diff options
639 files changed, 11571 insertions, 5089 deletions
diff --git a/app-office/visidata/visidata-2.8.ebuild b/app-office/visidata/visidata-2.8.ebuild index ab4d506ab..f3cf9e123 100644 --- a/app-office/visidata/visidata-2.8.ebuild +++ b/app-office/visidata/visidata-2.8.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 optfeature diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild index 432004f11..38e0dfbd0 100644 --- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild +++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..11} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit cmake python-any-r1 COMMIT="39f885951a9b8b11f931f917935a16066a945056" diff --git a/dev-cpp/highwayhash/highwayhash-20200922.ebuild b/dev-cpp/highwayhash/highwayhash-20200922.ebuild index 8483be41f..2eb0ccaa2 100644 --- a/dev-cpp/highwayhash/highwayhash-20200922.ebuild +++ b/dev-cpp/highwayhash/highwayhash-20200922.ebuild @@ -25,6 +25,6 @@ src_install() { LIBDIR="/usr/$(get_libdir)" \ install use static-libs || \ - rm "${ED}"/${EPREFIX}/usr/$(get_libdir)/lib*.a || die + rm "${ED}/usr/$(get_libdir)"/lib*.a || die einstalldocs } diff --git a/dev-cpp/xsimd/Manifest b/dev-cpp/xsimd/Manifest new file mode 100644 index 000000000..1411b4acf --- /dev/null +++ b/dev-cpp/xsimd/Manifest @@ -0,0 +1 @@ +DIST xsimd-10.0.0.tar.gz 212082 BLAKE2B 2a3c6dd711f9e7ffd32ce3fd9a6056a56768a0f5b6ff412d2c5cd5f82682cac87ed0a68109a449ab6337f89a4719e9ab25f94060d3f675783ce00c79e3378512 SHA512 bd7a363bbebc9196954c8c87271f14f05ca177569fcf080dac91be06ad2801c43fccbb385afd700b80d58c83d77f26ba199a7105672e4a1e55c517d15dd6e8e3 diff --git a/dev-cpp/xsimd/files/remove-libdir-in-pc.patch b/dev-cpp/xsimd/files/remove-libdir-in-pc.patch new file mode 100644 index 000000000..4548f0ab4 --- /dev/null +++ b/dev-cpp/xsimd/files/remove-libdir-in-pc.patch @@ -0,0 +1,12 @@ +libdir is not used in this header-only package +And this line cause QA notice: +key=libdir does not respect EPREFIX libdir=/lib64 +=================================================================== +--- xsimd-10.0.0.orig/xsimd.pc.in ++++ xsimd-10.0.0/xsimd.pc.in +@@ -1,5 +1,4 @@ + prefix=@CMAKE_INSTALL_PREFIX@ +-libdir=@libdir_for_pc_file@ + includedir=@includedir_for_pc_file@ + + Name: xsimd diff --git a/dev-cpp/xsimd/metadata.xml b/dev-cpp/xsimd/metadata.xml new file mode 100644 index 000000000..7e8334e1b --- /dev/null +++ b/dev-cpp/xsimd/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>xgreenlandforwyy@gmail.com</email> + <name>Yiyang Wu</name> + </maintainer> + <upstream> + <remote-id type="github">xtensor-stack/xsimd</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-cpp/xsimd/xsimd-10.0.0.ebuild b/dev-cpp/xsimd/xsimd-10.0.0.ebuild new file mode 100644 index 000000000..1a34b725b --- /dev/null +++ b/dev-cpp/xsimd/xsimd-10.0.0.ebuild @@ -0,0 +1,27 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="C++ wrappers for SIMD intrinsics and math implementations" +HOMEPAGE="https://github.com/xtensor-stack/xsimd" +SRC_URI="https://github.com/xtensor-stack/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND="test? ( dev-cpp/doctest )" +RDEPEND="${DEPEND}" +BDEPEND="" + +PATCHES=( "${FILESDIR}"/remove-libdir-in-pc.patch ) + +src_configure() { + local mycmakeargs=( -DBUILD_TESTS="$(usex test ON OFF)" ) + cmake_src_configure +} diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/dev-lang/icc/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/dev-lang/icc/icc-18.0.2.199-r1.ebuild b/dev-lang/icc/icc-18.0.2.199-r1.ebuild deleted file mode 100644 index 84641de62..000000000 --- a/dev-lang/icc/icc-18.0.2.199-r1.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2020 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 C/C++ Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -# avoid file collision with ifc #476330 -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=500M - -INTEL_DIST_DAT_RPMS=( - "icc-common-18.0.2-199-18.0.2-199.noarch.rpm" - "icc-common-ps-18.0.2-199-18.0.2-199.noarch.rpm" - "icc-common-ps-ss-bec-18.0.2-199-18.0.2-199.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "icc-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "icc-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "icc-doc-18.0-18.0.2-199.noarch.rpm" - "icc-doc-ps-18.0-18.0.2-199.noarch.rpm") - fi -} diff --git a/dev-lang/icc/icc-19.0.4.243.ebuild b/dev-lang/icc/icc-19.0.4.243.ebuild deleted file mode 100644 index 9a166f221..000000000 --- a/dev-lang/icc/icc-19.0.4.243.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel C/C++ Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -# avoid file collision with ifc #476330 -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=500M - -INTEL_DIST_DAT_RPMS=( - "icc-common-19.0.4-243-19.0.4-243.noarch.rpm" - "icc-common-ps-19.0.4-243-19.0.4-243.noarch.rpm" - "icc-common-ps-ss-bec-19.0.4-243-19.0.4-243.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "icc-19.0.4-243-19.0.4-243.x86_64.rpm" - "icc-ps-19.0.4-243-19.0.4-243.x86_64.rpm" - "icc-ps-ss-bec-19.0.4-243-19.0.4-243.x86_64.rpm") - -INTEL_DIST_X86_RPMS=( - "icc-32bit-19.0.4-243-19.0.4-243.x86_64.rpm" - "icc-ps-ss-bec-32bit-19.0.4-243-19.0.4-243.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "icc-doc-19.0-19.0.4-243.noarch.rpm" - "icc-doc-ps-19.0-19.0.4-243.noarch.rpm") - fi -} diff --git a/dev-lang/icc/icc-19.1.1.217.ebuild b/dev-lang/icc/icc-19.1.1.217.ebuild deleted file mode 100644 index 226b9c784..000000000 --- a/dev-lang/icc/icc-19.1.1.217.ebuild +++ /dev/null @@ -1,41 +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 C/C++ Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=500M - -MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630 - -QA_PREBUILT="*" - -INTEL_DIST_DAT_RPMS=( - "icc-common-${MY_PV}-${MY_PV}.noarch.rpm" - "icc-common-ps-${MY_PV}-${MY_PV}.noarch.rpm" - "idesupport-icc-common-ps-19.1-${MY_PV}.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "icc-${MY_PV}-${MY_PV}.x86_64.rpm" - "icc-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "icc-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -INTEL_DIST_X86_RPMS=( - "icc-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "icc-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "icc-doc-19.1-${MY_PV}.noarch.rpm" ) - fi -} diff --git a/dev-lang/icc/metadata.xml b/dev-lang/icc/metadata.xml deleted file mode 100644 index 7c4d1a96d..000000000 --- a/dev-lang/icc/metadata.xml +++ /dev/null @@ -1,16 +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 Intel® C++ Compiler is a full featured C/C++ compiler for Intel -based architectures. The compiler supports multi-threading, automatic -processor dispatch, vectorization, auto-parallelization, OpenMP, data -prefetching, loop unrolling. The package comes with extensive -documentation. The product can be installed as a non-commercial as -well. License, terms of qualifications can be found on the web site. -</longdescription> -</pkgmetadata> diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/dev-lang/ifc/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/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild b/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild deleted file mode 100644 index f37dd5491..000000000 --- a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild +++ /dev/null @@ -1,40 +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 FORTRAN Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=400M - -INTEL_DIST_DAT_RPMS=( "ifort-common-18.0.2-199-18.0.2-199.noarch.rpm" ) -INTEL_DIST_X86_RPMS=( "ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" ) -INTEL_DIST_AMD64_RPMS=( "ifort-18.0.2-199-18.0.2-199.x86_64.rpm" ) - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "ifort-doc-18.0-18.0.2-199.noarch.rpm" ) - fi -} - -src_install() { - # already provided in dev-libs/intel-common - rm \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/omp_lib.f90 \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib.mod \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib_kinds.mod \ - || die "rm failed" - - intel-sdp-r1_src_install -} diff --git a/dev-lang/ifc/ifc-19.0.4.243.ebuild b/dev-lang/ifc/ifc-19.0.4.243.ebuild deleted file mode 100644 index a45765a2f..000000000 --- a/dev-lang/ifc/ifc-19.0.4.243.ebuild +++ /dev/null @@ -1,39 +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 