev-lang/swig-2.0:0 - dev-cpp/castxml + dev-libs/castxml + ) + doc? ( app-text/doxygen ) +" +BDEPEND=" + test? ( + vtkglue? ( ${VIRTUALX_DEPEND} ) + python? ( + $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]') + ) ) - doc? ( app-doc/doxygen ) " - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" S="${WORKDIR}/${MY_P}" PATCHES=( - "${FILESDIR}"/tests.patch - "${FILESDIR}"/${P}-downloads.patch + "${FILESDIR}/${P}-upstream-fixes.patch" + "${FILESDIR}/${P}-system-tiff-has-64.patch" + "${FILESDIR}/${P}-fix-castxml-clang-attr-malloc.patch" + "${FILESDIR}/${P}-system-openjpeg.patch" ) pkg_pretend() { @@ -89,16 +106,42 @@ pkg_pretend() { } src_prepare() { - sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ - Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt - ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die + # drop bundled libs + local -a DROPS=( + DoubleConversion/src/double-conversion + Eigen3/src/itkeigen + Expat/src/expat + GDCM/src/gdcm + JPEG/src/itkjpeg + HDF5/src/itkhdf5 + OpenJPEG/src/openjpeg + PNG/src/itkpng + TIFF/src/itktiff + ZLIB/src/itkzlib + ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x%%/*}" + rm -r "Modules/ThirdParty/${x}" || die + eend $? + done + { + find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n' + printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,' + } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die + + # Remote modules + ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" Modules/External/ITKGenericLabelInterpolator || die + ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die + cmake_src_prepare + if use test; then cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die for i in "${GLI_TEST_HASHES[@]}"; do - cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die - cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die + cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die + cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die done fi } @@ -106,6 +149,7 @@ src_prepare() { src_configure() { local mycmakeargs=( -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" + -DITK_INSTALL_DOC_DIR="share/doc/${P}" -DBUILD_EXAMPLES="$(usex examples ON OFF)" -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING="$(usex test ON OFF)" @@ -118,8 +162,12 @@ src_configure() { -DITK_USE_SYSTEM_DCMTK=ON -DITK_USE_SYSTEM_DOUBLECONVERSION=ON -DITK_USE_SYSTEM_CASTXML=ON + -DITK_USE_SYSTEM_EIGEN=ON + -DITK_USE_SYSTEM_EXPAT=ON + -DITK_USE_SYSTEM_GDCM=ON -DITK_USE_SYSTEM_HDF5=ON -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_OPENJPEG=ON -DITK_USE_SYSTEM_PNG=ON -DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_TIFF=ON @@ -127,6 +175,7 @@ src_configure() { -DITK_USE_KWSTYLE=OFF -DITK_BUILD_DEFAULT_MODULES=ON -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + -DModule_AdaptiveDenoising:BOOL=ON -DModule_GenericLabelInterpolator:BOOL=ON -DModule_ITKReview:BOOL=ON -DWRAP_ITK_JAVA=OFF @@ -152,6 +201,7 @@ src_configure() { if use python; then mycmakeargs+=( -DITK_WRAP_PYTHON=ON + -DPython3_EXECUTABLE="${PYTHON}" -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" ) else @@ -171,13 +221,13 @@ src_install() { dodoc -r "${S}"/Examples/* fi - echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" + echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die + local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" if use python; then - echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die + ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} + echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die doenvd "${T}"/40${PN} if use doc; then @@ -187,4 +237,14 @@ src_install() { docinto api-docs dodoc -r * fi + + use python && python_optimize +} + +src_test() { + if use vtkglue; then + virtx cmake_src_test + else + cmake_src_test + fi } diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild new file mode 100644 index 000000000..b2c3af801 --- /dev/null +++ b/sci-libs/itk/itk-5.3.0-r1.ebuild @@ -0,0 +1,269 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +VIRTUALX_REQUIRED="manual" + +inherit cmake python-single-r1 virtualx + +MY_PN="InsightToolkit" +MY_P="${MY_PN}-${PV}" +GLI_V="1.2.0" +IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c" +TEST_HASH="bb6d3b9a932333901465c75417fe8859124f5fed" +declare -a GLI_TEST_HASHES=( + "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" + "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" +) + +GLI_TEST_SRC="" +for i in "${GLI_TEST_HASHES[@]}"; do + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} " +done + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="https://itk.org" +SRC_URI=" + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz -> ITKGenericLabelInterpolator-${GLI_V}.tar.gz + https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz + test? ( + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz + ${GLI_TEST_SRC} + ) + " + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/double-conversion:0= + dev-libs/expat:0= + dev-libs/icu:0= + media-libs/libjpeg-turbo:0= + media-libs/libpng:0= + media-libs/openjpeg:2 + media-libs/tiff:0=[jpeg] + sci-libs/dcmtk:0= + sci-libs/gdcm:0= + sci-libs/hdf5:0=[cxx] + sys-libs/zlib-ng + fftw? ( sci-libs/fftw:3.0=[threads] ) + vtkglue? ( + sci-libs/vtk:0=[rendering] + python? ( + sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}] + ) + ) + python? ( ${PYTHON_DEPS} ) +" +# Might also need: +# dev-libs/kwsys::guru +# kwiml +# minc +# metaio +# niftilib +# sci-lib/vxl::science +DEPEND="${RDEPEND} + sys-apps/coreutils + python? ( + >=dev-lang/swig-2.0:0 + dev-libs/castxml + ) + doc? ( app-text/doxygen ) +" +BDEPEND=" + test? ( + vtkglue? ( ${VIRTUALX_DEPEND} ) + python? ( + $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]') + ) + ) +" + +S="${WORKDIR}/${MY_P}" + +# uint patch applied by upstream for next release. +PATCHES=( + "${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch" + "${FILESDIR}/${PN}-5.3.0-system-openjpeg.patch" + "${FILESDIR}/${PN}-5.3.0-uint8.patch" +) + +pkg_pretend() { + if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then + elog "To tune ITK to make the best use of working memory you can set" + elog " ITK_COMPUTER_MEMORY_SIZE=XX" + elog "in make.conf, default is 1 (unit is GB)" + fi + if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_prepare() { + # drop bundled libs + local -a DROPS=( + DoubleConversion/src/double-conversion + Eigen3/src/itkeigen + Expat/src/expat + GDCM/src/gdcm + JPEG/src/itkjpeg + HDF5/src/itkhdf5 + OpenJPEG/src/openjpeg + PNG/src/itkpng + TIFF/src/itktiff + ZLIB/src/itkzlib-ng + ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x%%/*}" + rm -r "Modules/ThirdParty/${x}" || die + eend $? + done + { + find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n' + printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,' + } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die + + # Remote modules + ln -sr "../ITKGenericLabelInterpolator-${GLI_V}" Modules/External/ITKGenericLabelInterpolator || die + ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die + + cmake_src_prepare + + if use test; then + cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die + mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die + for i in "${GLI_TEST_HASHES[@]}"; do + cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die + cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die + done + fi +} + +src_configure() { + local mycmakeargs=( + -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" + -DITK_INSTALL_DOC_DIR="share/doc/${P}" + -DBUILD_EXAMPLES="$(usex examples ON OFF)" + -DBUILD_SHARED_LIBS=ON + -DBUILD_TESTING="$(usex test ON OFF)" + -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" + -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DITK_FORBID_DOWNLOADS:BOOL=ON + -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DITK_USE_REVIEW="$(usex review ON OFF)" + -DITK_USE_SYSTEM_ICU=ON + -DITK_USE_SYSTEM_DCMTK=ON + -DITK_USE_SYSTEM_DOUBLECONVERSION=ON + -DITK_USE_SYSTEM_CASTXML=ON + -DITK_USE_SYSTEM_EIGEN=ON + -DITK_USE_SYSTEM_EXPAT=ON + -DITK_USE_SYSTEM_GDCM=ON + -DITK_USE_SYSTEM_HDF5=ON + -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_OPENJPEG=ON + -DITK_USE_SYSTEM_PNG=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_USE_SYSTEM_TIFF=ON + -DITK_USE_SYSTEM_ZLIB=ON + -DITK_USE_KWSTYLE=OFF + -DITK_BUILD_DEFAULT_MODULES=ON + -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + -DModule_AdaptiveDenoising:BOOL=ON + -DModule_GenericLabelInterpolator:BOOL=ON + -DModule_ITKReview:BOOL=ON + -DWRAP_ITK_JAVA=OFF + -DWRAP_ITK_TCL=OFF + -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) + ) + if use fftw; then + mycmakeargs+=( + -DITK_USE_FFTWD:BOOL=ON + -DITK_USE_FFTWF:BOOL=ON + -DITK_USE_SYSTEM_FFTW:BOOL=ON + -DITK_WRAP_double=ON + -DITK_WRAP_vector_double=ON + -DITK_WRAP_covariant_vector_double=ON + -DITK_WRAP_complex_double=ON + ) + else + mycmakeargs+=( + -DITK_USE_FFTWD:BOOL=OFF + -DITK_USE_FFTWF:BOOL=OFF + -DITK_USE_SYSTEM_FFTW:BOOL=OFF + -DITK_WRAP_double=OFF + -DITK_WRAP_vector_double=OFF + -DITK_WRAP_covariant_vector_double=OFF + -DITK_WRAP_complex_double=OFF + ) + fi + if use vtkglue; then + mycmakeargs+=( + -DModule_ITKVtkGlue=ON + ) + fi + if use python; then + mycmakeargs+=( + -DITK_WRAP_PYTHON=ON + -DPython3_EXECUTABLE="${PYTHON}" + -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" + ) + else + mycmakeargs+=( + -DITK_WRAP_PYTHON=OFF + ) + fi + cmake_src_configure +} + +src_install() { + cmake_src_install + + if use examples; then + docinto examples + docompress -x /usr/share/doc/${PF}/examples + dodoc -r "${S}"/Examples/* + fi + + echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die + local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" + if use python; then + echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die + ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + fi + echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die + doenvd "${T}"/40${PN} + + if use doc; then + cd "${WORKDIR}"/html || die + rm *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto api-docs + dodoc -r * + fi + + use python && python_optimize +} + +src_test() { + if use vtkglue; then + virtx cmake_src_test + else + cmake_src_test + fi +} diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml index c41202e23..5da2678ec 100644 --- a/sci-libs/itk/metadata.xml +++ b/sci-libs/itk/metadata.xml @@ -19,6 +19,7 @@ <flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag> </use> <upstream> + <remote-id type="github">InsightSoftwareConsortium/ITK</remote-id> <remote-id type="sourceforge">itk</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/jhdf5/Manifest b/sci-libs/jhdf5/Manifest deleted file mode 100644 index 0adcfacbb..000000000 --- a/sci-libs/jhdf5/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sis-jhdf5-19.04.0.zip 16667536 BLAKE2B 54f7fa368cdcc04a4d22fcf761627a6a29c96643840b0185ab2b6ea7f65c72923cb21d80f52e3d441f2c50fe916047243bd00a2ab7f604bb46c0cc610f5b6fa6 SHA512 ea5fd9554d3729193252e97610f5643168dd927d6009e2f2c2e65e0ea838f8e1be942a9ee15d542740a6ec6f68a7c288cf33eea36dabcb9191814f66d209aa79 diff --git a/sci-libs/jhdf5/jhdf5-19.04.0.ebuild b/sci-libs/jhdf5/jhdf5-19.04.0.ebuild deleted file mode 100644 index 588503cfe..000000000 --- a/sci-libs/jhdf5/jhdf5-19.04.0.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java binding for HDF5 compatible with HDF5 1.6/1.8" -HOMEPAGE="https://wiki-bsse.ethz.ch/display/JHDF5" -SRC_URI="https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-${PV}.zip" -# first SIS release: https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.0-r33145.zip -# last CISD release: https://wiki-bsse.ethz.ch/download/attachments/26609237/cisd-jhdf5-13.06.2-r29633.zip - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - >=virtual/jdk-1.7:* - app-arch/unzip - dev-java/args4j:* - dev-java/commons-io:* - dev-java/commons-lang:* -" -RDEPEND="${DEPEND} - >=virtual/jre-1.7:*" - -S="${WORKDIR}/sis-jhdf5" - -src_install() { - dobin bin/h5ar - java-pkg_newjar lib/sis-${P}.jar sis-${PN}.jar - java-pkg_dolauncher sis-${PN} --jar sis-${PN}.jar - java-pkg_newjar lib/sis-${PN}-h5ar-cli-${PV}.jar sis-${PN}-h5ar-cli.jar - java-pkg_dolauncher sis-${PN}-h5ar-cli --jar sis-${PN}-h5ar-cli.jar - dodoc doc/JHDF5-${PV}.* -} diff --git a/sci-libs/labbookdb/labbookdb-0.1.ebuild b/sci-libs/labbookdb/labbookdb-0.1.ebuild index 4da4106a2..57c90a390 100644 --- a/sci-libs/labbookdb/labbookdb-0.1.ebuild +++ b/sci-libs/labbookdb/labbookdb-0.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch deleted file mode 100644 index 0f64b325f..000000000 --- a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- lib2bit-0.2.1/Makefile.ori 2017-03-31 22:09:48.387098439 +0200 -+++ lib2bit-0.2.1/Makefile 2017-03-31 22:10:29.889020564 +0200 -@@ -8,7 +8,7 @@ - LDLIBS = - INCLUDES = - --prefix = /usr/local -+prefix = $(DESTDIR)/usr/local - includedir = $(prefix)/include - libdir = $(exec_prefix)/lib - diff --git a/sci-libs/lib2bit/lib2bit-0.2.1.ebuild b/sci-libs/lib2bit/lib2bit-0.2.1.ebuild index 808c97b21..5f012de35 100644 --- a/sci-libs/lib2bit/lib2bit-0.2.1.ebuild +++ b/sci-libs/lib2bit/lib2bit-0.2.1.ebuild @@ -1,10 +1,8 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -inherit eutils - DESCRIPTION="C library for accessing 2bit files" HOMEPAGE="https://github.com/dpryan79/lib2bit" SRC_URI="https://github.com/dpryan79/lib2bit/archive/${PV}.tar.gz -> ${P}.tar.gz" @@ -14,9 +12,6 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="static" -DEPEND="" -RDEPEND="${DEPEND}" - PATCHES=( "${FILESDIR}"/${P}_respect_LDFLAGS.patch "${FILESDIR}"/${P}_test_support_python3.patch diff --git a/sci-libs/libflame-amd/Manifest b/sci-libs/libflame-amd/Manifest index 6da475e97..422282045 100644 --- a/sci-libs/libflame-amd/Manifest +++ b/sci-libs/libflame-amd/Manifest @@ -1 +1 @@ -DIST libflame-amd-2.2.tar.gz 28327573 BLAKE2B a53bef8c08bfb5ca14c145ac9ae11e6f41f9d0ef2755cab2b69df6103b2164a6786bb2e3e709faf7a11cad2b4a58310082637c6e5516a987bb65cb599837bfff SHA512 c68a9a1e37eac649d898f25bd5f4d89abecd3fdb8ff9c9678d4d2c0761660322f270f4508f93511f3db75ef074531a1c9824cc81ed88cfcec82bc9513d274ec0 +DIST libflame-amd-3.1.tar.gz 26635219 BLAKE2B 43f5db65bb53a818259e62e01d373ba8db2052c11b5839d28805e37e2b9033e16410efc4b6ce3379f3d92067511b834ef16dbca22987945608167a90e4f31871 SHA512 b6a05dbadd169e05645bc4ae456f00b6c84f2c3eeaf1e1bd74d273e540ca1f99915bd221427bce0e4f73fed050daf2db8902891451d5b2b9273af48c8e2f4479 diff --git a/sci-libs/libflame-amd/libflame-amd-2.2.ebuild b/sci-libs/libflame-amd/libflame-amd-3.1.ebuild index 45cc98a60..cdadccb5c 100644 --- a/sci-libs/libflame-amd/libflame-amd-2.2.ebuild +++ b/sci-libs/libflame-amd/libflame-amd-3.1.ebuild @@ -1,29 +1,23 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -inherit autotools fortran-2 +inherit fortran-2 FORTRAN_NEED_OPENMP=1 DESCRIPTION="AMD optimized high-performance object-based library for DLA computations" HOMEPAGE="https://developer.amd.com/amd-aocl/" +SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/libflame-${PV}" -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/amd/libflame" -else - SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/libflame-"${PV}" - KEYWORDS="~amd64" -fi - +KEYWORDS="~amd64" LICENSE="BSD" SLOT="0" CPU_FLAGS=( sse3 ) IUSE_CPU_FLAGS_X86="${CPU_FLAGS[@]/#/cpu_flags_x86_}" -IUSE="scc static-libs supermatrix ${IUSE_CPU_FLAGS_X86[@]}" +IUSE="scc supermatrix ${IUSE_CPU_FLAGS_X86[@]}" DEPEND="virtual/cblas" RDEPEND="${DEPEND}" @@ -39,17 +33,14 @@ src_configure() { --enable-max-arg-list-hack --enable-dynamic-build --enable-vector-intrinsics=$(usex cpu_flags_x86_sse3 sse none) - $(use_enable static-libs static-build) $(use_enable scc) $(use_enable supermatrix) ) econf "${myconf[@]}" } -src_compile() { - default -} - src_install() { - emake -j1 DESTDIR="${D}" install + # -j1 because otherwise cannot create file that already exists + DESTDIR="${ED}" emake -j1 install + einstalldocs } diff --git a/sci-libs/libflame-amd/libflame-amd-9999.ebuild b/sci-libs/libflame-amd/libflame-amd-9999.ebuild deleted file mode 100644 index 45cc98a60..000000000 --- a/sci-libs/libflame-amd/libflame-amd-9999.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools fortran-2 -FORTRAN_NEED_OPENMP=1 - -DESCRIPTION="AMD optimized high-performance object-based library for DLA computations" -HOMEPAGE="https://developer.amd.com/amd-aocl/" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/amd/libflame" -else - SRC_URI="https://github.com/amd/libflame/archive/${PV}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/libflame-"${PV}" - KEYWORDS="~amd64" -fi - -LICENSE="BSD" -SLOT="0" - -CPU_FLAGS=( sse3 ) -IUSE_CPU_FLAGS_X86="${CPU_FLAGS[@]/#/cpu_flags_x86_}" -IUSE="scc static-libs supermatrix ${IUSE_CPU_FLAGS_X86[@]}" - -DEPEND="virtual/cblas" -RDEPEND="${DEPEND}" -BDEPEND="dev-vcs/git" - -src_configure() { - local myconf=( - --disable-optimizations - --enable-multithreading=openmp - --enable-verbose-make-output - --enable-lapack2flame - --enable-cblas-interfaces - --enable-max-arg-list-hack - --enable-dynamic-build - --enable-vector-intrinsics=$(usex cpu_flags_x86_sse3 sse none) - $(use_enable static-libs static-build) - $(use_enable scc) - $(use_enable supermatrix) - ) - econf "${myconf[@]}" -} - -src_compile() { - default -} - -src_install() { - emake -j1 DESTDIR="${D}" install -} diff --git a/sci-libs/libmatheval/files/libmatheval-1.1.11_update_configure.ac.patch b/sci-libs/libmatheval/files/libmatheval-1.1.11_update_configure.ac.patch new file mode 100644 index 000000000..0dd3a3abe --- /dev/null +++ b/sci-libs/libmatheval/files/libmatheval-1.1.11_update_configure.ac.patch @@ -0,0 +1,40 @@ +Update configure.ac build script +Remove references to guile which is only used for tests and breaks the package due to needing masked guile-1* +sed command in ebuild removes references to these tests +Taken from git repo which has updated the package: https://gitlab.com/Grimler/libmatheval/-/blob/master/configure.ac + +--- a/configure.ac ++++ b/configure.ac +@@ -21,10 +21,8 @@ dnl Process this file with autoconf to produce a configure script. + AC_PREREQ(2.53) + AC_INIT([libmatheval],[1.1.11],[asamardzic@gnu.org]) + AC_CONFIG_AUX_DIR([config]) +-AC_CONFIG_MACRO_DIR([m4]) +-AC_SUBST([ac_aux_dir]) +-AM_INIT_AUTOMAKE([libmatheval], [1.1.11]) +-AC_CONFIG_SRCDIR([configure.in]) ++AC_CONFIG_MACRO_DIRS([m4]) ++AM_INIT_AUTOMAKE + AM_CONFIG_HEADER([config.h]) + + dnl Initialize the test suite. +@@ -44,7 +42,6 @@ AC_PROG_LIBTOOL + AC_PROG_MAKE_SET + AC_PROG_YACC + AM_MISSING_PROG([AUTOM4TE], [autom4te]) +-GUILE_FLAGS + + dnl Checks for libraries. + +@@ -59,11 +56,5 @@ AC_TYPE_SIZE_T + dnl Checks for library functions. + AC_CHECK_FUNCS([bzero memset], [break]) + +-dnl Additional Guile feature checks. +-AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include <libguile.h>]) +-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) +- + AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile]) + AC_OUTPUT(libmatheval.pc) diff --git a/sci-libs/libmatheval/libmatheval-1.1.11-r1.ebuild b/sci-libs/libmatheval/libmatheval-1.1.11-r1.ebuild new file mode 100644 index 000000000..9fad1cafa --- /dev/null +++ b/sci-libs/libmatheval/libmatheval-1.1.11-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools + +DESCRIPTION="library to parse and evaluate symbolic expressions" +HOMEPAGE="https://www.gnu.org/software/libmatheval/" +SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +PATCHES=( "${FILESDIR}"/"${P}"_update_configure.ac.patch ) + +src_prepare() { + # rename configure.in -> configure.ac for Q/A + mv configure.in configure.ac || die + # patch configure.ac + default + # remove test subdirectory depends on masked guile-1* + # Bug: https://bugs.gentoo.org/755353 + sed -e 's/SUBDIRS = doc lib tests/SUBDIRS = doc lib/' -i Makefile.am || die + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} diff --git a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild index ff5583090..4b50c2030 100644 --- a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild +++ b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild @@ -1,10 +1,8 @@ -# Copyright 2019-2020 Gentoo Authors +# Copyright 2019-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -inherit autotools - release_data="20191120141844" DESCRIPTION="Library for biobambam2" HOMEPAGE="https://github.com/gt1/libmaus" diff --git a/sci-libs/libsufr/Manifest b/sci-libs/libsufr/Manifest index 7faa3abc0..2ba7a16c9 100644 --- a/sci-libs/libsufr/Manifest +++ b/sci-libs/libsufr/Manifest @@ -1 +1 @@ -DIST libsufr-0.7.5.tar.gz 200473 BLAKE2B b1835af6acea211623cf545aef8f224648c12059f155d17e632432eb328ea977f2c028a246bb16d97911c9dfd33520e3e69bebe3cc9af0d4bacb01e925db2260 SHA512 5b6ee5b166f7e306ec4ce0df8542ca5439a8113e53a6fa6e27e52ca9b9e7e7793b1a839f4c734df7b9e5bec37c073ee409c42038d360c5a1036ff2b7047693cc +DIST libsufr-0.7.7.tar.gz 207409 BLAKE2B ba366ee8ce19c6b4fed0d45cf8bde39bc9589f46e4e428cc0346966f76e8a185edec6947fb14a5ff63414b3c08b8df56c2367b4f47fe53ed96ae0d26e1d67951 SHA512 c24cb69361f8db31396e554a48eb864b7cc2c8ac437b2c0d3113e02adf9a53017973e2ff49cc9a7a6debeaaea5d9f20c8aa8d505b23e1974f19b3560fded9ca4 diff --git a/sci-libs/libsufr/libsufr-0.7.5-r1.ebuild b/sci-libs/libsufr/libsufr-0.7.7.ebuild index 0f0cc83fe..cd49de6b5 100644 --- a/sci-libs/libsufr/libsufr-0.7.5-r1.ebuild +++ b/sci-libs/libsufr/libsufr-0.7.7.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 CMAKE_BUILD_TYPE=Release -inherit cmake fortran-2 CMAKE_MAKEFILE_GENERATOR="emake" +inherit cmake fortran-2 DESCRIPTION="LIBrary of Some Useful Fortran Routines" HOMEPAGE="http://libsufr.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" @@ -23,7 +23,6 @@ DOCS=( "CHANGELOG" "README" "VERSION" ) src_unpack() { default - gunzip -r "${S}"/man || die } diff --git a/sci-libs/lwpr/lwpr-1.2.5.ebuild b/sci-libs/lwpr/lwpr-1.2.5.ebuild index c7289f921..2f040a86e 100644 --- a/sci-libs/lwpr/lwpr-1.2.5.ebuild +++ b/sci-libs/lwpr/lwpr-1.2.5.ebuild @@ -5,11 +5,11 @@ EAPI=7 DOCS_BUILDER="doxygen" -inherit autotools docs +inherit docs DESCRIPTION="The Locally Weighted Projection Regression Library" HOMEPAGE="https://web.inf.ed.ac.uk/slmc" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="LGPL-2.1" SLOT="0" diff --git a/sci-libs/miopen/Manifest b/sci-libs/miopen/Manifest deleted file mode 100644 index d36ff9285..000000000 --- a/sci-libs/miopen/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST MIOpen-4.0.0.tar.gz 35574627 BLAKE2B 6741d653ab251ead275d3b015086e77a32f4b3e9aa2e1af3bb54cc519ab1cf456eac39670a6cbd6fab1db25330e3cb1e74f66cc4aeb5de7a9151a1284d630dc1 SHA512 32f3e7f04260921e0658f50817079f6394fbc469c31afe72b40925c0429b47056dd07a931ec4ee5c41fc9c5388a1b25ecafb7ea74879ed77b2506784471acce3 diff --git a/sci-libs/miopen/metadata.xml b/sci-libs/miopen/metadata.xml deleted file mode 100644 index 336bdb639..000000000 --- a/sci-libs/miopen/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - </maintainer> - <maintainer type="person"> - <email>gentoo@holzke.net</email> - <name>Wilfried Holzke</name> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/miopen/miopen-4.0.0-r1.ebuild b/sci-libs/miopen/miopen-4.0.0-r1.ebuild deleted file mode 100644 index 7197880df..000000000 --- a/sci-libs/miopen/miopen-4.0.0-r1.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="AMD's Machine Intelligence Library" -HOMEPAGE="https://github.com/ROCmSoftwarePlatform/MIOpen" -SRC_URI="https://github.com/ROCmSoftwarePlatform/MIOpen/archive/rocm-${PV}.tar.gz -> MIOpen-${PV}.tar.gz" - -LICENSE="MIT" -KEYWORDS="~amd64" -SLOT="0" - -RDEPEND=" - >=dev-util/hip-${PV} - >=dev-libs/half-1.12.0 - <dev-libs/half-2 - dev-libs/ocl-icd - =dev-util/rocm-clang-ocl-${PV}* - sci-libs/rocBLAS - =dev-libs/boost-1.72*" - -DEPEND="${RDEPEND}" -BDEPEND="app-admin/chrpath" - -S="${WORKDIR}/MIOpen-rocm-${PV}" - -src_prepare() { - sed -e "s:PATHS /opt/rocm/llvm:PATHS ""${EPREFIX}""/usr/lib/llvm/roc/ NO_DEFAULT_PATH:" \ - -e '/set( MIOPEN_INSTALL_DIR/s:miopen:${CMAKE_INSTALL_PREFIX}:' \ - -e '/set(MIOPEN_SYSTEM_DB_PATH/s:${CMAKE_INSTALL_PREFIX}/::' \ - -e '/MIOPEN_TIDY_ERRORS ALL/d' \ - -i CMakeLists.txt || die - - sed -e "/rocm_install_symlink_subdir(\${MIOPEN_INSTALL_DIR})/d" -i src/CMakeLists.txt || die - - sed -e "s:\${AMD_DEVICE_LIBS_PREFIX}/lib:${EPREFIX}/usr/lib/amdgcn/bitcode:" -i cmake/hip-config.cmake || die - - cmake_src_prepare -} - -src_configure() { - export CXX="hipcc" - - local mycmakeargs=( - -DCMAKE_INSTALL_PREFIX="${EPREFIX}/usr" - -DCMAKE_BUILD_TYPE=Release - -DMIOPEN_BACKEND=HIP - -DBoost_USE_STATIC_LIBS=OFF - ) - - cmake_src_configure -} - -src_install() { - cmake_src_install - chrpath --delete "${ED}/usr/bin/MIOpenDriver" || die - chrpath --delete "${ED}/usr/lib64/libMIOpen.so.1.0" || die -} diff --git a/sci-libs/mlpack/Manifest b/sci-libs/mlpack/Manifest deleted file mode 100644 index 827319a78..000000000 --- a/sci-libs/mlpack/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST mlpack-3.4.1.tar.gz 5782241 BLAKE2B d5a1050489c61a934330a0f3d1142e7949f7fdd9c31f679d7963208fc8aaea8fd8c0eb7e45920c3799712cb059808c75098e31b913557ec3c2af2f1d32e561f0 SHA512 53de83c2ca36829a0ae952357b25bee44bf85d01c2414848fe2c5f09ebe4732bd0a1d3c72de202646345fa66964fbc3247ddeb6a327e87459c036a215fe55fc2 -DIST mlpack-3.4.2.tar.gz 5782921 BLAKE2B d775124462357b489f91f6ef75f5f908d9a9234082c48223f19a728ab9e41cb6576fca9b4b59415d3096471f4ab2d2970296387954977652169a447b8e036263 SHA512 05a66b73cba8d83f630b0999023913e7a4a3214632930ff3c598d964d52bcae4eab113018eecf385130c0e7e9c16c25380b31dd62a2e0ecf419b4bf3856b34b0 diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml deleted file mode 100644 index f587c48a7..000000000 --- a/sci-libs/mlpack/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - mlpack is a C++ machine learning library with emphasis on - scalability, speed, and ease-of-use. Its aim is to make machine - learning possible for novice users by means of a simple, consistent - API, while simultaneously exploiting C++ language features to - provide maximum performance and maximum flexibility for expert - users. - </longdescription> - <use> - <flag name="arma-debug">build with armadillo dbug symbols</flag> - <flag name="go">build go bindings</flag> - <flag name="julia">build julia bindings</flag> - <flag name="matlab">build matlab bindings</flag> - <flag name="R">build R bindings</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/mlpack/mlpack-3.4.1.ebuild b/sci-libs/mlpack/mlpack-3.4.1.ebuild deleted file mode 100644 index bc5f8d642..000000000 --- a/sci-libs/mlpack/mlpack-3.4.1.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit cmake python-single-r1 toolchain-funcs - -DESCRIPTION="scalable C++ machine learning library" -HOMEPAGE="https://www.mlpack.org/" -SRC_URI="https://www.mlpack.org/files/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE+="arma-debug debug doc go julia matlab openmp profile R test" -REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )" -RESTRICT="!test? ( test )" - -CDEPEND=" - ${PYTHON_DEPS} - julia? ( || ( - dev-lang/julia - dev-lang/julia-bin:* - ) - ) - go? ( dev-lang/go ) - R? ( dev-lang/R ) -" - -RDEPEND=" - ${CDEPEND} - $(python_gen_cond_dep ' - dev-libs/boost[${PYTHON_USEDEP}] - dev-libs/libxml2[${PYTHON_USEDEP}] - ') - dev-python/pandas - dev-python/cython - dev-python/numpy - dev-libs/stb - >=sci-libs/armadillo-8.4.0[arpack,blas,lapack] - sci-libs/ensmallen -" -DEPEND="${RDEPEND}" -BDEPEND=" - ${CDEPEND} - app-text/txt2man - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-libs/mathjax - ) - test? ( $( python_gen_cond_dep ' - dev-python/pytest[${PYTHON_USEDEP}] - ') - ) -" - -pkg_setup() { - elog "If you want to build matlab bindings then you" - elog "need to make sure that matlab has been installed" - elog "prior to building this package and it is available" - elog "in the standard locations to be found by" - elog "CMake, library finders, header includes and other" - elog "trinkets that are used while compiling." - elog "Matlab will not be entertained as a first class" - elog "citizen until we have enough personnel" - - python-single-r1_pkg_setup -} - -src_prepare() { - sed -i \ - -e "s:share/doc/mlpack:share/doc/${PF}:" \ - -e 's/-O3//g' \ - CMakeLists.txt || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DDISABLE_DOWNLOADS=ON - -DDOWNLOAD_ENSMALLEN=OFF - -DDOWNLOAD_STB_IMAGE=OFF - -DBUILD_WITH_COVERAGE=OFF - -DBUILD_PYTHON_BINDINGS=ON - -DBUILD_SHARED_LIBS=ON - -DBUILD_CLI_EXECUTABLES=ON - -DTEST_VERBOSE=$(usex test) - -DBUILD_TESTS=$(usex test) - -DDEBUG=$(usex debug) - -DPROFILE=$(usex profile) - -DARMA_EXTRA_DEBUG=$(usex arma-debug) - -DUSE_OPENMP=$(usex openmp) - -DMATLAB_BINDINGS=$(usex matlab) - -DBUILD_GO_SHLIB=$(usex go) - -DBUILD_JULIA_BINDINGS=$(usex julia) - -DBUILD_GO_BINDINGS=$(usex go) - -DBUILD_R_BINDINGS=$(usex R) - -DBUILD_MARKDOWN_BINDINGS=$(usex doc) - -DMATHJAX=$(usex doc) - ${EXTRA_ECONF[@]} - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - - python_optimize -} diff --git a/sci-libs/mlpack/mlpack-3.4.2.ebuild b/sci-libs/mlpack/mlpack-3.4.2.ebuild deleted file mode 100644 index bc5f8d642..000000000 --- a/sci-libs/mlpack/mlpack-3.4.2.