commit: edd4bbf46b30ee203ab8845e618dbd32534510d5 Author: Alessandro Barbieri <lssndrbarbieri <AT> gmail <DOT> com> AuthorDate: Tue May 3 23:24:37 2022 +0000 Commit: Haelwenn Monnier <contact <AT> hacktivis <DOT> me> CommitDate: Tue May 3 23:27:49 2022 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=edd4bbf4
sci-libs/mlpack: new package, add 3.4.2_p20220501 Signed-off-by: Alessandro Barbieri <lssndrbarbieri <AT> gmail.com> sci-libs/mlpack/Manifest | 19 +++ .../mlpack-3.4.2_p20220501-no-backports.patch | 53 ++++++ sci-libs/mlpack/files/mlpack-link-armadillo.patch | 7 + .../mlpack/files/mlpack-no-pytest-runner.patch | 11 ++ sci-libs/mlpack/metadata.xml | 22 +++ sci-libs/mlpack/mlpack-3.4.2_p20220501.ebuild | 179 +++++++++++++++++++++ 6 files changed, 291 insertions(+) diff --git a/sci-libs/mlpack/Manifest b/sci-libs/mlpack/Manifest new file mode 100644 index 000000000..9e645dd8e --- /dev/null +++ b/sci-libs/mlpack/Manifest @@ -0,0 +1,19 @@ +DIST github.com%2Fajstarks%2Fsvgo%2F@v%2Fv0.0.0-20180226025133-644b8db467af.mod 32 BLAKE2B b8647c299d1f9a1c4f8ade152cfcb58f73d4bba4b6803f7fed7e0584607c6da369f9f622e70c1a415af2f5f53cdd1c8de7f29a7843b3ce505821ff1ffacaaec7 SHA512 031c2c2f683d57f81b504c68d24aa328a8f03af7d3ab9021b0acffd541d9a295a80cc7b1c9051d19ba30caad619d3e454ec5b804f14e24e9e39b008ec27dfaf5 +DIST github.com%2Ffogleman%2Fgg%2F@v%2Fv1.2.1-0.20190220221249-0403632d5b90.mod 30 BLAKE2B 725b27caadd05c18fc518e46ce4f1a213cd6ed7b4da3edb02cd74b7c7d3dc37891692f195144bbfc455bdc9bc77e683b41122bb3d646796555e92f565cc0133c SHA512 d64a7c87d6a40c48684a61ed0f6a7e75590df7d72d55242863f1bf18af9bb9ef51c40ecf0c41fbc039e06f1651898a238375afb12f41af5978195887a9a16c9c +DIST github.com%2Fgolang%2Ffreetype%2F@v%2Fv0.0.0-20170609003504-e2365dfdc4a0.mod 34 BLAKE2B 55487f18e815e30ee3653a5dcc9370d2cf044641f7cf12c566e165fa173efe9af3ab18fed752dc36ee0fa25ae2e81a5094e18cebaa61d997ae599b9cc3d09bf1 SHA512 a34e950c565fa284163c40712c9f5e53881996c85153f972a78f27a5cdcaebfdbcce60556e173bbef2db32939f1b8721325846b705ef1504a1c5680598343b10 +DIST github.com%2Fjung-kurt%2Fgofpdf%2F@v%2Fv1.0.3-0.20190309125859-24315acbbda5.mod 35 BLAKE2B c1b6f3da9b37c5e0888f6ae304f7885901fb5f90bd94de7c980b7089d2477ea25f0fecf30b502f55fdb6a8dd7ba49683f33b89d761de0acd0e9ccbeff53a183b SHA512 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9615629f1bf7d58419f5b73842e19f6be3a8c8cefb217364917f1aaf68aec00de41d96700378b048d6cc385e154ed6d3db59256b4a00e9165bac7951cd0bcbab SHA512 9131017b8ab0c2362b74e0c010daeb849689025aa31cb464dc379b0e34d0fcdb66749329b111041127997440bac052249dab522ab27239858405c056e3ac5dbf +DIST golang.org%2Fx%2Fexp%2F@v%2Fv0.0.0-20190125153040-c74c464bbbf2.zip 1453241 BLAKE2B 3cefe5395bcd715cedaeff2add4c77d057025fb96b9bec7732d044cfcad027fd6c47633543957560194c04f4649646c72e12f998b17d6709965eb9c196ab4f14 SHA512 904202536557a2a73c421e242cbba38c1d68a94d49e3b80649c85f3353b7612cf0005325dbdc7b1c0b10d4334f2b59599278d5686843c479944eca58e8d84134 +DIST golang.org%2Fx%2Fimage%2F@v%2Fv0.0.0-20180708004352-c73c2afc3b81.mod 26 BLAKE2B 99ea5bcf900233680c1e0fd7526b1e12c79143afc9e545e59796fe734cb5b788536d332179d2432924b39670e4067fb3d13752735e59b8b19b3d27e9de9403ef SHA512 e78afa02a8d030fcd336ae1c1d5d4071d14f2873a1ad72af64a744c0e5e3ec795957fbc527557f4ba5b747cbcdf31c0109b43a6d75342d85a69fac6cf97f233a +DIST golang.org%2Fx%2Ftools%2F@v%2Fv0.0.0-20180525024113-a5b4c53f6e8b.mod 26 BLAKE2B 2a44c2cc034af3473d9a1d4e1c23b0f4542333853bfc0ecbfcf9eacacbb3593b449fcfc94d23f49ccc16e5a844bc72a3462a3e08a5c26194106a64d1f2732e0a SHA512 3c166b18c0ce47a47e95da9eeede63879a92b0205bd4589d554f7bae89699be0efa83e1f5bba8e50f47714ea23e759b07f4543fe06301995d39373da2db16fc0 +DIST golang.org%2Fx%2Ftools%2F@v%2Fv0.0.0-20190206041539-40960b6deb8e.mod 26 BLAKE2B 2a44c2cc034af3473d9a1d4e1c23b0f4542333853bfc0ecbfcf9eacacbb3593b449fcfc94d23f49ccc16e5a844bc72a3462a3e08a5c26194106a64d1f2732e0a SHA512 3c166b18c0ce47a47e95da9eeede63879a92b0205bd4589d554f7bae89699be0efa83e1f5bba8e50f47714ea23e759b07f4543fe06301995d39373da2db16fc0 +DIST gonum.org%2Fv1%2Fgonum%2F@v%2Fv0.0.0-20180816165407-929014505bf4.mod 147 BLAKE2B 6124c221210cb16cf7f0ea44ad962d904b2e8b050b4a86777f8a21114609c99866c53cd32572005bce9778317e2e13425cafee613ccacefa52933ae35c2fa65f SHA512 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SHA512 1576aa0b64384add0cbec0e1e5187ba992022ba5d1ac2ed6ad2d3cd888a8f97218bd42aeb8cb5e53677e8192dc4db4c7800b15fb18c6bcc320a2c67b5bd07a37 +DIST gonum.org%2Fv1%2Fnetlib%2F@v%2Fv0.0.0-20190313105609-8cb42192e0e0.zip 220616 BLAKE2B ee0e947ce59df10c713766f1c8fdf27d37f64da46ffb095e7ff30da8583309f8ee15c9fa38a1790b71da466fadf87b1918600b5610fc632cd051658da32bfa50 SHA512 4439ea5da9742ca27d2ccb0604edae491594299db5b2062a4a117e8f2c08a64c6e3a87c5a3d9a606d816e89aab5eb870c13a0849b79cbb47b2659840efebc355 +DIST gonum.org%2Fv1%2Fplot%2F@v%2Fv0.0.0-20190515093506-e2840ee46a6b.mod 471 BLAKE2B 92356c493b1e94781571e05eb5096e6b40beb88c57927a955f899e8610597192fe82622f8e8f84b4c96ec00b1965552e6d5fb9166a6e3fa4f603d4fba72a4913 SHA512 ee8422d1041c7ba9306c5a49eb3bebb8c8243563250b7b3f19326769a3fb08660414625130cc1941077e7778104f6243aa5a5eb45797b72b4daf4f6abddaa32b +DIST mlpack-3.4.2_p20220501.tar.gz 5944464 BLAKE2B c4c27bddaa7dd177a1f39131e7bae159ad044fe41fbb863dbbc0d2207e1bccca75807f607de567725e69818f28a72e9de09c4c5eaac2c76aee0c8f06f3a42b3d SHA512 ed6762c9be2e7c63a926bafedc8d2cea0c9946eca9313db84cfcca40a562ba90199829daf438a1196bfa8c7c20882c180a18b449f9c9fe4b69324233d521417d +DIST rsc.io%2Fpdf%2F@v%2Fv0.1.1.mod 18 BLAKE2B 02f32b5a77e5009f179cf1fdc9acbb977fe219698f19ef41acee8129e0de7ad93b0b39ce82ac1538c82a7cdd33776e270f0acec114716c791727b021a4d3e147 SHA512 f911a889614d9177295952c82f8b4a0942fcbb7b4fca7378c0b98a63ed0e37e1319d51905f906ad08144eb0f3f829a2ccc2af04c2147e60cc2ac1ea8d7dab16f diff --git