FORTRAN Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=400M - -INTEL_DIST_DAT_RPMS=( "ifort-common-19.0.4-243-19.0.4-243.noarch.rpm" ) -INTEL_DIST_AMD64_RPMS=( "ifort-19.0.4-243-19.0.4-243.x86_64.rpm" ) -INTEL_DIST_X86_RPMS=( "ifort-32bit-19.0.4-243-19.0.4-243.x86_64.rpm" ) - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.0-19.0.4-243.noarch.rpm" ) - fi -} - -src_install() { - # already provided in dev-libs/intel-common - rm \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/omp_lib.f90 \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib.mod \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib_kinds.mod \ - || die "rm failed" - - intel-sdp-r1_src_install -} diff --git a/dev-lang/ifc/ifc-19.1.1.217.ebuild b/dev-lang/ifc/ifc-19.1.1.217.ebuild deleted file mode 100644 index 4157a3eec..000000000 --- a/dev-lang/ifc/ifc-19.1.1.217.ebuild +++ /dev/null @@ -1,43 +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 FORTRAN Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630 - -QA_PREBUILT="*" - -CHECKREQS_DISK_BUILD=400M - -INTEL_DIST_DAT_RPMS=( "ifort-common-${MY_PV}-${MY_PV}.noarch.rpm" ) -INTEL_DIST_AMD64_RPMS=( "ifort-${MY_PV}-${MY_PV}.x86_64.rpm" ) -INTEL_DIST_X86_RPMS=( "ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.1-${MY_PV}.noarch.rpm" ) - fi -} - -src_install() { - # already provided in dev-libs/intel-common - rm \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/omp_lib.f90 \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib.mod \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib_kinds.mod \ - || die "rm failed" - - intel-sdp-r1_src_install -} diff --git a/dev-lang/ifc/metadata.xml b/dev-lang/ifc/metadata.xml deleted file mode 100644 index 0cc12d890..000000000 --- a/dev-lang/ifc/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 Intel® Fortran Compiler is a full featured FORTRAN 77/95 and -substantial FORTRAN 2003 compiler for Intel based architectures. The -compiler supports multi-threading with automatic processor dispatch, -vectorization, auto-parallelization, OpenMP, data prefetching, loop -unrolling. The package comes with extensive documentation. -The product can be installed as a non-commercial as well. License, -terms of qualifications can be found on the web site. -</longdescription> -</pkgmetadata> diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/dev-lang/vtune/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/dev-lang/vtune/metadata.xml b/dev-lang/vtune/metadata.xml deleted file mode 100644 index 718cc299c..000000000 --- a/dev-lang/vtune/metadata.xml +++ /dev/null @@ -1,15 +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 Intel® VTune™ Profiler collects key profiling data and presents -it with a powerful interface that simplifies its analysis and -interpretation. The package comes with extensive documentation. The -product can be installed as a non-commercial as well. License, terms -of qualifications can be found on the web site. -</longdescription> -</pkgmetadata> diff --git a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild b/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild deleted file mode 100644 index 9ec0beef6..000000000 --- a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild +++ /dev/null @@ -1,49 +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 -INTEL_SUBDIR=vtune_amplifier - -inherit intel-sdp-r1 - -DESCRIPTION="Intel VTune Amplifier XE" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-18.0.2.199[compiler]" - -INTEL_DIST_DAT_RPMS=( - "vtune-amplifier-2018-cli-common-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-common-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-common-pset-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-gui-common-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-sep-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-target-2018.2-551022.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "vtune-amplifier-2018-cli-2018.2-551022.x86_64.rpm" - "vtune-amplifier-2018-collector-64linux-2018.2-551022.x86_64.rpm" - "vtune-amplifier-2018-gui-2018.2-551022.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "vtune-amplifier-2018-cli-32bit-2018.2-551022.i486.rpm" - "vtune-amplifier-2018-collector-32linux-2018.2-551022.i486.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2018-doc-2018.2-551022.noarch.rpm" ) - fi -} - -src_install() { - intel-sdp-r1_src_install - - local path="PATH=" - use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64" - use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32" - echo "${path}" > "${T}"/35vtune || die - doenvd "${T}"/35vtune -} diff --git a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild b/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild deleted file mode 100644 index e090c10b7..000000000 --- a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition -INTEL_SUBDIR=vtune_amplifier - -inherit intel-sdp-r1 - -DESCRIPTION="Intel VTune Amplifier XE" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-19.0.4.243[compiler]" - -INTEL_DIST_DAT_RPMS=( - "vtune-amplifier-2019-cli-common-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-common-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-common-pset-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-gui-common-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-sep-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-target-2019.4-597835.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "vtune-amplifier-2019-cli-2019.4-597835.x86_64.rpm" - "vtune-amplifier-2019-collector-64linux-2019.4-597835.x86_64.rpm" - "vtune-amplifier-2019-gui-2019.4-597835.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "vtune-amplifier-2019-cli-32bit-2019.4-597835.i486.rpm" - "vtune-amplifier-2019-collector-32linux-2019.4-597835.i486.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2019-doc-2019.4-597835.noarch.rpm" ) - fi -} - -src_install() { - intel-sdp-r1_src_install - - local path="PATH=" - use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64" - use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32" - echo "${path}" > "${T}"/35vtune || die - doenvd "${T}"/35vtune -} diff --git a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild b/dev-lang/vtune/vtune-2020.1.0.607630.ebuild deleted file mode 100644 index e1ec58882..000000000 --- a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild +++ /dev/null @@ -1,52 +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 -INTEL_SUBDIR=vtune_profiler - -inherit intel-sdp-r1 - -DESCRIPTION="Intel VTune Profiler" -HOMEPAGE="https://software.intel.com/en-us/vtune" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]" - -MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630 - -QA_PREBUILT="*" - -INTEL_DIST_DAT_RPMS=( - "vtune-profiler-2020-cli-common-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-common-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-common-pset-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-sep-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-target-${MY_PV}.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "vtune-profiler-2020-cli-${MY_PV}.x86_64.rpm" - "vtune-profiler-2020-collector-64linux-${MY_PV}.x86_64.rpm" - "vtune-profiler-2020-gui-${MY_PV}.x86_64.rpm" - "vtune-profiler-2020-vpp-server-${MY_PV}.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "vtune-profiler-2020-cli-32bit-${MY_PV}.i486.rpm" - "vtune-profiler-2020-collector-32linux-${MY_PV}.i486.