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit cmake python-single-r1 toolchain-funcs - -DESCRIPTION="scalable C++ machine learning library" -HOMEPAGE="https://www.mlpack.org/" -SRC_URI="https://www.mlpack.org/files/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE+="arma-debug debug doc go julia matlab openmp profile R test" -REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )" -RESTRICT="!test? ( test )" - -CDEPEND=" - ${PYTHON_DEPS} - julia? ( || ( - dev-lang/julia - dev-lang/julia-bin:* - ) - ) - go? ( dev-lang/go ) - R? ( dev-lang/R ) -" - -RDEPEND=" - ${CDEPEND} - $(python_gen_cond_dep ' - dev-libs/boost[${PYTHON_USEDEP}] - dev-libs/libxml2[${PYTHON_USEDEP}] - ') - dev-python/pandas - dev-python/cython - dev-python/numpy - dev-libs/stb - >=sci-libs/armadillo-8.4.0[arpack,blas,lapack] - sci-libs/ensmallen -" -DEPEND="${RDEPEND}" -BDEPEND=" - ${CDEPEND} - app-text/txt2man - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-libs/mathjax - ) - test? ( $( python_gen_cond_dep ' - dev-python/pytest[${PYTHON_USEDEP}] - ') - ) -" - -pkg_setup() { - elog "If you want to build matlab bindings then you" - elog "need to make sure that matlab has been installed" - elog "prior to building this package and it is available" - elog "in the standard locations to be found by" - elog "CMake, library finders, header includes and other" - elog "trinkets that are used while compiling." - elog "Matlab will not be entertained as a first class" - elog "citizen until we have enough personnel" - - python-single-r1_pkg_setup -} - -src_prepare() { - sed -i \ - -e "s:share/doc/mlpack:share/doc/${PF}:" \ - -e 's/-O3//g' \ - CMakeLists.txt || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DDISABLE_DOWNLOADS=ON - -DDOWNLOAD_ENSMALLEN=OFF - -DDOWNLOAD_STB_IMAGE=OFF - -DBUILD_WITH_COVERAGE=OFF - -DBUILD_PYTHON_BINDINGS=ON - -DBUILD_SHARED_LIBS=ON - -DBUILD_CLI_EXECUTABLES=ON - -DTEST_VERBOSE=$(usex test) - -DBUILD_TESTS=$(usex test) - -DDEBUG=$(usex debug) - -DPROFILE=$(usex profile) - -DARMA_EXTRA_DEBUG=$(usex arma-debug) - -DUSE_OPENMP=$(usex openmp) - -DMATLAB_BINDINGS=$(usex matlab) - -DBUILD_GO_SHLIB=$(usex go) - -DBUILD_JULIA_BINDINGS=$(usex julia) - -DBUILD_GO_BINDINGS=$(usex go) - -DBUILD_R_BINDINGS=$(usex R) - -DBUILD_MARKDOWN_BINDINGS=$(usex doc) - -DMATHJAX=$(usex doc) - ${EXTRA_ECONF[@]} - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - - python_optimize -} diff --git a/sci-libs/mpfun90/Manifest b/sci-libs/mpfun90/Manifest new file mode 100644 index 000000000..56d64f14c --- /dev/null +++ b/sci-libs/mpfun90/Manifest @@ -0,0 +1 @@ +DIST 2023-02-26.tar.gz 66883 BLAKE2B 3b93099977b614e0d9a16df76f7f3c1eda9b76905664db3f0dc0ad0bd00b503105649aeb4c960d7293e7d536e3a902dbe8cb62f89be3bce655e9bae963097f35 SHA512 7280ecba6cb95f15cea91ea95f5cf21b69f76a490a3c92bef40cf8a1dfadd651cb93480bddddd684d0f18144db65cdb1590964df11d37a9f35eaeeb94f369d63 diff --git a/sci-libs/mpfun90/metadata.xml b/sci-libs/mpfun90/metadata.xml new file mode 100644 index 000000000..e3eb0d9c1 --- /dev/null +++ b/sci-libs/mpfun90/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + This package permits one to perform floating-point computations (real and complex) to arbitrarily high numeric precision + </longdescription> + <upstream> + <remote-id type="github">APN-Pucky/mpfun90</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild new file mode 100644 index 000000000..4f885fa2c --- /dev/null +++ b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild @@ -0,0 +1,29 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs fortran-2 + +DESCRIPTION="High-Precision Software" +HOMEPAGE=" + https://www.davidhbailey.com/dhbsoftware/ + https://github.com/APN-Pucky/mpfun90 +" +MY_PV=$(ver_rs 1- '-') +SRC_URI="https://github.com/APN-Pucky/mpfun90/archive/refs/tags/${MY_PV}.tar.gz" +S="${WORKDIR}/mpfun90-${MY_PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +src_compile() { + emake -j1 dynamic +} + +src_install() { + doheader *.mod + dolib.so libmpfun90.so + dolib.a libmpfun90.a +} diff --git a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild index b19a65fbe..58d8264cf 100644 --- a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild +++ b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild @@ -29,7 +29,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - app-doc/doxygen[dot] + app-text/doxygen[dot] " pkg_setup() { diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest index 31eb1f65e..d50b1b3b7 100644 --- a/sci-libs/nibabel/Manifest +++ b/sci-libs/nibabel/Manifest @@ -1,3 +1,2 @@ -DIST nibabel-2.5.1.tar.gz 4281663 BLAKE2B 361f1118d850a76fb8d2aa3ac6ebf0da711cf8df93aa6e2689201f3e713f35e028442ef00f69ce7a4a96d3c376b4966d0b76a087005123101f743b4d6074d3b2 SHA512 49de1a42113e64a56336e02f3143588b574c7b063b10b892ee125048451be701955e505bd1d51183327e2ee221f8364005fdd9fa7d256343113ab6ca1994820d -DIST nibabel-3.0.2.tar.gz 4336181 BLAKE2B b95ea57f28265eab627caea71f65c8ad1b0f868d40d80efb68f2dbb1e81f7d4f10b2da21d33f803abcd9441f3afe2c861f96828f8701f3981e4b7a4b2f97308e SHA512 51a10a72ade0382e43a006a0b9453b0c00f962a1c0d32c7a9da6ce3b9c95db05cd3bd672389d514107768b688a8315cba2e34d52bc845db3ca3e7912a1a0a8ac -DIST nibabel-3.2.1.tar.gz 4442534 BLAKE2B 5a76275c0c3746bbe094789350f4f6d9dc17e332915c9f567660138c44ba50672415272d21d7b0834c77f4f9660950bda8c684f7664d58f0e5784b782384cb2f SHA512 5c5d95313f4b22462ba67c23d52dd34ed5d690c72a3137b21ac0bdbc4d20aa4f0c1d87d23c675f8c2f6e4335dc51fb9ab788ac8c63be56eec8ab8657ed95a6d7 +DIST nibabel-5.0.0.tar.gz 4480342 BLAKE2B ef5c8fcd27fda60ae85fb657b360453a3b6ae58ea2b8e4eb55bfeb4bdecf6aa94cf1594d0b90a3187f6f3bad32fa9c721bba0827ec0966f799e5b59720778956 SHA512 5f27c03518c47856ecb33b878e9969ea33c7ebb717e6f4f9d89d9fdf415459e47675353051cdb824efea4e6a819759e0bf61cf49caa7212411c63423a77ed0d4 +DIST nibabel-5.1.0.tar.gz 4522882 BLAKE2B 62ffd86e14f66ab57bcfa127e9d0da0b46a04224739b61493080848305295f25136b51bc6fae69c0ec653b4185a28a1b5c323573588abc02f6ebb7372808b8fe SHA512 a07b4c2742ac3af8c0a87a0fa0562ed55c1377fb2067a7813fa2482cab4fc407f013b13b541dd863fa9620c644058296040487aeaba0b26818ff783b2dc2474e diff --git a/sci-libs/nibabel/nibabel-2.5.1.ebuild b/sci-libs/nibabel/nibabel-2.5.1.ebuild deleted file mode 100644 index 3316b84d5..000000000 --- a/sci-libs/nibabel/nibabel-2.5.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dicom doc test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom - dev-python/pillow[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - ${RDEPEND} - dev-python/nose[${PYTHON_USEDEP}] - ) - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) -" - -python_test() { - cd "${BUILD_DIR}" || die - echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. nosetests || die -} diff --git a/sci-libs/nibabel/nibabel-3.0.2.ebuild b/sci-libs/nibabel/nibabel-3.0.2.ebuild deleted file mode 100644 index 3316b84d5..000000000 --- a/sci-libs/nibabel/nibabel-3.0.2.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dicom doc test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom - dev-python/pillow[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - ${RDEPEND} - dev-python/nose[${PYTHON_USEDEP}] - ) - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) -" - -python_test() { - cd "${BUILD_DIR}" || die - echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. nosetests || die -} diff --git a/sci-libs/nibabel/nibabel-3.2.1.ebuild b/sci-libs/nibabel/nibabel-5.0.0.ebuild index d469867f9..0fec805b1 100644 --- a/sci-libs/nibabel/nibabel-3.2.1.ebuild +++ b/sci-libs/nibabel/nibabel-5.0.0.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=hatchling inherit distutils-r1 @@ -21,15 +21,14 @@ RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] dicom? ( - sci-libs/pydicom dev-python/pillow[${PYTHON_USEDEP}] - ) + sci-libs/pydicom + ) " BDEPEND="test? ( - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + dev-python/pytest-httpserver[${PYTHON_USEDEP}] )" distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild index 283ad8804..0fec805b1 100644 --- a/sci-libs/nibabel/nibabel-9999.ebuild +++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild @@ -1,36 +1,34 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=hatchling -inherit distutils-r1 git-r3 +inherit distutils-r1 DESCRIPTION="Access a cacophony of neuro-imaging file formats" HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/nipy/nibabel.git" +SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64 ~x86" IUSE="dicom" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] dicom? ( - sci-libs/pydicom dev-python/pillow[${PYTHON_USEDEP}] - ) + sci-libs/pydicom + ) " BDEPEND="test? ( - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + dev-python/pytest-httpserver[${PYTHON_USEDEP}] )" distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest index d9bac81b5..9444a9dd3 100644 --- a/sci-libs/nipy/Manifest +++ b/sci-libs/nipy/Manifest @@ -1 +1 @@ -DIST nipy-0.4.2.tar.gz 2403688 BLAKE2B 883377356787652450bb5a8090be48708144c9d11473232248d48e8bc36eb292cdd672ae30b337de6fb8c5e593a772489908c9575c2f97a8dbd82a8e4d6ad0df SHA512 730654e422c9fd15c0abf7ce0e0cb5e9569788527a35e9cc6deb71e2384b0ed2dbbf82f9eafe9cd739647bb1dc3a3d43606d0244fae5accd0896f1fc5bb3a8cc +DIST nipy-0.6.0.gh.tar.gz 1650342 BLAKE2B 5f375e23fb2d895cfb4320b8ec92cefcf902f3768b6b8dc2ba26b4db30168eb4a29d38be1241e2ae5ae9d87013beb64427c8aca1ac2adaa92d083c700dc0453a SHA512 a59485ccd677c443b9d1e2358c3b3d523ddfa9f390c180661e9afaf3b69943e1b1670c44410954e1bba11c88b9ca20e9e586392804b5c99e9f58b5b68df4641f diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml index 327dd23d3..30440d9a2 100644 --- a/sci-libs/nipy/metadata.xml +++ b/sci-libs/nipy/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">nipy</remote-id> + <remote-id type="github">nipy/nipy</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/nipy/nipy-0.4.2.ebuild b/sci-libs/nipy/nipy-0.4.2.ebuild deleted file mode 100644 index 3749f7ae2..000000000 --- a/sci-libs/nipy/nipy-0.4.2.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 eutils multilib flag-o-matic - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://nipy.org/" -SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - dev-python/prov[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] - >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - " - -DEPEND=" - ${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - " - -python_prepare_all() { - distutils-r1_python_prepare_all - # bug #397605 - [[ ${CHOST} == *-darwin* ]] \ - && append-ldflags -bundle "-undefined dynamic_lookup" \ - || append-ldflags -shared - - # nipy uses the horrible numpy.distutils automagic -} - -python_test() { - distutils-r1_install_for_testing - cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/" - cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/" - cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests" - cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii" - mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cd "${BUILD_DIR}" || die - echo "backend : agg" > matplotlibrc - nosetests || die -} diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild new file mode 100644 index 000000000..8f8ea83e8 --- /dev/null +++ b/sci-libs/nipy/nipy-0.6.0.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=meson-python +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_EXT=1 + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging tools for Python" +HOMEPAGE="https://nipy.org/" +SRC_URI="https://github.com/nipy/nipy/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Test data unavailable: +# https://github.com/nipy/nipy/issues/561#event-11866547632 +RESTRICT="test" + +RDEPEND=" + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/sympy[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + " +DEPEND="" + +distutils_enable_tests pytest + +python_test() { + rm -rf nipy || die + epytest +} diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild deleted file mode 100644 index 7e0f61d2d..000000000 --- a/sci-libs/nipy/nipy-9999.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 eutils multilib flag-o-matic git-r3 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://nipy.org/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/nipy/nipy" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" -IUSE="" - -RDEPEND=" - dev-python/prov[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] - >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - " - -DEPEND=" - ${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - " - -python_prepare_all() { - distutils-r1_python_prepare_all - # bug #397605 - [[ ${CHOST} == *-darwin* ]] \ - && append-ldflags -bundle "-undefined dynamic_lookup" \ - || append-ldflags -shared - - # nipy uses the horrible numpy.distutils automagic -} - -python_test() { - distutils-r1_install_for_testing - cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/" - cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/" - cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests" - cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii" - mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cd "${BUILD_DIR}" || die - echo "backend : agg" > matplotlibrc - nosetests || die -} diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest index a3c77d4ff..6c9059e1c 100644 --- a/sci-libs/nipype/Manifest +++ b/sci-libs/nipype/Manifest @@ -1 +1,2 @@ -DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85 +DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b +DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec diff --git a/sci-libs/nipype/files/nipype-1.5.0-collections.patch b/sci-libs/nipype/files/nipype-1.5.0-collections.patch new file mode 100644 index 000000000..e784ba48b --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.5.0-collections.patch @@ -0,0 +1,28 @@ +--- a/nipype/interfaces/base/traits_extension.py 2020-06-03 11:08:30.000000000 -0400 ++++ b/nipype/interfaces/base/traits_extension.py 2022-07-11 14:09:31.847784312 -0400 +@@ -19,7 +19,10 @@ + (usually by Robert Kern). + + """ +-from collections import Sequence ++try: ++ from collections import Sequence ++except ImportError: ++ from collections.abc import Sequence + + # perform all external trait imports here + from traits import __version__ as traits_version +--- a/nipype/utils/misc.py 2020-06-03 11:08:30.000000000 -0400 ++++ b/nipype/utils/misc.py 2020-06-03 14:08:57.951408897 -0400 +@@ -6,7 +6,10 @@ + import os + import sys + import re +-from collections import Iterator ++try: ++ from collections import Iterator ++except ImportError: ++ from collections.abc import Iterator + from warnings import warn + + from distutils.version import LooseVersion diff --git a/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch new file mode 100644 index 000000000..9811139e7 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch @@ -0,0 +1,575 @@ +From a31870d0f9dc0e774f1cf9d18351586f78ecb252 Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 08:11:54 -0500 +Subject: [PATCH 1/9] FIX: Set dtypes for integer test images + +NiBabel 4 began warning that int64 images would error, and NiBabel 5 +began erroring if not passed an explicit dtype or header. + +We don't need int64 images, just set some sensible dtypes. +--- + nipype/algorithms/tests/test_ErrorMap.py | 2 +- + nipype/algorithms/tests/test_TSNR.py | 3 ++- + nipype/algorithms/tests/test_metrics.py | 2 +- + 3 files changed, 4 insertions(+), 3 deletions(-) + +diff --git a/nipype/algorithms/tests/test_ErrorMap.py b/nipype/algorithms/tests/test_ErrorMap.py +index 98f05d8e17..adac507bad 100644 +--- a/nipype/algorithms/tests/test_ErrorMap.py ++++ b/nipype/algorithms/tests/test_ErrorMap.py +@@ -17,7 +17,7 @@ def test_errormap(tmpdir): + volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]]) + # Alan Turing's birthday + volume2 = np.array([[[0.0, 7.0], [2.0, 3.0]], [[1.0, 9.0], [1.0, 2.0]]]) +- mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]]) ++ mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]], dtype=np.uint8) + + img1 = nb.Nifti1Image(volume1, np.eye(4)) + img2 = nb.Nifti1Image(volume2, np.eye(4)) +diff --git a/nipype/algorithms/tests/test_TSNR.py b/nipype/algorithms/tests/test_TSNR.py +index 26c1019b63..320bec8ab2 100644 +--- a/nipype/algorithms/tests/test_TSNR.py ++++ b/nipype/algorithms/tests/test_TSNR.py +@@ -131,5 +131,6 @@ def assert_unchanged(self, expected_ranges): + [ + [[[2, 4, 3, 9, 1], [3, 6, 4, 7, 4]], [[8, 3, 4, 6, 2], [4, 0, 4, 4, 2]]], + [[[9, 7, 5, 5, 7], [7, 8, 4, 8, 4]], [[0, 4, 7, 1, 7], [6, 8, 8, 8, 7]]], +- ] ++ ], ++ dtype=np.int16, + ) +diff --git a/nipype/algorithms/tests/test_metrics.py b/nipype/algorithms/tests/test_metrics.py +index ad7502992e..3652fc2ce5 100644 +--- a/nipype/algorithms/tests/test_metrics.py ++++ b/nipype/algorithms/tests/test_metrics.py +@@ -45,7 +45,7 @@ def test_fuzzy_overlap(tmpdir): + + # Just considering the mask, the central pixel + # that raised the index now is left aside. +- data = np.zeros((3, 3, 3), dtype=int) ++ data = np.zeros((3, 3, 3), dtype=np.uint8) + data[0, 0, 0] = 1 + data[2, 2, 2] = 1 + nb.Nifti1Image(data, np.eye(4)).to_filename("mask.nii.gz") + +From 443492e82f3b197ad739cb244912ced652853a8d Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 08:43:07 -0500 +Subject: [PATCH 2/9] FIX: Coerce depidx to lil_matrix + +--- + nipype/pipeline/plugins/base.py | 18 +++++++++++++----- + 1 file changed, 13 insertions(+), 5 deletions(-) + +diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py +index a927b24686..3d600dda55 100644 +--- a/nipype/pipeline/plugins/base.py ++++ b/nipype/pipeline/plugins/base.py +@@ -21,6 +21,18 @@ + logger = logging.getLogger("nipype.workflow") + + ++def _graph_to_lil_matrix(graph, nodelist): ++ """Provide a sparse linked list matrix across various NetworkX versions""" ++ import scipy.sparse as ssp ++ ++ try: ++ from networkx import to_scipy_sparse_array ++ except ImportError: # NetworkX < 2.7 ++ from networkx import to_scipy_sparse_matrix as to_scipy_sparse_array ++ ++ return ssp.lil_matrix(to_scipy_sparse_array(graph, nodelist=nodelist, format="lil")) ++ ++ + class PluginBase(object): + """Base class for plugins.""" + +@@ -431,12 +443,8 @@ def _task_finished_cb(self, jobid, cached=False): + + def _generate_dependency_list(self, graph): + """Generates a dependency list for a list of graphs.""" +- import networkx as nx +- + self.procs, _ = topological_sort(graph) +- self.depidx = nx.to_scipy_sparse_matrix( +- graph, nodelist=self.procs, format="lil" +- ) ++ self.depidx = _graph_to_lil_matrix(graph, nodelist=self.procs) + self.refidx = self.depidx.astype(int) + self.proc_done = np.zeros(len(self.procs), dtype=bool) + self.proc_pending = np.zeros(len(self.procs), dtype=bool) + +From 34ef6c2ff89f327fcf2951b792ef38b6d56f8c4e Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 11:57:54 -0500 +Subject: [PATCH 3/9] FIX: Accept "str" in dipy type (includes "string") + +--- + nipype/interfaces/dipy/base.py | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py +index d8a1c0fbf5..161ed33227 100644 +--- a/nipype/interfaces/dipy/base.py ++++ b/nipype/interfaces/dipy/base.py +@@ -110,7 +110,7 @@ def convert_to_traits_type(dipy_type, is_file=False): + """Convert DIPY type to Traits type.""" + dipy_type = dipy_type.lower() + is_mandatory = bool("optional" not in dipy_type) +- if "variable" in dipy_type and "string" in dipy_type: ++ if "variable" in dipy_type and "str" in dipy_type: + return traits.ListStr, is_mandatory + elif "variable" in dipy_type and "int" in dipy_type: + return traits.ListInt, is_mandatory +@@ -120,9 +120,9 @@ def convert_to_traits_type(dipy_type, is_file=False): + return traits.ListBool, is_mandatory + elif "variable" in dipy_type and "complex" in dipy_type: + return traits.ListComplex, is_mandatory +- elif "string" in dipy_type and not is_file: ++ elif "str" in dipy_type and not is_file: + return traits.Str, is_mandatory +- elif "string" in dipy_type and is_file: ++ elif "str" in dipy_type and is_file: + return File, is_mandatory + elif "int" in dipy_type: + return traits.Int, is_mandatory + +From 83c8cf86d6bbb0dc04aa58dbe5119fd864342d9c Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 11:55:34 -0500 +Subject: [PATCH 4/9] MNT: Update requirements from info.py + +--- + requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index afec34ebfd..331e2c5def 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -2,8 +2,7 @@ + click>=6.6.0 + networkx>=2.0 + nibabel>=2.1.0 +-numpy>=1.13 ; python_version < "3.7" +-numpy>=1.15.3 ; python_version >= "3.7" ++numpy>=1.17 + packaging + prov>=1.5.2 + pydot>=1.2.3 +@@ -11,6 +10,7 @@ python-dateutil>=2.2 + rdflib>=5.0.0 + scipy>=0.14 + simplejson>=3.8.0 +-traits>=4.6,!=5.0 ++traits>=4.6,<6.4,!=5.0 + filelock>=3.0.0 + etelemetry>=0.2.0 ++looseversion + +From 24c55a6f48aa658320ff35283b6f91ec38b13a40 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Thu, 26 Jan 2023 02:28:33 -0500 +Subject: [PATCH 5/9] Writing pickles directly as networkx no longer ships + write_gpickle + +--- + nipype/interfaces/cmtk/cmtk.py | 12 ++++++++---- + nipype/interfaces/cmtk/nbs.py | 7 +++++-- + nipype/interfaces/cmtk/nx.py | 12 ++++++++---- + nipype/interfaces/cmtk/tests/test_nbs.py | 4 +++- + 4 files changed, 24 insertions(+), 11 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index 8775a8517e..8df7a1c5ad 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -226,7 +226,8 @@ def cmat( + # Add node information from specified parcellation scheme + path, name, ext = split_filename(resolution_network_file) + if ext == ".pck": +- gp = nx.read_gpickle(resolution_network_file) ++ with open(resolution_network_file, 'rb') as f: ++ gp = pickle.load(f) + elif ext == ".graphml": + gp = nx.read_graphml(resolution_network_file) + else: +@@ -379,7 +380,8 @@ def cmat( + fibdev.add_edge(u, v, weight=di["fiber_length_std"]) + + iflogger.info("Writing network as %s", matrix_name) +- nx.write_gpickle(G, op.abspath(matrix_name)) ++ with open(op.abspath(matrix_name), 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + + numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) + numfib_dict = {"number_of_fibers": numfib_mlab} +@@ -394,7 +396,8 @@ def cmat( + path, name, ext = split_filename(matrix_name) + intersection_matrix_name = op.abspath(name + "_intersections") + ext + iflogger.info("Writing intersection network as %s", intersection_matrix_name) +- nx.write_gpickle(I, intersection_matrix_name) ++ with open(intersection_matrix_name, 'wb') as f: ++ pickle.dump(I, f, pickle.HIGHEST_PROTOCOL) + + path, name, ext = split_filename(matrix_mat_name) + if not ext == ".mat": +@@ -1070,7 +1073,8 @@ def create_nodes(roi_file, resolution_network_file, out_filename): + ) + ) + G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]]) +- nx.write_gpickle(G, out_filename) ++ with open(out_filename, 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + return out_filename + + +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 4e1db9ffb7..57d63897c7 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -6,6 +6,7 @@ + + import numpy as np + import networkx as nx ++import pickle + + from ... import logging + from ..base import ( +@@ -172,12 +173,14 @@ def _run_interface(self, runtime): + + path = op.abspath("NBS_Result_" + details) + iflogger.info(path) +- nx.write_gpickle(nbsgraph, path) ++ with open(path, 'wb') as f: ++ pickle.dump(nbsgraph, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving output NBS edge network as %s", path) + + pval_path = op.abspath("NBS_P_vals_" + details) + iflogger.info(pval_path) +- nx.write_gpickle(nbs_pval_graph, pval_path) ++ with open(pval_path, 'wb') as f: ++ pickle.dump(nbs_pval_graph, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving output p-value network as %s", pval_path) + return runtime + +diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py +index aaf4bece39..a662eb65c6 100644 +--- a/nipype/interfaces/cmtk/nx.py ++++ b/nipype/interfaces/cmtk/nx.py +@@ -200,7 +200,8 @@ def average_networks(in_files, ntwk_res_file, group_id): + + # Writes the networks and returns the name + network_name = group_id + "_average.pck" +- nx.write_gpickle(avg_ntwk, op.abspath(network_name)) ++ with open(op.abspath(network_name), 'wb') as f: ++ pickle.dump(avg_ntwk, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving average network as %s", op.abspath(network_name)) + avg_ntwk = fix_keys_for_gexf(avg_ntwk) + network_name = group_id + "_average.gexf" +@@ -483,7 +484,8 @@ def _run_interface(self, runtime): + for key in list(node_measures.keys()): + newntwk = add_node_data(node_measures[key], ntwk) + out_file = op.abspath(self._gen_outfilename(key, "pck")) +- nx.write_gpickle(newntwk, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL) + nodentwks.append(out_file) + if isdefined(self.inputs.out_node_metrics_matlab): + node_out_file = op.abspath(self.inputs.out_node_metrics_matlab) +@@ -497,7 +499,8 @@ def _run_interface(self, runtime): + for key in list(edge_measures.keys()): + newntwk = add_edge_data(edge_measures[key], ntwk) + out_file = op.abspath(self._gen_outfilename(key, "pck")) +- nx.write_gpickle(newntwk, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL) + edgentwks.append(out_file) + if isdefined(self.inputs.out_edge_metrics_matlab): + edge_out_file = op.abspath(self.inputs.out_edge_metrics_matlab) +@@ -521,7 +524,8 @@ def _run_interface(self, runtime): + out_file = op.abspath( + self._gen_outfilename(self.inputs.out_k_crust, "pck") + ) +- nx.write_gpickle(ntwk_measures[key], out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(ntwk_measures[key], f, pickle.HIGHEST_PROTOCOL) + kntwks.append(out_file) + gpickled.extend(kntwks) + +diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py +index 46da939f1a..7a60b407a4 100644 +--- a/nipype/interfaces/cmtk/tests/test_nbs.py ++++ b/nipype/interfaces/cmtk/tests/test_nbs.py +@@ -2,6 +2,7 @@ + from ....utils.misc import package_check + import numpy as np + import networkx as nx ++import pickle + import pytest + + have_cv = True +@@ -20,7 +21,8 @@ def creating_graphs(tmpdir): + G = nx.from_numpy_matrix(graph) + out_file = tmpdir.strpath + graphnames[idx] + ".pck" + # Save as pck file +- nx.write_gpickle(G, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + graphlist.append(out_file) + return graphlist + + +From b9a8e2000be9ce30a94aca85453d5cf4e32e10ec Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Thu, 26 Jan 2023 02:03:39 -0500 +Subject: [PATCH 6/9] updating networkx from_numpy_{matrix,array} + +--- + nipype/interfaces/cmtk/cmtk.py | 2 +- + nipype/interfaces/cmtk/nbs.py | 4 ++-- + nipype/interfaces/cmtk/tests/test_nbs.py | 2 +- + 3 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index 8df7a1c5ad..fc730b1166 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -264,7 +264,7 @@ def cmat( + ) + intersection_matrix = np.matrix(intersection_matrix) + I = G.copy() +- H = nx.from_numpy_matrix(np.matrix(intersection_matrix)) ++ H = nx.from_numpy_array(np.matrix(intersection_matrix)) + H = nx.relabel_nodes(H, lambda x: x + 1) # relabel nodes so they start at 1 + I.add_weighted_edges_from( + ((u, v, d["weight"]) for u, v, d in H.edges(data=True)) +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 57d63897c7..b0a8b5df33 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -150,8 +150,8 @@ def _run_interface(self, runtime): + pADJ[x, y] = PVAL[idx] + + # Create networkx graphs from the adjacency matrix +- nbsgraph = nx.from_numpy_matrix(ADJ) +- nbs_pval_graph = nx.from_numpy_matrix(pADJ) ++ nbsgraph = nx.from_numpy_array(ADJ) ++ nbs_pval_graph = nx.from_numpy_array(pADJ) + + # Relabel nodes because they should not start at zero for our convention + nbsgraph = nx.relabel_nodes(nbsgraph, lambda x: x + 1) +diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py +index 7a60b407a4..6323546c1e 100644 +--- a/nipype/interfaces/cmtk/tests/test_nbs.py ++++ b/nipype/interfaces/cmtk/tests/test_nbs.py +@@ -18,7 +18,7 @@ def creating_graphs(tmpdir): + graphnames = ["name" + str(i) for i in range(6)] + for idx, name in enumerate(graphnames): + graph = np.random.rand(10, 10) +- G = nx.from_numpy_matrix(graph) ++ G = nx.from_numpy_array(graph) + out_file = tmpdir.strpath + graphnames[idx] + ".pck" + # Save as pck file + with open(out_file, 'wb') as f: + +From 7aa7c5968cf28afed9aca658bca28470afbfeb9f Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 12:45:17 -0500 +Subject: [PATCH 7/9] FIX: Purge nx.to_numpy_matrix + +--- + nipype/interfaces/cmtk/cmtk.py | 8 ++++---- + nipype/interfaces/cmtk/nbs.py | 2 +- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index fc730b1166..00c134fc37 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -383,13 +383,13 @@ def cmat( + with open(op.abspath(matrix_name), 'wb') as f: + pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + +- numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) ++ numfib_mlab = nx.to_numpy_array(numfib, dtype=int) + numfib_dict = {"number_of_fibers": numfib_mlab} +- fibmean_mlab = nx.to_numpy_matrix(fibmean, dtype=np.float64) ++ fibmean_mlab = nx.to_numpy_array(fibmean, dtype=np.float64) + fibmean_dict = {"mean_fiber_length": fibmean_mlab} +- fibmedian_mlab = nx.to_numpy_matrix(fibmedian, dtype=np.float64) ++ fibmedian_mlab = nx.to_numpy_array(fibmedian, dtype=np.float64) + fibmedian_dict = {"median_fiber_length": fibmedian_mlab} +- fibdev_mlab = nx.to_numpy_matrix(fibdev, dtype=np.float64) ++ fibdev_mlab = nx.to_numpy_array(fibdev, dtype=np.float64) + fibdev_dict = {"fiber_length_std": fibdev_mlab} + + if intersections: +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index b0a8b5df33..2560ed8e3c 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -40,7 +40,7 @@ def ntwks_to_matrices(in_files, edge_key): + raise KeyError( + "the graph edges do not have {} attribute".format(edge_key) + ) +- matrix[:, :, idx] = nx.to_numpy_matrix(graph) # Retrieve the matrix ++ matrix[:, :, idx] = nx.to_numpy_array(graph) # Retrieve the matrix + return matrix + + + +From f20035c303a88fba3e207ac60388397665bb97be Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 12:45:38 -0500 +Subject: [PATCH 8/9] FIX: Purge nx.read_gpickle + +--- + nipype/interfaces/cmtk/convert.py | 9 ++++++++- + nipype/interfaces/cmtk/nbs.py | 11 ++++++++--- + nipype/interfaces/cmtk/nx.py | 11 ++++++++--- + 3 files changed, 24 insertions(+), 7 deletions(-) + +diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py +index 321a40fbba..a45daddcd6 100644 +--- a/nipype/interfaces/cmtk/convert.py ++++ b/nipype/interfaces/cmtk/convert.py +@@ -18,6 +18,13 @@ + from .base import CFFBaseInterface, have_cfflib + + ++def _read_pickle(fname): ++ import pickle ++ ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + class CFFConverterInputSpec(BaseInterfaceInputSpec): + graphml_networks = InputMultiPath( + File(exists=True), desc="list of graphML networks" +@@ -135,7 +142,7 @@ def _run_interface(self, runtime): + unpickled = [] + for ntwk in self.inputs.gpickled_networks: + _, ntwk_name, _ = split_filename(ntwk) +- unpickled = nx.read_gpickle(ntwk) ++ unpickled = _read_pickle(ntwk) + cnet = cf.CNetwork(name=ntwk_name) + cnet.set_with_nxgraph(unpickled) + a.add_connectome_network(cnet) +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 2560ed8e3c..a2bd42abee 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -24,13 +24,18 @@ + iflogger = logging.getLogger("nipype.interface") + + ++def _read_pickle(fname): ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + def ntwks_to_matrices(in_files, edge_key): +- first = nx.read_gpickle(in_files[0]) ++ first = _read_pickle(in_files[0]) + files = len(in_files) + nodes = len(first.nodes()) + matrix = np.zeros((nodes, nodes, files)) + for idx, name in enumerate(in_files): +- graph = nx.read_gpickle(name) ++ graph = _read_pickle(name) + for u, v, d in graph.edges(data=True): + try: + graph[u][v]["weight"] = d[ +@@ -162,7 +167,7 @@ def _run_interface(self, runtime): + else: + node_ntwk_name = self.inputs.in_group1[0] + +- node_network = nx.read_gpickle(node_ntwk_name) ++ node_network = _read_pickle(node_ntwk_name) + iflogger.info( + "Populating node dictionaries with attributes from %s", node_ntwk_name + ) +diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py +index a662eb65c6..991ca89dcf 100644 +--- a/nipype/interfaces/cmtk/nx.py ++++ b/nipype/interfaces/cmtk/nx.py +@@ -24,11 +24,16 @@ + iflogger = logging.getLogger("nipype.interface") + + ++def _read_pickle(fname): ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + def read_unknown_ntwk(ntwk): + if not isinstance(ntwk, nx.classes.graph.Graph): + _, _, ext = split_filename(ntwk) + if ext == ".pck": +- ntwk = nx.read_gpickle(ntwk) ++ ntwk = _read_pickle(ntwk) + elif ext == ".graphml": + ntwk = nx.read_graphml(ntwk) + return ntwk +@@ -121,7 +126,7 @@ def average_networks(in_files, ntwk_res_file, group_id): + counting_ntwk = ntwk.copy() + # Sums all the relevant variables + for index, subject in enumerate(in_files): +- tmp = nx.read_gpickle(subject) ++ tmp = _read_pickle(subject) + iflogger.info("File %s has %i edges", subject, tmp.number_of_edges()) + edges = list(tmp.edges()) + for edge in edges: +@@ -461,7 +466,7 @@ def _run_interface(self, runtime): + edgentwks = list() + kntwks = list() + matlab = list() +- ntwk = nx.read_gpickle(self.inputs.in_file) ++ ntwk = _read_pickle(self.inputs.in_file) + + # Each block computes, writes, and saves a measure + # The names are then added to the output .pck file list + +From f6bf0af19c044709de5be79a4488dcfd4d08f305 Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 13:23:33 -0500 +Subject: [PATCH 9/9] FIX: Add dtypes to nilearn interface/tests + +--- + nipype/interfaces/nilearn.py | 2 +- + nipype/interfaces/tests/test_nilearn.py | 5 +++-- + 2 files changed, 4 insertions(+), 3 deletions(-) + +diff --git a/nipype/interfaces/nilearn.py b/nipype/interfaces/nilearn.py +index 053902e2bd..95494e7f5f 100644 +--- a/nipype/interfaces/nilearn.py ++++ b/nipype/interfaces/nilearn.py +@@ -155,7 +155,7 @@ def _process_inputs(self): + if self.inputs.include_global: + global_label_data = label_data.dataobj.sum(axis=3) # sum across all regions + global_label_data = ( +- np.rint(global_label_data).astype(int).clip(0, 1) ++ np.rint(global_label_data).clip(0, 1).astype('u1') + ) # binarize + global_label_data = self._4d(global_label_data, label_data.affine) + global_masker = nl.NiftiLabelsMasker( +diff --git a/nipype/interfaces/tests/test_nilearn.py b/nipype/interfaces/tests/test_nilearn.py +index 2066c00768..4f94bbb87b 100644 +--- a/nipype/interfaces/tests/test_nilearn.py ++++ b/nipype/interfaces/tests/test_nilearn.py +@@ -184,10 +184,11 @@ def assert_expected_output(self, labels, wanted): + [[2, -2, -1, -2, -5], [3, 0, 3, -5, -2]], + [[-4, -2, -2, 1, -2], [3, 1, 4, -3, -2]], + ], +- ] ++ ], ++ np.int16, + ) + +- fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]]) ++ fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]], np.uint8) + + fake_equiv_4d_label_data = np.array( + [ diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch new file mode 100644 index 000000000..b5c223422 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch @@ -0,0 +1,50 @@ +diff --git a/nipype/__init__.py b/nipype/__init__.py +index 06084e823..2e42dcbce 100644 +--- a/nipype/__init__.py ++++ b/nipype/__init__.py +@@ -73,23 +73,6 @@ from .interfaces import ( + ) + + +-def check_latest_version(raise_exception=False): +- """ +- Check for the latest version of the library. +- +- Parameters +- ---------- +- raise_exception: bool +- Raise a RuntimeError if a bad version is being used +- """ +- import etelemetry +- +- logger = logging.getLogger("nipype.utils") +- return etelemetry.check_available_version( +- "nipy/nipype", __version__, logger, raise_exception +- ) +- +- + # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL + if config.getboolean("execution", "check_version"): + import __main__ +@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"): + from .interfaces.base import BaseInterface + + if BaseInterface._etelemetry_version_data is None: +- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a" ++ BaseInterface._etelemetry_version_data = "n/a" +diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py +index c8099be63..f7770dbfc 100644 +--- a/nipype/interfaces/base/core.py ++++ b/nipype/interfaces/base/core.py +@@ -183,10 +183,9 @@ class BaseInterface(Interface): + config.getboolean("execution", "check_version") + and "NIPYPE_NO_ET" not in os.environ + ): +- from ... import check_latest_version + + if BaseInterface._etelemetry_version_data is None: +- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a" ++ BaseInterface._etelemetry_version_data = "n/a" + + if not self.input_spec: + raise Exception("No input_spec in class: %s" % self.__class__.__name__) diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild index 35792adbc..7c2e801ff 100644 --- a/sci-libs/nipype/nipype-1.5.0.ebuild +++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild @@ -1,20 +1,21 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) PYTHON_REQ_USE="threads(+),sqlite" inherit distutils-r1 DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" -HOMEPAGE="http://nipy.sourceforge.net/nipype/" +HOMEPAGE="https://nipype.readthedocs.io/" SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" IUSE="test" RESTRICT="!test? ( test )" @@ -28,30 +29,28 @@ DEPEND=" ${RDEPEND} ) " -# Dependency disabled as upstream test configuration which requires it fails -#dev-python/pytest-xdist[${PYTHON_USEDEP}] RDEPEND=" - >=dev-python/click-6.6[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] dev-python/networkx[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] dev-python/pydot[${PYTHON_USEDEP}] - dev-python/pydotplus[${PYTHON_USEDEP}] dev-python/python-dateutil[${PYTHON_USEDEP}] - >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/traits[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] " PATCHES=( - "${FILESDIR}/${P}"-version_check.patch + "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch" ) src_prepare() { # Remove etelemetry - sed -i '/"etelemetry/d' nipype/info.py || die + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die # Mark failing tests sed -i \ @@ -68,11 +67,16 @@ python_install_all() { doenvd "${FILESDIR}/98nipype" } +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + python_test() { # Setting environment variable to disable etelemetry version check: # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 - NIPYPE_NO_ET=1 pytest -vv\ - || die + NIPYPE_NO_ET=1 epytest # Upstream test configuration fails #-c nipype/pytest.ini\ #--doctest-modules nipype\ diff --git a/sci-libs/nipype/nipype-1.8.4-r2.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild new file mode 100644 index 000000000..4c3da70b3 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch" + "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch" +) + +src_prepare() { + # Remove etelemetry + # Doing this separately since the file is affected by another patch. + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild new file mode 100644 index 000000000..88bc23395 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.6.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Tests fail with numpy import error: +# https://github.com/nipy/nipype/issues/3626 +RESTRICT="test" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch" +) + +src_prepare() { + # Remove etelemetry + # Doing this separately since the file is affected by another patch. + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-libs/oneDAL/Manifest b/sci-libs/oneDAL/Manifest new file mode 100644 index 000000000..4ea34591f --- /dev/null +++ b/sci-libs/oneDAL/Manifest @@ -0,0 +1,4 @@ +DIST mklfpk_lnx_20221214.tgz 88817211 BLAKE2B 3416ce8fe8c768c0d8598536d23f68aafe9e47590d854ce19e8ac79108aa5f10a2fd2fdbf7c96aec9f083ef8ad3ae7a1515e5f5b0e565f0c1686cc5fc0eeb02d SHA512 c0a0beb56c3f41deff9b587d116e7cd366ff31b393a78d4ad608ef620d5b503bc80b720eb61b9355c8d5547a3a566f223d5deb3421c97498fbff90997d8d7e62 +DIST mklgpufpk_lnx_20221214.tgz 15283052 BLAKE2B 54137083613cef5114cd95cade61e58456a0858bd46ecc9fe2294ba06d5bd405bbb1259b16f9003ba466a91cfa0b3801dc8485338fd11d612f09811741ff25a2 SHA512 2cf035133269ac24fa7d39aecaa673d21a65b772d86179a04fec20e4d6e1ad20122ae8ce262f2814ad768272258c512e6fedf0ab978ed687ba54949bb7b6b3b5 +DIST oneDAL-2023.0.1.tar.gz 61208026 BLAKE2B 2a9509fe59808ee1211b39b2ae0da34b37ba73e747316fdb407112611bbba1b808d451f5aef0afc9552178839adaae71bbe80c2fdeea39a23048674f87b159c1 SHA512 58e9aacc5c09bae67d5bdc6477b7e5d6f0c696513e532d778ae427314e35f629c6c3b8d94f382638ab736786f4ae965dcbdf2e25ab018efc863ee21000116894 +DIST oneDAL-2023.2.1.tar.gz 50938584 BLAKE2B c14bbdc7a1d4faf5266f47a0849a1a9403824c6824ca392f5bafc5fe7c9e6abd6448647cb73d1ffd9cec8b347bba2ca3d58d86306af185896a0a5880132e593a SHA512 d412bd8f353a017929b31411ff2788fada04ceee9cb4f6d98828e5bb10a50a28dc4d73f89da0a0db21baf1cb4accebfb647198331748f95a6af9299c4977d5b7 diff --git a/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch b/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch new file mode 100644 index 000000000..553e742ab --- /dev/null +++ b/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch @@ -0,0 +1,164 @@ +diff --git a/dev/bazel/deps/onedal.bzl b/dev/bazel/deps/onedal.bzl +index f0f7662..6b9d11f 100644 +--- a/dev/bazel/deps/onedal.bzl ++++ b/dev/bazel/deps/onedal.bzl +@@ -21,18 +21,12 @@ onedal_repo = repos.prebuilt_libs_repo_rule( + "include", + ], + libs = [ +- # Static +- "lib/intel64/libonedal_core.a", +- "lib/intel64/libonedal_thread.a", +- "lib/intel64/libonedal.a", +- "lib/intel64/libonedal_dpc.a", +- "lib/intel64/libonedal_sycl.a", +- + # Dynamic + "lib/intel64/libonedal_core.so", + "lib/intel64/libonedal_thread.so", + "lib/intel64/libonedal.so", + "lib/intel64/libonedal_dpc.so", ++ "lib/intel64/libonedal_sycl.so", + ], + build_template = "@onedal//dev/bazel/deps:onedal.tpl.BUILD", + ) +diff --git a/dev/bazel/deps/onedal.tpl.BUILD b/dev/bazel/deps/onedal.tpl.BUILD +index 60be678..0f7990e 100644 +--- a/dev/bazel/deps/onedal.tpl.BUILD ++++ b/dev/bazel/deps/onedal.tpl.BUILD +@@ -9,62 +9,17 @@ cc_library( + includes = [ "include" ], + ) + +-cc_library( +- name = "core_static", +- srcs = [ +- "lib/intel64/libonedal_core.a", +- ], +- deps = [ +- ":headers", +- # TODO: Currently vml_ipp lib depends on TBB, but it shouldn't +- # Remove TBB from deps once problem with vml_ipp is resolved +- "@tbb//:tbb_binary", +- ], +-) +- +-cc_library( +- name = "thread_static", +- srcs = [ +- "lib/intel64/libonedal_thread.a", +- ], +- deps = [ +- ":headers", +- "@tbb//:tbb_binary", +- "@tbb//:tbbmalloc_binary", +- ], +-) + + cc_library( + name = "onedal_sycl", + srcs = [ +- "lib/intel64/libonedal_sycl.a", +- ], +- deps = [ +- ":headers", +- ], +-) +- +-cc_library( +- name = "onedal_static", +- srcs = [ +- "lib/intel64/libonedal.a", ++ "lib/intel64/libonedal_sycl.so", + ], + deps = [ + ":headers", + ], + ) + +-cc_library( +- name = "onedal_static_dpc", +- srcs = [ +- "lib/intel64/libonedal_dpc.a", +- ], +- deps = [ +- ":headers", +- ":onedal_sycl", +- ], +-) +- + cc_library( + name = "core_dynamic", + srcs = [ +diff --git a/dev/make/cmplr.dpcpp.mk b/dev/make/cmplr.dpcpp.mk +index 2ac2ed9..bd0e182 100644 +--- a/dev/make/cmplr.dpcpp.mk ++++ b/dev/make/cmplr.dpcpp.mk +@@ -28,13 +28,13 @@ CORE.SERV.COMPILER.dpcpp = generic + -Zl.dpcpp = + -DEBC.dpcpp = -g + +-COMPILER.lnx.dpcpp = icpx -fsycl $(if $(IA_is_ia32),-m32,-m64) -stdlib=libstdc++ -fgnu-runtime -fwrapv \ +- -Werror -Wreturn-type -fsycl-device-code-split=per_kernel +-COMPILER.win.dpcpp = icx -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ ++COMPILER.lnx.dpcpp = $(CXX) $(CXXFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -stdlib=libstdc++ -fgnu-runtime -fwrapv \ ++ -Wreturn-type -fsycl-device-code-split=per_kernel ++COMPILER.win.dpcpp = $(CC) $(CFLAGS) -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ + -Wno-deprecated-declarations -fsycl-device-code-split=per_kernel + +-link.dynamic.lnx.dpcpp = icpx -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel +-link.dynamic.win.dpcpp = icx -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel ++link.dynamic.lnx.dpcpp = $(CXX) $(LDFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel ++link.dynamic.win.dpcpp = $(CC) $(LDFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel + + pedantic.opts.lnx.dpcpp = -pedantic \ + -Wall \ +diff --git a/dev/make/cmplr.icx.mk b/dev/make/cmplr.icx.mk +index 28ce293..7c478b0 100644 +--- a/dev/make/cmplr.icx.mk ++++ b/dev/make/cmplr.icx.mk +@@ -24,14 +24,14 @@ CMPLRDIRSUFF.icx = _icx + + CORE.SERV.COMPILER.icx = generic + +--Zl.icx = -no-intel-lib=libirc ++-Zl.icx = + -DEBC.icx = -g + +-COMPILER.lnx.icx = icpx $(if $(IA_is_ia32),-m32,-m64) \ +- -Werror -Wreturn-type ++COMPILER.lnx.icx = $(CXX) $(CXXFLAGS) $(if $(IA_is_ia32),-m32,-m64) \ ++ -Wreturn-type + + +-link.dynamic.lnx.icx = icpx $(if $(IA_is_ia32),-m32,-m64) ++link.dynamic.lnx.icx = $(CXX) $(LDFLAGS) $(if $(IA_is_ia32),-m32,-m64) + + pedantic.opts.icx = -pedantic \ + -Wall \ +diff --git a/makefile b/makefile +index 9c51bad..20aaff5 100644 +--- a/makefile ++++ b/makefile +@@ -219,7 +219,7 @@ TBBDIR.2 := $(if $(TBBDIR.2),$(TBBDIR.2),$(error Can`t find TBB neither in $(DIR + + TBBDIR.include := $(if $(TBBDIR),$(TBBDIR)/include/tbb $(TBBDIR)/include) + +-TBBDIR.libia.prefix := $(TBBDIR.2)/lib ++TBBDIR.libia.prefix := $(TBBDIR.2)/lib64 + + TBBDIR.libia.win.vc1 := $(if $(OS_is_win),$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt),$(TBBDIR.libia.prefix)/$(_IA)/vc_mt,$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc14),$(TBBDIR.libia.prefix)/$(_IA)/vc14))) + TBBDIR.libia.win.vc2 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc1),,$(firstword $(filter $(call topf,$$TBBROOT)%,$(subst ;,$(space),$(call topf,$$LIB)))))) +@@ -227,10 +227,10 @@ TBBDIR.libia.win.vc22 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc2),$(wildca + + TBBDIR.libia.win:= $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc22),$(TBBDIR.libia.win.vc2),$(if $(TBBDIR.libia.win.vc1),$(TBBDIR.libia.win.vc1),$(error Can`t find TBB libs nether in $(call frompf,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt not in $(firstword $(filter $(TBBROOT)%,$(subst ;,$(space),$(LIB)))).)))) + +-TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8/*),$(TBBDIR.libia.prefix)/$(_IA)/gcc4.8)) ++TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.lnx.gcc2 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))))) + TBBDIR.libia.lnx.gcc22 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc2),$(wildcard $(TBBDIR.libia.lnx.gcc2)/libtbb.so))) +-TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8 not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) ++TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix) not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) + + TBBDIR.libia.mac.clang1 := $(if $(OS_is_mac),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.mac.clang2 := $(if $(OS_is_mac),$(if $(TBBDIR.libia.mac.clang1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LIBRARY_PATH)))))) diff --git a/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch b/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch new file mode 100644 index 000000000..50731570d --- /dev/null +++ b/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch @@ -0,0 +1,162 @@ +diff --git a/dev/bazel/deps/onedal.bzl b/dev/bazel/deps/onedal.bzl +index f0f7662c0..6b9d11ff2 100644 +--- a/dev/bazel/deps/onedal.bzl ++++ b/dev/bazel/deps/onedal.bzl +@@ -21,18 +21,12 @@ onedal_repo = repos.prebuilt_libs_repo_rule( + "include", + ], + libs = [ +- # Static +- "lib/intel64/libonedal_core.a", +- "lib/intel64/libonedal_thread.a", +- "lib/intel64/libonedal.a", +- "lib/intel64/libonedal_dpc.a", +- "lib/intel64/libonedal_sycl.a", +- + # Dynamic + "lib/intel64/libonedal_core.so", + "lib/intel64/libonedal_thread.so", + "lib/intel64/libonedal.so", + "lib/intel64/libonedal_dpc.so", ++ "lib/intel64/libonedal_sycl.so", + ], + build_template = "@onedal//dev/bazel/deps:onedal.tpl.BUILD", + ) +diff --git a/dev/bazel/deps/onedal.tpl.BUILD b/dev/bazel/deps/onedal.tpl.BUILD +index 60be67856..0f7990ef5 100644 +--- a/dev/bazel/deps/onedal.tpl.BUILD ++++ b/dev/bazel/deps/onedal.tpl.BUILD +@@ -9,62 +9,17 @@ cc_library( + includes = [ "include" ], + ) + +-cc_library( +- name = "core_static", +- srcs = [ +- "lib/intel64/libonedal_core.a", +- ], +- deps = [ +- ":headers", +- # TODO: Currently vml_ipp lib depends on TBB, but it shouldn't +- # Remove TBB from deps once problem with vml_ipp is resolved +- "@tbb//:tbb_binary", +- ], +-) +- +-cc_library( +- name = "thread_static", +- srcs = [ +- "lib/intel64/libonedal_thread.a", +- ], +- deps = [ +- ":headers", +- "@tbb//:tbb_binary", +- "@tbb//:tbbmalloc_binary", +- ], +-) + + cc_library( + name = "onedal_sycl", + srcs = [ +- "lib/intel64/libonedal_sycl.a", +- ], +- deps = [ +- ":headers", +- ], +-) +- +-cc_library( +- name = "onedal_static", +- srcs = [ +- "lib/intel64/libonedal.a", ++ "lib/intel64/libonedal_sycl.so", + ], + deps = [ + ":headers", + ], + ) + +-cc_library( +- name = "onedal_static_dpc", +- srcs = [ +- "lib/intel64/libonedal_dpc.a", +- ], +- deps = [ +- ":headers", +- ":onedal_sycl", +- ], +-) +- + cc_library( + name = "core_dynamic", + srcs = [ +diff --git a/dev/make/cmplr.dpcpp.mk b/dev/make/cmplr.dpcpp.mk +index 2a78043b7..b431e1255 100644 +--- a/dev/make/cmplr.dpcpp.mk ++++ b/dev/make/cmplr.dpcpp.mk +@@ -28,13 +28,13 @@ CORE.SERV.COMPILER.dpcpp = generic + -Zl.dpcpp = + -DEBC.dpcpp = -g + +-COMPILER.lnx.dpcpp = icpx -fsycl -m64 -stdlib=libstdc++ -fgnu-runtime -fwrapv \ ++COMPILER.lnx.dpcpp = $(CXX) $(CXXFLAGS) -fsycl -m64 -stdlib=libstdc++ -fgnu-runtime -fwrapv \ + -Werror -Wreturn-type -fsycl-device-code-split=per_kernel +-COMPILER.win.dpcpp = icx -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ ++COMPILER.win.dpcpp = $(CC) $(CFLAGS) -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ + -Wno-deprecated-declarations -fsycl-device-code-split=per_kernel + +-link.dynamic.lnx.dpcpp = icpx -fsycl -m64 -fsycl-device-code-split=per_kernel +-link.dynamic.win.dpcpp = icx -fsycl -m64 -fsycl-device-code-split=per_kernel ++link.dynamic.lnx.dpcpp = $(CXX) $(LDFLAGS) -fsycl -m64 -fsycl-device-code-split=per_kernel ++link.dynamic.win.dpcpp = $(CC) $(LDFLAGS) -fsycl -m64 -fsycl-device-code-split=per_kernel + + pedantic.opts.lnx.dpcpp = -pedantic \ + -Wall \ +diff --git a/dev/make/cmplr.icx.mk b/dev/make/cmplr.icx.mk +index cbcde1a7e..61ef3583c 100644 +--- a/dev/make/cmplr.icx.mk ++++ b/dev/make/cmplr.icx.mk +@@ -24,14 +24,14 @@ CMPLRDIRSUFF.icx = _icx + + CORE.SERV.COMPILER.icx = generic + +--Zl.icx = -no-intel-lib=libirc ++-Zl.icx = + -DEBC.icx = -g + +-COMPILER.lnx.icx = icpx -m64 \ ++COMPILER.lnx.icx = $(CXX) $(CXXFLAGS) -m64 \ + -Werror -Wreturn-type + + +-link.dynamic.lnx.icx = icpx -m64 ++link.dynamic.lnx.icx = $(CXX) $(LDFLAGS) -m64 + + pedantic.opts.icx = -pedantic \ + -Wall \ +diff --git a/makefile b/makefile +index 525e52728..db864e9cb 100644 +--- a/makefile ++++ b/makefile +@@ -215,7 +215,7 @@ TBBDIR.2 := $(if $(TBBDIR.2),$(TBBDIR.2),$(error Can`t find TBB neither in $(DIR + + TBBDIR.include := $(if $(TBBDIR),$(TBBDIR)/include/tbb $(TBBDIR)/include) + +-TBBDIR.libia.prefix := $(TBBDIR.2)/lib ++TBBDIR.libia.prefix := $(TBBDIR.2)/lib64 + + TBBDIR.libia.win.vc1 := $(if $(OS_is_win),$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt),$(TBBDIR.libia.prefix)/$(_IA)/vc_mt,$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc14),$(TBBDIR.libia.prefix)/$(_IA)/vc14))) + TBBDIR.libia.win.vc2 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc1),,$(firstword $(filter $(call topf,$$TBBROOT)%,$(subst ;,$(space),$(call topf,$$LIB)))))) +@@ -223,10 +223,10 @@ TBBDIR.libia.win.vc22 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc2),$(wildca + + TBBDIR.libia.win:= $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc22),$(TBBDIR.libia.win.vc2),$(if $(TBBDIR.libia.win.vc1),$(TBBDIR.libia.win.vc1),$(error Can`t find TBB libs nether in $(call frompf,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt not in $(firstword $(filter $(TBBROOT)%,$(subst ;,$(space),$(LIB)))).)))) + +-TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8/*),$(TBBDIR.libia.prefix)/$(_IA)/gcc4.8)) ++TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.lnx.gcc2 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))))) + TBBDIR.libia.lnx.gcc22 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc2),$(wildcard $(TBBDIR.libia.lnx.gcc2)/libtbb.so))) +-TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8 not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) ++TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix) not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) + + TBBDIR.libia.mac.clang1 := $(if $(OS_is_mac),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.mac.clang2 := $(if $(OS_is_mac),$(if $(TBBDIR.libia.mac.clang1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LIBRARY_PATH)))))) diff --git a/sci-libs/geom/metadata.xml b/sci-libs/oneDAL/metadata.xml index b34b297d6..2793ac235 100644 --- a/sci-libs/geom/metadata.xml +++ b/sci-libs/oneDAL/metadata.xml @@ -6,6 +6,6 @@ <name>Gentoo Science Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">salomegeometry</remote-id> + <remote-id type="github">oneapi-src/oneDAL</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild b/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild new file mode 100644 index 000000000..589a74960 --- /dev/null +++ b/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild @@ -0,0 +1,85 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +inherit python-any-r1 java-pkg-2 + +MKLFPK_VER="20221214" +MKLGPUFPK_VER="20221214" + +DESCRIPTION="oneAPI Data Analytics Library" +HOMEPAGE="https://github.com/oneapi-src/oneDAL" +# Secondary urls extracted from dev/download_micromkl.sh +SRC_URI=" + https://github.com/oneapi-src/oneDAL/archive/${PV}.tar.gz -> ${P}.tar.gz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklfpk_lnx_${MKLFPK_VER}.tgz +" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND="sys-devel/DPC++" + +RDEPEND=" + dev-cpp/tbb:= + dev-libs/opencl-icd-loader + virtual/jdk:17 +" +DEPEND=" + ${DEPEND} + ${PYTHON_DEPS} +" + +PATCHES=( + "${FILESDIR}/${PN}-2021.7.1_p20221207-fix-compile.patch" +) + +pkg_setup() { + python-any-r1_pkg_setup + java-pkg-2_pkg_setup +} + +src_unpack() { + unpack "${P}.tar.gz" + mkdir -p "${S}/__deps/mklfpk/" "${S}/__deps/mklgpufpk/lnx" || die + cd "${S}/__deps/mklfpk/" || die + unpack "mklfpk_lnx_${MKLFPK_VER}.tgz" + cd "${S}/__deps/mklgpufpk/lnx" || die + unpack "mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz" +} + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export TBBROOT="${ESYSROOT}/usr" + export CPLUS_INCLUDE_PATH="./cpp/daal/include:${ESYSROOT}/usr/lib/llvm/intel/include" + export JAVA_HOME="${ESYSROOT}/usr/lib64/openjdk-17/" + export PATH="${JAVA_HOME}/bin:${PATH}" + export CPATH="${JAVA_HOME}/include:${JAVA_HOME}/include/linux:${CPATH}" + + default +} + +src_compile() { + emake PLAT=lnx32e COMPILER=icx daal oneapi +} + +src_install() { + einstalldocs + cd __release_lnx_icx/daal/latest || die + docinto examples + dodoc -r examples/* + docinto samples + dodoc -r samples/* + doheader -r include/* + dolib.so lib/intel64/*.so* + dolib.a lib/intel64/*.a* + insinto /usr/share/pkgconfig + doins -r lib/pkgconfig/* + java-pkg_dojar lib/*.jar +} diff --git a/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild b/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild new file mode 100644 index 000000000..9007f7a51 --- /dev/null +++ b/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild @@ -0,0 +1,85 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +inherit python-any-r1 java-pkg-2 + +MKLFPK_VER="20221214" +MKLGPUFPK_VER="20221214" + +DESCRIPTION="oneAPI Data Analytics Library" +HOMEPAGE="https://github.com/oneapi-src/oneDAL" +# Secondary urls extracted from dev/download_micromkl.sh +SRC_URI=" + https://github.com/oneapi-src/oneDAL/archive/${PV}.tar.gz -> ${P}.tar.gz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklfpk_lnx_${MKLFPK_VER}.tgz +" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND="sys-devel/DPC++" + +RDEPEND=" + dev-cpp/tbb:= + dev-libs/opencl-icd-loader + virtual/jdk:17 +" +DEPEND=" + ${DEPEND} + ${PYTHON_DEPS} +" + +PATCHES=( + "${FILESDIR}/${PN}-2023.2.1-fix-compile.patch" +) + +pkg_setup() { + python-any-r1_pkg_setup + java-pkg-2_pkg_setup +} + +src_unpack() { + unpack "${P}.tar.gz" + mkdir -p "${S}/__deps/mklfpk/" "${S}/__deps/mklgpufpk/lnx" || die + cd "${S}/__deps/mklfpk/" || die + unpack "mklfpk_lnx_${MKLFPK_VER}.tgz" + cd "${S}/__deps/mklgpufpk/lnx" || die + unpack "mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz" +} + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export TBBROOT="${ESYSROOT}/usr" + export CPLUS_INCLUDE_PATH="./cpp/daal/include:${ESYSROOT}/usr/lib/llvm/intel/include" + export JAVA_HOME="${ESYSROOT}/usr/lib64/openjdk-17/" + export PATH="${JAVA_HOME}/bin:${PATH}" + export CPATH="${JAVA_HOME}/include:${JAVA_HOME}/include/linux:${CPATH}" + + default +} + +src_compile() { + emake PLAT=lnx32e COMPILER=icx daal oneapi +} + +src_install() { + einstalldocs + cd __release_lnx_icx/daal/latest || die + docinto examples + dodoc -r examples/* + docinto samples + dodoc -r samples/* + doheader -r include/* + dolib.so lib/intel64/*.so* + dolib.a lib/intel64/*.a* + insinto /usr/share/pkgconfig + doins -r lib/pkgconfig/* + java-pkg_dojar lib/*.jar +} diff --git a/sci-libs/oneMKL/Manifest b/sci-libs/oneMKL/Manifest new file mode 100644 index 000000000..9999712a5 --- /dev/null +++ b/sci-libs/oneMKL/Manifest @@ -0,0 +1,2 @@ +DIST oneMKL-0.2_p20221201.tar.gz 958514 BLAKE2B 14fe7ca0095440f90ae74f9480be1693677c405071d123b10044d3ce09c7e2f8cb42f262ecfe617ba7d68efdf506ccd6aa31c52e376ff3bd1789f4923597b2b5 SHA512 e474f3d37aa58978aba417073f466507c91e428477c7a4b6f52206584e4ba6c307df7157b5b6e6e9b82e8bd1d9b6537eebef569fe8170cf053f6d1d87d2c1176 +DIST oneMKL-0.2_p20230221.tar.gz 983270 BLAKE2B 73f399301989938c78620dfd833cc895050e253d5880d4b7b6a416438179ac3299278f7dfef8198ba81aa55c33e95bb37d62c523345aa5d876177ca482cbaab7 SHA512 b502b0511613927e74e0d40186c0d91864f12bd23880eb029876a30b89cf1d495f0af9bfefe0278ee102b6d0bb7f698b50a3280ad53b33a9ebce32ec5ce84e85 diff --git a/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch b/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch new file mode 100644 index 000000000..2c2fc1367 --- /dev/null +++ b/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch @@ -0,0 +1,22 @@ +diff --git a/cmake/FindLAPACKE.cmake b/cmake/FindLAPACKE.cmake +index 42a5b7d..080108a 100644 +--- a/cmake/FindLAPACKE.cmake ++++ b/cmake/FindLAPACKE.cmake +@@ -19,13 +19,13 @@ + + include_guard() + +-find_library(LAPACKE64_file NAMES lapacke64.dll.lib lapacke64.lib lapacke64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(LAPACKE64_file NAMES lapacke64.dll.lib lapacke64.lib lapacke HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS LAPACKE64_file) +-find_library(LAPACK64_file NAMES lapack64.dll.lib lapack64.lib lapack64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(LAPACK64_file NAMES lapack64.dll.lib lapack64.lib lapack HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS LAPACK64_file) +-find_library(CBLAS64_file NAMES cblas64.dll.lib cblas64.lib cblas64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(CBLAS64_file NAMES cblas64.dll.lib cblas64.lib cblas HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS CBLAS64_file) +-find_library(BLAS64_file NAMES blas64.dll.lib blas64.lib blas64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(BLAS64_file NAMES blas64.dll.lib blas64.lib blas HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS BLAS64_file) + + get_filename_component(LAPACKE64_LIB_DIR ${LAPACKE64_file} DIRECTORY) diff --git a/sci-libs/oneMKL/metadata.xml b/sci-libs/oneMKL/metadata.xml new file mode 100644 index 000000000..77e2dd702 --- /dev/null +++ b/sci-libs/oneMKL/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">oneapi-src/oneMKL</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild b/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild new file mode 100644 index 000000000..35d773397 --- /dev/null +++ b/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild @@ -0,0 +1,59 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +COMMIT="f4866ab2648cd7cff4a047b91be5f94ff7b73ba1" + +DESCRIPTION="oneAPI Math Kernel Library Interfaces " +HOMEPAGE="https://github.com/oneapi-src/oneMKL" +SRC_URI="https://github.com/oneapi-src/oneMKL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +# Tests don't compile properly +# RESTRICT="!test? ( test )" +RESTRICT="test" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-cpp/tbb:= + sci-libs/lapack[lapacke] + sci-libs/mkl +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-find-lapacke.patch" +) + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_CXX_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + -DCMAKE_C_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + -DMKL_ROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + -DBUILD_FUNCTIONAL_TESTS="$(usex test)" + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + # Move into the correct libdid + mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die +} diff --git a/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild b/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild new file mode 100644 index 000000000..896ed4566 --- /dev/null +++ b/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild @@ -0,0 +1,59 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +COMMIT="793c771c60f5105c12eaf59e1534eeb21d1cfe4a" + +DESCRIPTION="oneAPI Math Kernel Library Interfaces " +HOMEPAGE="https://github.com/oneapi-src/oneMKL" +SRC_URI="https://github.com/oneapi-src/oneMKL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +# Tests don't compile properly +# RESTRICT="!test? ( test )" +RESTRICT="test" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-cpp/tbb:= + sci-libs/lapack[lapacke] + sci-libs/mkl +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-0.2_p20221201-find-lapacke.patch" +) + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_CXX_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + -DCMAKE_C_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + -DMKL_ROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + -DBUILD_FUNCTIONAL_TESTS="$(usex test)" + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + # Move into the correct libdir + mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die +} diff --git a/sci-libs/pg2plplot/Manifest b/sci-libs/pg2plplot/Manifest index 762415606..7a4b1af78 100644 --- a/sci-libs/pg2plplot/Manifest +++ b/sci-libs/pg2plplot/Manifest @@ -1 +1 @@ -DIST pg2plplot-5.13.0.tar.gz 39330 BLAKE2B 45221573132f4d4556612e7d6ae280ed225a8c3e08c860a269c39c566cd36513a51ad1c9108d8bf053bf71725f72bb990e88b60f8a5792ef06191581cbdc13bb SHA512 38261e2bed8b2700c2b797a6d220a9ede0f18ddfb00260ef1eccfcdf3c7f8bef23918d659927650644e10976a4a7cb7855a01aa6da0b033dace8bb356b141345 +DIST pg2plplot-5.13.1.tar.gz 39935 BLAKE2B c233e68548652145dd845640ec54de6d7f64dc89b52b2f6794b1eb2ee3d02af6333c192c3754d69cd2655474b7fd14f03e7e8e827493e91eae03c4f6374bee2d SHA512 d594630b1154b56009ed9b8f97b2d4e9d401ce06387954eda05e04de230586965b3868fd7a257a8628e53ac1624092850bfa4ccf0e8238daecfc40c3bc6af03c diff --git a/sci-libs/pg2plplot/pg2plplot-5.13.0.ebuild b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild index 5b5373e58..123404533 100644 --- a/sci-libs/pg2plplot/pg2plplot-5.13.0.ebuild +++ b/sci-libs/pg2plplot/pg2plplot-5.13.1.ebuild @@ -1,29 +1,32 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 CMAKE_BUILD_TYPE=Release -inherit cmake fortran-2 CMAKE_MAKEFILE_GENERATOR="emake" +inherit cmake fortran-2 DESCRIPTION="Assist the transition from PGPlot to PLplot in Fortran programs" HOMEPAGE="http://pg2plplot.sourceforge.net" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="X png postscript static-libs" -DEPEND="virtual/fortran - sci-libs/plplot[fortran]" +DEPEND=" + virtual/fortran + sci-libs/plplot[fortran] +" # If USE="png" or "postscript", ensure PLplot has USE="cairo": RDEPEND="${DEPEND} - sci-libs/plplot[fortran,X?] - png? ( sci-libs/plplot[cairo] ) - postscript? ( sci-libs/plplot[cairo] )" + sci-libs/plplot[fortran,X?] + png? ( sci-libs/plplot[cairo] ) + postscript? ( sci-libs/plplot[cairo] ) +" src_configure() { local mycmakeargs=( @@ -31,5 +34,3 @@ src_configure() { ) cmake_src_configure } - -DOCS="CHANGELOG README VERSION" diff --git a/sci-libs/pybids/Manifest b/sci-libs/pybids/Manifest index 28c1b4626..fc1863ad9 100644 --- a/sci-libs/pybids/Manifest +++ b/sci-libs/pybids/Manifest @@ -1,4 +1,3 @@ DIST pybids-0.10.2.tar.gz 3013772 BLAKE2B 70255fbca7a7d5a51efa454ee20d30a9527703d6028a965b51da883aa10f8b63d180f72fd127e12b27249c3f388825a9bb2ba4604680c57f3a512ec7093c01c4 SHA512 c90b7e471d73b070e86452ca5d03639d0263e74c3c79386b52ed2c5fc49576f985bc923f2327882ee56bc4691631105c831ebe40f78aade5b9943be83909ba16 -DIST pybids-0.11.1.tar.gz 3026079 BLAKE2B 9ca7d1299a074f4b7ae51e7d6ff29a55664b6c32c85511913fb69459bd66a0c09b63dddfef2c433c5cccf47c4e358720cbd101f85e7794e22a9935bd6a36ac65 SHA512 bcc1cc3a06b6921e8336990e83e820439c217cfdce6aee3b4b93f2c1ee04acf0bf9009fa2fc80fd50cd59bd9b1a2a3ceb934589b5fd590612de386e91e4f7340 DIST pybids-0.12.4.tar.gz 3031862 BLAKE2B de9d1ba0a0eb400da1de44189f4920a8d1f003dba1c47b18e339d593c68b5a80c340a9acc5267dbfbf730a59aad004035568a1f8b0de30dbab9c211b11790fbd SHA512 1f2f3a784a1e3f0e74919c6ada2ae0365ab89315d724f0a6b6b38a0416c1e6f7e938966b2dda80f090ef2bbf84ce0bcf0bb214a652743432b1d193d9569eb7b1 DIST pybids-0.6.5.tar.gz 2915557 BLAKE2B d7765b872917bbffcd2706488d7c789976be5bbb1eb5d112cb0b7bcedb483236643f8bf7c177f4a64a44a4d50787a4df1d39fbec8e826bfffd2e2e6f891b3ef3 SHA512 9eef42f00440dddf0147d91f90e07db81f9f95a650f0e47c04304771173ca8691cdb366bd0df1d752c0444f102a4aa010c2343ba75df96528cceb9a98f9d8a0e diff --git a/sci-libs/pybids/pybids-0.10.2.ebuild b/sci-libs/pybids/pybids-0.10.2.ebuild index 062cad939..5f2776855 100644 --- a/sci-libs/pybids/pybids-0.10.2.ebuild +++ b/sci-libs/pybids/pybids-0.10.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -29,12 +29,4 @@ RDEPEND=" dev-python/scipy[${PYTHON_USEDEP}] " -#RESTRICT="test" -# Fails because fixtures are called directly -# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673 - -python_test() { - #rm bids/tests/test_config.py || die - distutils_install_for_testing - pytest -vv || die -} +distutils_enable_tests pytest diff --git a/sci-libs/pybids/pybids-0.11.1.ebuild b/sci-libs/pybids/pybids-0.11.1.ebuild deleted file mode 100644 index 062cad939..000000000 --- a/sci-libs/pybids/pybids-0.11.1.ebuild +++ /dev/null @@ -1,40 +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 package to access BIDS datasets" -HOMEPAGE="https://github.com/INCF/pybids" -SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="" -RDEPEND=" - dev-python/num2words[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/patsy[${PYTHON_USEDEP}] - dev-python/sqlalchemy[${PYTHON_USEDEP}] - sci-libs/bids-validator[${PYTHON_USEDEP}] - sci-libs/nibabel[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - " - -#RESTRICT="test" -# Fails because fixtures are called directly -# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673 - -python_test() { - #rm bids/tests/test_config.py || die - distutils_install_for_testing - pytest -vv || die -} diff --git a/sci-libs/pybids/pybids-0.12.4.ebuild b/sci-libs/pybids/pybids-0.12.4.ebuild index 40a8adc17..7860d69c9 100644 --- a/sci-libs/pybids/pybids-0.12.4.ebuild +++ b/sci-libs/pybids/pybids-0.12.4.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 @@ -16,9 +16,7 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64" -BDEPEND="dev-python/versioneer[${PYTHON_USEDEP}] - test? ( dev-python/mock[${PYTHON_USEDEP}] ) -" +BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )" RDEPEND=" dev-python/click[${PYTHON_USEDEP}] @@ -32,4 +30,4 @@ RDEPEND=" dev-python/scipy[${PYTHON_USEDEP}] " -distutils_enable_tests --install pytest +distutils_enable_tests pytest diff --git a/sci-libs/pybids/pybids-0.6.5.ebuild b/sci-libs/pybids/pybids-0.6.5.ebuild index 521ef9947..6103c3191 100644 --- a/sci-libs/pybids/pybids-0.6.5.ebuild +++ b/sci-libs/pybids/pybids-0.6.5.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-libs/pydicom/Manifest b/sci-libs/pydicom/Manifest index 90e3ca3eb..b5e5f2a75 100644 --- a/sci-libs/pydicom/Manifest +++ b/sci-libs/pydicom/Manifest @@ -1,2 +1,2 @@ -DIST pydicom-1.1.0.tar.gz 6724086 BLAKE2B efdcdd722bc877b9b9cf137ecd2a3fa6fb2b7da022bdab49f03dbcdb5a3e3dc8bc24b6b0d8eb9ab946934ec182c13ec1df671461c357476f543afb6f435f604c SHA512 ffca9eb4333d29accea1d6e5a5b4c3c0bd0f8c12fdf00c5c84d83769db621e8f348c9200dff1dc1cd6016cbf5d76b00f08c3b112ba653433a84ce31ad1ab33d5 -DIST pydicom-1.4.2.tar.gz 35237997 BLAKE2B 0b4db847150153519cc7d805a9a7b9c5c4d9ed46496bd561a24e5ede1cd3b5f176581a9741aba65c31cdd0533fb6a33905cc21003f0237c7cd7e603ef672c67a SHA512 8fc0a2e5f0a8578b98d49b749912cca98d51bdcae2b3bd5759e03e13cd2a2d4f45ce0e2a22d80526abfa5f428a4a71b5fad2c9f36bafc4f3fa2866cd687ac015 +DIST pydicom-2.2.2.tar.gz 2149674 BLAKE2B d109975c6ac0081a02c534bb014040ca767968d276fb841a0000ab4f7b4884ab604276b7092f8cc699d24d0429426cf5be3225ae56b8b8ebdad89cf541ab065a SHA512 5f1829d445c462884debb75328f59471dea4da51701835a3a97a1c22c1c0b75730e0688558cb76ef3f7a4b29f350028190a515d73f88968a7fda09ed414ec145 +DIST pydicom-2.3.1.tar.gz 2164956 BLAKE2B ffdf14c582a7a783ae963008de9d8d9dd54c6d6889f10ebb767ff87abf00ab36406ea3dbab50304bcf1902af745b871b9dc1702d8824fb9ed163d1d909e88ac5 SHA512 bf2856b8afa13f6477a37abdc7d723337f532746705832b0eb01cfcf468f318ec4b74af5aade3b8629d050947a87e87fb39aca965ff98d0a348170a900d7dd57 diff --git a/sci-libs/pydicom/pydicom-1.4.2.ebuild b/sci-libs/pydicom/pydicom-2.2.2.ebuild index f02b71a97..69cbed0c7 100644 --- a/sci-libs/pydicom/pydicom-1.4.2.ebuild +++ b/sci-libs/pydicom/pydicom-2.2.2.ebuild @@ -1,22 +1,24 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="http://www.pydicom.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://pydicom.github.io/pydicom/dev/" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="test" -RESTRICT="!test? ( test )" +# Reported upstream: +# https://github.com/pydicom/pydicom/issues/1800 +RESTRICT="test" DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" diff --git a/sci-libs/pydicom/pydicom-1.1.0.ebuild b/sci-libs/pydicom/pydicom-2.3.1.ebuild index 523da2654..69cbed0c7 100644 --- a/sci-libs/pydicom/pydicom-1.1.0.ebuild +++ b/sci-libs/pydicom/pydicom-2.3.1.ebuild @@ -1,27 +1,28 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="http://www.pydicom.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://pydicom.github.io/pydicom/dev/" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="test" -# Upstream bug: https://github.com/pydicom/pydicom/issues/663 +# Reported upstream: +# https://github.com/pydicom/pydicom/issues/1800 RESTRICT="test" DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" python_test() { distutils-r1_install_for_testing - py.test --cov=pydicom -r sx --pyargs pydicom --verbose || die + py.test -r sx --pyargs pydicom --verbose || die } diff --git a/sci-libs/pytorch/Manifest b/sci-libs/pytorch/Manifest deleted file mode 100644 index 65e5fc7a8..000000000 --- a/sci-libs/pytorch/Manifest +++ /dev/null @@ -1,81 +0,0 @@ -DIST FP16-4dfe081c.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e -DIST FP16-4dfe081cf.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e 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NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz 219318 BLAKE2B 6b6619c8a706ef9630f20fda1e276314b2ef7f6c9aed26836a48bdaa0ae198a86383e68b04c651f37c07d34e400bc54b5daa75b06fc18cdb0a9c55e2cb33bbe1 SHA512 f0b261e8698b412d12dd739e5d0cf71c284965ae28da735ae22814a004358ba3ecaea6cd26fa17b594c0245966b7dd2561c1e05c6cbf0592fd7b85ea0f21eb37 -DIST PeachPy-07d8fde8.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa -DIST PeachPy-07d8fde8a.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa -DIST PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa -DIST QNNPACK-7d2a4e99.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127 -DIST QNNPACK-7d2a4e993.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127 -DIST QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127 -DIST XNNPACK-1b354636.tar.gz 1353346 BLAKE2B ce286e1a1f14aa195baffa48ef8c21c4ae0ec85ae89169a429fc06077e34f28302930e081cf464dbe78252bb065a247b65b61d8aa3872375043176d150f97651 SHA512 9e7528334a8e3df18a54fce44a122fb6d989a946bb456b01f81772f160bd6532fad460e787c976bbdd76ebaa78cd1c64329ffeb498c5d27e1cd53195bb8a9db4 -DIST XNNPACK-1b354636b.tar.gz 1353346 BLAKE2B ce286e1a1f14aa195baffa48ef8c21c4ae0ec85ae89169a429fc06077e34f28302930e081cf464dbe78252bb065a247b65b61d8aa3872375043176d150f97651 SHA512 9e7528334a8e3df18a54fce44a122fb6d989a946bb456b01f81772f160bd6532fad460e787c976bbdd76ebaa78cd1c64329ffeb498c5d27e1cd53195bb8a9db4 -DIST XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz 3955905 BLAKE2B d787d4a965c53c8d65887f3b111da950f3b5558cd28ce468764c5bf8efbaddeea567803cfcd89a1aab4a0bc781816871dcca2901e762257aaf96a1d8f868ffd2 SHA512 72c3e53b00d77cfd94db93c60276ca7fd419554dadddf74286e85e0500dbdad0bf65694e451e832de89ea17e7731a9ec9e9f1d831b03c1b81946e0dacb96197d -DIST asmjit-9057aa30.tar.gz 534633 BLAKE2B faec98981c67110294e4135a9cb7f47b038d44a02483728a4c79c7094da62b8a6a1c805eba69f1258a99b24b699823f02516c50d166a96eb5ff65227406f402e SHA512 678e5ce4a8d96961be4c10aac67d43aa8949ff022dce855a92cf6d626738be8667668c48953d43b6ef21ad7c5f913d07f7f692ad719870700aa97deb80662baf -DIST benchmark-505be96a.tar.gz 129647 BLAKE2B d9f435f464fa1db18b86258947b8c5077b8b20b9c26ca00aeeca79da604f299f776673c374b7d0db10a5d40cbc84774642b29e756a83f02cda5d085280387346 SHA512 2ec79b66c31d4741b214c04f7865cf0139b4c0b14a8fb2a70bf332cf90e73821282b510719689bc2fe59542ee51c87e9f9b49a47b6a67cad897f7f906f0b05e9 -DIST benchmark-505be96ab.tar.gz 129647 BLAKE2B d9f435f464fa1db18b86258947b8c5077b8b20b9c26ca00aeeca79da604f299f776673c374b7d0db10a5d40cbc84774642b29e756a83f02cda5d085280387346 SHA512 2ec79b66c31d4741b214c04f7865cf0139b4c0b14a8fb2a70bf332cf90e73821282b510719689bc2fe59542ee51c87e9f9b49a47b6a67cad897f7f906f0b05e9 -DIST benchmark-5b7683f4.tar.gz 102332 BLAKE2B a7210a2c7a173a9df8bf03b83fc9712d5b52ded13c932e4d13a93004b93ad816895b722acc941b1d94c6b403e4ccb846141f5a38f42baafc5fb3cb108c039559 SHA512 a4e69ee8ec824e418abd713cb3597175cd40ecee9bc539e2d3592f9ec0f8ee54e7466984874f410b78beee82b4c396a7f2824880f808c4217704cf9970411ebf -DIST benchmark-e776aa02.tar.gz 126890 BLAKE2B 389a4fc0bfedc20227de31d4b1447b8370300a8e3cbea8a8d4b1c82ee90757c2a035ea0324e762217f5a6279a4277f431b7e511d8a9a3bcf226fe31c0022b83c SHA512 d9f70c617af75683dfcf5a0d7ff14b3374258bcf869e3b69b23e85c980366cc4f9859fef3d3dd84a2a92933729053eb02663eaf4bbe0a020a2e001f42b85230d -DIST benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz 176771 BLAKE2B 22280c0777635d57574852e6e3ad276683d582eed9b17ef93f09f6a5560dc3d06bbabdead9cfc72f5059570436515855a841118c47f23c3793e1b83e368cc75b SHA512 aa4455fa0f8546ec5762f14065e0be6667b5874e6991ca6dd21dc7b29e38c7c74cfddb2c99c7a1ed2f7636aa7bdec8fc0fc1523967b179f5642c2dc2e968089c -DIST cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz 3496223 BLAKE2B 4da452faf12138fbc1abd266d8ae6e0a0192f48a84faccb55fd05c3ac85d0bea2ecbd80b5eda69bb51c6704a223f90dd83d1f0fc79d56d35dd21cae5c5b8fab5 SHA512 50e537b61d991e8579577fb1ecf8d9ceb2171dbad96dfe159a062eadfdc0b2372b94988fc6f223c20e327453c7f55042ee06779f5b5fe0922f4470f746c9686b -DIST cpuinfo-63b25457.tar.gz 3495405 BLAKE2B bb7cefa2bfe6e44134c52b8ba8048a84f0063623e566e89dd92ed6ff5e383a150c554a45b66ee5c4ba6d1544de948ac978ab6e53101399d4768bace20110b4e6 SHA512 44f4a55eea9c0d707818dedfec26f007c2bc2271c7bf9375e6e30171384fb0fa2e1d5731cb946570c717e6d88e6b1496d498e6e55dbf37d66174a4c675a3a006 -DIST cpuinfo-63b254577.tar.gz 3495405 BLAKE2B bb7cefa2bfe6e44134c52b8ba8048a84f0063623e566e89dd92ed6ff5e383a150c554a45b66ee5c4ba6d1544de948ac978ab6e53101399d4768bace20110b4e6 SHA512 44f4a55eea9c0d707818dedfec26f007c2bc2271c7bf9375e6e30171384fb0fa2e1d5731cb946570c717e6d88e6b1496d498e6e55dbf37d66174a4c675a3a006 -DIST cpuinfo-d5e37adf.tar.gz 3489028 BLAKE2B aa6b7719eb9871b6cc71318cb4a9c2e2397e665662b7978daecd9e8380304691a78b95118eba5cbbb738c4b490352a847f6ce6b5c4ae29de0543b95ecc557cbb SHA512 ecd2115340fa82a67db7889ce286c3070d5ab9c30b02372b08aac893e90ccebc65c6b3e66aa02a9ae9c57892d2d8c3b77cb836e5fc3b88df2c75d33e574d90d2 -DIST cub-d106ddb9.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835 -DIST cub-d106ddb99.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835 -DIST cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835 -DIST fbgemm-1d710393.tar.gz 259645 BLAKE2B 7b159c67ee66679985758f59b001aea02f141e2a36af2dd12731bd260ba5a5834a2a5eefd9b8b43454a0d4c75df929fa302e7ba0e5210ee67c150b405d3b4cac SHA512 19bbc9ed274bced7b8453d9ec4f43bb998725764aeeee72782abff36fc77e9ef918396f5c462da7b448e9a3bb7a834f143cfdf6777ef0cdddada63bc2bf98761 -DIST fbgemm-7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz 444575 BLAKE2B 97c0672119eee2e0a770445fbc7d3fad8d91d86d7a860f75e20b0a9b8dabae555b324f12d63092463eb1882ccb9d587e73cbb34013acaa3a76f015f093792e9f SHA512 b4cb8964e84dbe4065d7b9292c5877305a43b7dc21e896e3d20d3082c208eca2afe2348face8ce2236256e436c611d6adf9c9f729ef07b2ae9f939e25ec21e00 -DIST fbgemm-87c378172.tar.gz 244850 BLAKE2B 322d892cc34921c9ffd7b9faf67804f3cfc3a427281e12afeeca4af3df37a8aa47198695e28e33feb836605d29925f566a4a290206ce6209478af87883561564 SHA512 42e678560dc774694ed6e2eb7d62a0284532be9c206aa1e056810e00bb7c06d557541e0ce56446735e163d480b504854e45cce9d7f23368974c500ecfe6e9961 -DIST fmt-9bdd1596c.tar.gz 733867 BLAKE2B b5c62ea43bfd99268dd120d5a09eb5f80bc29411268367e63bdf7034aeb98c9aed00da019ad6e259922adbb849b4484353142e9d3449a256909e72f4a50ddee4 SHA512 3639b4984a88fc5495c6cb1a0a09bb0a13f5dc05286f5a2b15e60dfda780bcc1fe213497006cc27247c3c358be27d8af4dd995db2b3de0f6a5a1288dc1058585 -DIST fmt-cd4af11e.tar.gz 740467 BLAKE2B da998415363b8205cb3be5c677ff8c3ea4aa5636741a5cfe45d7b6e54c1f6d0a36696158e2e21f37978323a11150e01efb2793de6a42af4ed19aac52381e0afc SHA512 24b42288be97849533dc82282fc08833d74642ad2afeb511e65c6389d88c709cf25345dec5b550c18af3705f4c0847fa0d4066308b51cd41ccfdda1a2c3babd0 -DIST fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz 740467 BLAKE2B da998415363b8205cb3be5c677ff8c3ea4aa5636741a5cfe45d7b6e54c1f6d0a36696158e2e21f37978323a11150e01efb2793de6a42af4ed19aac52381e0afc SHA512 24b42288be97849533dc82282fc08833d74642ad2afeb511e65c6389d88c709cf25345dec5b550c18af3705f4c0847fa0d4066308b51cd41ccfdda1a2c3babd0 -DIST foxi-4aba696e.tar.gz 28740 BLAKE2B 54b2eb9610f402b89ed64b0f487326a58c8ecf9a195d0081329e4b55cc531bca45065f10176ba29ff7cc18b29c89ba7f0aa5046c35a78c562986e8dab40451e8 SHA512 6aec53e9489f87fab6ef70ddef20854f551ccc54368800f7c465c73858f13fd6db8f031fb6db43c9e26c1fd13d65389501d1db97148afc518277f4f95a5367d6 -DIST foxi-8015abb72.tar.gz 28571 BLAKE2B d64b00bb81e43a9b1f55f640ab6e6845d33e01520daf7e1b56cd6ef3f82b38c5c8d6cb5c54d55302524f46a6ca2fbc43ef1aa3ee0fba563a8de502a8c4720175 SHA512 94c8c25d90273941161e04bedee521d3f7bbb296c125083e1d3c1421210b18758917d95c95bbd213c8eb19ad36f4e088c943816505e7fc462aecf12e00ebd2f6 -DIST foxi-c278588e34e535f0bb8f00df3880d26928038cad.tar.gz 28960 BLAKE2B 06c960f829b090eec4fe9e8c981e119578f358724e0b63991173bb7e318d23654261b901d1e15efeb6240bba75cc05fd45ab32fb30bbdf48369e139cf152f398 SHA512 ad42cfd70e40ba0f0a9187b34ae9e3bd361c8c0038669f4c1591c4f7421d12ad93f76f42b33c2575eea1a3ddb3ff781da2895cdc636df5b60422598f450203c7 -DIST gemmlowp-3fb5c176.tar.gz 826382 BLAKE2B c5e68cb78429fe8ce96c752270e747382287937d0a0c1af26b444eda495a78438193c54900cd7906b34b369e170d582c5599f541d23d1280e38f972d6daea1ea SHA512 1c97bba41931c7fddf0e7c01312892cfa3d87abe2a4cdaf4cd20d846a102c5ad3d85329ccdb386f7047f2f037e92639cbcf91b317c2bf38bee11c12e71584afc -DIST gemmlowp-3fb5c176c.tar.gz 826382 BLAKE2B c5e68cb78429fe8ce96c752270e747382287937d0a0c1af26b444eda495a78438193c54900cd7906b34b369e170d582c5599f541d23d1280e38f972d6daea1ea SHA512 1c97bba41931c7fddf0e7c01312892cfa3d87abe2a4cdaf4cd20d846a102c5ad3d85329ccdb386f7047f2f037e92639cbcf91b317c2bf38bee11c12e71584afc -DIST gloo-3d08580f9.tar.gz 227739 BLAKE2B 3b011cc8ae08da36a917860dd58b87bc5b08c7189926b2f5bfaf839a9d53c5e7dee881e836f659e90269149eba6d80807e3a8e450b31f71220ba442ab59a389a SHA512 3dee533b350862cabce410f054fd943b4524b60394da1e92b9c73830e143b9abd30e5a493fe0c064d6fee8c15bd09b12620f0b528122170df329548c57116bd1 -DIST gloo-3dc0328f.tar.gz 231048 BLAKE2B aa06ea3ca8c522652a405c0b56662bc5bd0eba5ef38770aaa2a078a8fd19fd1eeaa2e1007e537e584c5b07a84abe991c810f2a9c73e5b8df820dacde703bb81a SHA512 a6401f4b5e91130a7880a6742c075fdeb94026c3a04a57ce59b6dabc78b44d2f5e93803b3a7289e0c116bde4366536bb55f6dfd91a9a0d8af9640a81e3e4fe7b -DIST gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz 247789 BLAKE2B a8b72ee81c47d6b52559a5a7dc7a74dec56747c2fa46437fc9b3be9535b2ac577031a235c1a2cc7029c840a1ad28e58d2e91d7db820af3c0ce474e2a3ebea8a8 SHA512 1aa7bd5511a55ecb7a318cafa6ae1bde94d7cbc4d1483727e3b07c86a4c6e32864aa740d5a58a452d7cb7f37d84a928fa740f1fdb73e3309061d88b018083c56 -DIST googletest-0fc5466d.tar.gz 993626 BLAKE2B f80e5d7e92c665a964add6370b6420ac00b0309768d21d52ce74e87b548293e05271456c63d171eb36389c601febc3514ea81d991145b1921e27f38e5fc0e084 SHA512 ac57b52454c027d4c14b0ca339ff4b5d36b66da38c7420164c44c11c214b617c79cf690b74b6f2f233b5df5dff200d97afa40c9b814f8b6117cd3d9e382a20c5 -DIST googletest-2fe3bd99.tar.gz 993527 BLAKE2B fa631eadc310607dbe19cec6d66d8fb1c5e99e2dfc5031fff26f8c12c951d7798ad2062edf21589020cafc821bfe4b5e89310ee4e85f45d7d7fcd435ddd5eef9 SHA512 130182d2c1067bcd263fb27999c164d240f5d06d837475e71e7cadbf65c7211de00154dc1e15deae0b6ec2963799e55c0c21ee971e1c588064c5063e69a2bf1e -DIST googletest-2fe3bd994.tar.gz 993527 BLAKE2B fa631eadc310607dbe19cec6d66d8fb1c5e99e2dfc5031fff26f8c12c951d7798ad2062edf21589020cafc821bfe4b5e89310ee4e85f45d7d7fcd435ddd5eef9 SHA512 130182d2c1067bcd263fb27999c164d240f5d06d837475e71e7cadbf65c7211de00154dc1e15deae0b6ec2963799e55c0c21ee971e1c588064c5063e69a2bf1e -DIST googletest-5ec7f0c4.tar.gz 961649 BLAKE2B 2c518a4006e7a9decff3d4b81c30a910c01f6bf2a71593da25f6e74d5117cbf56de486078a3caf6be255df473fc1c2a04de5317cf882396114be0625d67d041b SHA512 623b077b3334958fafcbc34aa85891883277994af33be530efd903f47738a3e3562001cbf3b6da1a5e7d03803c5bd51bcc1fab81490db85d5a4f2b15e7de1495 -DIST googletest-e2239ee6043f73722e7aa812a459f54a28552929.tar.gz 887296 BLAKE2B 8f29b7028a6dd8190a113cd93398705b23b61d88bee38beaf9dcc0dfc8a463aed7fcd3719f6f1b131d4363aa57231629aaeffa108f6558efb58416cfface6d6e SHA512 cf9e7f3fd3e31ce6677eac355fb8bfe19c5b56a8ec3af8b9417d0904cdf5da92f99f7411a08131cc9fa4fc7d38e6a71fcfac993648e47b269a74a27de7607f7a -DIST ideep-938cc6889.tar.gz 27315 BLAKE2B 967bff56175d6f6b6e9895ef8e7ecf22f2bcbc4aa33074654b8c527165beb280e70c1b39da37ae2cd432eaa8d0ec600b83282d86faac05e17319dbd647f22107 SHA512 24a3f0b35756e3892af99658f7de7d17dff369601ffa7d39a6e2c3609c9c667f341cc66b6664fb69c4d938a1f7b3454e7106b8e27ec9995be5ad2d541927e2e1 -DIST ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz 30949 BLAKE2B 07028f6544e5e088c01b111e89defd02eed022663536c4b1fe582e3b8da65a383aeb75e191f433e4cf497236630dcc531fa16a2758cd9be6db504c6b04f2a9b0 SHA512 0b51c41124ed033fd608b1ae7a6de3ebbb5c8b96c53cea594966178b5e0bd38d8b1b2773c4ba5e8f7b2f4af6d6ce1aef8fcb84bbe05780822976644d0e79b20f -DIST ideep-ba885200.tar.gz 27307 BLAKE2B 710dde31a8784315c88df9869e50c3940416263958ab653bce9876d60786906565b12f36c2d716a8a1f6009bc9e532e06733ddfac0d4079dba13ea153b8acbd9 SHA512 0c1bca04adbe797e5767f8b86fb3b247a2a287ffa2b3b19a918f976312175b459a6488166d12cf55e68c9aced84038fcda0d1d1c51a5034c83f844f51d462727 -DIST kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz 7245955 BLAKE2B 09e6b1b1e15c485bbcc20713d07dab42fcc1b075557b6f202089696944b379d9fb3a860f68c16946b6f3eb76b12cf52a7fbc99a14af1baa40fb09b3f6d295c4e SHA512 6c479c3a14887c0703843416a961b6c92169caada029683a1d6d8463b4001a5bf8606dcd480df509c0f1fe53206001ab7428c9352fa638acc581523f55687e2b -DIST libnop-aa95422e.tar.gz 124202 BLAKE2B 5a74ecbf473dba09db1a11172a4aa432d81b14adb3826bef9aa8bae1bf1e2d0d5a7bf775fd4343fa9d7b235b17cafe949e47c903e92fd5eae9cc0717a552ea45 SHA512 62b21be874d2117294925c2497394d166da43d534776764c9c124699b5799d99790a2c6420804f8e143e1a18a536106852082f3a9d0052a726abc624fc19f937 -DIST libuv-02a9e1be.tar.gz 1250418 BLAKE2B 49d7c6161614218bf856f7e23cd3e483bf1ac682bdc78b9624b9b5b52edde31aae005638bbc01e89f01421097e0bd4e07893db464326741ca6d1abaf45e633fe SHA512 de6d5d014b61804884a3945f2992f4aecf642fdd330927aa9a3bc17b76c29c51f6615d3d04542b24bb9ccdfd5207155e282f2fcd3aac14233d5bde4b1bc30284 -DIST mkl-dnn-5ef631a0.tar.gz 5799312 BLAKE2B ea2aafcf45adadb0546781b00b44a0e9712c28e4937ef4daeef8b910e76bbb152e5434e45bec2aae0f6cb86fd7b5098e61842d7e99258db6fa846a79996d2e23 SHA512 66df9ea574010616df46d85ef25d23bd9ed31f9719cdbec4c727de58728fe095cd412d7663c2d456dba2f26848e45c1d67e34bffe4e25beeef9c1d40f187e8d6 -DIST nccl-033d7995.tar.gz 146624 BLAKE2B b6f15d5d4690a5cbcf882c10826def400a14c58ff5f5af276b5b9a615a567de36ca907120cc681cdf2f2eb207f22bc87ee87d145a365097a64fb3d9de82432fb SHA512 3b3e087cb729b10e3251dfef52196bddd33e3e777df289c5fc537e99473e78f8720255fbd3e14ae2d2a6126d1e9d59aa6d57d7c7958d919e65834fef92c1c835 -DIST nccl-5949d96f3.tar.gz 147548 BLAKE2B f3d3dd222ae90ac9ac1457a9695f112a21f5652a5b40e10ac049da910f07707b1c3910f59734fbe5e2c6523c1e83f3801f809efa77d122a57e859828c74ba8c2 SHA512 d9ea83caf7940fb47134293236fcb7478c0d4e40365d3b0a29427758e2e2dbb980c5e8c05fc9fc3956ed5e21a82ec0efaa31d973fe9c73fa3f50465f76756131 -DIST onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz 9332964 BLAKE2B 20858ed93a7e2064624f13bb345ad7ad699ddc8c5e9ce9af27ae49d14bd7db9a0d9ff463919dd0c840595916ac7a720344608c586e87b522d5e2b78fde42eb6a SHA512 bcc1edbc4ce29b1c3c9f1ac4854f13d547d9efa6b712ddb5afb3d84637687aba1dbb2224ac4278a2b2e677ee485397c432554e7f02d51333c57a1ed7e0909d32 -DIST onnx-765f5ee8.tar.gz 2379139 BLAKE2B 3e3299e2f3c1184937820b137d5fb492abe216ae3a054f4a17c6cb037168f4a77d8c90db0ba657ba9c9f7af2099f71ae0b8658a573c9f2f6d29fbc9d5f0f1b8a SHA512 7e10717546d1ed0bab780768e907f957294bfda47748b4c7576b75a761f5e006fdd21f0b014ce6d761a0ac6ae59dd8bc71592785b67167a6b3692d1a56dbbda9 -DIST onnx-a82c6a70.