a/sci-libs/mlpack/files/mlpack-3.4.2_p20220501-no-backports.patch b/sci-libs/mlpack/files/mlpack-3.4.2_p20220501-no-backports.patch new file mode 100644 index 000000000..eae88d692 --- /dev/null +++ b/sci-libs/mlpack/files/mlpack-3.4.2_p20220501-no-backports.patch @@ -0,0 +1,53 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -111,7 +111,7 @@ + enable_testing() + + # Set required standard to C++11. +-set(CMAKE_CXX_STANDARD 11) ++set(CMAKE_CXX_STANDARD 17) + set(CMAKE_CXX_STANDARD_REQUIRED ON) + + # Ensure that GCC is new enough, if the compiler is GCC. +--- a/src/mlpack/bindings/python/setup.py.in ++++ b/src/mlpack/bindings/python/setup.py.in +@@ -52,7 +52,7 @@ + else: + cxx_flags = '${CMAKE_CXX_FLAGS}'.strip() + cxx_flags = re.sub(' +', ' ', cxx_flags) +- extra_args = ['-DBINDING_TYPE=BINDING_TYPE_PYX', '-std=c++11'] ++ extra_args = ['-DBINDING_TYPE=BINDING_TYPE_PYX', '-std=c++17'] + if '${OpenMP_CXX_FLAGS}' != '': + extra_args.append('${OpenMP_CXX_FLAGS}') + if cxx_flags: +--- a/src/mlpack/bindings/R/mlpack/src/Makevars ++++ b/src/mlpack/bindings/R/mlpack/src/Makevars +@@ -1,3 +1,3 @@ + PKG_CXXFLAGS = -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=false -I. $(SHLIB_OPENMP_CXXFLAGS) + PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +-CXX_STD = CXX11 ++CXX_STD = CXX17 +--- a/src/mlpack/core/cereal/CMakeLists.txt ++++ b/src/mlpack/core/cereal/CMakeLists.txt +@@ -4,10 +4,8 @@ + array_wrapper.hpp + is_loading.hpp + is_saving.hpp +- pair_associative_container.hpp + pointer_wrapper.hpp + pointer_vector_wrapper.hpp +- unordered_map.hpp + ) + + # add directory name to sources +--- a/src/mlpack/prereqs.hpp ++++ b/src/mlpack/prereqs.hpp +@@ -110,7 +110,7 @@ + #include <cereal/types/array.hpp> + #include <cereal/types/string.hpp> + #include <cereal/types/tuple.hpp> +-#include <mlpack/core/cereal/unordered_map.hpp> ++#include <cereal/types/unordered_map.hpp> + #include <cereal/types/utility.hpp> + #include <cereal/types/vector.hpp> + diff --git a/sci-libs/mlpack/files/mlpack-link-armadillo.patch b/sci-libs/mlpack/files/mlpack-link-armadillo.patch new file mode 100644 index 000000000..d37d12f4f --- /dev/null +++ b/sci-libs/mlpack/files/mlpack-link-armadillo.patch @@ -0,0 +1,7 @@ +--- a/src/mlpack/bindings/R/mlpack/src/Makevars ++++ b/src/mlpack/bindings/R/mlpack/src/Makevars +@@ -1,3 +1,3 @@ + PKG_CXXFLAGS = -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=false -I. $(SHLIB_OPENMP_CXXFLAGS) +-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -larmadillo + CXX_STD = CXX11 diff --git a/sci-libs/mlpack/files/mlpack-no-pytest-runner.patch b/sci-libs/mlpack/files/mlpack-no-pytest-runner.patch new file mode 100644 index 000000000..649d407d9 --- /dev/null +++ b/sci-libs/mlpack/files/mlpack-no-pytest-runner.patch @@ -0,0 +1,11 @@ +--- a/src/mlpack/bindings/python/setup.py.in ++++ b/src/mlpack/bindings/python/setup.py.in +@@ -137,7 +137,7 @@ + packages=['mlpack'], + cmdclass={ 'build_ext': build_ext }, + ext_modules = modules, +- setup_requires=['cython', 'pytest-runner'], ++ setup_requires=['cython'], + tests_require=['pytest>3;python_version>"3.4"', 'pytest>3,<=4.6;python_version<="3.4"', + 'more-itertools>=4.0.0,<6.0.0;python_version<="2.7"', + 'more-itertools>=4.0.0;python_version>"2.7"'], diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml new file mode 100644 index 000000000..083fe9f20 --- /dev/null +++ b/sci-libs/mlpack/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <description>co-maintainers welcome</description> + <email>lssndrbarbi...@gmail.com</email> + <name>Alessandro Barbieri</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="go">build go bindings</flag> + <flag name="julia">build julia bindings</flag> + <flag name="R">build R bindings</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/mlpack/mlpack-3.4.2_p20220501.ebuild b/sci-libs/mlpack/mlpack-3.4.2_p20220501.ebuild new file mode 100644 index 000000000..8c4e12677 --- /dev/null +++ b/sci-libs/mlpack/mlpack-3.4.2_p20220501.ebuild @@ -0,0 +1,179 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_IN_SOURCE_BUILD=1 +CMAKE_MAKEFILE_GENERATOR="emake" +COMMIT="54c6ebe03a07d7c32db46a6a06a03e8b821da4f2" +EGO_PN="mlpack.org/v1/mlpack" +EGO_SUM=( + "github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod" + "github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod" + "github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod" + "github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod" + "golang.org/x/exp v0.0.0-20180321215751-8460e604b9de/go.mod" + "golang.org/x/exp v0.0.0-20180807140117-3d87b88a115f/go.mod" + "golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2" + "golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2/go.mod" + "golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod" + "golang.org/x/tools v0.0.0-20180525024113-a5b4c53f6e8b/go.mod" + "golang.org/x/tools v0.0.0-20190206041539-40960b6deb8e/go.mod" + "gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod" + "gonum.org/v1/gonum v0.7.0" + "gonum.org/v1/gonum v0.7.0/go.mod" + "gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0" + "gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0/go.mod" + "gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod" + "rsc.io/pdf v0.1.1/go.mod" + ) +GO_OPTIONAL=1 +PYTHON_COMPAT=( python3_{8..9} ) + +inherit cmake flag-o-matic go-module python-single-r1 + +go-module_set_globals + +DESCRIPTION="scalable C++ machine learning library" +HOMEPAGE=" + https://www.mlpack.org + https://github.com/mlpack/mlpack +" +SRC_URI=" + https://github.com/mlpack/mlpack/archive/${COMMIT}.tar.gz -> ${PF}.tar.gz + go? ( ${EGO_SUM_SRC_URI} ) +" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="LGPL-3 BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="debug