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "vtune-profiler-2020-doc-${MY_PV}.noarch.rpm" ) - fi -} - -src_install() { - intel-sdp-r1_src_install - - local path="PATH=" - use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64" - use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32" - echo "${path}" > "${T}"/35vtune || die - doenvd "${T}"/35vtune -} diff --git a/dev-libs/apache-arrow/Manifest b/dev-libs/apache-arrow/Manifest new file mode 100644 index 000000000..42267587e --- /dev/null +++ b/dev-libs/apache-arrow/Manifest @@ -0,0 +1,3 @@ +DIST apache-arrow-11.0.0.tar.gz 19956186 BLAKE2B dff0faecbde9e2d19f092fd0c48a7ac7a401da6dbfd17f30af1b35c9e3fd3e1ba5611311f5bcb08383368de195cff783a178a9397a63a1c4f740a81349f8b8d3 SHA512 46df4fb5a703d38d0a74fde9838e9f9702b24b442cb225517516c335a5ab18955699000bf0b2fc7d1698ada6d2e890ba3860933b6280f5160b0fce8a07484d0e +DIST apache-arrow-arrow-data-11.0.0.tar.gz 3570422 BLAKE2B df1f8d1c4e321ca0abdce598b09945aa9e63114199e7f2eb0fc549323dadf703b917efd90c04a2d540d763a44128d76c6ee12788a983d4b9536d04297316b656 SHA512 0be19960b0d22fc2e07bf84f11148e69d6fa82f10627eb2a5e4b762b1d4cf4e151a57c5a1dc761d6d8ed29881ea589e4cfe0cd47d5c7cbf7b6107143b4a45e82 +DIST apache-arrow-parquet-data-11.0.0.tar.gz 1013835 BLAKE2B cb4e544b6588ddad503f9692ee2eee5d4f1e931f10654b7253e11ffd2feb4c957dec047a1b1644c1f1538a3bf7ea726e5a9ae9b7d0c3bb0d55d27f088b5c5be3 SHA512 d4c2af20d6a88c1beb44770982f4aa324ea4ee375e8f556339074875af15c48f4398d972c1eec35eba5d209e9e62df4bdbf73ebc8148a7bb05ffa2d69c97df61 diff --git a/dev-libs/apache-arrow/apache-arrow-11.0.0.ebuild b/dev-libs/apache-arrow/apache-arrow-11.0.0.ebuild new file mode 100644 index 000000000..8a763531a --- /dev/null +++ b/dev-libs/apache-arrow/apache-arrow-11.0.0.ebuild @@ -0,0 +1,90 @@ +# Copyright 2021-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +IUSE="+bzip2 +brotli +csv +lz4 +parquet snappy test +zlib +zstd" + +DESCRIPTION="A cross-language development platform for in-memory data." +HOMEPAGE="https://arrow.apache.org/" +PARQUET_DATA_GIT_HASH=b2e7cc755159196e3a068c8594f7acbaecfdaaac +ARROW_DATA_GIT_HASH=d2c73bf78246331d8e58b6f11aa8aa199cbb5929 +SRC_URI="mirror://apache/arrow/arrow-${PV}/${P}.tar.gz +test? ( https://github.com/apache/parquet-testing/archive/${PARQUET_DATA_GIT_HASH}.tar.gz -> ${PN}-parquet-data-${PV}.tar.gz + https://github.com/apache/arrow-testing/archive/${ARROW_DATA_GIT_HASH}.tar.gz -> ${PN}-arrow-data-${PV}.tar.gz )" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/lz4 + >=dev-cpp/xsimd-8.1 + lz4? ( app-arch/lz4:= ) + brotli? ( app-arch/brotli ) + bzip2? ( app-arch/bzip2 ) + parquet? ( + dev-libs/libutf8proc:= + dev-libs/re2:= + dev-libs/thrift + ) + snappy? ( app-arch/snappy ) + zlib? ( sys-libs/zlib ) + zstd? ( app-arch/zstd:= ) +" +DEPEND=" + ${RDEPEND} + dev-libs/rapidjson + net-libs/grpc + >=dev-cpp/xsimd-8.1 + test? ( + dev-libs/flatbuffers + dev-cpp/gflags + dev-cpp/gtest + ) +" + +S="${WORKDIR}/${P}/cpp" + +PATCHES=( "${FILESDIR}/arrow-11.0-shared-lz4.patch" ) + +src_prepare() { + # use Gentoo CXXFLAGS, specify docdir at src_configure. + sed -e '/SetupCxxFlags/d' \ + -e '/set(ARROW_DOC_DIR.*)/d' \ + -i CMakeLists.txt || die + # xsimd version is managed by Gentoo. + sed -e 's/resolve_dependency(xsimd.*)/resolve_dependency(xsimd)/' \ + -i cmake_modules/ThirdpartyToolchain.cmake || die + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DARROW_DEPENDENCY_SOURCE=SYSTEM + -DARROW_BUILD_STATIC=OFF + -DARROW_CSV=$(usex csv ON OFF) + -DARROW_DATASET=ON + -DARROW_DOC_DIR=share/doc/${PF} + -DARROW_JEMALLOC=OFF + -DARROW_SUBSTRAIT=OFF + -DARROW_BUILD_TESTS=$(usex test ON OFF) + -DARROW_MIMALLOC=OFF + -DARROW_PARQUET=$(usex parquet ON OFF) + -DARROW_WITH_BZ2=$(usex bzip2 ON OFF) + -DARROW_WITH_LZ4=$(usex lz4 ON OFF) + -DARROW_WITH_SNAPPY=$(usex snappy ON OFF) + -DARROW_WITH_ZLIB=$(usex zlib ON OFF) + -DARROW_WITH_ZSTD=$(usex zstd ON OFF) + ) + cmake_src_configure +} + +src_test() { + export PARQUET_TEST_DATA="${WORKDIR}/parquet-testing-${PARQUET_DATA_GIT_HASH}/data" + export ARROW_TEST_DATA="${WORKDIR}/arrow-testing-${ARROW_DATA_GIT_HASH}/data" + cmake_src_test +} diff --git a/dev-libs/apache-arrow/files/arrow-11.0-shared-lz4.patch b/dev-libs/apache-arrow/files/arrow-11.0-shared-lz4.patch new file mode 100644 index 000000000..fdb26196d --- /dev/null +++ b/dev-libs/apache-arrow/files/arrow-11.0-shared-lz4.patch @@ -0,0 +1,14 @@ +Index: cpp/cmake_modules/Findlz4Alt.cmake +=================================================================== +--- cpp.orig/cmake_modules/Findlz4Alt.cmake ++++ cpp/cmake_modules/Findlz4Alt.cmake +@@ -32,8 +32,8 @@ if(lz4_FOUND) + # Conan uses lz4::lz4 not LZ4::lz4 + if(NOT TARGET LZ4::lz4 AND TARGET lz4::lz4) + add_library(LZ4::lz4 ALIAS lz4::lz4) ++ return() + endif() +- return() + endif() + + if(MSVC_TOOLCHAIN AND NOT DEFINED LZ4_MSVC_LIB_PREFIX) diff --git a/dev-libs/apache-arrow/metadata.xml b/dev-libs/apache-arrow/metadata.xml new file mode 100644 index 000000000..8df604998 --- /dev/null +++ b/dev-libs/apache-arrow/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>xgreenlandforwyy@gmail.com</email> + <name>Yiyang Wu</name> + </maintainer> + <upstream> + <remote-id type="github">arrow-testing/tree</remote-id> + <remote-id type="github">apache/parquet-testing</remote-id> + </upstream> + <use> + <flag name='brotli'>Enable brotli compression suppor</flag> + <flag name='csv'>Enables read/write csv format</flag> + <flag name='parquet'>Enables read/write parquet data format</flag> + </use> +</pkgmetadata> diff --git a/dev-libs/intel-common/Manifest b/dev-libs/intel-common/Manifest deleted file mode 100644 index 21dea448d..000000000 --- a/dev-libs/intel-common/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update3_professional_edition.tgz 4777019188 BLAKE2B 1ebbc23d1370bb396b452dc73d4a79b4ea7be0e304e3d38b3cba77372df6af097ea1109535d166b56a6c50e28e3330a1ed49c6a9270411b14ccf48f32a9eaedd SHA512 622b1a8877f06247a0a93cb98d2cc6d5b359aa2c9cf7ff6f45a8e1dca34fecea10d603d632a7b3454d809d6e38cb860b40ae3f782e250279768937af6ceb015d -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/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild b/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild deleted file mode 100644 index 5397d76b6..000000000 --- a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild +++ /dev/null @@ -1,95 +0,0 @@ -# Copyright 1999-2021 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="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -CHECKREQS_DISK_BUILD=750M - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-18.0.2-199-18.0.2-199.noarch.rpm" - "comp-l-all-common-18.0.2-199-18.0.2-199.noarch.rpm" - "comp-l-all-vars-18.0.2-199-18.0.2-199.noarch.rpm" - "comp-nomcu-vars-18.0.2-199-18.0.2-199.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-18.0-18.0.2-199.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-2018.2-199-2018.2-199.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-2018-2018.2-199.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-18.0.2-199-18.0.2-199.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-18.0.2-199-18.0.2-199.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-18.0.2-199-18.0.2-199.noarch.rpm" - "openmp-common-ifort-18.0.2-199-18.0.2-199.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-18.0.2-199-18.0.2-199.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild b/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild deleted file mode 100644 index dc06e4551..000000000 --- a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild +++ /dev/null @@ -1,101 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update3_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -SLOT="0" - -MY_PV=$(ver_rs 3 '-') # 19.0.3-199 -MY_PV2=$(ver_cut 1-2) # 19.0 -MY_PV3='20'$(ver_cut 1) # 2019 -MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199 - -CHECKREQS_DISK_BUILD=750M - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm" - "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild b/dev-libs/intel-common/intel-common-19.0.4.243.ebuild deleted file mode 100644 index df8f5574c..000000000 --- a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild +++ /dev/null @@ -1,101 +0,0 @@ -# Copyright 1999-2021 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="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -SLOT="0" - -MY_PV=$(ver_rs 3 '-') # 19.0.3-199 -MY_PV2=$(ver_cut 1-2) # 19.0 -MY_PV3='20'$(ver_cut 1) # 2019 -MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199 - -CHECKREQS_DISK_BUILD=750M - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm" - "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild b/dev-libs/intel-common/intel-common-19.1.1.217.ebuild deleted file mode 100644 index 4ba98edad..000000000 --- a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild +++ /dev/null @@ -1,102 +0,0 @@ -# Copyright 1999-2021 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="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -SLOT="0" - -MY_PV="$(ver_rs 3 '-')" # 19.1.1-217 -MY_PV2="$(ver_cut 1-2)" # 19.1 -MY_PV3="2019" # 2019 -MY_PV4="${MY_PV3}.7-$(ver_cut 4)" # 2019.7-217 sic! - -CHECKREQS_DISK_BUILD=750M - -QA_PREBUILT="*" - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm" - "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/metadata.xml b/dev-libs/intel-common/metadata.xml deleted file mode 100644 index 026b5a33d..000000000 --- a/dev-libs/intel-common/metadata.xml +++ /dev/null @@ -1,15 +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"> -This package contains the core files to be installed for the Intel -compilers and libraries. Probably useless if installed standalone. -</longdescription> - <use> - <flag name="compiler">Install the libraries needed for the icc and ifort compilers</flag> - </use> -</pkgmetadata> diff --git a/dev-libs/lief/lief-0.11.5.ebuild b/dev-libs/lief/lief-0.11.5.ebuild index 519729525..c2c38e5ba 100644 --- a/dev-libs/lief/lief-0.11.5.ebuild +++ b/dev-libs/lief/lief-0.11.5.ebuild @@ -4,7 +4,7 @@ EAPI=7 CMAKE_ECLASS=cmake -PYTHON_COMPAT=( python3_{8..10} pypy3 ) +PYTHON_COMPAT=( python3_10 pypy3 ) # Upstream has two alternate approaches to building its Python API: # 1. A working "CMakeList.txt" only supporting a single Python target. diff --git a/dev-libs/oneCCL/Manifest b/dev-libs/oneCCL/Manifest new file mode 100644 index 000000000..95c5b9e72 --- /dev/null +++ b/dev-libs/oneCCL/Manifest @@ -0,0 +1,2 @@ +DIST oneCCL-2021.7.1.tar.gz 35807233 BLAKE2B 0608b548f42c28983453a1e693c922aff0f6c77ffbf35f92b69113ba9fb02263bf8e1efa94ba47330559bb97b81493923cac10ce2c68c5fb50181677152fcc28 SHA512 e77d836afdcccbc2a1d2f9903916f17698a0d5ad795cd76dbb19a835375e89d0ecfa4695d87758e1ca6078bc23e30416d0a228ad3060816409b91851ad0b0790 +DIST oneCCL-2021.8.tar.gz 36868388 BLAKE2B b27f04efaddf2c31befd70388f0aa84b9cb5266b5d4e4a300064e0dc98e4d7eee3590288dc0b8cc1640fe0a9b928a0dfdf16a2ea45db9bd1517a8ca2dd00bdfe SHA512 879d1b73e594d5ff2c5a5aee08dfb4aded11c4974a9efcc199e7c2ee87b00c2441edb1dcb073bb4ed2587d752efcafe338072959b7b0f89fc1692dc377f748c2 diff --git a/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch new file mode 100644 index 000000000..e92608f4a --- /dev/null +++ b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch @@ -0,0 +1,104 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 74c4fc0..92c4d16 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -87,15 +87,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE + SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support") + + set(CCL_COMMON_INSTALL_PREFIX "intel64") +-set(CMAKE_INSTALL_LIBDIR "lib") + set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") + set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}") + set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}") + set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}") +-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env") +-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc") +-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing") +-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles") ++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env") ++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}") ++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles") + set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples") + set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests") + set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") +@@ -103,23 +101,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") + # setup dependency directories + set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps") + +-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/") +-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/") ++set(MPI_INCLUDE_DIR "/usr/include/") ++set(MPI_LIB_DIR "/usr/lib64/") + message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}") + message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}") + + if ("${LIBFABRIC_DIR}" STREQUAL "") +- set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include") +- set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/") ++ set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/") ++ set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/") + else() + set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/") +- set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib") ++ set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/") + endif() + message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}") + message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}") + +-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/") +-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/") ++set(HWLOC_INCLUDE_DIR "/usr/include/") ++set(HWLOC_LIB_DIR "/usr/lib64/") + message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}") + message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}") + +@@ -128,7 +126,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64") + message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}") + message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}") + +-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/") ++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero") + message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}") + + set(CMAKE_SKIP_INSTALL_RPATH TRUE) +@@ -241,8 +239,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party- + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE}) +-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE}) +-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE}) + + # copy kernels + if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels") +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 7b4cff9..e8296a0 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -263,8 +263,8 @@ list(APPEND SRC_LINK_LIBS + pthread + ${EXTERNAL_LIBS} + fabric +- ${HWLOC_LIB_DIR}/libhwloc.a +- ${ITT_LIB_DIR}/libittnotify.a) ++ libhwloc.so ++ libittnotify.so) + + if (ENABLE_MPI) + set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI") +@@ -335,16 +335,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "") + install(DIRECTORY ${DEPS_DIR}/ofi/lib/ + DESTINATION ${CCL_INSTALL_LIB}) + endif() +- +-if (ENABLE_MPI) +- file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*") +- install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN}) +- install(DIRECTORY ${DEPS_DIR}/mpi/include/ +- DESTINATION ${CCL_INSTALL_INCLUDE}) +- install(DIRECTORY ${DEPS_DIR}/mpi/lib/ +- DESTINATION ${CCL_INSTALL_LIB}) +- install(DIRECTORY ${DEPS_DIR}/mpi/etc/ +- DESTINATION ${CCL_INSTALL_ETC}) +- install(DIRECTORY ${DEPS_DIR}/mpi/licensing/ +- DESTINATION ${CCL_INSTALL_LICENSE}/mpi/) +-endif() diff --git a/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch new file mode 100644 index 000000000..dbb3a9e5f --- /dev/null +++ b/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch @@ -0,0 +1,104 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1e65ce9..cabbff9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -109,15 +109,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE + SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support") + + set(CCL_COMMON_INSTALL_PREFIX "intel64") +-set(CMAKE_INSTALL_LIBDIR "lib") + set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") + set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}") + set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}") + set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}") +-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env") +-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc") +-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing") +-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles") ++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env") ++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}") ++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles") + set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples") + set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests") + set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") +@@ -125,23 +123,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") + # setup dependency directories + set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps") + +-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/") +-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/") ++set(MPI_INCLUDE_DIR "/usr/include/") ++set(MPI_LIB_DIR "/usr/lib64/") + message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}") + message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}") + + if ("${LIBFABRIC_DIR}" STREQUAL "") +- set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include") +- set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/") ++ set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/") ++ set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/") + else() + set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/") +- set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib") ++ set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/") + endif() + message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}") + message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}") + +-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/") +-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/") ++set(HWLOC_INCLUDE_DIR "/usr/include/") ++set(HWLOC_LIB_DIR "/usr/lib64/") + message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}") + message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}") + +@@ -150,7 +148,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64") + message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}") + message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}") + +-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/") ++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero") + message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}") + + message(STATUS "DRM_INCLUDE_DIR: ${DRM_INCLUDE_DIR}") +@@ -290,8 +288,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party- + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE}) +-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE}) +-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE}) + + # copy kernels + if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels") +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 3948373..168a690 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -279,8 +279,8 @@ list(APPEND SRC_LINK_LIBS + dl + pthread + ${EXTERNAL_LIBS} +- ${HWLOC_LIB_DIR}/libhwloc.a +- ${ITT_LIB_DIR}/libittnotify.a) ++ libhwloc.so ++ libittnotify.so) + + if (ENABLE_MPI) + set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI") +@@ -350,16 +350,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "") + install(DIRECTORY ${DEPS_DIR}/ofi/lib/ + DESTINATION ${CCL_INSTALL_LIB}) + endif() +- +-if (ENABLE_MPI) +- file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*") +- install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN}) +- install(DIRECTORY ${DEPS_DIR}/mpi/include/ +- DESTINATION ${CCL_INSTALL_INCLUDE}) +- install(DIRECTORY ${DEPS_DIR}/mpi/lib/ +- DESTINATION ${CCL_INSTALL_LIB}) +- install(DIRECTORY ${DEPS_DIR}/mpi/etc/ +- DESTINATION ${CCL_INSTALL_ETC}) +- install(DIRECTORY ${DEPS_DIR}/mpi/licensing/ +- DESTINATION ${CCL_INSTALL_LICENSE}/mpi/) +-endif() diff --git a/sci-libs/ipp/metadata.xml b/dev-libs/oneCCL/metadata.xml index 7bd17909e..cbb320b12 100644 --- a/sci-libs/ipp/metadata.xml +++ b/dev-libs/oneCCL/metadata.xml @@ -5,9 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> - <longdescription lang="en"> -Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a -library of multi-core-ready, optimized software functions for -multimedia data processing, and communications applications. -</longdescription> + <upstream> + <remote-id type="github">oneapi-src/oneCCL</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild new file mode 100644 index 000000000..76ab29af2 --- /dev/null +++ b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild @@ -0,0 +1,61 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="oneAPI Collective Communications Library" +HOMEPAGE="https://github.com/oneapi-src/oneCCL" +SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="mpi" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-libs/level-zero:= + sys-apps/hwloc:= + sys-block/libfabric:= + sys-devel/ittapi + mpi? ( virtual/mpi ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-2021.7.1-use-system-libs.patch" +) + +src_prepare() { + # No -Werror + find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die + + # Use system libs instead + rm -r deps/* || die + + # 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=( + -DBUILD_EXAMPLES=OFF + # BUILD_CONFIG causes sandbox violation + -DBUILD_CONFIG=OFF + -DCCL_ENABLE_ZE=ON + # TODO: Find out how to execute the tests + -DBUILD_FT=OFF + -DENABLE_MPI_TESTS=OFF + -DENABLE_MPI="$(usex mpi)" + # Use system fabric + -DLIBFABRIC_DIR="${ESYSROOT}/usr" + ) + cmake_src_configure +} diff --git a/dev-libs/oneCCL/oneCCL-2021.8.ebuild b/dev-libs/oneCCL/oneCCL-2021.8.ebuild new file mode 100644 index 000000000..a67659f4a --- /dev/null +++ b/dev-libs/oneCCL/oneCCL-2021.8.ebuild @@ -0,0 +1,62 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="oneAPI Collective Communications Library" +HOMEPAGE="https://github.com/oneapi-src/oneCCL" +SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="mpi" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-libs/level-zero:= + sys-apps/hwloc:= + sys-block/libfabric:= + sys-devel/ittapi + sys-cluster/pmix + mpi? ( virtual/mpi ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-2021.8-use-system-libs.patch" +) + +src_prepare() { + # No -Werror + find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die + + # Use system libs instead + rm -r deps/* || die + + # 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=( + -DBUILD_EXAMPLES=OFF + # BUILD_CONFIG causes sandbox violation + -DBUILD_CONFIG=OFF + -DCCL_ENABLE_ZE=ON + # TODO: Find out how to execute the tests + -DBUILD_FT=OFF + -DENABLE_MPI_TESTS=OFF + -DENABLE_MPI="$(usex mpi)" + # Use system fabric + -DLIBFABRIC_DIR="${ESYSROOT}/usr" + ) + cmake_src_configure +} diff --git a/dev-libs/oneDNN/Manifest b/dev-libs/oneDNN/Manifest new file mode 100644 index 000000000..b66805cea --- /dev/null +++ b/dev-libs/oneDNN/Manifest @@ -0,0 +1,2 @@ +DIST oneDNN-2.7.2.tar.gz 6409290 BLAKE2B 8e6fb262a77469cfaddd633bf11334d04ffb641fa798f0de23e458086c66c9b7e932d45d52baf8a93453495df9280f6a97dc3f220d7674850d1ca6c525ce2a7f SHA512 faf8ea953f552afaafcc597f647a98187c8c6dabd8a532fc1b8037626fa77a8a6543dce3247d953a470391d39189ba421ab7de589a8bb7c4c38e22327ab1c401 +DIST oneDNN-3.0.1.tar.gz 7189577 BLAKE2B e55798bb3ab921945873040876514c0b22a77edce34d4bba249537cc56bbcd846eecb461dc22d2ea3bf4b1c47f9079a9c876307f3044e059f71e69b5669886aa SHA512 ca7d7d97469c878953507ddd7c4e3a09bb9955f160ce57529b5a943afd08db0ff82755ffded857518193fcab0e0be2b4ebe45f5e8bfba1a53006b0f161ac15b5 diff --git a/dev-libs/oneDNN/metadata.xml b/dev-libs/oneDNN/metadata.xml new file mode 100644 index 000000000..0d6dc84a7 --- /dev/null +++ b/dev-libs/oneDNN/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/oneDNN</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-libs/oneDNN/oneDNN-2.7.2.ebuild b/dev-libs/oneDNN/oneDNN-2.7.2.ebuild new file mode 100644 index 000000000..1c66ec72c --- /dev/null +++ b/dev-libs/oneDNN/oneDNN-2.7.2.ebuild @@ -0,0 +1,60 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DOCS_BUILDER="doxygen" +DOCS_DIR="${WORKDIR}/${P}_build" +# There is additional sphinx documentation but we are missing dependency doxyrest. +inherit cmake docs + +DESCRIPTION="oneAPI Deep Neural Network Library" +HOMEPAGE="https://github.com/oneapi-src/oneDNN" +SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +# TODO: get the tests up and running +#RESTRICT="!test? ( test )" +RESTRICT="test" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-cpp/tbb:= + dev-libs/level-zero:= + virtual/opencl +" +RDEPEND="${DEPEND}" + +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=( + -DDNNL_CPU_RUNTIME=DPCPP + -DDNNL_GPU_RUNTIME=DPCPP + -DDNNL_BUILD_TESTS="$(usex test)" + ) + cmake_src_configure +} + +src_compile() { + cmake_src_compile + docs_compile +} + +src_install() { + cmake_src_install + # Correct docdir + mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die + rm -r "${ED}/usr/share/doc/dnnl" || die +} diff --git a/dev-libs/oneDNN/oneDNN-3.0.1.ebuild b/dev-libs/oneDNN/oneDNN-3.0.1.ebuild new file mode 100644 index 000000000..1c66ec72c --- /dev/null +++ b/dev-libs/oneDNN/oneDNN-3.0.1.ebuild @@ -0,0 +1,60 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DOCS_BUILDER="doxygen" +DOCS_DIR="${WORKDIR}/${P}_build" +# There