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2 -DIST onnx-a82c6a701.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2 -DIST onnx-tensorrt-c1532114.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5 -DIST onnx-tensorrt-c15321141.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5 -DIST onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5 -DIST psimd-072586a7.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94 -DIST psimd-072586a71.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94 -DIST psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94 -DIST pthreadpool-029c8862.tar.gz 45970 BLAKE2B 09bd7d258f45fbe703238826b7435d8a5d013700cd734282b646420ba0854c0a386712f6bc3ed44e7496d51471b1e0a965f01ebdb09786e2020d979ecddb767a SHA512 b51099fa9d62065883cc43dcd5f9717a17be5ee2e87fc861667172a09acb3a62929c8bbc8a5c0c00885a638af0ec2ae4149adde2ba85bf3c80834f9b973c2d5b -DIST pthreadpool-029c88620.tar.gz 45970 BLAKE2B 09bd7d258f45fbe703238826b7435d8a5d013700cd734282b646420ba0854c0a386712f6bc3ed44e7496d51471b1e0a965f01ebdb09786e2020d979ecddb767a SHA512 b51099fa9d62065883cc43dcd5f9717a17be5ee2e87fc861667172a09acb3a62929c8bbc8a5c0c00885a638af0ec2ae4149adde2ba85bf3c80834f9b973c2d5b -DIST pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz 49011 BLAKE2B 7bfbca81321243e64aa53c668dfe380ce4f7b88477a1c794a4dea9062c9b0969ca745dbfe0abbb95fffbf44080763506609c387ed085d89f6c612be6804b5cc2 SHA512 5f5a1275bbcef13cea88e381010bf2654c9646d30c5fb061f1d6e9e9a0ae6398e137c5e4f7da69f7d8d8b58fb5a7e79f7a4c0c1c3bbaad8f3d0c896d21bc7691 -DIST pytorch-1.6.0.tar.gz 11376568 BLAKE2B 30aac34e14837ed6942ef7577aea77752cd9c809cb751fa837693b2b60eeda9a371421c4b4678fe94763a47e434b65ea60afc56aec7863887ba12bf362b96f0a SHA512 117ff1588ed1ebd0df15fbed066c65ea026893fe9a40d14aa1f73d848fab114b1b11bd7ed083815030f7fdf13a824480521cb40865f48a24c7028f4d195f2127 -DIST pytorch-1.7.1.tar.gz 13012087 BLAKE2B ff498814178281ca59ae80bfe51dde3ffb0cde1eaa762bd9b36c2ff7f07d4b5ae4d68e10c76158e5e9e4250fcb01265a3755575b761495e20cf677e9a9825454 SHA512 359e271093e7afd374202f48e40356d195f644f78377a0b88f38627ad7aeabb9201a18c12ff35fb4aaf0d731168e511504445d8b4c08e92eed50264e23d81bae -DIST pytorch-1.9.0.tar.gz 16772380 BLAKE2B 16f369cf2752082ab07fa0e497aaff7b90daf94cf39cce533c4a8b06a9237710089af0c137e29fbc79b4cf72d8d47681408e9ada1692431b573d90a07c373f1e SHA512 389ff114367a4337ab6e68178184f04751e4641fac685923afa019093951fa3a446f5265f6661f3aaad99c733c0107391431896c6e876796b8837f5ae75edd99 -DIST sleef-7f523de6.tar.gz 1174007 BLAKE2B 58ebdddea912c841a4d917111d81051860631e93abbed43fb9899eff9370181f9227419e87872799a650e6a50cf174d0bf3b90c699a0e0763e903976baf95c9c SHA512 d83b24c34e83b36314344d5b31f1c3b673e38b44bc2d2bbbfdaf2019c3f0e73a83f2d13c6d745ca99d1532c1a3e0fcb4a71bd212e423bec03d610af5dd49e3f3 -DIST sleef-7f523de65.tar.gz 1174007 BLAKE2B 58ebdddea912c841a4d917111d81051860631e93abbed43fb9899eff9370181f9227419e87872799a650e6a50cf174d0bf3b90c699a0e0763e903976baf95c9c SHA512 d83b24c34e83b36314344d5b31f1c3b673e38b44bc2d2bbbfdaf2019c3f0e73a83f2d13c6d745ca99d1532c1a3e0fcb4a71bd212e423bec03d610af5dd49e3f3 -DIST sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz 1642070 BLAKE2B 366fa96e35f429199e8462c63bc9cfbd1888aa65170d3203a5b0391fb855c29241eb225f847e416650e6ed5544f17a745c5a43a622a2847416ad7bd207572840 SHA512 13ea28745e796f8b77a40c99f679e0955e213128fb05d17b61cdcef102b7a758cbda04def3544767a81ddf170b7800f168d25fb1b55093614c7126456765cbea -DIST tensorpipe-3b8089c9c.tar.gz 141980 BLAKE2B 6c2a1e630412e9f8e039d5c44aaed4623f51516d59ee4237b9ec95d5b30970dbf4961aca0d84f1fee621ab8b8f668f0e8dbfbe558614d5651a00d9be21259a88 SHA512 1e9473532b11c23ec7dd9fdb148c0440263ae41f42a7826a4f7e098ed2a7e0c99d5e9df344b310e17098c3d70749a38d20d8af992c4820bebdbd5078d1a20dcc -DIST tensorpipe-95ff9319.tar.gz 155511 BLAKE2B bc074efe7501fd29fbff177c2782d4be1d514c8f2f5c9fe0fcdcbd0ca3a33bb91cab8fc95e8e5dac1bc4f65d904d0beef3d30f001eab9884b0506edbbee774fd SHA512 5ef38f10c65c49b3feea964c45564196005ebf47b365ed0cf60916215bac4fa04525ec9de007342fe520206b8e8663c0264fd838e89073a752d308418a2b1dd6 -DIST tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz 253518 BLAKE2B fcef24208f97c1a96a3b0d30a76c3956de4383823c908982bcf1ef7fdacd14f6ada6fa3b797d3b6c9bd3dea3d1dd4bfc6f7b2136057a385ab42b2909cd1beee3 SHA512 734e919df485b590ff3bc022b53bbe8aeda1c2178ab8c6938e9fb6d977b48d4fa9a395f65f3727f602d0b25d0a7d419ad9ea96566b644b83073291ae40c54856 diff --git a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch b/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch deleted file mode 100644 index de9fe9a0d..000000000 --- a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch +++ /dev/null @@ -1,30 +0,0 @@ -From e5003b88ad3a504eb04c0ba66c2f439149de2ee3 Mon Sep 17 00:00:00 2001 -From: Alexey Chernov <4ernov@gmail.com> -Date: Tue, 5 Nov 2019 00:58:17 +0300 -Subject: [PATCH 2/7] Don't build `libtorch` again for PyTorch - -If starting with building of `libtorch` using CMake, -don't build it again for the sake of running `setup.py` -to build Python version (PyTorch). ---- - setup.py | 7 ------- - 1 file changed, 7 deletions(-) - -Index: pytorch-1.4.0_p0/setup.py -=================================================================== ---- pytorch-1.4.0_p0.orig/setup.py -+++ pytorch-1.4.0_p0/setup.py -@@ -303,13 +303,6 @@ def build_deps(): - check_pydep('yaml', 'pyyaml') - check_pydep('typing', 'typing') - -- build_caffe2(version=version, -- cmake_python_library=cmake_python_library, -- build_python=True, -- rerun_cmake=RERUN_CMAKE, -- cmake_only=CMAKE_ONLY, -- cmake=cmake) -- - version_path = os.path.join(cwd, 'torch', 'version.py') - with open(version_path, 'w') as f: - f.write("__version__ = '{}'\n".format(version)) diff --git a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch b/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch deleted file mode 100644 index 16d2c1f2e..000000000 --- a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/setup.py b/setup.py -index 2db381644c..2241a33015 100644 ---- a/setup.py -+++ b/setup.py -@@ -307,13 +307,6 @@ def build_deps(): - check_pydep('yaml', 'pyyaml') - check_pydep('typing', 'typing') - -- build_caffe2(version=version, -- cmake_python_library=cmake_python_library, -- build_python=True, -- rerun_cmake=RERUN_CMAKE, -- cmake_only=CMAKE_ONLY, -- cmake=cmake) -- - if CMAKE_ONLY: - report('Finished running cmake. Run "ccmake build" or ' - '"cmake-gui build" to adjust build options and ' diff --git a/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch b/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch deleted file mode 100644 index f71ba17bc..000000000 --- a/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch +++ /dev/null @@ -1,46 +0,0 @@ -From dbb0bac77986016217cdfe779499a2ccd0e10570 Mon Sep 17 00:00:00 2001 -From: Alexey Chernov <4ernov@gmail.com> -Date: Wed, 6 Nov 2019 00:16:24 +0300 -Subject: [PATCH 3/4] Change path to `caffe2` build dir made by `libtorch` - -Setup and use properly `caffe2` build dir made while -`libtorch` building with CMake, so that it was used -by the Python installation. ---- - setup.py | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/setup.py b/setup.py -index f4bfdc99cd..60502b6add 100644 ---- a/setup.py -+++ b/setup.py -@@ -236,7 +236,7 @@ else: - cwd = os.path.dirname(os.path.abspath(__file__)) - lib_path = os.path.join(cwd, "torch", "lib") - third_party_path = os.path.join(cwd, "third_party") --caffe2_build_dir = os.path.join(cwd, "build") -+caffe2_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build")) - # lib/pythonx.x/site-packages - rel_site_packages = distutils.sysconfig.get_python_lib(prefix='') - # full absolute path to the dir above -@@ -279,7 +279,7 @@ elif sha != 'Unknown': - version += '+' + sha[:7] - report("Building wheel {}-{}".format(package_name, version)) - --cmake = CMake() -+cmake = CMake(caffe2_build_dir) - - # all the work we need to do _before_ setup runs - def build_deps(): -@@ -445,7 +445,7 @@ class build_ext(setuptools.command.build_ext.build_ext): - filename = self.get_ext_filename(fullname) - report("\nCopying extension {}".format(ext.name)) - -- src = os.path.join("torch", rel_site_packages, filename) -+ src = os.path.join(caffe2_build_dir, filename) - if not os.path.exists(src): - report("{} does not exist".format(src)) - del self.extensions[i] --- -2.23.0 - diff --git a/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch b/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch deleted file mode 100644 index c8f57d9e6..000000000 --- a/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch +++ /dev/null @@ -1,104 +0,0 @@ -From a0ace7295b6895954d2a0f8d6fe311a34a7c4e85 Mon Sep 17 00:00:00 2001 -From: Alexey Chernov <4ernov@gmail.com> -Date: Tue, 12 Nov 2019 02:01:36 +0300 -Subject: [PATCH 4/4] Don't fill rpath of Caffe2 library for system-wide - install - -Don't fill in runtime path of Caffe2 library for the case of -building for system-wide installation. ---- - CMakeLists.txt | 3 +++ - caffe2/CMakeLists.txt | 18 +++++++++++++++--- - cmake/Dependencies.cmake | 19 +++++++++++-------- - 3 files changed, 29 insertions(+), 11 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 20923c0544..45a882ae0e 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -193,6 +193,9 @@ option(USE_TBB "Use TBB" OFF) - # Used when building Caffe2 through setup.py - option(BUILDING_WITH_TORCH_LIBS "Tell cmake if Caffe2 is being built alongside torch libs" ON) - -+# Used when building Caffe2 for further system-wide installation -+option(BUILDING_SYSTEM_WIDE "Tell cmake if Caffe2 is being built for system-wide installation" OFF) -+ - # /Z7 override option - # When generating debug symbols, CMake default to use the flag /Zi. - # However, it is not compatible with sccache. So we rewrite it off. -diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt -index 1f7d037243..30d5615cdb 100644 ---- a/caffe2/CMakeLists.txt -+++ b/caffe2/CMakeLists.txt -@@ -1235,7 +1235,11 @@ if (BUILD_PYTHON) - if (MSVC AND BUILD_SHARED_LIBS) - install(FILES $<TARGET_PDB_FILE:caffe2_pybind11_state> DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python" OPTIONAL) - endif() -- set_target_properties(caffe2_pybind11_state PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}") -+ if (NOT BUILDING_SYSTEM_WIDE) -+ set_target_properties(caffe2_pybind11_state PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}") -+else() -+ set_target_properties(caffe2_pybind11_state PROPERTIES SKIP_BUILD_RPATH ON) -+ endif() - - if(USE_CUDA) - add_library(caffe2_pybind11_state_gpu MODULE ${Caffe2_GPU_PYTHON_SRCS}) -@@ -1261,7 +1265,11 @@ if (BUILD_PYTHON) - if (MSVC AND BUILD_SHARED_LIBS) - install(FILES $<TARGET_PDB_FILE:caffe2_pybind11_state_gpu> DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python" OPTIONAL) - endif() -- set_target_properties(caffe2_pybind11_state_gpu PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}") -+ if (NOT BUILDING_SYSTEM_WIDE) -+ set_target_properties(caffe2_pybind11_state_gpu PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}") -+ else() -+ set_target_properties(caffe2_pybind11_state_gpu PROPERTIES SKIP_BUILD_RPATH ON) -+ endif() - endif() - - if(USE_ROCM) -@@ -1284,7 +1292,11 @@ if (BUILD_PYTHON) - caffe2_pybind11_state_hip PROPERTIES LIBRARY_OUTPUT_DIRECTORY - ${CMAKE_BINARY_DIR}/caffe2/python) - install(TARGETS caffe2_pybind11_state_hip DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python") -- set_target_properties(caffe2_pybind11_state_hip PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}") -+ if (NOT BUILDING_SYSTEM_WIDE) -+ set_target_properties(caffe2_pybind11_state_hip PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}") -+ else() -+ set_target_properties(caffe2_pybind11_state_hip PROPERTIES SKIP_BUILD_RPATH ON) -+ endif() - endif() - - if (MSVC AND CMAKE_GENERATOR MATCHES "Visual Studio") -diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake -index a8e9769536..6ef9d7b0e2 100644 ---- a/cmake/Dependencies.cmake -+++ b/cmake/Dependencies.cmake -@@ -6,14 +6,17 @@ if (APPLE) - else() - set(_rpath_portable_origin $ORIGIN) - endif(APPLE) --# Use separate rpaths during build and install phases --set(CMAKE_SKIP_BUILD_RPATH FALSE) --# Don't use the install-rpath during the build phase --set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) --set(CMAKE_INSTALL_RPATH "${_rpath_portable_origin}") --# Automatically add all linked folders that are NOT in the build directory to --# the rpath (per library?) --set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) -+ -+if (NOT BUILDING_SYSTEM_WIDE) -+ # Use separate rpaths during build and install phases -+ set(CMAKE_SKIP_BUILD_RPATH FALSE) -+ # Don't use the install-rpath during the build phase -+ set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) -+ set(CMAKE_INSTALL_RPATH "${_rpath_portable_origin}") -+ # Automatically add all linked folders that are NOT in the build directory to -+ # the rpath (per library?) -+ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) -+endif() - - # UBSAN triggers when compiling protobuf, so we need to disable it. - set(UBSAN_FLAG "-fsanitize=undefined") --- -2.23.0 - diff --git a/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch b/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch deleted file mode 100644 index 324b8f682..000000000 --- a/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch +++ /dev/null @@ -1,31 +0,0 @@ -From 52019a3f395e5fa97b26d424152d91f73b400f8e Mon Sep 17 00:00:00 2001 -From: Alexey Chernov <4ernov@gmail.com> -Date: Wed, 13 Nov 2019 23:44:12 +0300 -Subject: [PATCH 5/5] Change library directory according to CMake build - -Change `lib_path` in favour of out-of-tree CMake build -directory, so that all the C++ libraries be found. ---- - setup.py | 5 +++-- - 1 file changed, 3 insertions(+), 2 deletions(-) - -diff --git a/setup.py b/setup.py -index 60502b6add..cbced52192 100644 ---- a/setup.py -+++ b/setup.py -@@ -234,9 +234,10 @@ else: - - # Constant known variables used throughout this file - cwd = os.path.dirname(os.path.abspath(__file__)) --lib_path = os.path.join(cwd, "torch", "lib") -+cmake_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build")) -+lib_path = os.path.join(cmake_build_dir, "lib") - third_party_path = os.path.join(cwd, "third_party") --caffe2_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build")) -+caffe2_build_dir = cmake_build_dir - # lib/pythonx.x/site-packages - rel_site_packages = distutils.sysconfig.get_python_lib(prefix='') - # full absolute path to the dir above --- -2.23.0 - diff --git a/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch b/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch deleted file mode 100644 index 49835d201..000000000 --- a/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch +++ /dev/null @@ -1,38 +0,0 @@ -From 0f3a0d9a948fdd8481a5f7751a255ecd9ed4d37a Mon Sep 17 00:00:00 2001 -From: Alexey Chernov <4ernov@gmail.com> -Date: Mon, 20 Jan 2020 01:21:22 +0300 -Subject: [PATCH 3/3] Remove conversion ambiguity in ternary operators - -It fails to compile with recent versions of Clang -(namely, version 10 used behind HCC compiler when -being built with ROCm support) with the -`conditional expression is ambiguous` error. ---- - caffe2/operators/relu_op.cu | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/caffe2/operators/relu_op.cu b/caffe2/operators/relu_op.cu -index f6edf7105e..ab49540fc9 100644 ---- a/caffe2/operators/relu_op.cu -+++ b/caffe2/operators/relu_op.cu -@@ -51,7 +51,7 @@ __global__ void ReluCUDAKernel<half2>(const int N, const half2* X, half2* Y) { - #else - const float2 xx = __half22float2(X[i]); - Y[i] = -- __floats2half2_rn(xx.x > 0.0f ? xx.x : 0.0f, xx.y > 0.0f ? xx.y : 0.0f); -+ __floats2half2_rn(xx.x > 0.0f ? float(xx.x) : 0.0f, xx.y > 0.0f ? float(xx.y) : 0.0f); - #endif - } - } -@@ -101,7 +101,7 @@ __global__ void ReluGradientCUDAKernel<half2>( - const float2 dy = __half22float2(dY[i]); - const float2 yy = __half22float2(Y[i]); - dX[i] = -- __floats2half2_rn(yy.x > 0.0f ? dy.x : 0.0f, yy.y > 0.0f ? dy.y : 0.0f); -+ __floats2half2_rn(yy.x > 0.0f ? float(dy.x) : 0.0f, yy.y > 0.0f ? float(dy.y) : 0.0f); - #endif - } - } --- -2.24.1 - diff --git a/sci-libs/pytorch/files/get_third_parties b/sci-libs/pytorch/files/get_third_parties deleted file mode 100644 index 8c38a9b73..000000000 --- a/sci-libs/pytorch/files/get_third_parties +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/bash - -path_url() { - local dir=$(dirname $1)/ - git config --file $1 --get-regexp '(path|url)' | sed -r -e "N;s,[^ ]* ([^ ]*)\n[^ ]* ([^ ]*),${dir#./}\1 \2," -} - -join \ - <(for gm in $(find . -name '.gitmodules' | sort -r); do path_url $gm; done | sort -u) \ - <(git submodule status --recursive | awk '{print $2 " " $1}' | sort -u) | \ -while read path url hash; do - [[ ${path} =~ (eigen|six|ios|neon2sse|protobuf|pybind11|python-enum|tbb|zstd|fbjni) ]] && continue - u=${url%.git} - hfull=${hash#-} - h=${hfull:0:8} - p=$(basename $u) - echo "${u}/archive/${h}.tar.gz -> ${p}-${h}.tar.gz" >> SRC_URI - [[ $p = fbgemm ]] && p=${p^^} - echo "rmdir ${path} && ln -sv \"\${WORKDIR}\"/${p}-${hfull} ${path}" >> src_prepare -done diff --git a/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch b/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch deleted file mode 100644 index 85e796a60..000000000 --- a/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch +++ /dev/null @@ -1,24 +0,0 @@ -Index: pytorch-1.4.0_p0/setup.py -=================================================================== ---- pytorch-1.4.0_p0.orig/setup.py -+++ pytorch-1.4.0_p0/setup.py -@@ -288,9 +288,7 @@ def build_deps(): - sys.exit(1) - - check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt")) -- check_file(os.path.join(third_party_path, "pybind11", "CMakeLists.txt")) - check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt')) -- check_file(os.path.join(third_party_path, 'tbb', 'Makefile')) - check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt')) - check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt')) - check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt')) -@@ -341,9 +339,6 @@ def build_deps(): - if not same: - shutil.copyfile(orig_file, sym_file) - -- dir_util.copy_tree('third_party/pybind11/include/pybind11/', -- 'torch/include/pybind11') -- - ################################################################################ - # Building dependent libraries - ################################################################################ diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch deleted file mode 100644 index 165e79dd4..000000000 --- a/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch +++ /dev/null @@ -1,28 +0,0 @@ -Index: nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf/makefiles/common.mk -=================================================================== ---- nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf.orig/makefiles/common.mk -+++ nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf/makefiles/common.mk -@@ -46,7 +46,7 @@ endif - CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR) -DCUDA_MINOR=$(CUDA_MINOR) -fPIC -fvisibility=hidden - CXXFLAGS += -Wall -Wno-unused-function -Wno-sign-compare -std=c++11 -Wvla - CXXFLAGS += -I $(CUDA_INC) --NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -lineinfo -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all -+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -lineinfo -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all - # Use addprefix so that we can specify more than one path - NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt - -@@ -60,14 +60,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler - # $(warning GCOV_FLAGS=${GCOV_FLAGS}) - ########## GCOV ########## - --ifeq ($(DEBUG), 0) --NVCUFLAGS += -O3 --CXXFLAGS += -O3 -g --else --NVCUFLAGS += -O0 -G -g --CXXFLAGS += -O0 -g -ggdb3 --endif -- - ifneq ($(VERBOSE), 0) - NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter - CXXFLAGS += -Wall -Wextra diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch b/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch deleted file mode 100644 index 3682469d7..000000000 --- a/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch +++ /dev/null @@ -1,28 +0,0 @@ -Disable expected test failures. - -TCPStoreTest is too slow to run. - -Reference: https://github.com/pytorch/pytorch/issues/13746 -Reference: https://github.com/pytorch/pytorch/issues/21873 - -Index: pytorch-1.4.0_p0/torch/lib/c10d/test/CMakeLists.txt -=================================================================== ---- pytorch-1.4.0_p0.orig/torch/lib/c10d/test/CMakeLists.txt -+++ pytorch-1.4.0_p0/torch/lib/c10d/test/CMakeLists.txt -@@ -14,7 +14,6 @@ function(c10d_add_test test_src) - endfunction() - - c10d_add_test(FileStoreTest.cpp c10d) --c10d_add_test(TCPStoreTest.cpp c10d) - - if(USE_CUDA) - if(USE_C10D_GLOO) -Index: pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt -=================================================================== ---- pytorch-1.4.0_p0.orig/caffe2/share/contrib/depthwise/CMakeLists.txt -+++ pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt -@@ -6,4 +6,3 @@ set(Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU - ) - - set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_CPU_SRC} PARENT_SCOPE) --set(Caffe2_CPU_TEST_SRCS ${Caffe2_CPU_TEST_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU_SRC} PARENT_SCOPE) diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch b/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch deleted file mode 100644 index 222a0f73e..000000000 --- a/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch +++ /dev/null @@ -1,15 +0,0 @@ -Give the location of sleef.h. - -Reference: https://github.com/pytorch/pytorch/issues/26555 -Index: pytorch-1.4.0/caffe2/CMakeLists.txt -=================================================================== ---- pytorch-1.4.0.orig/caffe2/CMakeLists.txt -+++ pytorch-1.4.0/caffe2/CMakeLists.txt -@@ -1062,6 +1062,7 @@ if (BUILD_TEST) - add_executable(${test_name} "${test_src}") - target_link_libraries(${test_name} ${Caffe2_MAIN_LIBS} gtest_main) - target_include_directories(${test_name} PRIVATE $<INSTALL_INTERFACE:include>) -+ target_include_directories(${test_name} PRIVATE $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>) - target_include_directories(${test_name} PRIVATE ${Caffe2_CPU_INCLUDE}) - add_test(NAME ${test_name} COMMAND $<TARGET_FILE:${test_name}>) - if (INSTALL_TEST) diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch b/sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch deleted file mode 100644 index 1e9388ff1..000000000 --- a/sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch +++ /dev/null @@ -1,15 +0,0 @@ -Don't hardcode the library path. Leave it to the dynamic loader. - -Index: pytorch-1.6.0/torch/__init__.py -=================================================================== ---- pytorch-1.6.0.orig/torch/__init__.py -+++ pytorch-1.6.0/torch/__init__.py -@@ -138,7 +138,7 @@ def _load_global_deps(): - here = os.path.abspath(__file__) - lib_path = os.path.join(os.path.dirname(here), 'lib', lib_name) - -- ctypes.CDLL(lib_path, mode=ctypes.RTLD_GLOBAL) -+ ctypes.CDLL(lib_name, mode=ctypes.RTLD_GLOBAL) - - - if (USE_RTLD_GLOBAL_WITH_LIBTORCH or os.getenv('TORCH_USE_RTLD_GLOBAL')) and \ diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch deleted file mode 100644 index 052474ee4..000000000 --- a/sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff -uprN nccl-5949d96f36d050e59d05872f8bbffd2549318e95/makefiles/common.mk nccl-patched/makefiles/common.mk ---- nccl-5949d96f36d050e59d05872f8bbffd2549318e95/makefiles/common.mk 2020-06-09 00:31:44.000000000 +0800 -+++ nccl-patched/makefiles/common.mk 2020-08-06 21:25:57.784279738 +0800 -@@ -54,7 +54,7 @@ CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR) - # Maxrregcount needs to be set accordingly to NCCL_MAX_NTHREADS (otherwise it will cause kernel launch errors) - # 512 : 120, 640 : 96, 768 : 80, 1024 : 60 - # We would not have to set this if we used __launch_bounds__, but this only works on kernels, not on functions. --NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all -+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all - # Use addprefix so that we can specify more than one path - NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt - -@@ -68,14 +68,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler - # $(warning GCOV_FLAGS=${GCOV_FLAGS}) - ########## GCOV ########## - --ifeq ($(DEBUG), 0) --NVCUFLAGS += -O3 --CXXFLAGS += -O3 -g --else --NVCUFLAGS += -O0 -G -g --CXXFLAGS += -O0 -g -ggdb3 --endif -- - ifneq ($(VERBOSE), 0) - NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter - CXXFLAGS += -Wall -Wextra diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-setup.patch b/sci-libs/pytorch/files/pytorch-1.6.0-setup.patch deleted file mode 100644 index 6a197a907..000000000 --- a/sci-libs/pytorch/files/pytorch-1.6.0-setup.patch +++ /dev/null @@ -1,14 +0,0 @@ -Index: pytorch-1.4.0_p0/setup.py -=================================================================== ---- pytorch-1.4.0_p0.orig/setup.py -+++ pytorch-1.4.0_p0/setup.py -@@ -288,9 +288,7 @@ def build_deps(): - sys.exit(1) - - check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt")) -- check_file(os.path.join(third_party_path, "pybind11", "CMakeLists.txt")) - check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt')) -- check_file(os.path.join(third_party_path, 'tbb', 'Makefile')) - check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt')) - check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt')) - check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt')) diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch b/sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch deleted file mode 100644 index 3ef2c533f..000000000 --- a/sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch +++ /dev/null @@ -1,14 +0,0 @@ -Disable expected test failures. - -Reference: https://github.com/pytorch/pytorch/issues/13746 -Reference: https://github.com/pytorch/pytorch/issues/21873 - -Index: pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt -=================================================================== ---- pytorch-1.4.0_p0.orig/caffe2/share/contrib/depthwise/CMakeLists.txt -+++ pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt -@@ -6,4 +6,3 @@ set(Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU - ) - - set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_CPU_SRC} PARENT_SCOPE) --set(Caffe2_CPU_TEST_SRCS ${Caffe2_CPU_TEST_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU_SRC} PARENT_SCOPE) diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch b/sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch deleted file mode 100644 index a4ba38322..000000000 --- a/sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch +++ /dev/null @@ -1,13 +0,0 @@ -Index: tensorpipe/cmake/pytorch.cmake -=================================================================== ---- tensorpipe.orig/cmake/pytorch.cmake -+++ tensorpipe/cmake/pytorch.cmake -@@ -138,7 +138,7 @@ endif() - - add_library(tensorpipe ${TENSORPIPE_SRC}) - --set(TP_BUILD_LIBUV ON) -+set(TP_BUILD_LIBUV OFF) - find_package(uv REQUIRED) - target_link_libraries(tensorpipe PRIVATE uv::uv) - diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch b/sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch deleted file mode 100644 index eabda092e..000000000 --- a/sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake -index b3a892cf88..2c8622870c 100644 ---- a/cmake/Dependencies.cmake -+++ b/cmake/Dependencies.cmake -@@ -4,7 +4,6 @@ if(APPLE) - set(CMAKE_MACOSX_RPATH ON) - set(_rpath_portable_origin "@loader_path") - else() -- set(_rpath_portable_origin $ORIGIN) - endif(APPLE) - # Use separate rpaths during build and install phases - set(CMAKE_SKIP_BUILD_RPATH FALSE) diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-setup.patch b/sci-libs/pytorch/files/pytorch-1.7.1-setup.patch deleted file mode 100644 index 28db5692c..000000000 --- a/sci-libs/pytorch/files/pytorch-1.7.1-setup.