doc go julia openmp profile R source test" + +CDEPEND=" + ${PYTHON_DEPS} + go? ( >=dev-lang/go-1.11.0 ) + julia? ( || ( >=dev-lang/julia-1.3.0 >=dev-lang/julia-bin-1.3.0:* ) ) + R? ( >=dev-lang/R-4.0 ) +" +RDEPEND=" + ${CDEPEND} + R? ( + dev-R/BH + >=dev-R/Rcpp-0.12.12 + dev-R/RcppArmadillo + dev-R/RcppEnsmallen + dev-R/roxygen2 + >=dev-R/testthat-2.1.0 + ) + + $(python_gen_cond_dep ' + >=dev-libs/boost-1.58[python,${PYTHON_USEDEP}] + dev-libs/libxml2[${PYTHON_USEDEP}] + >=dev-python/cython-0.24[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + ') + + >=dev-libs/cereal-1.1.2 + dev-libs/stb + >=sci-libs/armadillo-8.4.0[arpack,blas,lapack] + >=sci-libs/ensmallen-2.10.0 +" +DEPEND=" + ${RDEPEND} + R? ( dev-R/pkgbuild ) +" +BDEPEND=" + app-arch/unzip + app-text/txt2man + virtual/pkgconfig + + doc? ( + app-doc/doxygen + dev-libs/mathjax + ) + test? ( $(python_gen_cond_dep 'dev-python/pytest[${PYTHON_USEDEP}]') ) +" + +PATCHES=( + "${FILESDIR}/${PN}-no-pytest-runner.patch" + "${FILESDIR}/${PN}-link-armadillo.patch" + "${FILESDIR}/${PN}-3.4.2_p20220501-no-backports.patch" +) +RESTRICT="!test? ( test )" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +src_unpack() { + go-module_src_unpack + use go && go-module_setup_proxy +} + +src_prepare() { + rm -r src/mlpack/core/std_backport || die + rm -r src/mlpack/core/cereal/{pair_associative_container,unordered_map}.hpp || die + + sed -i \ + -e "s:share/doc/mlpack:share/doc/${PF}:" \ + -e 's/-O3//g' \ + CMakeLists.txt || die + cmake_src_prepare +} + +src_compile() { + cmake_src_compile +} + +src_configure() { + use R && append-cxxflags "-larmadillo" + + local mycmakeargs=( + -DBUILD_CLI_EXECUTABLES=ON + -DBUILD_PYTHON_BINDINGS=ON + -DBUILD_SHARED_LIBS=ON + -DDOWNLOAD_DEPENDENCIES=OFF + + -DARMADILLO_INCLUDE_DIR="${EPREFIX}/usr/include" + -DARMADILLO_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libarmadillo.so" + -DCEREAL_INCLUDE_DIR="${EPREFIX}/usr/include" + -DENSMALLEN_INCLUDE_DIR="${EPREFIX}/usr/include" + -DSTB_IMAGE_INCLUDE_DIR="${EPREFIX}/usr/include/stb" + + -DARMA_EXTRA_DEBUG=$(usex debug) + -DBUILD_DOCS=$(usex doc) + -DBUILD_GO_BINDINGS=OFF + -DFORCE_BUILD_GO_BINDINGS=$(usex go) + -DBUILD_GO_SHLIB=$(usex go) + -DBUILD_JULIA_BINDINGS=$(usex julia) + -DBUILD_MARKDOWN_BINDINGS=$(usex doc) + -DBUILD_R_BINDINGS=$(usex R) + -DBUILD_TESTS=$(usex test) + -DDEBUG=$(usex debug) + -DMATHJAX=$(usex doc) + -DPROFILE=$(usex profile) + -DTEST_VERBOSE=$(usex test) + -DUSE_OPENMP=$(usex openmp) + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + + if use R; then + pushd "${BUILD_DIR}/src/mlpack/bindings/R/" || die + insinto "/usr/$(get_libdir)/R/site-library" + rm -r mlpack/src || die + doins -r mlpack + popd || die + fi + + if use source; then + gosrc="$(go env GOROOT)/src" || die + insinto "${gosrc}/${EGO_PN}" + doins -r src/mlpack/bindings/go/mlpack/* + fi + + python_optimize +}