is additional sphinx documentation but we are missing dependency doxyrest. +inherit cmake docs + +DESCRIPTION="oneAPI Deep Neural Network Library" +HOMEPAGE="https://github.com/oneapi-src/oneDNN" +SRC_URI="https://github.com/oneapi-src/oneDNN/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +# TODO: get the tests up and running +#RESTRICT="!test? ( test )" +RESTRICT="test" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-cpp/tbb:= + dev-libs/level-zero:= + virtual/opencl +" +RDEPEND="${DEPEND}" + +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=( + -DDNNL_CPU_RUNTIME=DPCPP + -DDNNL_GPU_RUNTIME=DPCPP + -DDNNL_BUILD_TESTS="$(usex test)" + ) + cmake_src_configure +} + +src_compile() { + cmake_src_compile + docs_compile +} + +src_install() { + cmake_src_install + # Correct docdir + mv "${ED}/usr/share/doc/dnnl/"* "${ED}/usr/share/doc/${PF}" || die + rm -r "${ED}/usr/share/doc/dnnl" || die +} diff --git a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild new file mode 100644 index 000000000..6f675dc80 --- /dev/null +++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Create calibration matrix to correct for magneto-resistance in resistive sensors" +HOMEPAGE="https://gitlab.science.ru.nl/hfml/MRcalib" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] +" diff --git a/dev-python/MagnetoResistance-tool/Manifest b/dev-python/MagnetoResistance-tool/Manifest new file mode 100644 index 000000000..b8d0afd21 --- /dev/null +++ b/dev-python/MagnetoResistance-tool/Manifest @@ -0,0 +1 @@ +DIST MagnetoResistance-tool-0.0.2.tar.gz 21657 BLAKE2B 5d1a2f497f742df04aac5db6afe83373e6e3e3cea3891585c22d1585186665f0d597b3dccd5f2adfef4e58bc41f680b974974cb12c56e3ef29f69122407cfff5 SHA512 4866197feb96912edc19691ba7ea54303ed168d8ab72c534ad910a3a77ce6e8ccf0f19744eca5044936c29bde131d4c352abbd57547f1c30b3ae59d4aac36986 diff --git a/dev-python/MagnetoResistance-tool/metadata.xml b/dev-python/MagnetoResistance-tool/metadata.xml new file mode 100644 index 000000000..aed122741 --- /dev/null +++ b/dev-python/MagnetoResistance-tool/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>andrewammerlaan@gentoo.org</email> + <name>Andrew Ammerlaan</name> + </maintainer> + <upstream> + <remote-id type="pypi">MagnetoResistance-tool</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/affine/affine-2.3.0.ebuild b/dev-python/affine/affine-2.3.0.ebuild index a298cec26..7cc363d92 100644 --- a/dev-python/affine/affine-2.3.0.ebuild +++ b/dev-python/affine/affine-2.3.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/amply/amply-0.1.4.ebuild b/dev-python/amply/amply-0.1.4.ebuild index db2b71b73..ae3e3b63d 100644 --- a/dev-python/amply/amply-0.1.4.ebuild +++ b/dev-python/amply/amply-0.1.4.ebuild @@ -15,7 +15,7 @@ LICENSE="EPL-1.0" KEYWORDS="~amd64 ~x86" SLOT="0" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" RDEPEND=" dev-python/docutils[${PYTHON_USEDEP}] diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild index b35e3c274..90511a157 100644 --- a/dev-python/annexremote/annexremote-1.5.0.ebuild +++ b/dev-python/annexremote/annexremote-1.5.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Helper module to easily develop git-annex remotes" @@ -14,6 +14,9 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="examples" +# Reported upstream: +# https://github.com/Lykos153/AnnexRemote/issues/61 +RESTRICT="test" COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]" RDEPEND=" diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild index b35e3c274..90511a157 100644 --- a/dev-python/annexremote/annexremote-1.6.0.ebuild +++ b/dev-python/annexremote/annexremote-1.6.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Helper module to easily develop git-annex remotes" @@ -14,6 +14,9 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="examples" +# Reported upstream: +# https://github.com/Lykos153/AnnexRemote/issues/61 +RESTRICT="test" COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]" RDEPEND=" diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild index d74bb76f9..659e797cf 100644 --- a/dev-python/anys/anys-0.2.1.ebuild +++ b/dev-python/anys/anys-0.2.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest new file mode 100644 index 000000000..5351b4321 --- /dev/null +++ b/dev-python/archspec/Manifest @@ -0,0 +1 @@ +DIST archspec-0.1.4.tar.gz 35184 BLAKE2B fe05cab539163d986e639e7e9cf57db208f9cce7ee447d2d3207af0bad68f2d5410e720e5f73376f950b9672602885fe34942fb885d7acbb8ad7e31b7f139ee0 SHA512 28da79ba1469db38ab1424be49feba87378c252ead5ad07fca8ae752dc3503d281f2f3f30391fe6209b118800f357b5219593c2d0d11608d683e56c95ca8f286 diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild new file mode 100644 index 000000000..5e8eee157 --- /dev/null +++ b/dev-python/archspec/archspec-0.1.4.ebuild @@ -0,0 +1,20 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=poetry +inherit distutils-r1 + +DESCRIPTION="labels for various aspects of a system architecture like CPU, etc." +HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/six-1.16.0[${PYTHON_USEDEP}] + <=dev-python/six-2.0.0[${PYTHON_USEDEP}] + >=dev-python/click-7.1.2[${PYTHON_USEDEP}] +" +BDEPEND="${RDEPEND}" diff --git a/dev-python/archspec/metadata.xml b/dev-python/archspec/metadata.xml new file mode 100644 index 000000000..3688592b1 --- /dev/null +++ b/dev-python/archspec/metadata.xml @@ -0,0 +1,20 @@ +<?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"> + Archspec aims at providing a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them. + </longdescription> + <upstream> + <remote-id type="pypi">archspec</remote-id> + <remote-id type="github">archspec/archspec</remote-id> + <bugs-to>https://github.com/archspec/archspec/issues</bugs-to> + </upstream> +</pkgmetadata> diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild index 57c0eb7a2..3f8f82f8b 100644 --- a/dev-python/asciitree/asciitree-0.3.3.ebuild +++ b/dev-python/asciitree/asciitree-0.3.3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="ASCII trees in python" diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest index 3b2cf6ef8..fc182f25b 100644 --- a/dev-python/asdf/Manifest +++ b/dev-python/asdf/Manifest @@ -1 +1,2 @@ +DIST asdf-2.14.3.tar.gz 489097 BLAKE2B 26e3da88f4b0ada5a995ff77fdb55a26aa9af1b53c4e90723b36080526ee218581d09295b169bddd998a4055d1b9818e793bfdafdc786a27f5ea87021e9f85e7 SHA512 125015a1d3a26034c8d483bebf609af02489d0710973828e443dea5cfa46cb33826078714b9ccbd385fcc92fd6b2d92253e80c32ca90565a48f45e4ff47b8655 DIST asdf-2.8.3.tar.gz 513853 BLAKE2B 73afb6f5799a13689bd2be73b8d9b45d5bb4a1f093654e3d8a0796a6342f03deabe64c6de4d33213ba762e3b2508541a25b24cccc490f0685714180af6790c43 SHA512 c3b72ed7fefd33958413c962d81213d2d141072473e08c767059a3ff46ba03f0135c9435a7893eb0eb43b199e2c701d62f263a487872a120465979dfec8988df diff --git a/dev-python/asdf/asdf-2.14.3.ebuild b/dev-python/asdf/asdf-2.14.3.ebuild new file mode 100644 index 000000000..d5e292123 --- /dev/null +++ b/dev-python/asdf/asdf-2.14.3.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2023 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 pypi + +DESCRIPTION="Python library for the Advanced Scientific Data Format" +HOMEPAGE="https://asdf.readthedocs.io/en/latest/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Reported upstream: +# https://github.com/asdf-format/asdf/issues/1319 +RESTRICT="test" + +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/astropy[${PYTHON_USEDEP}] + dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/gwcs[${PYTHON_USEDEP}] + ) + doc? ( media-gfx/graphviz ) +" + +RDEPEND=" + >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}] + >=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.10[${PYTHON_USEDEP}] + >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}] + >=dev-python/semantic_version-2.8[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-python/matplotlib dev-python/docutils + +python_test() { + # discovers things in docs dir if we do not + # explicitly set it to run on the tests dir + epytest asdf/tests +} diff --git a/dev-python/asdf/asdf-2.8.3.ebuild b/dev-python/asdf/asdf-2.8.3.ebuild index 96663e49a..09aab4068 100644 --- a/dev-python/asdf/asdf-2.8.3.ebuild +++ b/dev-python/asdf/asdf-2.8.3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..10} ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 @@ -15,8 +15,11 