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/setup.py b/setup.py -index 2db381644c..01a2e57aea 100644 ---- a/setup.py -+++ b/setup.py -@@ -294,7 +294,6 @@ def build_deps(): - - check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt")) - check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt')) -- check_file(os.path.join(third_party_path, 'tbb', 'Makefile')) - check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt')) - check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt')) - check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt')) diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch b/sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch deleted file mode 100644 index 960ae3618..000000000 --- a/sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake -index d1e4bdaed6..85821a78df 100644 ---- a/cmake/Dependencies.cmake -+++ b/cmake/Dependencies.cmake -@@ -1308,7 +1308,6 @@ if(USE_DISTRIBUTED AND USE_TENSORPIPE) - if(MSVC) - message(WARNING "Tensorpipe cannot be used on Windows.") - else() -- set(TP_BUILD_LIBUV ON CACHE BOOL "" FORCE) - set(TP_ENABLE_SHM OFF CACHE BOOL "" FORCE) - set(TP_ENABLE_CMA OFF CACHE BOOL "" FORCE) - set(TP_STATIC_OR_SHARED STATIC CACHE STRING "" FORCE) diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch b/sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch deleted file mode 100644 index 44b27cac3..000000000 --- a/sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/torch/__init__.py b/torch/__init__.py -index 03f6eca622..297fb169a4 100644 ---- a/torch/__init__.py -+++ b/torch/__init__.py -@@ -412,7 +412,7 @@ def manager_path(): - - - # Shared memory manager needs to know the exact location of manager executable --_C._initExtension(manager_path()) -+_C._initExtension(b"@GENTOO_PORTAGE_EPREFIX@/usr/bin/torch_shm_manager") - del manager_path - - # Appease the type checker: it can't deal with direct setting of globals(). diff --git a/sci-libs/pytorch/metadata.xml b/sci-libs/pytorch/metadata.xml deleted file mode 100644 index 01e2b2703..000000000 --- a/sci-libs/pytorch/metadata.xml +++ /dev/null @@ -1,39 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>4ernov@gmail.com</email> - <name>Alexey Chernov</name> - </maintainer> - <maintainer type="person"> - <email>heroxbd@gentoo.org</email> - <name>Benda Xu</name> - </maintainer> - <use> - <flag name="asan">Build with address sanitizer (ASAN)</flag> - <flag name="atlas">Use ATLAS as BLAS implementation</flag> - <flag name="cuda">Enable support for nVidia CUDA</flag> - <flag name="eigen">Use Eigen as BLAS implementation</flag> - <flag name="fbgemm">Enable FBGEMM (Facebook GEneral Matrix Multiplication) support</flag> - <flag name="gflags">Build with gflags</flag> - <flag name="glog">Build with glog support</flag> - <flag name="gloo">Build gloo distributed communication backend support</flag> - <flag name="leveldb">Enable support for LevelDB</flag> - <flag name="lmdb">Enable support for LMDB</flag> - <flag name="mkl">Use Intel MKL as BLAS implementation</flag> - <flag name="mkldnn">Build with Intel MKL-DNN support</flag> - <flag name="namedtensor">Enable support for named tensors</flag> - <flag name="nnpack">Enable NNPACK support</flag> - <flag name="numa">Enable support for NUMA</flag> - <flag name="numpy">Enable NumPy support</flag> - <flag name="observers">Build observers</flag> - <flag name="openblas">Use OpenBLAS as BLAS implementation</flag> - <flag name="opencv">Enable support for OpenCV</flag> - <flag name="opencl">Enable support for OpenCL</flag> - <flag name="qnnpack">Enable QNNPACK support</flag> - <flag name="redis">Enable support for Redis</flag> - <flag name="rocm">Enable AMD ROCm</flag> - <flag name="tools">Build binary tools</flag> - <flag name="zeromq">Enable support for ZeroMQ</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/pytorch/pytorch-1.6.0-r2.ebuild b/sci-libs/pytorch/pytorch-1.6.0-r2.ebuild deleted file mode 100644 index 280089c6e..000000000 --- a/sci-libs/pytorch/pytorch-1.6.0-r2.ebuild +++ /dev/null @@ -1,287 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8} ) - -inherit distutils-r1 cmake cuda - -MPV=${PV/_p/a} - -DESCRIPTION="Tensors and Dynamic neural networks in Python with strong GPU acceleration" -HOMEPAGE="https://pytorch.org/" -SRC_URI="https://github.com/pytorch/${PN}/archive/v${MPV}.tar.gz -> ${P}.tar.gz -https://github.com/google/benchmark/archive/505be96ab.tar.gz -> benchmark-505be96ab.tar.gz -https://github.com/pytorch/cpuinfo/archive/63b254577.tar.gz -> cpuinfo-63b254577.tar.gz -https://github.com/NVlabs/cub/archive/d106ddb99.tar.gz -> cub-d106ddb99.tar.gz -https://github.com/pytorch/fbgemm/archive/87c378172.tar.gz -> fbgemm-87c378172.tar.gz -https://github.com/fmtlib/fmt/archive/9bdd1596c.tar.gz -> fmt-9bdd1596c.tar.gz -https://github.com/houseroad/foxi/archive/8015abb72.tar.gz -> foxi-8015abb72.tar.gz -https://github.com/Maratyszcza/FP16/archive/4dfe081cf.tar.gz -> FP16-4dfe081cf.tar.gz -https://github.com/Maratyszcza/FXdiv/archive/b408327ac.tar.gz -> FXdiv-b408327ac.tar.gz -https://github.com/google/gemmlowp/archive/3fb5c176c.tar.gz -> gemmlowp-3fb5c176c.tar.gz -https://github.com/facebookincubator/gloo/archive/3d08580f9.tar.gz -> gloo-3d08580f9.tar.gz -https://github.com/google/googletest/archive/2fe3bd994.tar.gz -> googletest-2fe3bd994.tar.gz -https://github.com/intel/ideep/archive/938cc6889.tar.gz -> ideep-938cc6889.tar.gz -cuda? ( https://github.com/NVIDIA/nccl/archive/5949d96f3.tar.gz -> nccl-5949d96f3.tar.gz ) -https://github.com/Maratyszcza/NNPACK/archive/24b55303f.tar.gz -> NNPACK-24b55303f.tar.gz -https://github.com/onnx/onnx/archive/a82c6a701.tar.gz -> onnx-a82c6a701.tar.gz -https://github.com/onnx/onnx-tensorrt/archive/c15321141.tar.gz -> onnx-tensorrt-c15321141.tar.gz -https://github.com/Maratyszcza/psimd/archive/072586a71.tar.gz -> psimd-072586a71.tar.gz -https://github.com/Maratyszcza/pthreadpool/archive/029c88620.tar.gz -> pthreadpool-029c88620.tar.gz -https://github.com/Maratyszcza/PeachPy/archive/07d8fde8a.tar.gz -> PeachPy-07d8fde8a.tar.gz -https://github.com/pytorch/QNNPACK/archive/7d2a4e993.tar.gz -> QNNPACK-7d2a4e993.tar.gz -https://github.com/shibatch/sleef/archive/7f523de65.tar.gz -> sleef-7f523de65.tar.gz -https://github.com/pytorch/tensorpipe/archive/3b8089c9c.tar.gz -> tensorpipe-3b8089c9c.tar.gz -https://github.com/google/XNNPACK/archive/1b354636b.tar.gz -> XNNPACK-1b354636b.tar.gz -https://github.com/asmjit/asmjit/archive/9057aa30.tar.gz -> asmjit-9057aa30.tar.gz - " - -# git clone git@github.com:pytorch/pytorch.git && cd pytorch -# src_uri() { -# join \ -# <(git config --file .gitmodules --get-regexp url | sed -r -e 's/^submodule.(.*).url (.*)/\1 \2/' -e 's,NNPACK_deps/,,' -e 's/third-party/third_party/' | sort) \ -# <(git submodule status | awk '{print $2 " " $1}' | sort) | \ -# while read path url hash; do -# [[ ${path} =~ (eigen|six|ios|neon2sse|protobuf|pybind11|enum34|tbb|zstd|fbjni) ]] && continue -# u=${url%.git} -# h=${hash#-} -# h=${h:0:8} -# echo "${u}/archive/${h}.tar.gz -> $(basename ${u})-${h}.tar.gz" -# done -# } -# src_uri - -# git submodule update --init third_party/fbgemm && cd third_party/fbgemm -# src_uri | grep asmjit -# cd ../.. - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -IUSE="asan atlas cuda eigen +fbgemm ffmpeg gflags glog +gloo leveldb lmdb mkl mkldnn mpi namedtensor +nnpack numa +numpy +observers +openblas opencl opencv +openmp +python +qnnpack redis static test tools zeromq" -RESTRICT="!test? ( test )" - -REQUIRED_USE=" - python? ( ${PYTHON_REQUIRED_USE} ) - numpy? ( python ) - ^^ ( atlas eigen mkl openblas ) -" - -RDEPEND=" - dev-libs/protobuf - dev-python/pyyaml[${PYTHON_USEDEP}] - atlas? ( sci-libs/atlas ) - cuda? ( dev-libs/cudnn - dev-cpp/eigen[cuda] ) - ffmpeg? ( media-video/ffmpeg ) - gflags? ( dev-cpp/gflags ) - glog? ( dev-cpp/glog ) - leveldb? ( dev-libs/leveldb ) - lmdb? ( dev-db/lmdb ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - numpy? ( dev-python/numpy[${PYTHON_USEDEP}] ) - openblas? ( sci-libs/openblas ) - opencl? ( dev-libs/clhpp virtual/opencl ) - opencv? ( media-libs/opencv ) - python? ( ${PYTHON_DEPS} - dev-python/pybind11[${PYTHON_USEDEP}] - ) - redis? ( dev-db/redis ) - zeromq? ( net-libs/zeromq ) - eigen? ( dev-cpp/eigen ) - dev-libs/libuv -" - -#ATen code generation -BDEPEND="dev-python/pyyaml" - -DEPEND="${RDEPEND} - test? ( dev-python/pytest[${PYTHON_USEDEP}] ) - dev-python/setuptools[${PYTHON_USEDEP}] - dev-cpp/tbb - app-arch/zstd - dev-python/protobuf-python[${PYTHON_USEDEP}] - dev-python/pybind11[${PYTHON_USEDEP}] - sys-fabric/libibverbs - sys-process/numactl -" - -PATCHES=( - "${FILESDIR}"/${PN}-1.6.0-setup.patch - "${FILESDIR}"/${PN}-1.6.0-skip-tests.patch - "${FILESDIR}"/${PN}-1.6.0-global-dlopen.patch - "${FILESDIR}"/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch - "${FILESDIR}"/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch - "${FILESDIR}"/0005-Change-library-directory-according-to-CMake-build.patch -) - -src_unpack() { - default - - [[ -d ${P} ]] || mv -v ${PN}-${MPV} ${P} || die -} - -src_prepare() { - cmake_src_prepare - eapply_user - - mv -v third_party/miniz-* ../ || die - rm -r third_party || die - ln -s .. third_party || die - cd .. || die - for d in *; do - case ${d} in - ${PN}* | miniz-*) continue ;; - PeachPy-*) mv -v ${d} python-peachpy || die ;; - *) mv -v ${d} ${d%-*} || die ;; - esac - done - - mv -v FBGEMM fbgemm || die - cd fbgemm || die - rm -r third_party || die - ln -s .. third_party || die - - cd ../onnx || die - rm -r third_party || die - ln -s .. third_party || die - - if use cuda; then - cd ../nccl || die - eapply "${FILESDIR}"/${PN}-1.6.0-nccl-nvccflags.patch - ln -s . nccl || die - - addpredict /dev/nvidiactl - cuda_src_prepare - export CUDAHOSTCXX=$(cuda_gccdir)/g++ - fi - - cd ../tensorpipe || die - eapply "${FILESDIR}"/${PN}-1.6.0-tensorpipe-unbundle-libuv.patch -} - -src_configure() { - local blas="Eigen" - - if use atlas; then - blas="ATLAS" - elif use mkl; then - blas="MKL" - elif use openblas; then - blas="OpenBLAS" - fi - - local mycmakeargs=( - -DTORCH_BUILD_VERSION=${PV} - -DTORCH_INSTALL_LIB_DIR=$(get_libdir) - -DBUILD_BINARY=$(usex tools ON OFF) - -DBUILD_CUSTOM_PROTOBUF=OFF - -DBUILD_PYTHON=$(usex python ON OFF) - -DBUILD_SHARED_LIBS=$(usex static OFF ON) - -DBUILD_TEST=$(usex test ON OFF) - -DUSE_ASAN=$(usex asan ON OFF) - -DUSE_CUDA=$(usex cuda ON OFF) - -DUSE_NCCL=$(usex cuda ON OFF) - -DUSE_SYSTEM_NCCL=OFF - -DUSE_ROCM=OFF - -DUSE_FBGEMM=$(usex fbgemm ON OFF) - -DUSE_FFMPEG=$(usex ffmpeg ON OFF) - -DUSE_GFLAGS=$(usex gflags ON OFF) - -DUSE_GLOG=$(usex glog ON OFF) - -DUSE_LEVELDB=$(usex leveldb ON OFF) - -DUSE_LITE_PROTO=OFF - -DUSE_LMDB=$(usex lmdb ON OFF) - -DCAFFE2_USE_MKL=$(usex mkl ON OFF) - -DUSE_MKLDNN=$(usex mkldnn ON OFF) - -DUSE_MKLDNN_CBLAS=OFF - -DUSE_NNPACK=$(usex nnpack ON OFF) - -DUSE_NUMPY=$(usex numpy ON OFF) - -DUSE_NUMA=$(usex numa ON OFF) - -DUSE_OBSERVERS=$(usex observers ON OFF) - -DUSE_OPENCL=$(usex opencl ON OFF) - -DUSE_OPENCV=$(usex opencv ON OFF) - -DUSE_OPENMP=$(usex openmp ON OFF) - -DUSE_TBB=OFF - -DUSE_PROF=OFF - -DUSE_QNNPACK=$(usex qnnpack ON OFF) - -DUSE_REDIS=$(usex redis ON OFF) - -DUSE_ROCKSDB=OFF - -DUSE_ZMQ=$(usex zeromq ON OFF) - -DUSE_MPI=$(usex mpi ON OFF) - -DUSE_GLOO=$(usex gloo ON OFF) - -DUSE_SYSTEM_EIGEN_INSTALL=ON - -DBUILD_NAMEDTENSOR=$(usex namedtensor ON OFF) - -DBLAS=${blas} - ) - - cmake_src_configure - - if use python; then - CMAKE_BUILD_DIR="${BUILD_DIR}" distutils-r1_src_configure - fi - - # do not rerun cmake and the build process in src_install - sed '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die -} - -src_compile() { - cmake_src_compile - - if use python; then - CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_compile - fi -} - -src_install() { - cmake_src_install - - local LIB=$(get_libdir) - if [[ ${LIB} != lib ]]; then - mv -fv "${ED}"/usr/lib/*.so "${ED}"/usr/${LIB}/ || die - fi - - rm -rfv "${ED}/torch" - rm -rfv "${ED}/var" - rm -rfv "${ED}/usr/lib" - - rm -fv "${ED}/usr/include/*.{h,hpp}" - rm -rfv "${ED}/usr/include/asmjit" - rm -rfv "${ED}/usr/include/c10d" - rm -rfv "${ED}/usr/include/fbgemm" - rm -rfv "${ED}/usr/include/fp16" - rm -rfv "${ED}/usr/include/gloo" - rm -rfv "${ED}/usr/include/include" - rm -rfv "${ED}/usr/include/var" - - cp -rv "${WORKDIR}/${P}/third_party/pybind11/include/pybind11" "${ED}/usr/include/" - - rm -fv "${ED}/usr/lib64/libtbb.so" - rm -rfv "${ED}/usr/lib64/cmake" - - if use python; then - install_shm_manager() { - TORCH_BIN_DIR="${D}$(python_get_sitedir)/torch/bin" - - mkdir -pv ${TORCH_BIN_DIR} - cp -v "${ED}/usr/bin/torch_shm_manager" "${TORCH_BIN_DIR}" - } - - python_foreach_impl install_shm_manager - - scanelf -r --fix "${BUILD_DIR}/caffe2/python" - CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_install - - python_foreach_impl python_optimize - fi - - find "${ED}/usr/${LIB}" -name "*.a" -exec rm -fv {} \; - - use test && rm -rfv "${ED}/usr/test" "${ED}"/usr/bin/test_{api,jit} - - # Remove the empty directories by CMake Python: - find "${ED}" -type d -empty -delete || die -} diff --git a/sci-libs/pytorch/pytorch-1.7.1-r2.ebuild b/sci-libs/pytorch/pytorch-1.7.1-r2.ebuild deleted file mode 100644 index 99cc2e750..000000000 --- a/sci-libs/pytorch/pytorch-1.7.1-r2.ebuild +++ /dev/null @@ -1,292 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake cuda distutils-r1 prefix - -DESCRIPTION="Tensors and Dynamic neural networks in Python with strong GPU acceleration" -HOMEPAGE="https://pytorch.org/" -SRC_URI="https://github.com/pytorch/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz -https://github.com/google/benchmark/archive/505be96a.tar.gz -> benchmark-505be96a.tar.gz -https://github.com/pytorch/cpuinfo/archive/63b25457.tar.gz -> cpuinfo-63b25457.tar.gz -https://github.com/NVlabs/cub/archive/d106ddb9.tar.gz -> cub-d106ddb9.tar.gz -https://github.com/pytorch/fbgemm/archive/1d710393.tar.gz -> fbgemm-1d710393.tar.gz -https://github.com/asmjit/asmjit/archive/9057aa30.tar.gz -> asmjit-9057aa30.tar.gz -https://github.com/pytorch/cpuinfo/archive/d5e37adf.tar.gz -> cpuinfo-d5e37adf.tar.gz -https://github.com/google/googletest/archive/0fc5466d.tar.gz -> googletest-0fc5466d.tar.gz -https://github.com/fmtlib/fmt/archive/cd4af11e.tar.gz -> fmt-cd4af11e.tar.gz -https://github.com/houseroad/foxi/archive/4aba696e.tar.gz -> foxi-4aba696e.tar.gz -https://github.com/Maratyszcza/FP16/archive/4dfe081c.tar.gz -> FP16-4dfe081c.tar.gz -https://github.com/Maratyszcza/FXdiv/archive/b408327a.tar.gz -> FXdiv-b408327a.tar.gz -https://github.com/google/gemmlowp/archive/3fb5c176.tar.gz -> gemmlowp-3fb5c176.tar.gz -https://github.com/facebookincubator/gloo/archive/3dc0328f.tar.gz -> gloo-3dc0328f.tar.gz -https://github.com/google/googletest/archive/2fe3bd99.tar.gz -> googletest-2fe3bd99.tar.gz -https://github.com/intel/ideep/archive/ba885200.tar.gz -> ideep-ba885200.tar.gz -https://github.com/intel/mkl-dnn/archive/5ef631a0.tar.gz -> mkl-dnn-5ef631a0.tar.gz -cuda? ( https://github.com/NVIDIA/nccl/archive/033d7995.tar.gz -> nccl-033d7995.tar.gz ) -https://github.com/Maratyszcza/NNPACK/archive/24b55303.tar.gz -> NNPACK-24b55303.tar.gz -https://github.com/onnx/onnx/archive/a82c6a70.tar.gz -> onnx-a82c6a70.tar.gz -https://github.com/onnx/onnx-tensorrt/archive/c1532114.tar.gz -> onnx-tensorrt-c1532114.tar.gz -https://github.com/onnx/onnx/archive/765f5ee8.tar.gz -> onnx-765f5ee8.tar.gz -https://github.com/google/benchmark/archive/e776aa02.tar.gz -> benchmark-e776aa02.tar.gz -https://github.com/google/benchmark/archive/5b7683f4.tar.gz -> benchmark-5b7683f4.tar.gz -https://github.com/google/googletest/archive/5ec7f0c4.tar.gz -> googletest-5ec7f0c4.tar.gz -https://github.com/Maratyszcza/psimd/archive/072586a7.tar.gz -> psimd-072586a7.tar.gz -https://github.com/Maratyszcza/pthreadpool/archive/029c8862.tar.gz -> pthreadpool-029c8862.tar.gz -https://github.com/Maratyszcza/PeachPy/archive/07d8fde8.tar.gz -> PeachPy-07d8fde8.tar.gz -https://github.com/pytorch/QNNPACK/archive/7d2a4e99.tar.gz -> QNNPACK-7d2a4e99.tar.gz -https://github.com/shibatch/sleef/archive/7f523de6.tar.gz -> sleef-7f523de6.tar.gz -https://github.com/pytorch/tensorpipe/archive/95ff9319.tar.gz -> tensorpipe-95ff9319.tar.gz -https://github.com/google/googletest/archive/2fe3bd99.tar.gz -> googletest-2fe3bd99.tar.gz -https://github.com/google/libnop/archive/aa95422e.tar.gz -> libnop-aa95422e.tar.gz -https://github.com/libuv/libuv/archive/02a9e1be.tar.gz -> libuv-02a9e1be.tar.gz -https://github.com/google/XNNPACK/archive/1b354636.tar.gz -> XNNPACK-1b354636.tar.gz - " - -# git clone git@github.com:pytorch/pytorch.git && cd pytorch -# git submodules update --init --recursive -# ${FILESDIR}/get_third_paries -# cat SRC_URI src_prepare - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -IUSE="asan blas cuda +fbgemm ffmpeg gflags glog +gloo leveldb lmdb mkldnn mpi namedtensor +nnpack numa +observers opencl opencv +openmp +python +qnnpack redis rocm static test tools zeromq" -RESTRICT="!test? ( test )" -REQUIRED_USE=" - ?? ( cuda rocm ) -" - -RDEPEND=" - dev-python/pyyaml[${PYTHON_USEDEP}] - blas? ( virtual/blas ) - cuda? ( dev-libs/cudnn - dev-cpp/eigen[cuda] ) - rocm? ( >=dev-util/hip-4.0.0-r1 - >=dev-libs/rccl-4 - >=sci-libs/rocThrust-4 - >=sci-libs/hipCUB-4 - >=sci-libs/rocPRIM-4 - >=sci-libs/miopen-4 - >=sci-libs/rocBLAS-4 - >=sci-libs/rocRAND-4 - >=sci-libs/hipSPARSE-4 - >=sci-libs/rocFFT-4 - >=dev-util/roctracer-4 ) - ffmpeg? ( media-video/ffmpeg ) - gflags? ( dev-cpp/gflags ) - glog? ( dev-cpp/glog ) - leveldb? ( dev-libs/leveldb ) - lmdb? ( dev-db/lmdb ) - mpi? ( virtual/mpi ) - opencl? ( dev-libs/clhpp virtual/opencl ) - opencv? ( media-libs/opencv ) - python? ( ${PYTHON_DEPS} - dev-python/pybind11[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/protobuf-python:0/22 - ) - redis? ( dev-db/redis ) - zeromq? ( net-libs/zeromq ) - dev-cpp/eigen - dev-libs/protobuf:0/22 - dev-libs/libuv -" - -#ATen code generation -BDEPEND="dev-python/pyyaml" - -DEPEND="${RDEPEND} - test? ( dev-python/pytest[${PYTHON_USEDEP}] ) - dev-python/setuptools[${PYTHON_USEDEP}] - dev-cpp/tbb - app-arch/zstd - dev-python/pybind11[${PYTHON_USEDEP}] - sys-fabric/libibverbs - sys-process/numactl -" - -PATCHES=( - "${FILESDIR}"/${PN}-1.7.1-setup.patch - "${FILESDIR}"/${PN}-1.6.0-skip-tests.patch - "${FILESDIR}"/${PN}-1.6.0-global-dlopen.patch - "${FILESDIR}"/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch - "${FILESDIR}"/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch - "${FILESDIR}"/0005-Change-library-directory-according-to-CMake-build.patch - "${FILESDIR}"/${PN}-1.7.1-no-rpath.patch - "${FILESDIR}"/${PN}-1.7.1-tensorpipe-unbundle-libuv.patch - "${FILESDIR}"/${PN}-1.7.1-torch_shm_manager.patch -) - -src_prepare() { - cmake_src_prepare - eprefixify torch/__init__.py - eapply_user - - rmdir third_party/benchmark && ln -sv "${WORKDIR}"/benchmark-505be96ab23056580a3a2315abba048f4428b04e third_party/benchmark - rmdir third_party/cpuinfo && ln -sv "${WORKDIR}"/cpuinfo-63b254577ed77a8004a9be6ac707f3dccc4e1fd9 third_party/cpuinfo - rmdir third_party/cub && ln -sv "${WORKDIR}"/cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4 third_party/cub - rmdir third_party/fbgemm && ln -sv "${WORKDIR}"/FBGEMM-1d710393d5b7588f5de3b83f51c22bbddf095229 third_party/fbgemm - rmdir third_party/fbgemm/third_party/asmjit && ln -sv "${WORKDIR}"/asmjit-9057aa30b620f0662ff51e2230c126a345063064 third_party/fbgemm/third_party/asmjit - rmdir third_party/fbgemm/third_party/cpuinfo && ln -sv "${WORKDIR}"/cpuinfo-d5e37adf1406cf899d7d9ec1d317c47506ccb970 third_party/fbgemm/third_party/cpuinfo - rmdir third_party/fbgemm/third_party/googletest && ln -sv "${WORKDIR}"/googletest-0fc5466dbb9e623029b1ada539717d10bd45e99e third_party/fbgemm/third_party/googletest - rmdir third_party/fmt && ln -sv "${WORKDIR}"/fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05 third_party/fmt - rmdir third_party/foxi && ln -sv "${WORKDIR}"/foxi-4aba696ec8f31794fd42880346dc586486205e0a third_party/foxi - rmdir third_party/FP16 && ln -sv "${WORKDIR}"/FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3 third_party/FP16 - rmdir third_party/FXdiv && ln -sv "${WORKDIR}"/FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1 third_party/FXdiv - rmdir third_party/gemmlowp/gemmlowp && ln -sv "${WORKDIR}"/gemmlowp-3fb5c176c17c765a3492cd2f0321b0dab712f350 third_party/gemmlowp/gemmlowp - rmdir third_party/gloo && ln -sv "${WORKDIR}"/gloo-3dc0328fe6a9d47bd47c0c6ca145a0d8a21845c6 third_party/gloo - rmdir third_party/googletest && ln -sv "${WORKDIR}"/googletest-2fe3bd994b3189899d93f1d5a881e725e046fdc2 third_party/googletest - rmdir third_party/ideep && ln -sv "${WORKDIR}"/ideep-ba885200dbbc1f144c7b58eba487378eb324f281 third_party/ideep - rmdir third_party/ideep/mkl-dnn && ln -sv "${WORKDIR}"/mkl-dnn-5ef631a030a6f73131c77892041042805a06064f third_party/ideep/mkl-dnn - rmdir third_party/nccl/nccl && ln -sv "${WORKDIR}"/nccl-033d799524fb97629af5ac2f609de367472b2696 third_party/nccl/nccl - rmdir third_party/NNPACK && ln -sv "${WORKDIR}"/NNPACK-24b55303f5cf65d75844714513a0d1b1409809bd third_party/NNPACK - rmdir third_party/onnx && ln -sv "${WORKDIR}"/onnx-a82c6a7010e2e332d8f74ad5b0c726fd47c85376 third_party/onnx - rmdir third_party/onnx-tensorrt && ln -sv "${WORKDIR}"/onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f third_party/onnx-tensorrt - rmdir third_party/onnx-tensorrt/third_party/onnx && ln -sv "${WORKDIR}"/onnx-765f5ee823a67a866f4bd28a9860e81f3c811ce8 third_party/onnx-tensorrt/third_party/onnx - rmdir third_party/onnx-tensorrt/third_party/onnx/third_party/benchmark && ln -sv "${WORKDIR}"/benchmark-e776aa0275e293707b6a0901e0e8d8a8a3679508 third_party/onnx-tensorrt/third_party/onnx/third_party/benchmark - rmdir third_party/onnx/third_party/benchmark && ln -sv "${WORKDIR}"/benchmark-e776aa0275e293707b6a0901e0e8d8a8a3679508 third_party/onnx/third_party/benchmark - rmdir third_party/psimd && ln -sv "${WORKDIR}"/psimd-072586a71b55b7f8c584153d223e95687148a900 third_party/psimd - rmdir third_party/pthreadpool && ln -sv "${WORKDIR}"/pthreadpool-029c88620802e1361ccf41d1970bd5b07fd6b7bb third_party/pthreadpool - rmdir third_party/python-peachpy && ln -sv "${WORKDIR}"/PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473 third_party/python-peachpy - rmdir third_party/QNNPACK && ln -sv "${WORKDIR}"/QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c third_party/QNNPACK - rmdir third_party/sleef && ln -sv "${WORKDIR}"/sleef-7f523de651585fe25cade462efccca647dcc8d02 third_party/sleef - rmdir third_party/tensorpipe && ln -sv "${WORKDIR}"/tensorpipe-95ff9319161fcdb3c674d2bb63fac3e94095b343 third_party/tensorpipe - rmdir third_party/tensorpipe/third_party/googletest && ln -sv "${WORKDIR}"/googletest-2fe3bd994b3189899d93f1d5a881e725e046fdc2 third_party/tensorpipe/third_party/googletest - rmdir third_party/tensorpipe/third_party/libnop && ln -sv "${WORKDIR}"/libnop-aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2 third_party/tensorpipe/third_party/libnop - rmdir third_party/tensorpipe/third_party/libuv && ln -sv "${WORKDIR}"/libuv-02a9e1be252b623ee032a3137c0b0c94afbe6809 third_party/tensorpipe/third_party/libuv - rmdir third_party/XNNPACK && ln -sv "${WORKDIR}"/XNNPACK-1b354636b5942826547055252f3b359b54acff95 third_party/XNNPACK - - if use cuda; then - cd third_party/nccl/nccl || die - eapply "${FILESDIR}"/${PN}-1.6.0-nccl-nvccflags.patch - - addpredict /dev/nvidiactl - cuda_src_prepare - export CUDAHOSTCXX=$(cuda_gccdir)/g++ - fi - - if use rocm; then - #Allow escaping sandbox - addread /dev/kfd - addread /dev/dri - addwrite /dev/kfd - addwrite /dev/dri - - ebegin "HIPifying cuda sources" - tools/amd_build/build_amd.py - eend $? - - export PYTORCH_ROCM_ARCH=$(rocminfo | egrep -o "gfx[0-9]+" | uniq | awk -vORS=';' "{print $1}" | sed 's/;$/\n/') || die - sed -e "/set(roctracer_INCLUDE_DIRS/s,\${ROCTRACER_PATH}/include,${EPREFIX}/usr/include/roctracer," \ - -i cmake/public/LoadHIP.cmake || die - fi -} - -src_configure() { - local mycmakeargs=( - -DTORCH_BUILD_VERSION=${PV} - -DTORCH_INSTALL_LIB_DIR=$(get_libdir) - -DBUILD_BINARY=$(usex tools ON OFF) - -DBUILD_CUSTOM_PROTOBUF=OFF - -DBUILD_PYTHON=$(usex python ON OFF) - -DBUILD_SHARED_LIBS=$(usex static OFF ON) - -DBUILD_TEST=$(usex test ON OFF) - -DUSE_ASAN=$(usex asan ON OFF) - -DUSE_CUDA=$(usex cuda ON OFF) - -DUSE_NCCL=$(usex cuda ON OFF) - -DUSE_SYSTEM_NCCL=OFF - -DUSE_ROCM=$(usex rocm ON OFF) - -DUSE_FBGEMM=$(usex fbgemm ON OFF) - -DUSE_FFMPEG=$(usex ffmpeg ON OFF) - -DUSE_GFLAGS=$(usex gflags ON OFF) - -DUSE_GLOG=$(usex glog ON OFF) - -DUSE_LEVELDB=$(usex leveldb ON OFF) - -DUSE_LITE_PROTO=OFF - -DUSE_LMDB=$(usex lmdb ON OFF) - -DUSE_MKLDNN=$(usex mkldnn ON OFF) - -DUSE_MKLDNN_CBLAS=OFF - -DUSE_NNPACK=$(usex nnpack ON OFF) - -DUSE_NUMPY=$(usex python ON OFF) - -DUSE_NUMA=$(usex numa ON OFF) - -DUSE_OBSERVERS=$(usex observers ON OFF) - -DUSE_OPENCL=$(usex opencl ON OFF) - -DUSE_OPENCV=$(usex opencv ON OFF) - -DUSE_OPENMP=$(usex openmp ON OFF) - -DUSE_TBB=OFF - -DUSE_PROF=OFF - -DUSE_QNNPACK=$(usex qnnpack ON OFF) - -DUSE_REDIS=$(usex redis ON OFF) - -DUSE_ROCKSDB=OFF - -DUSE_ZMQ=$(usex zeromq ON OFF) - -DUSE_MPI=$(usex mpi ON OFF) - -DUSE_GLOO=$(usex gloo ON OFF) - -DUSE_SYSTEM_EIGEN_INSTALL=ON - -DBUILD_NAMEDTENSOR=$(usex namedtensor ON OFF) - -DBLAS=$(usex blas Generic Eigen) - -DTP_BUILD_LIBUV=OFF - -Wno-dev - ) - - cmake_src_configure - - if use python; then - CMAKE_BUILD_DIR="${BUILD_DIR}" distutils-r1_src_configure - fi - - # do not rerun cmake and the build process in src_install - sed '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die -} - -src_compile() { - cmake_src_compile - - if use python; then - CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_compile - fi -} - -src_install() { - cmake_src_install - - local LIB=$(get_libdir) - if [[ ${LIB} != lib ]]; then - mv -fv "${ED}"/usr/lib/*.so "${ED}"/usr/${LIB}/ || die - fi - - rm -rfv "${ED}/torch" - rm -rfv "${ED}/var" - rm -rfv "${ED}/usr/lib" - - rm -fv "${ED}/usr/include/*.{h,hpp}" - rm -rfv "${ED}/usr/include/asmjit" - rm -rfv "${ED}/usr/include/c10d" - rm -rfv "${ED}/usr/include/fbgemm" - rm -rfv "${ED}/usr/include/fp16" - rm -rfv "${ED}/usr/include/gloo" - rm -rfv "${ED}/usr/include/include" - rm -rfv "${ED}/usr/include/var" - - cp -rv "${WORKDIR}/${P}/third_party/pybind11/include/pybind11" "${ED}/usr/include/" - - rm -fv "${ED}/usr/${LIB}/libtbb.so" - rm -rfv "${ED}/usr/${LIB}/cmake" - - if use python; then - scanelf -r --fix "${BUILD_DIR}/caffe2/python" - CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_install - - python_foreach_impl python_optimize - fi - - find "${ED}/usr/${LIB}" -name "*.a" -exec rm -fv {} \; - - use test && rm -rfv "${ED}/usr/test" "${ED}"/usr/bin/test_{api,jit} - - # Remove the empty directories by CMake Python: - find "${ED}" -type d -empty -delete || die -} diff --git a/sci-libs/pytorch/pytorch-1.9.0.ebuild b/sci-libs/pytorch/pytorch-1.9.0.ebuild deleted file mode 100644 index c997f8da8..000000000 --- a/sci-libs/pytorch/pytorch-1.9.0.ebuild +++ /dev/null @@ -1,321 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake cuda distutils-r1 prefix - -DESCRIPTION="Tensors and Dynamic neural networks in Python with strong GPU acceleration" -HOMEPAGE="https://pytorch.org/" -SRC_URI="https://github.com/pytorch/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz -https://github.com/google/benchmark/archive/e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz -> benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz -https://github.com/pytorch/cpuinfo/archive/63b25457.tar.gz -> cpuinfo-63b25457.tar.gz -https://github.com/NVlabs/cub/archive/d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz -> cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz -https://github.com/pytorch/fbgemm/archive/7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz -> fbgemm-7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz -https://github.com/asmjit/asmjit/archive/9057aa30.tar.gz -> asmjit-9057aa30.tar.gz -https://github.com/pytorch/cpuinfo/archive/5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz -> cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz -https://github.com/google/googletest/archive/0fc5466d.tar.gz -> googletest-0fc5466d.tar.gz -https://github.com/fmtlib/fmt/archive/cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz -> fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz -https://github.com/houseroad/foxi/archive/c278588e34e535f0bb8f00df3880d26928038cad.tar.gz -> foxi-c278588e34e535f0bb8f00df3880d26928038cad.tar.gz -https://github.com/Maratyszcza/FP16/archive/4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz -> FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz -https://github.com/Maratyszcza/FXdiv/archive/b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz -> FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz -https://github.com/google/gemmlowp/archive/3fb5c176.tar.gz -> gemmlowp-3fb5c176.tar.gz -https://github.com/facebookincubator/gloo/archive/c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz -> gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz -https://github.com/google/googletest/archive/e2239ee6043f73722e7aa812a459f54a28552929.tar.gz -> googletest-e2239ee6043f73722e7aa812a459f54a28552929.tar.gz -https://github.com/intel/ideep/archive/9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz -> ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz -https://github.com/intel/mkl-dnn/archive/5ef631a0.tar.gz -> mkl-dnn-5ef631a0.tar.gz -cuda? ( https://github.com/NVIDIA/nccl/archive/033d7995.tar.gz -> nccl-033d7995.tar.gz ) -https://github.com/Maratyszcza/NNPACK/archive/c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz -> NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz -https://github.com/onnx/onnx/archive/a82c6a70.tar.gz -> onnx-a82c6a70.tar.gz -https://github.com/onnx/onnx-tensorrt/archive/c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz -> onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz -https://github.com/onnx/onnx/archive/29e7aa7048809784465d06e897f043a4600642b2.tar.gz -> onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz -https://github.com/google/benchmark/archive/e776aa02.tar.gz -> benchmark-e776aa02.tar.gz -https://github.com/google/benchmark/archive/5b7683f4.tar.gz -> benchmark-5b7683f4.tar.gz -https://github.com/google/googletest/archive/5ec7f0c4.tar.gz -> googletest-5ec7f0c4.tar.gz -https://github.com/Maratyszcza/psimd/archive/072586a71b55b7f8c584153d223e95687148a90.tar.gz -> psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz -https://github.com/Maratyszcza/pthreadpool/archive/a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz -> pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz -https://github.com/Maratyszcza/PeachPy/archive/07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz -> PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz -https://github.com/pytorch/QNNPACK/archive/7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz -> QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz -https://github.com/shibatch/sleef/archive/e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz -> sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz -https://github.com/pytorch/tensorpipe/archive/c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz -> tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz -https://github.com/google/googletest/archive/2fe3bd99.tar.gz -> googletest-2fe3bd99.tar.gz -https://github.com/google/libnop/archive/aa95422e.tar.gz -> libnop-aa95422e.tar.gz -https://github.com/libuv/libuv/archive/02a9e1be.tar.gz -> libuv-02a9e1be.tar.gz -https://github.com/google/XNNPACK/archive/79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz -> XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz -https://github.com/pytorch/kineto/archive/dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz -> kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz -" - -# git clone git@github.com:pytorch/pytorch.git && cd pytorch -# git submodules update --init --recursive -# ${FILESDIR}/get_third_paries -# cat SRC_URI src_prepare - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" - -IUSE="asan blas cuda +fbgemm ffmpeg gflags glog +gloo leveldb lmdb mkldnn mpi namedtensor +nnpack numa +observers opencl opencv +openmp +python +qnnpack redis rocm static test tools zeromq" -RESTRICT="!test? ( test )" -REQUIRED_USE=" - ?? ( cuda rocm ) -" - -RDEPEND=" - dev-python/pyyaml[${PYTHON_USEDEP}] - blas? ( virtual/blas ) - cuda? ( dev-libs/cudnn - dev-cpp/eigen[cuda] ) - rocm? ( >=dev-util/hip-4.0.0-r1 - >=dev-libs/rccl-4 - >=sci-libs/rocThrust-4 - >=sci-libs/hipCUB-4 - >=sci-libs/rocPRIM-4 - >=sci-libs/miopen-4 - >=sci-libs/rocBLAS-4 - >=sci-libs/rocRAND-4 - >=sci-libs/hipSPARSE-4 - >=sci-libs/rocFFT-4 - >=dev-util/roctracer-4 ) - ffmpeg? ( media-video/ffmpeg ) - gflags? ( dev-cpp/gflags ) - glog? ( dev-cpp/glog ) - leveldb? ( dev-libs/leveldb ) - lmdb? ( dev-db/lmdb ) - mpi? ( virtual/mpi ) - opencl? ( dev-libs/clhpp virtual/opencl ) - opencv? ( media-libs/opencv ) - python? ( ${PYTHON_DEPS} - dev-python/pybind11[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/protobuf-python:0/22 - ) - redis? ( dev-db/redis ) - zeromq? ( net-libs/zeromq ) - dev-cpp/eigen - dev-libs/protobuf:0/22 - dev-libs/libuv -" - -#ATen code generation -BDEPEND="dev-python/pyyaml" - -DEPEND="${RDEPEND} - test? ( dev-python/pytest[${PYTHON_USEDEP}] ) - dev-cpp/tbb - app-arch/zstd - dev-python/pybind11[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - sys-fabric/libibverbs - sys-process/numactl -" - -PATCHES=( - "${FILESDIR}"/${PN}-1.6.0-skip-tests.patch - "${FILESDIR}"/${PN}-1.6.0-global-dlopen.patch - "${FILESDIR}"/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch - "${FILESDIR}"/${PN}-1.7.1-no-rpath.patch - "${FILESDIR}"/${PN}-1.7.1-torch_shm_manager.patch -) - -src_prepare() { - cmake_src_prepare - eprefixify torch/__init__.py - - rmdir third_party/benchmark || die - ln -sv "${WORKDIR}"/benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd third_party/benchmark || die - rmdir third_party/cpuinfo || die - ln -sv "${WORKDIR}"/cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d third_party/cpuinfo || die - rmdir third_party/cub || die - ln -sv "${WORKDIR}"/cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4 third_party/cub || die - rmdir third_party/fbgemm || die - ln -sv "${WORKDIR}"/FBGEMM-7495417ad31c38a06b1b13db66b355b6f23cd96d third_party/fbgemm || die - rmdir third_party/fbgemm/third_party/asmjit || die - ln -sv "${WORKDIR}"/asmjit-9057aa30b620f0662ff51e2230c126a345063064 third_party/fbgemm/third_party/asmjit || die - rmdir third_party/fbgemm/third_party/cpuinfo || die - ln -sv "${WORKDIR}"/cpuinfo-d5e37adf1406cf899d7d9ec1d317c47506ccb970 third_party/fbgemm/third_party/cpuinfo || die - rmdir third_party/fbgemm/third_party/googletest || die - ln -sv "${WORKDIR}"/googletest-0fc5466dbb9e623029b1ada539717d10bd45e99e third_party/fbgemm/third_party/googletest || die - rmdir third_party/fmt || die - ln -sv "${WORKDIR}"/fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05 third_party/fmt || die - rmdir third_party/foxi || die - ln -sv "${WORKDIR}"/foxi-c278588e34e535f0bb8f00df3880d26928038cad third_party/foxi || die - rmdir third_party/FP16 || die - ln -sv "${WORKDIR}"/FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3 third_party/FP16 || die - rmdir third_party/FXdiv - ln -sv "${WORKDIR}"/FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1 third_party/FXdiv || die - rmdir third_party/gemmlowp/gemmlowp || die - ln -sv "${WORKDIR}"/gemmlowp-3fb5c176c17c765a3492cd2f0321b0dab712f350 third_party/gemmlowp/gemmlowp || die - rmdir third_party/gloo || die - ln -sv "${WORKDIR}"/gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f third_party/gloo || die - rmdir third_party/googletest || die - ln -sv "${WORKDIR}"/googletest-e2239ee6043f73722e7aa812a459f54a28552929 third_party/googletest || die - rmdir third_party/ideep || die - ln -sv "${WORKDIR}"/ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40 third_party/ideep || die - rmdir third_party/ideep/mkl-dnn || die - ln -sv "${WORKDIR}"/mkl-dnn-5ef631a030a6f73131c77892041042805a06064f third_party/ideep/mkl-dnn || die - rmdir third_party/nccl/nccl || die - ln -sv "${WORKDIR}"/nccl-033d799524fb97629af5ac2f609de367472b2696 third_party/nccl/nccl || die - rmdir third_party/NNPACK || die - ln -sv "${WORKDIR}"/NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73 third_party/NNPACK || die - rmdir third_party/onnx || die - ln -sv "${WORKDIR}"/onnx-29e7aa7048809784465d06e897f043a4600642b2 third_party/onnx || die - rmdir third_party/onnx-tensorrt || die - ln -sv "${WORKDIR}"/onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f third_party/onnx-tensorrt || die - rmdir third_party/onnx-tensorrt/third_party/onnx || die - ln -sv "${WORKDIR}"/onnx-765f5ee823a67a866f4bd28a9860e81f3c811ce8 third_party/onnx-tensorrt/third_party/onnx || die - rmdir third_party/onnx/third_party/benchmark || die - ln -sv "${WORKDIR}"/benchmark-e776aa0275e293707b6a0901e0e8d8a8a3679508 third_party/onnx/third_party/benchmark || die - rmdir third_party/psimd || die - ln -sv "${WORKDIR}"/psimd-072586a71b55b7f8c584153d223e95687148a900 third_party/psimd || die - rmdir third_party/pthreadpool || die - ln -sv "${WORKDIR}"/pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413 third_party/pthreadpool || die - rmdir third_party/python-peachpy || die - ln -sv "${WORKDIR}"/PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473 third_party/python-peachpy || die - rmdir third_party/QNNPACK || die - ln -sv "${WORKDIR}"/QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c third_party/QNNPACK || die - rmdir third_party/sleef || die - ln -sv "${WORKDIR}"/sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff third_party/sleef || die - rmdir third_party/tensorpipe || die - ln -sv "${WORKDIR}"/tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9 third_party/tensorpipe || die - rmdir third_party/tensorpipe/third_party/googletest || die - ln -sv "${WORKDIR}"/googletest-2fe3bd994b3189899d93f1d5a881e725e046fdc2 third_party/tensorpipe/third_party/googletest || die - rmdir third_party/tensorpipe/third_party/libnop || die - ln -sv "${WORKDIR}"/libnop-aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2 third_party/tensorpipe/third_party/libnop || die - rmdir third_party/tensorpipe/third_party/libuv || die - ln -sv "${WORKDIR}"/libuv-02a9e1be252b623ee032a3137c0b0c94afbe6809 third_party/tensorpipe/third_party/libuv || die - rmdir third_party/XNNPACK || die - ln -sv "${WORKDIR}"/XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db third_party/XNNPACK || die - rmdir third_party/kineto || die - ln -sv "${WORKDIR}"/kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b third_party/kineto || die - - if use cuda; then - cd third_party/nccl/nccl || die - eapply "${FILESDIR}"/${PN}-1.6.0-nccl-nvccflags.patch - -# addpredict /dev/nvidiactl - cuda_src_prepare - export CUDAHOSTCXX=$(cuda_gccdir)/g++ - fi - - if use rocm; then - #Allow escaping sandbox - addread /dev/kfd - addread /dev/dri - addwrite /dev/kfd - addwrite /dev/dri - - ebegin "HIPifying cuda sources" - tools/amd_build/build_amd.py - eend $? - - export PYTORCH_ROCM_ARCH=$(rocminfo | egrep -o "gfx[0-9]+" | uniq | awk -vORS=';' "{print $1}" | sed 's/;$/\n/') || die - sed -e "/set(roctracer_INCLUDE_DIRS/s,\${ROCTRACER_PATH}/include,${EPREFIX}/usr/include/roctracer," \ - -i cmake/public/LoadHIP.cmake || die - fi -} - -src_configure() { - local mycmakeargs=( - -DTORCH_BUILD_VERSION=${PV} - -DTORCH_INSTALL_LIB_DIR=$(get_libdir) - -DBUILD_BINARY=$(usex tools ON OFF) - -DBUILD_CUSTOM_PROTOBUF=OFF - -DBUILD_PYTHON=$(usex python ON OFF) - -DBUILD_SHARED_LIBS=$(usex static OFF ON) - -DBUILD_TEST=$(usex test ON OFF) - -DUSE_ASAN=$(usex asan ON OFF) - -DUSE_CUDA=$(usex cuda ON OFF) - -DUSE_NCCL=$(usex cuda ON OFF) - -DUSE_SYSTEM_NCCL=OFF - -DUSE_ROCM=$(usex rocm ON OFF) - -DUSE_FBGEMM=$(usex fbgemm ON OFF) - -DUSE_FFMPEG=$(usex ffmpeg ON OFF) - -DUSE_GFLAGS=$(usex gflags ON OFF) - -DUSE_GLOG=$(usex glog ON OFF) - -DUSE_LEVELDB=$(usex leveldb ON OFF) - -DUSE_LITE_PROTO=OFF - -DUSE_LMDB=$(usex lmdb ON OFF) - -DUSE_MKLDNN=$(usex mkldnn ON OFF) - -DUSE_MKLDNN_CBLAS=OFF - -DUSE_NNPACK=$(usex nnpack ON OFF) - -DUSE_NUMPY=$(usex python ON OFF) - -DUSE_NUMA=$(usex numa ON OFF) - -DUSE_OBSERVERS=$(usex observers ON OFF) - -DUSE_OPENCL=$(usex opencl ON OFF) - -DUSE_OPENCV=$(usex opencv ON OFF) - -DUSE_OPENMP=$(usex openmp ON OFF) - -DUSE_TBB=OFF - -DUSE_PROF=OFF - -DUSE_QNNPACK=$(usex qnnpack ON OFF) - -DUSE_REDIS=$(usex redis ON OFF) - -DUSE_ROCKSDB=OFF - -DUSE_ZMQ=$(usex zeromq ON OFF) - -DUSE_MPI=$(usex mpi ON OFF) - -DUSE_GLOO=$(usex gloo ON OFF) - -DUSE_SYSTEM_EIGEN_INSTALL=ON - -DBUILD_NAMEDTENSOR=$(usex namedtensor ON OFF) - -DBLAS=$(usex blas Generic Eigen) - -DTP_BUILD_LIBUV=OFF - -Wno-dev - ) - - cmake_src_configure - - if use python; then - CMAKE_BUILD_DIR="${BUILD_DIR}" distutils-r1_src_configure - fi - - # do not rerun cmake and the build process in src_install - sed '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die -} - -src_compile() { - cmake_src_compile - - if use python; then - CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_compile - fi -} - -src_install() { - cmake_src_install - - local LIB=$(get_libdir) - if [[ ${LIB} != lib ]]; then - mv -fv "${ED}"/usr/lib/*.so "${ED}"/usr/${LIB}/ || die - fi - - rm -rfv "${ED}/torch" - rm -rfv "${ED}/var" - rm -rfv "${ED}/usr/lib" - - rm -fv "${ED}/usr/include/*.{h,hpp}" - rm -rfv "${ED}/usr/include/asmjit" - rm -rfv "${ED}/usr/include/c10d" - rm -rfv "${ED}/usr/include/fbgemm" - rm -rfv "${ED}/usr/include/fp16" - rm -rfv "${ED}/usr/include/gloo" - rm -rfv "${ED}/usr/include/include" - rm -rfv "${ED}/usr/include/var" - - cp -rv "${WORKDIR}/${P}/third_party/pybind11/include/pybind11" "${ED}/usr/include/" - - rm -fv "${ED}/usr/${LIB}/libtbb.so" - rm -rfv "${ED}/usr/${LIB}/cmake" - - if use python; then - scanelf -r --fix "${BUILD_DIR}/caffe2/python" - CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_install - - python_foreach_impl python_optimize - fi - - find "${ED}/usr/${LIB}" -name "*.a" -exec rm -fv {} \; - - use test && rm -rfv "${ED}/usr/test" "${ED}"/usr/bin/test_{api,jit} - - # Remove the empty directories by CMake Python: - find "${ED}" -type d -empty -delete || die -} diff --git a/sci-libs/rdkit/Manifest b/sci-libs/rdkit/Manifest index 94554cc96..50005a850 100644 --- a/sci-libs/rdkit/Manifest +++ b/sci-libs/rdkit/Manifest @@ -1,4 +1 @@ -DIST coordgenlibs-1.4.0.tar.gz 154413 BLAKE2B f8965135d15c3f0b0c70577907990221df61f480dc5c23df17944ef799044825f82ce5dd774f7e23f5a28394e4da9370a0abc0c2b983555c0eacc1c9b0f74c8b SHA512 8fcf8e959797dcefbac0f713fdb5f1f120c8a0ffd0e7619a675a22882a5dcee79352bad85ba91df9a7a30a6b832e5f59300be08a5e9aa7313edeec8efac1a95a -DIST maeparser-1.2.3.tar.gz 38435 BLAKE2B 666bad8d53b53702ecba434a77ae23fbc006eaa509d5b709c722416a2a1f551a23ea22c302789da6c1b62d96009d75f510e641d8996624a157a5eb6a62a425dd SHA512 fbe398a65dd3f375e320a44464bce57b37382ac78460e34875180d72f319b5fcf4bdbc0ce3b4787767f2d3d3d84cff752ed02e7b1c4890dc40760d9efe036e1b -DIST rapidjson-1.1.0.tar.gz 1019402 BLAKE2B e1564b3cfa020f76437b0a35048a42ff2cd98b5ce285e63f228e158885182e5cecda13407cdf30c03fa39b47cbc579ff0065f6c2682d04b806e8f9ea8d36fc4e SHA512 2e82a4bddcd6c4669541f5945c2d240fb1b4fdd6e239200246d3dd50ce98733f0a4f6d3daa56f865d8c88779c036099c52a9ae85d47ad263686b68a88d832dff -DIST rdkit-2020.03.6.tar.gz 60759026 BLAKE2B 9f7e9ad832bc779bc687d7de6109d58588c8a1151d50483a4c09c16281d1cf97e596e5075d4122e7f97e3ca67c981aa7d1e3bb09bb97ce6b4230e63f3280f4c3 SHA512 bc0a1ca21eaced83332de52f0d8ca81a5efc9585013edbccf277cf791672dac20cef16eff459441c9a699d6486064108311968247122d403e690f3d391b16b68 +DIST rdkit-2021.09.4.tar.gz 78474802 BLAKE2B 8c78c787a0e414b5e035998d9575322edca955acecb6d2df173610398f91cffd0b9053e7fc2c9284a2117afd720f313b7a63ed7e9ab67c708f25a5735b838f59 SHA512 c761fd5c3340ec38141165996b8666c3dcd4ed46ab91ca0d5a43ae3daedfc423ae36ec5882f085e1bd0c4c13dfe1f09497d05ec95e4847048c0acff8bcd0b1db diff --git a/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch b/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch deleted file mode 100644 index 2f7656245..000000000 --- a/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch +++ /dev/null @@ -1,59 +0,0 @@ ---- a/External/catch/CMakeLists.txt 2020-09-28 05:09:11.307595711 -0400 -+++ b/External/catch/CMakeLists.txt 2020-09-28 05:10:35.188570785 -0400 -@@ -13,9 +13,6 @@ - message("-- Catch not found in ${CATCH_DIR}") - include(RDKitUtils) - set(RELEASE_NO "2.1.2") -- downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz" -- "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz" -- "4c5740d7446d9b4e3735dcff0951aaca") - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) ---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:13:38.351584109 -0400 -+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:15:49.396007762 -0400 -@@ -38,9 +38,6 @@ - - if(NOT EXISTS "${MAEPARSER_DIR}/MaeParser.hpp") - set(RELEASE_NO "1.2.3") -- set(MD5 "4ead02a0bf87110d1caae79ab42a5747") -- downloadAndCheckMD5("https://github.com/schrodinger/maeparser/archive/v${RELEASE_NO}.tar.gz" -- "${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz" ${MD5}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) ---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:31:21.353305949 -0400 -+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:32:04.187783628 -0400 -@@ -67,9 +67,6 @@ - - if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h") - set(RELEASE_NO "1.4.0") -- set(MD5 "5f663c8809b494f0548dd504c011c739") -- downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz" -- "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz" ${MD5}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) ---- a/External/RingFamilies/CMakeLists.txt 2020-09-18 11:18:37.000000000 -0400 -+++ b/External/RingFamilies/CMakeLists.txt 2020-09-28 05:35:04.427800305 -0400 -@@ -8,9 +8,6 @@ - - if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h") - set(RELEASE_NO "1.1.3_rdkit") -- set(MD5 "e9a0bcdda8b921a35e812b9888a9a874") -- downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz" -- "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) ---- a/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-18 11:18:37.000000000 -0400 -+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-28 05:36:47.759960868 -0400 -@@ -1,8 +1,5 @@ - - if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") -- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" -- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" -- "badd12c511e081fec6c89c43a7027bce") - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch new file mode 100644 index 000000000..94a209e0f --- /dev/null +++ b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch @@ -0,0 +1,22 @@ +diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt +index 8027444..6a8c715 100644 +--- a/Code/GraphMol/MolInterchange/CMakeLists.txt ++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt +@@ -1,16 +1,5 @@ + +-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") +- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" +- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" +- "badd12c511e081fec6c89c43a7027bce") +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf +- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz +- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) +-else() +- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") +-endif() +- +-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) ++include_directories(/usr/include/rapidjson) + + + rdkit_library(MolInterchange diff --git a/sci-libs/rdkit/rdkit-2020.03.6.ebuild b/sci-libs/rdkit/rdkit-2020.03.6.ebuild deleted file mode 100644 index b73817270..000000000 --- a/sci-libs/rdkit/rdkit-2020.03.6.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit cmake python-r1 - -DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python" -HOMEPAGE="http://www.rdkit.org/" -SRC_URI=" - https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz - https://github.com/schrodinger/maeparser/archive/v1.2.3.tar.gz -> maeparser-1.2.3.tar.gz - https://github.com/schrodinger/coordgenlibs/archive/v1.4.0.tar.gz -> coordgenlibs-1.4.0.tar.gz - https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz -> rapidjson-1.1.0.tar.gz - " -# issues with bundled packages; dev-libs/rapidjson, at least, should be unbundled: -# https://github.com/rdkit/rdkit/issues/3443 - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" -# build configuration issues https://github.com/rdkit/rdkit/issues/3444 -IUSE="+python static-libs" -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND="dev-libs/boost - python? ( - dev-libs/boost[python,${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - ${PYTHON_DEPS} - ) - >=dev-db/sqlite-3" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/rdkit-Release_${PV//./_} - -PATCHES=( "${FILESDIR}"/${P}-no_dynamic_checking.patch ) - -src_prepare() { - cp ../maeparser-* -rf External/CoordGen/ || die - cp ../coordgenlibs-* -rf External/CoordGen/ || die - cp ../rapidjson-* -rf External/ || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr - -DRDK_INSTALL_INTREE=0 - -DRDK_BUILD_CPP_TESTS=OFF - -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)" - -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)" - ) - cmake_src_configure -} diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2021.09.4.ebuild new file mode 100644 index 000000000..a1621ea79 --- /dev/null +++ b/sci-libs/rdkit/rdkit-2021.09.4.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) + +inherit cmake python-single-r1 + +DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python" +HOMEPAGE="http://www.rdkit.org/" +SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/rdkit-Release_${PV//./_}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+python static-libs test" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" +RESTRICT="!test? ( test )" + +RDEPEND="dev-libs/boost + python? ( + $(python_gen_cond_dep ' + dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + ') + ${PYTHON_DEPS} + ) + dev-cpp/catch:0 + dev-libs/rapidjson + >=dev-db/sqlite-3" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch" +) + +src_configure() { + local mycmakeargs=( + -DCATCH_DIR="${EPREFIX}/usr/include/catch2" + -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr" + -DRDK_INSTALL_INTREE=0 + -DRDK_BUILD_CPP_TESTS="$(usex test)" + -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)" + -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)" + # Disable things that trigger fetching and are not packaged + -DRDK_INSTALL_COMIC_FONTS=OFF + -DRDK_BUILD_COORDGEN_SUPPORT=OFF + -DRDK_BUILD_MAEPARSER_SUPPORT=OFF + -DRDK_USE_URF=OFF + ) + cmake_src_configure +} + +src_test() { + RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test +} diff --git a/sci-libs/scikit-learn-intelx/Manifest b/sci-libs/scikit-learn-intelx/Manifest new file mode 100644 index 000000000..d14b31510 --- /dev/null +++ b/sci-libs/scikit-learn-intelx/Manifest @@ -0,0 +1 @@ +DIST scikit-learn-intelx-2023.0.2.tar.gz 13864043 BLAKE2B dfc082a8b008553e0d20cf7a24417fecd510dd8e6b3286a57a633b1e3b79cecc87fc1189df6f4a3440d7ccb74077c54a9f6eaf58bfbb19181cb4b437b3e06ae6 SHA512 dd8c983365d4f32d2640caab17319970c86bfed5ad6852d15dce35ba66a3584c51b94fa5ef0d8073b917332ea18a8c9af95ef8da125edb47190f27e9b8cab424 diff --git a/sci-libs/scikit-learn-intelx/metadata.xml b/sci-libs/scikit-learn-intelx/metadata.xml new file mode 100644 index 000000000..247707c87 --- /dev/null +++ b/sci-libs/scikit-learn-intelx/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">intel/scikit-learn-intelex</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild b/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild new file mode 100644 index 000000000..29288cbcf --- /dev/null +++ b/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild @@ -0,0 +1,49 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Seamless way to speed up your Scikit-learn application" +HOMEPAGE="https://github.com/intel/scikit-learn-intelex" +SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/scikit-learn-intelex-${PV}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/daal4py[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl" + export MPIROOT="${ESYSROOT}/usr" + export DALROOT="${ESYSROOT}/usr" + + # remove the daal4py setup files, and rename skleanex setup files + rm setup.py setup.cfg || die + mv setup_sklearnex.cfg setup.cfg || die + mv setup_sklearnex.py setup.py || die + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/sci-libs/scikits_video/Manifest b/sci-libs/scikits_video/Manifest deleted file mode 100644 index d18395f99..000000000 --- a/sci-libs/scikits_video/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST scikits_video-1.1.11_p20200115.tar.gz 32060067 BLAKE2B 2f2c14ed89638f46b3c7e27b5d7562429a17f86982442f66015392173dcda89fa3ef810e4529dca9f4dccdb59287f12af2d897411124e4d15abb6197e7d13fc5 SHA512 ca3c4eaf343075934d83c540ff11cb4f2e611838bcbfd9f06efb69b00875ffc77dac1f0f32978d554a7cb126c8d689013fb103b61cda39b7d4d9f85c81542b2d diff --git a/sci-libs/scikits_video/metadata.xml b/sci-libs/scikits_video/metadata.xml deleted file mode 100644 index 186bb5c9c..000000000 --- a/sci-libs/scikits_video/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - Scikit-video is designed for easy video processing using Python. It is - modeled in the spirit of other successful scikits such as scikit-learn - and scikit-image. This project aims to provide an all-in-one solution to - make video algorithms easy to access for students, engineers, - instructors, and researchers. - </longdescription> - <upstream> - <remote-id type="pypi">scikit-video</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild b/sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild deleted file mode 100644 index bb8efaa24..000000000 --- a/sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -MY_PN="scikit-video" -MY_HASH="87c7113a84b50679d9853ba81ba34b557f516b05" - -DESCRIPTION="Video processing in Python" -HOMEPAGE="https://scikit-image.org/" -SRC_URI="https://github.com/scikit-video/scikit-video/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - media-video/ffmpeg - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] - media-video/mediainfo -" - -S="${WORKDIR}/${MY_PN}-${MY_HASH}" - -distutils_enable_tests pytest diff --git a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild index afc114669..26e0c688d 100644 --- a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild +++ b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_10 ) LUA_COMPAT=( lua5-{1..3} ) -inherit lua-single toolchain-funcs cmake python-single-r1 +inherit lua-single cmake python-single-r1 MY_PN="SimpleITK" diff --git a/sci-libs/spams-python/Manifest b/sci-libs/spams-python/Manifest deleted file mode 100644 index d58c9e869..000000000 --- a/sci-libs/spams-python/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST spams-python-2.6.2.tar.gz 315332 BLAKE2B 1aa972a65c2f69de859391b98a28972ebbd30f166ea3d44083933f746e119105d45d6ee5adff99064dc396f5522c31e5dd4055210c82e93c1217a06bf4bce2f2 SHA512 dec2ce2abe5abeb78bf470952c5f854501bf9ea21019dda1de66683f813153e78cc9b87b5376e91ac74beedb4d13854cc053e54e97bfded4177728c540812a9f diff --git a/sci-libs/spams-python/metadata.xml b/sci-libs/spams-python/metadata.xml deleted file mode 100644 index 4cb1814dc..000000000 --- a/sci-libs/spams-python/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - SPAMS (SPArse Modeling Software) is an optimization toolbox for solving - various sparse estimation problems, such as: Dictionary learning and - matrix factorization (NMF, sparse PCA, ...); solving sparse decomposition - problems with LARS, coordinate descent, OMP, SOMP, proximal methods; and - Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse - group lasso, tree-structured regularization, structured sparsity with - overlapping groups,...). - </longdescription> - <upstream> - <remote-id type="github">samuelstjean/spams-python</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/spams-python/spams-python-2.6.2.ebuild b/sci-libs/spams-python/spams-python-2.6.2.ebuild deleted file mode 100644 index 99b1e6370..000000000 --- a/sci-libs/spams-python/spams-python-2.6.2.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 toolchain-funcs - -DESCRIPTION="Optimization toolbox for solving various sparse estimation problems" -HOMEPAGE="http://spams-devel.gforge.inria.fr/index.html" -SRC_URI="https://github.com/samuelstjean/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-python/distro[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - sci-libs/openblas - virtual/lapack - " -RDEPEND="${DEPEND} - dev-python/scipy[${PYTHON_USEDEP}] - " - -pc_libdir() { - $(tc-getPKG_CONFIG) --libs-only-L $@ | \ - sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^,||' -} - -pc_libs() { - $(tc-getPKG_CONFIG) --libs-only-l $@ | \ - sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ - -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ - | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' -} -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -python_prepare_all() { - local libdir="${EPREFIX}"/usr/$(get_libdir) - MY_LAPACK=$(pc_libs lapack) - MY_BLAS=$(pc_libs blas) - MY_LIBDIRS="$(pc_libdir blas lapack)'${libdir}'" - sed -i -e "s/'blas', 'lapack'/'${MY_BLAS}', '${MY_LAPACK}'/g" setup.py || die - sed -i -e "s|libdirs = \[\]|libdirs = [${MY_LIBDIRS}]|g" setup.py || die - distutils-r1_python_prepare_all -} - -python_test() { - ${EPYTHON} test_spams.py -} diff --git a/sci-libs/spyking-circus/Manifest b/sci-libs/spyking-circus/Manifest index 8550f6bab..d74a84da5 100644 --- a/sci-libs/spyking-circus/Manifest +++ b/sci-libs/spyking-circus/Manifest @@ -1 +1 @@ -DIST spyking-circus-1.0.6.tar.gz 4814284 BLAKE2B 171aff57a6ab23c54c497f4486b3453666029aef27bb6c1051ddac2be4131d78e065d08feea9c193dd52cb6723db5bdd3aaacfe92cbdc7be35c90631957d4ded SHA512 908aea4f7c4fd47fdd9b67b70873708ae5dd5e461b12dbbe3b519ea058ce63235bede94800204d2e48dbde9bfed8b90c9f6bb40e93134bb8950f1b958103ecdf +DIST spyking-circus-1.1.0.tar.gz 4822364 BLAKE2B e862cc40618db0dab45d0d8d2461a0e72b6ba442af7701ccb2af8c96afe4116715b5a8758670ac37b462fdfc5e5b2815a7ffb4d485c3d5bfec667fb6137a3b41 SHA512 87aa7f6c6efd1a419fd9394cc2e5467d4d8da96afdca46761df10215a1f5fd198e78a39cf75f4b0c5310b21ada9db831d2a14878c6ad0de37c86c63bd9ce4807 diff --git a/sci-libs/spyking-circus/metadata.xml b/sci-libs/spyking-circus/metadata.xml index 844f386de..89a208f6f 100644 --- a/sci-libs/spyking-circus/metadata.xml +++ b/sci-libs/spyking-circus/metadata.xml @@ -16,4 +16,7 @@ on datasets coming from in vitro retina with 252 electrodes MEA, from in vivo hippocampus with tetrodes, and in vivo and in vitro cortex data. </longdescription> + <upstream> + <remote-id type="github">spyking-circus/spyking-circus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild index f453c6986..9b9233020 100644 --- a/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild +++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -13,9 +13,9 @@ SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz - LICENSE="CeCILL-2" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" -# TODO: Fix this +# Wants to run mpirun (and fails) RESTRICT="test" RDEPEND=" @@ -26,13 +26,10 @@ RDEPEND=" >=dev-python/matplotlib-2.2.4[${PYTHON_USEDEP}] >=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}] >=dev-python/numpy-1.17.4[${PYTHON_USEDEP}] - >=dev-python/pandas-0.21[${PYTHON_USEDEP}] >=dev-python/psutil-5.6.7[${PYTHON_USEDEP}] - >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] >=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}] >=dev-python/scipy-1.3.1[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.21.3 - || ( <=sys-cluster/openmpi-3.0.0 >=sys-cluster/mpich-2.0 ) " DEPEND="${RDEPEND}" diff --git a/sci-libs/superlu_dist/Manifest b/sci-libs/superlu_dist/Manifest deleted file mode 100644 index 5b7c716f7..000000000 --- a/sci-libs/superlu_dist/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST superlu_dist-6.4.0.tar.gz 1710130 BLAKE2B 82a14c8fe671bc16daa1f9ae9014dd39300566057af25acda3a9a5fd6581157a7d40baff9c9520cf6a93726418407bdfbeffe77c60dfe261fd41511d79059167 SHA512 e9de825ad65979df238cfdd5d07fefe0775ba705b247b2cca2ce6b7cd775f39c45320617553f5e0e05f39be17c5d3c8d1d40f03272fd87303a3c230b3a120172 diff --git a/sci-libs/superlu_dist/metadata.xml b/sci-libs/superlu_dist/metadata.xml deleted file mode 100644 index 0bd32bba5..000000000 --- a/sci-libs/superlu_dist/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> -SuperLU is a general purpose library for the direct solution of -large, sparse, nonsymmetric systems of linear equations on high -performance machines. The library is written in C and is callable -from either C or Fortran. The library routines will perform an LU -decomposition with partial pivoting and triangular system solves -through forward and back substitution. The LU factorization routines -can handle non-square matrices but the triangular solves are -performed only for square matrices. The matrix columns may be -preordered (before factorization) either through library or user -supplied routines. This preordering for sparsity is completely -separate from the factorization. Working precision iterative -refinement subroutines are provided for improved backward -stability. Routines are also provided to equilibrate the system, -estimate the condition number, calculate the relative backward -error, and estimate error bounds for the refined solutions. -This is the distributed version (MPI based). -</longdescription> -</pkgmetadata> diff --git a/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild b/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild deleted file mode 100644 index 8c0b87423..000000000 --- a/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DOCS_BUILDER="doxygen" -DOCS_CONFIG_NAME="DoxyConfig" - -inherit cmake docs multilib - -MYPN=SuperLU_DIST - -DESCRIPTION="MPI distributed sparse LU factorization library" -HOMEPAGE="https://portal.nersc.gov/project/sparse/superlu/ https://github.com/xiaoyeli/superlu_dist" -SRC_URI="https://github.com/xiaoyeli/superlu_dist/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples test" -RESTRICT="!test? ( test )" - -RDEPEND=" - sci-libs/parmetis[mpi(-)] - virtual/mpi" -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -src_configure() { - local mycmakeargs=( - -DTPL_PARMETIS_LIBRARIES="/usr/$(get_libdir)/libmetis.so" - -DTPL_PARMETIS_INCLUDE_DIRS="/usr/include/" - -Denable_examples=$(usex examples ON OFF) - -Denable_tests=$(usex test ON OFF) - ) - cmake_src_configure -} - -src_compile() { - cmake_src_compile - default -} diff --git a/sci-libs/torchvision/Manifest b/sci-libs/torchvision/Manifest new file mode 100644 index 000000000..7cf5fa956 --- /dev/null +++ b/sci-libs/torchvision/Manifest @@ -0,0 +1,2 @@ +DIST torchvision-0.14.1.tar.gz 9265179 BLAKE2B 0708635b00ac7c2cf4e54799f1190f01f3240f53233695819f691313b8a369b8922520e2f3cf96184bab671877b5826b84e0936d9ca5b58004d6e2a098c6cbbf SHA512 08fb1e35da1c3f1d0446ef879d9b6a7ae839a5137c3b5b46ef8111c2ae890299e2b555d1bd3b3d61f96b8778b831d8f895487cf8a4e36e371fcd4b8acda67d1f +DIST torchvision-0.17.1.tar.gz 13091686 BLAKE2B db25faab565412f2892ca4cf8d13c459b8045aaab83009a686a93272f0b3e3e8c0da930f1d7b0682e0adc7a600195b035ca19f71fd15a26f77b349206e3ed324 SHA512 c9ef5704a337a43c1ab3a5865b2a20d09d07a9b5eeda66c7aa1e1931772bad9acee822bb400cf627960a84ace01188cd32e95f0e709eb392bf9028d36cfc50be diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch new file mode 100644 index 000000000..7a3637f3a --- /dev/null +++ b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch @@ -0,0 +1,36 @@ +From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?= + <zboszor@gmail.com> +Date: Tue, 7 Nov 2023 10:43:11 +0100 +Subject: [PATCH] Fix build with ffmpeg 6.0 +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Signed-off-by: Zoltán Böszörményi <zboszor@gmail.com> +--- + torchvision/csrc/io/decoder/stream.cpp | 11 ++--------- + 1 file changed, 2 insertions(+), 9 deletions(-) + +diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp +index 0d625ef211c..8c914050587 100644 +--- a/torchvision/csrc/io/decoder/stream.cpp ++++ b/torchvision/csrc/io/decoder/stream.cpp +@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector<DecoderMetadata>* metadata, int num_threads) { + codecCtx_->thread_count = num_threads; + } else { + // otherwise set sensible defaults +- // with the special case for the different MPEG4 codecs +- // that don't have threading context functions +- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) { +- codecCtx_->thread_type = FF_THREAD_FRAME; +- codecCtx_->thread_count = 2; +- } else { +- codecCtx_->thread_count = 8; +- codecCtx_->thread_type = FF_THREAD_SLICE; +- } ++ codecCtx_->thread_count = 8; ++ codecCtx_->thread_type = FF_THREAD_SLICE; + } + + int ret; diff --git a/sci-libs/torchvision/metadata.xml b/sci-libs/torchvision/metadata.xml new file mode 100644 index 000000000..9c4ddaefd --- /dev/null +++ b/sci-libs/torchvision/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>jpizarrocallejas@gmail.com</email> + <name>Jorge Pizarro Callejas</name> + </maintainer> + <upstream> + <remote-id type="github">pytorch/vision</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/torchvision/torchvision-0.14.1.ebuild b/sci-libs/torchvision/torchvision-0.14.1.ebuild new file mode 100644 index 000000000..7f40fe556 --- /dev/null +++ b/sci-libs/torchvision/torchvision-0.14.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 2020-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_SINGLE_IMPL=1 +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Datasets, transforms and models to specific to computer vision" +HOMEPAGE="https://github.com/pytorch/vision" +SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/vision-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ') + sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] + media-video/ffmpeg + dev-qt/qtcore:5 +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + $(python_gen_cond_dep ' + dev-python/mock[${PYTHON_USEDEP}] + ') + )" + +distutils_enable_tests pytest diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild b/sci-libs/torchvision/torchvision-0.17.1.ebuild new file mode 100644 index 000000000..e0c72684c --- /dev/null +++ b/sci-libs/torchvision/torchvision-0.17.1.ebuild @@ -0,0 +1,45 @@ +# Copyright 2020-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_SINGLE_IMPL=1 +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +inherit distutils-r1 multiprocessing + +DESCRIPTION="Datasets, transforms and models to specific to computer vision" +HOMEPAGE="https://github.com/pytorch/vision" +SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/vision-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +RESTRICT="test" + +RDEPEND=" + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ') + sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] + media-video/ffmpeg:= +" +DEPEND="${RDEPEND}" + +PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" ) + +src_compile() +{ + export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS + + # Ensure some ext_module sources are compiled before linking + export MAKEOPTS="-j1" + + distutils-r1_src_compile +} diff --git a/sci-libs/vegas/Manifest b/sci-libs/vegas/Manifest new file mode 100644 index 000000000..c636ac4c2 --- /dev/null +++ b/sci-libs/vegas/Manifest @@ -0,0 +1 @@ +DIST vegas-6.0.1.tar.gz 1535565 BLAKE2B 3cd30387e9369ce7efe62e1f5838f87c73bb93e1690c131602a8e0b77a6671e9d9cadb6b909e1f9ba548cd4a32cb09bd6d1d50bfaf536b7c3fbd269c4595ed04 SHA512 ead47a9f194846d704e229d62163233a7b063dab504e665d620f59be5c9abe2b31facf14cad612b102d4bf64d60d9f6f53c0b4bca0ba78d1e62cbd9bda77e0b1 diff --git a/sci-libs/vegas/metadata.xml b/sci-libs/vegas/metadata.xml new file mode 100644 index 000000000..8ae183900 --- /dev/null +++ b/sci-libs/vegas/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + The vegas package is for evaluating multidimensional integrals using an improved version of the adaptive Monte Carlo vegas algorithm (G. P. Lepage, J. Comput. Phys. 27(1978) 192). + </longdescription> + <upstream> + <remote-id type="pypi">vegas</remote-id> + <remote-id type="github">gplepage/vegas</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/vegas/vegas-6.0.1.ebuild b/sci-libs/vegas/vegas-6.0.1.ebuild new file mode 100644 index 000000000..7654563e4 --- /dev/null +++ b/sci-libs/vegas/vegas-6.0.1.ebuild @@ -0,0 +1,24 @@ +EAPI=8 + +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Adaptive multidimensional Monte Carlo integration." +HOMEPAGE="https://github.com/gplepage/vegas" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~arm64" + +RDEPEND=" + >=dev-python/numpy-1.16[${PYTHON_USEDEP}] + >=sci-libs/gvar-13.0.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + >=dev-python/cython-0.17[${PYTHON_USEDEP}] +" + +distutils_enable_tests unittest diff --git a/sci-libs/vxl/metadata.xml b/sci-libs/vxl/metadata.xml index 22feba67c..f7d43af09 100644 --- a/sci-libs/vxl/metadata.xml +++ b/sci-libs/vxl/metadata.xml @@ -13,5 +13,6 @@ written in ANSI/ISO C++ and is designed to be portable over many platforms. </longdescription> <upstream> <remote-id type="sourceforge">vxl</remote-id> + <remote-id type="github">vxl/vxl</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/vxl/vxl-2.0.2.ebuild b/sci-libs/vxl/vxl-2.0.2.ebuild index 0680cceb3..4db9621f4 100644 --- a/sci-libs/vxl/vxl-2.0.2.ebuild +++ b/sci-libs/vxl/vxl-2.0.2.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit cmake multilib +inherit cmake DESCRIPTION="C++ computer vision research libraries" HOMEPAGE="https://vxl.github.io/" diff --git a/sci-libs/wannier90/files/wannier90-1.1-0001.patch b/sci-libs/wannier90/files/wannier90-1.1-0001.patch deleted file mode 100644 index e68c5f4fe..000000000 --- a/sci-libs/wannier90/files/wannier90-1.1-0001.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -urN wannier90-1.1.old/src/wannier_lib.F90 wannier90-1.1.new/src/wannier_lib.F90 ---- wannier90-1.1.old/src/wannier_lib.F90 2007-12-20 10:58:37.000000000 +0100 -+++ wannier90-1.1.new/src/wannier_lib.F90 2008-04-28 17:27:19.000000000 +0200 -@@ -166,6 +166,12 @@ - exclude_bands_loc(1:num_exclude_bands) = exclude_bands(1:num_exclude_bands) - end if - -+ if (postproc_setup) then -+ call kmesh_write() -+ write(stdout,'(1x,a25,f11.3,a)') 'Time to write kmesh ',io_time(),' (sec)' -+ write(stdout,'(/a)') ' '//trim(seedname)//'.nnkp written.' -+ endif -+ - - call kmesh_dealloc() - call param_dealloc() diff --git a/sci-libs/wannier90/files/wannier90-1.1-0002.patch b/sci-libs/wannier90/files/wannier90-1.1-0002.patch deleted file mode 100644 index 391a34ca2..000000000 --- a/sci-libs/wannier90/files/wannier90-1.1-0002.patch +++ /dev/null @@ -1,105 +0,0 @@ -diff -urN wannier90-1.1.old/src/disentangle.F90 wannier90-1.1.new/src/disentangle.F90 ---- wannier90-1.1.old/src/disentangle.F90 2009-03-07 15:44:11.000000000 +0100 -+++ wannier90-1.1.new/src/disentangle.F90 2009-03-07 15:48:05.000000000 +0100 -@@ -1784,9 +1784,9 @@ - ! [BIG ITERATION LOOP (iter)] - - if (.not.dis_converged) then -- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement & -- &iterations reached >>>' -- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>' -+ write(stdout,'(/5x,a)') & -+ '<<< Warning: Maximum number of disentanglement iterations reached >>>' -+ write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>' - endif - - if (icompflag.eq.1) then -@@ -2551,8 +2551,8 @@ - ! [BIG ITERATION LOOP (iter)] - - if (.not.dis_converged) then -- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement & -- &iterations reached >>>' -+ write(stdout,'(/5x,a)') & -+ '<<< Warning: Maximum number of disentanglement iterations reached >>>' - write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>' - endif - -diff -urN wannier90-1.1.old/src/overlap.F90 wannier90-1.1.new/src/overlap.F90 ---- wannier90-1.1.old/src/overlap.F90 2009-03-07 15:44:11.000000000 +0100 -+++ wannier90-1.1.new/src/overlap.F90 2009-03-07 15:48:36.000000000 +0100 -@@ -141,8 +141,8 @@ - nn_found=.true. - nn=inn - else -- call io_error('Error reading '//trim(seedname)//'.mmn.& -- & More than one matching nearest neighbour found') -+ call io_error('Error reading '//trim(seedname)// & -+ '.mmn. More than one matching nearest neighbour found') - endif - endif - end do -diff -urN wannier90-1.1.old/src/parameters.F90 wannier90-1.1.new/src/parameters.F90 ---- wannier90-1.1.old/src/parameters.F90 2009-03-07 15:44:11.000000000 +0100 -+++ wannier90-1.1.new/src/parameters.F90 2009-03-07 15:50:46.000000000 +0100 -@@ -1054,8 +1054,9 @@ - write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+' - do nsp=1,num_species - do nat=1,atoms_species_num(nsp) -- write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),& -- '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|' -+ write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') & -+& '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),& -+& '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|' - end do - end do - write(stdout,'(1x,a)') '*----------------------------------------------------------------------------*' -@@ -1073,8 +1074,8 @@ - write(stdout,'(1x,a)') '| Frac. Coord. l mr r z-axis x-axis Z/a |' - write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+' - do nsp=1,num_proj -- write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),& -- & 2x,f4.1,1x,a1)') '|',proj_site(1,nsp),proj_site(2,nsp),& -+ write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),2x,f4.1,1x,a1)')& -+& '|',proj_site(1,nsp),proj_site(2,nsp),& - proj_site(3,nsp),proj_l(nsp), proj_m(nsp),proj_radial(nsp),& - proj_z(1,nsp),proj_z(2,nsp),proj_z(3,nsp),proj_x(1,nsp),& - proj_x(2,nsp),proj_x(3,nsp),proj_zona(nsp),'|' -@@ -2738,8 +2739,8 @@ - dummy=utility_strip(in_data(line)) - dummy=adjustl(dummy) - pos1=index(dummy,':') -- if(pos1==0) call io_error('param_read_projection: malformed projection & -- &definition: '//trim(dummy)) -+ if(pos1==0) & -+ call io_error('param_read_projection: malformed projection definition: '//trim(dummy)) - sites=0 - ctemp=dummy(:pos1-1) - ! Read the atomic site -@@ -2980,11 +2981,11 @@ - endif - end if - if(sites==-1) then -- if(counter+sum(ang_states) > num_proj) call io_error('param_get_projection: & -- &too many projections defined') -+ if(counter+sum(ang_states) > num_proj) & -+ call io_error('param_get_projection: too many projections defined') - else -- if(counter+sites*sum(ang_states) > num_proj) call io_error('param_get_projection:& -- & too many projections defined') -+ if(counter+sites*sum(ang_states) > num_proj) & -+ call io_error('param_get_projection: too many projections defined') - end if - ! - if(sites==-1) then -@@ -3025,8 +3026,8 @@ - - ! check there are enough projections and add random projections if required - if (.not. lpartrandom) then -- if (counter.ne.num_proj) call io_error('param_get_projections:& -- & Fewer projections defined than the number of Wannier functions requested') -+ if (counter.ne.num_proj) call io_error(& -+ 'param_get_projections: Fewer projections defined than the number of Wannier functions requested') - else - call random_seed() - do loop=counter+1,num_proj diff --git a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch b/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch deleted file mode 100644 index c9656ac31..000000000 --- a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naurp wannier90-2.0.1.1.orig/tests/run_test.pl wannier90-2.0.1.1/tests/run_test.pl ---- wannier90-2.0.1.1.orig/tests/run_test.pl 2016-02-08 11:51:52.000000000 +0000 -+++ wannier90-2.0.1.1/tests/run_test.pl 2017-01-05 12:10:29.584850729 +0000 -@@ -2,7 +2,7 @@ - # - use Cwd; - my $cwd = cwd(); --$wanex="../wannier90.x" ; -+$wanex="../src/wannier90.x" ; - $wanex=$cwd."/".$wanex ; - print " Running test set of inputs\n"; - @tests_found = <./test*>; diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml index a7ac8e977..273952673 100644 --- a/sci-libs/wannier90/metadata.xml +++ b/sci-libs/wannier90/metadata.xml @@ -18,5 +18,6 @@ <upstream> <doc>http://www.wannier.org/</doc> <remote-id type="launchpad">wannier90</remote-id> + <remote-id type="github">wannier-developers/wannier90</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/wannier90/wannier90-3.1.0.ebuild b/sci-libs/wannier90/wannier90-3.1.0.ebuild index 28bd897c4..ca53b3863 100644 --- a/sci-libs/wannier90/wannier90-3.1.0.ebuild +++ b/sci-libs/wannier90/wannier90-3.1.0.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit fortran-2 multilib toolchain-funcs +inherit fortran-2 toolchain-funcs DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)" HOMEPAGE="http://www.wannier.org/" diff --git a/sci-libs/xblas/Manifest b/sci-libs/xblas/Manifest deleted file mode 100644 index 4919da836..000000000 --- a/sci-libs/xblas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xblas-1.0.248.tar.gz 2087424 BLAKE2B 47f446f95f033260baec4053f4d761eda54e753bd39477cdf0636f3b68f1a3748f6c48aa32eaa693a486a8bb92b259b2742e42a2663fa1b3a75de1d3ff93daac SHA512 4a3c3a6aea0e12a5620ba1c4d328ca9f20764da4871b2bac48c21366c25afed31daa3a3ef291973159b890b2bbf033bdc14503634637b50ff4514f425b4356ad diff --git a/sci-libs/xblas/metadata.xml b/sci-libs/xblas/metadata.xml deleted file mode 100644 index 11b4b52f7..000000000 --- a/sci-libs/xblas/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> -The XBLAS library of routines is part of a reference implementation for -the Dense and Banded Basic Linear Algebra Subroutines, along with their -Extended and Mixed Precision versions, as documented in Chapters 2 and 4 -of the new BLAS Standard. -</longdescription> - <use> - <flag name="int64">Build the 64 bits integer library</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/xblas/xblas-1.0.248-r1.ebuild b/sci-libs/xblas/xblas-1.0.248-r1.ebuild deleted file mode 100644 index 1467ccc19..000000000 --- a/sci-libs/xblas/xblas-1.0.248-r1.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -NUMERIC_MODULE_NAME="xblas" -FORTRAN_NEEDED=fortran - -inherit flag-o-matic fortran-2 numeric-int64-multibuild toolchain-funcs - -DESCRIPTION="Extra Precise Basic Linear Algebra Subroutines" -HOMEPAGE="https://www.netlib.org/xblas/" -SRC_URI="https://www.netlib.org/xblas/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc fortran static-libs" - -RDEPEND="" -DEPEND="${RDEPEND} - sys-devel/m4" - -static_to_shared() { - local libstatic=${1}; shift - local libname=$(basename ${libstatic%.a}) - local soname=${libname}$(get_libname $(ver_cut 1-2)) - local libdir=$(dirname ${libstatic}) - - einfo "Making ${soname} from ${libstatic}" - if [[ ${CHOST} == *-darwin* ]] ; then - ${LINK:-$(tc-getCC)} ${LDFLAGS} \ - -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ - -Wl,-all_load -Wl,${libstatic} \ - "$@" -o ${libdir}/${soname} || die "${soname} failed" - else - ${LINK:-$(tc-getCC)} ${LDFLAGS} \ - -shared -Wl,-soname=${soname} \ - -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ - "$@" -o ${libdir}/${soname} || die "${soname} failed" - [[ ${#PV} -gt 1 ]] && \ - ln -s ${soname} ${libdir}/${libname}$(get_libname $(ver_cut 0-1)) || die - ln -s ${soname} ${libdir}/${libname}$(get_libname) || die - fi -} - -pkg_setup() { - use fortran && fortran-2_pkg_setup -} - -src_prepare() { - default - numeric-int64-multibuild_copy_sources -} - -src_configure() { - xblas_configure() { - export FCFLAGS="${FCFLAGS} $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)" - econf $(use_enable fortran) - } - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_configure -} - -src_compile() { - xblas_src_compile() { - local profname=$(numeric-int64_get_module_name) - local libname="${profname//-/_}" - # default target builds and runs tests - split - # build first static libs because of fPIC afterwards - # and we link tests with shared ones - if use static-libs; then - emake makefiles - emake lib XBLASLIB=lib${libname}_nonpic.a - emake clean - fi - sed -i \ - -e 's:\(CFLAGS.*\).*:\1 -fPIC:' \ - make.inc || die - emake makefiles - emake lib XBLASLIB=lib${libname}.a - static_to_shared lib${libname}.a - } - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_src_compile -} - -src_test() { - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir emake tests -} - -src_install() { - xblas_src_install() { - local profname=$(numeric-int64_get_module_name) - local libname="${profname//-/_}" - if numeric-int64_is_static_build; then - use static-libs && newlib.a lib${libname}_nonpic.a lib${libname}.a - else - dolib.so lib${libname}$(get_libname)* - - create_pkgconfig \ - --name ${profname} \ - --libs "-L\${libdir} -l${libname}" \ - --cflags "-I\${includedir} $(numeric-int64_get_fortran_int64_abi_fflags)" \ - ${profname} - fi - } - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_src_install - - dodoc README README.devel - use doc && dodoc doc/report.ps -} diff --git a/sci-libs/xraylib/Manifest b/sci-libs/xraylib/Manifest deleted file mode 100644 index 9ca464e07..000000000 --- a/sci-libs/xraylib/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xraylib-4.0.0.tar.gz 7844625 BLAKE2B 3db521e15147d9bae4ce8aa08c488460a57233143df2b71518fddffdcf14de34b44ffde0262ad44bcddd39fa067badc304d341d841e0beedee99d36a46cd364f SHA512 ce5cc0d628d397921e10a812251c21a159f529165589b9408fa43112024cd44f3c7fe710a4f1fc51778645850896a23ea32fddbda21ebeebf9e53eefaf1e5b29 diff --git a/sci-libs/xraylib/metadata.xml b/sci-libs/xraylib/metadata.xml deleted file mode 100644 index a7d2f91fb..000000000 --- a/sci-libs/xraylib/metadata.xml +++ /dev/null @@ -1,42 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>cjk34@cam.ac.uk</email> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> -Quantitative estimate of elemental composition by spectroscopic and imaging -techniques using X-ray fluorescence requires the availability of accurate data -of X-ray interaction with matter. Although a wide number of computer codes -and data sets are reported in literature, none of them is presented in the -form of freely available library functions which can be easily included in -software applications for X-ray fluorescence. This work presents a compilation -of data sets from different published works and an xraylib interface in the -form of callable functions. Although the target applications are on X-ray -fluorescence, cross sections of interactions like photoionization, coherent -scattering and Compton scattering, as well as form factors and anomalous -scattering functions, are also available. - -xraylib provides access to some of the most respected databases of physical -data in the field of x-rays. The core of xraylib is a library, written in ANSI -C, containing over 40 functions to be used to retrieve data from these -databases. This C library can be directly linked with any program written in -C, C++ or Objective-C. Furthermore, the xraylib package contains bindings to -several popular programming languages: Fortran 2003, Perl, Python, Java, IDL, -Lua and .NET, as well as a command-line utility which can be used as a -pocket-calculator. Although not officially supported, xraylib has been -reported to be useable from within Matlab and LabView. - -Reference: T. Schoonjans, A. Brunetti, B. Golosio, M. Sanchez del Rio, -V. A. Solé, C. Ferrero and L. Vincze, "The xraylib library for X-ray--matter -interactions. Recent developments", Spectrochimica Acta B 66 (2011) 776-784 -( doi: http://dx.doi.org/10.1016/j.sab.2011.09.011 ) -</longdescription> - <upstream> - <remote-id type="github">tschoonj/xraylib</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/xraylib/xraylib-4.0.0.ebuild b/sci-libs/xraylib/xraylib-4.0.0.ebuild deleted file mode 100644 index 6dfde6dae..000000000 --- a/sci-libs/xraylib/xraylib-4.0.0.ebuild +++ /dev/null @@ -1,96 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -AUTOTOOLS_AUTORECONF=true -FORTRAN_NEEDED=fortran -FORTRAN_STANDARD=2003 -PYTHON_COMPAT=( python3_{7,8,9} ) # python 3 supported by github master -LUA_COMPAT=( lua5-{1..3} ) -USE_RUBY="ruby27 ruby30" - -inherit python-single-r1 lua-single ruby-single java-pkg-opt-2 fortran-2 - -DESCRIPTION="X-ray matter interaction cross sections for X-ray fluorescence library" -HOMEPAGE="https://github.com/tschoonj/xraylib" -SRC_URI="http://lvserver.ugent.be/xraylib/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -#IUSE="examples fortran java lua perl python" -# jave now uses the gradle build system which is not supported by portage -IUSE="examples fortran lua perl php python ruby" - -REQUIRED_USE=" - python? ( ${PYTHON_REQUIRED_USE} ) - lua? ( ${LUA_REQUIRED_USE} ) -" - -RDEPEND=" - lua? ( ${LUA_DEPS} ) - perl? ( dev-lang/perl ) - php? ( <dev-lang/php-8:* ) - python? ( - ${PYTHON_DEPS} - $(python_gen_cond_dep \ - 'dev-python/numpy[${PYTHON_USEDEP}]' - ) - ) - ruby? ( ${RUBY_DEPS} ) -" # java? ( >=virtual/jre-1.7:* ) - -DEPEND="${RDEPEND}" -# java? ( >=virtual/jdk-1.7:* ) - -DOCS=( AUTHORS Changelog README TODO ) - -pkg_setup() { - fortran-2_pkg_setup - java-pkg-opt-2_pkg_setup - use python && python-single-r1_pkg_setup -} - -src_configure() { - econf \ - --disable-idl \ - $(use_enable fortran fortran2003) \ - $(use_enable lua) \ - $(use_enable perl) \ - $(use_enable perl perl-integration) \ - $(use_enable php) \ - $(use_enable php php-integration) \ - $(use_enable python) \ - $(use_enable python python-integration) \ - $(use_enable python python-numpy) \ - $(use_enable ruby) \ - $(use_enable ruby ruby-integration) \ - # $(use_enable java) -} - -src_test() { - # see https://github.com/tschoonj/xraylib/issues/11 - emake -j1 check -} - -src_install() { - default - use python && python_optimize - - if use examples; then - docinto /usr/share/doc/${PF}/examples - dodoc example/*.c example/*.cpp - use fortran && dodoc example/*.f90 - use lua && dodoc example/*.lua - use perl && dodoc example/*.pl - use php && dodoc example/*.php - use python && dodoc example/*.py - use ruby && dodoc example/*.rb - # use java && dodoc example/*.java - docompress -x /usr/share/doc/${PF}/examples # Don't compress examples - fi - - # use java && java-pkg_regso /usr/share/xraylib/java/libxraylib.so -} |