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" +# Reported upstream: +# https://github.com/asdf-format/asdf/issues/1319 +RESTRICT="test" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}] +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}] test? ( dev-python/astropy[${PYTHON_USEDEP}] dev-python/pytest-doctestplus[${PYTHON_USEDEP}] diff --git a/dev-python/asdf/metadata.xml b/dev-python/asdf/metadata.xml index 4f4367037..332ed9dd0 100644 --- a/dev-python/asdf/metadata.xml +++ b/dev-python/asdf/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">asdf</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy-healpix/Manifest b/dev-python/astropy-healpix/Manifest index 0845b8ed4..ee0baaaa9 100644 --- a/dev-python/astropy-healpix/Manifest +++ b/dev-python/astropy-healpix/Manifest @@ -1 +1 @@ -DIST astropy_healpix-0.6.tar.gz 104224 BLAKE2B a06474de29f2848d18dedb45202ea63ba5893d6993ef39ebb91e02b55c0f5e100522c267198a233c8771f3920c620f7eddb83f08c82c3cb4151432e1815b00d8 SHA512 c54a41e50c7eaa51126b20abc88e5fc8f7c02521baeb4a69a5a8eac42f59350273e8f30c17926daf628c7866550eec141980ce0349028ff72a4ac2786275f428 +DIST astropy_healpix-0.7.tar.gz 107330 BLAKE2B c1daed6475b63d59debd19ad97fc3547917df93b9b6998aef51f38a7e4014a543f25f6823dac12e93745fa8cd6c17b418035730b4d37f85b7df250e8d4fd6026 SHA512 33e23a616a0a36880066d96a50b949b1a96b4a1cecc1ebe8584c817a10587d26eb58879fb175c3fd675c3fbc98d4be1cfa9b19aa9ad4ac7a1528a8e6d32f7436 diff --git a/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild index ce6ec0cd3..36f38c205 100644 --- a/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild +++ b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -25,7 +26,7 @@ KEYWORDS="~amd64 ~x86" # pytest-filter-subpackage>=0.1 RESTRICT="test" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" RDEPEND=" >=dev-python/astropy-3.2[${PYTHON_USEDEP}] @@ -33,4 +34,4 @@ RDEPEND=" " distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib -distutils_enable_tests --install pytest +distutils_enable_tests pytest diff --git a/dev-python/astropy-healpix/metadata.xml b/dev-python/astropy-healpix/metadata.xml index 4f4367037..2d40d7328 100644 --- a/dev-python/astropy-healpix/metadata.xml +++ b/dev-python/astropy-healpix/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astropy-healpix</remote-id> + <remote-id type="pypi">astropy-healpix</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild index 393066583..34b71dbda 100644 --- a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild +++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 xdg-utils diff --git a/dev-python/astropy-helpers/metadata.xml b/dev-python/astropy-helpers/metadata.xml index 8bc35edb7..8bd2cb74a 100644 --- a/dev-python/astropy-helpers/metadata.xml +++ b/dev-python/astropy-helpers/metadata.xml @@ -15,5 +15,6 @@ </maintainer> <upstream> <remote-id type="github">astropy/astropy-helpers</remote-id> + <remote-id type="pypi">astropy-helpers</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild index 844b614bd..5b63931b8 100644 --- a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild +++ b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild @@ -3,14 +3,14 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="The sphinx theme for Astropy and affiliated packages" HOMEPAGE="https://github.com/astropy/astropy-sphinx-theme" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/astropy-sphinx-theme/metadata.xml b/dev-python/astropy-sphinx-theme/metadata.xml index 4f4367037..7db317173 100644 --- a/dev-python/astropy-sphinx-theme/metadata.xml +++ b/dev-python/astropy-sphinx-theme/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astropy-sphinx-theme</remote-id> + <remote-id type="pypi">astropy-sphinx-theme</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest index c8278e21a..da0e68d73 100644 --- a/dev-python/astropy/Manifest +++ b/dev-python/astropy/Manifest @@ -1 +1,2 @@ DIST astropy-5.0.tar.gz 7823746 BLAKE2B e769f9ea26e156a2342dc75b307c16c2c38108adf0dfd931812b2eb3234941055c013378a492306f2247c16b4804fe569ba1cbfd8427df1aac2b808976082cf9 SHA512 3c0b0cdef434f27ee399fbfc3d55b95ce8395624caf8e73a205dba7742c39d8a2bcea9bf61c2c20235da7388d40c657c5474bfc7e3dc3c9e5911e39bab47cdb9 +DIST astropy-5.2.1.tar.gz 8284422 BLAKE2B ded3556d6b16fe7abbbd019c23c0297f4690b13f054a1b98ab6aaeb20b92debefbc6e7c6c5eff8c65dfaa271826885027d6ba4a92f94218632162501a30b025b SHA512 46da7b065e119fa36233ced928abab31d6022fd116d2ed6825cb88b456ab57130772eea1de8cff7b5b7f30aadf46b933ad56a47cf6d2d68c0fa7593f322a6ea0 diff --git a/dev-python/astropy/astropy-5.0.ebuild b/dev-python/astropy/astropy-5.0.ebuild index c650533d6..6f32f60ed 100644 --- a/dev-python/astropy/astropy-5.0.ebuild +++ b/dev-python/astropy/astropy-5.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -37,7 +37,7 @@ BDEPEND="${RDEPEND} dev-python/astropy-helpers[${PYTHON_USEDEP}] dev-python/extension-helpers[${PYTHON_USEDEP}] dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools_scm[${PYTHON_USEDEP}] + dev-python/setuptools-scm[${PYTHON_USEDEP}] test? ( dev-libs/libxml2 dev-python/h5py[${PYTHON_USEDEP}] diff --git a/dev-python/astropy/astropy-5.2.1.ebuild b/dev-python/astropy/astropy-5.2.1.ebuild new file mode 100644 index 000000000..ac5c388b0 --- /dev/null +++ b/dev-python/astropy/astropy-5.2.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Core functionality for performing astrophysics with Python" +HOMEPAGE="https://www.astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +RDEPEND=" + dev-libs/expat:0= + >=dev-python/numpy-1.18[${PYTHON_USEDEP}] + >=dev-python/pyerfa-2.0[${PYTHON_USEDEP}] + >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}] + >=dev-python/packaging-19.0[${PYTHON_USEDEP}] + sci-astronomy/wcslib:0= + >=sci-libs/cfitsio-3.350:0= + sys-libs/zlib:0= +" +BDEPEND="${RDEPEND} + dev-python/astropy-helpers[${PYTHON_USEDEP}] + dev-python/extension-helpers[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-libs/libxml2 + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/ipython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/objgraph[${PYTHON_USEDEP}] + dev-python/pytest-xdist[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + )" + +distutils_enable_tests pytest +# TODO: Fix this +# NameError: name 'disabled_intersphinx_mapping' is not defined +#distutils_enable_sphinx docs \ +# dev-python/matplotlib \ +# dev-python/graphviz \ +# dev-python/sphinx-astropy \ +# dev-python/pyyaml \ +# dev-python/scipy diff --git a/dev-python/astropy/metadata.xml b/dev-python/astropy/metadata.xml index 3d1dc456d..3891d8cc8 100644 --- a/dev-python/astropy/metadata.xml +++ b/dev-python/astropy/metadata.xml @@ -9,4 +9,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">astropy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astroquery/Manifest b/dev-python/astroquery/Manifest index 5d34a7193..2472dec6d 100644 --- a/dev-python/astroquery/Manifest +++ b/dev-python/astroquery/Manifest @@ -1 +1 @@ -DIST astroquery-0.4.1.tar.gz 6525892 BLAKE2B 9ee1d57f265e0370df4f302b6422955701c5fd8deb27c4dd76b5746f3c307e5b4d09b29a8746ff0f6b406065b0d339b3afa59e974806e47d9d9ee6fef3e18e09 SHA512 71e160c9495532c0bf0060574996187d7801feeecac526b50b3aebd0ce147ae3877a2a235ab5c49690733d5833050bd3f8365be7ba6f97f2db8a416766f12c15 +DIST astroquery-0.4.6.tar.gz 6070636 BLAKE2B 9ea912661e3d0ad59ca42087527eeee5657062c39c389a2635e699a5cb683eb6f4324b9c546e227f26e57b645057ad6bde0b2dad7f71cf5f7b090792ca9f4afc SHA512 4ec5e2fbd9754ae0be614011a0020218fbdd7d7cf4511836b40cefcf99fa0feb88cc247c2c83e556aa11ff10930b9e4d7784d175039f9581a4551bb4667a3529 diff --git a/dev-python/astroquery/astroquery-0.4.1.ebuild b/dev-python/astroquery/astroquery-0.4.6.ebuild index a7884eb1d..3e140280c 100644 --- a/dev-python/astroquery/astroquery-0.4.1.ebuild +++ b/dev-python/astroquery/astroquery-0.4.6.ebuild @@ -1,15 +1,15 @@ # Copyright 1999-2021 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} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A collection of packages to access online astronomical resources" -HOMEPAGE="https://www.astropy.org/astroquery/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://astroquery.readthedocs.io/" LICENSE="BSD" SLOT="0" diff --git a/dev-python/astroquery/metadata.xml b/dev-python/astroquery/metadata.xml index bb6a20b51..b70564de2 100644 --- a/dev-python/astroquery/metadata.xml +++ b/dev-python/astroquery/metadata.xml @@ -12,5 +12,6 @@ to support many services with a uniform API. </longdescription> <upstream> <remote-id type="github">astropy/astroquery</remote-id> + <remote-id type="pypi">astroquery</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild index f4ef741da..cd34136af 100644 --- a/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild +++ b/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild @@ -3,21 +3,19 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Speedy Cosmic Ray Annihilation Package in Python" HOMEPAGE="https://github.com/astropy/astroscrappy" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" #TODO: Fix this -# ModuleNotFoundError: No module named 'astroscrappy.astroscrappy' -# happens even with --install argument RESTRICT="test" RDEPEND=" @@ -28,4 +26,4 @@ BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" # Requires self to already be installed #distutils_enable_sphinx docs dev-python/sphinx-astropy -distutils_enable_tests --install pytest +distutils_enable_tests pytest diff --git a/dev-python/astroscrappy/metadata.xml b/dev-python/astroscrappy/metadata.xml index 4f4367037..b308f644b 100644 --- a/dev-python/astroscrappy/metadata.xml +++ b/dev-python/astroscrappy/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astroscrappy</remote-id> + <remote-id type="pypi">astroscrappy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild index 57a8bbdfb..91c9535df 100644 --- a/dev-python/av/av-8.0.3.ebuild +++ b/dev-python/av/av-8.0.3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild index 263546dbf..02581b74c 100644 --- a/dev-python/bokeh/bokeh-2.4.2.ebuild +++ b/dev-python/bokeh/bokeh-2.4.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_SETUPTOOLS=rdepend DISTUTILS_IN_SOURCE_BUILD=1 inherit distutils-r1 optfeature diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest index 4818fac84..9b34bca41 100644 --- a/dev-python/cadquery-ocp/Manifest +++ b/dev-python/cadquery-ocp/Manifest @@ -1,2 +1 @@ -DIST cadquery-ocp-7.5.2_beta.tar.gz 5571554 BLAKE2B 552e44b301b69f1b1b4f6c26c46638bcf94a5f753d4d35e2cbbd6e1d963a23c685d6c05ead56c970c6532a3adbbf7b1f2bd572e72fb482ccd2dac04585764910 SHA512 041d12632678b96f23528f289516e31457a4e0d3251db6f01e3fc2bb2ccc41d2df8b825c94db0cebd7419cf82070c75d20852f25d91f05377502d75adf493fd8 DIST cadquery-ocp-7.5.3.0.tar.gz 5571719 BLAKE2B ba31d7ae2f54e2f4c17f0914cab1299b91254a3fab7d07f18b2d698ce6e47e9ea174e449e18971197b39f08fa755c4d16d8cba24f894372f5bd515ec6686935e SHA512 b89dc91f224ee87e288bd7e3a10cb3b2c6559e2b36c24aac2f675fb05ecda755b723721122a7e58d87ba4253024892795369b1e747fb77684c739d01d516d1a2 diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild deleted file mode 100644 index ec0b8526d..000000000 --- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild +++ /dev/null @@ -1,195 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..9} ) - -# OCP uses "python-single-r1" only because VTK uses "python-single-r1". -inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs - -MY_PN=OCP -MY_PV="${PV//_/-}" -MY_P="${MY_PN}-${MY_PV}" -OCCT_PV=$(ver_cut 1-3) - -DESCRIPTION="Python wrapper for OCCT generated using pywrap" -HOMEPAGE="https://github.com/CadQuery/OCP" -SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -KEYWORDS="~amd64 ~x86" -SLOT="0" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file -# generated by the src_prepare() phase. OCP currently requires opencascade -# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also: -# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994 -BDEPEND=" - >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}] - >=dev-util/cmake-3.16 -" -RDEPEND=" - ${PYTHON_DEPS} - sci-libs/opencascade:0/7.5[json,tbb,vtk] - >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}] -" -DEPEND="${RDEPEND} - $(python_gen_cond_dep ' - >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]') -" - -S="${WORKDIR}/${MY_P}" - -# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare(). -CMAKE_IN_SOURCE_BUILD=True - -# Ensure the path returned by get_llvm_prefix() contains clang. -llvm_check_deps() { - has_version -r "sys-devel/clang:${LLVM_SLOT}" -} - -cadquery-ocp_check_reqs() { - CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE} -} - -pkg_pretend() { - cadquery-ocp_check_reqs -} - -pkg_setup() { - cadquery-ocp_check_reqs - llvm_pkg_setup - python-single-r1_pkg_setup -} - -# OCP currently requires manual configuration, compilation, and installation -# loosely inspired by the conda-specific "build-bindings-job.yml" file. -# -# Note that the cmake_src_prepare() function called below handles user patches. -src_prepare() { - # Most recently installed version of Clang. - local _CLANG_VERSION="$(CPP=clang clang-fullversion)" - - # Most recently installed version (excluding trailing patch) of VTK. - local _VTK_VERSION="$(best_version -r sci-libs/vtk)" - _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")" - - # Absolute dirname of the most recently installed Clang include directory, - # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also: - # https://bugs.gentoo.org/619490 - local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include" - - # Absolute filename of the most recently installed Clang shared library. - local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so" - - # Absolute dirname of OCCT's include and shared library directories. - local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade-${OCCT_PV}" - local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade-${OCCT_PV}" - - # Absolute dirname of a temporary directory to store symbol tables for this - # OCCT version dumped below by the "dump_symbols.py" script. - local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols" - local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux" - - # Absolute dirname of VTK's include directory, - local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}" - - # Ensure the above paths exist as a crude sanity test. - test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found." - test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found." - test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found." - test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found." - test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found." - - # "dev-python/clang-python" atom targeting this Clang version. - local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}" - - # Ensure "dev-python/clang-python" targets this Clang version. - has_version -r "=${_CLANG_PYTHON_ATOM}" || - die "${_CLANG_PYTHON_ATOM} not installed." - - # Remove all vendored paths. - rm -r conda opencascade pywrap *.dat || die - - # Inject a symlink to OCCT's include directory. - ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die - - # Inject a symlink from OCCT's shared library directory into this temporary - # directory as required by the "dump_symbols.py" script. - mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die - ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die - - # Update all hardcoded OCCT shared library versions in "dump_symbols.py". - sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \ - dump_symbols.py || die - - # Dump (i.e., generate) symbol tables for this OCCT version. - einfo 'Dumping OCCT symbol tables...' - ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die - - # Generate OCCT bindings in the "OCP/" subdirectory. - einfo 'Building OCP CMake binary tree...' - ${EPYTHON} -m bindgen \ - --verbose \ - --njobs $(makeopts_jobs) \ - --libclang "${_CLANG_LIB_FILE}" \ - --include "${_CLANG_INCLUDE_DIR}" \ - --include "${_VTK_INCLUDE_DIR}" \ - all ocp.toml || die - - # Remove the source "FindOpenCascade.cmake" after generating bindings, - # which copied that file to the target "OCP/FindOpenCascade.cmake". - rm FindOpenCascade.cmake || die - - #FIXME: Submit an issue recommending upstream replace their - #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level - #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl - # find_package(vtk 9 CONFIG REQUIRED) - # if(TARGET VTK::VTK) - # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES) - # endif() - - # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with - # standard OCCT paths derived above. That file is both fundamentally - # broken and useless, as the ${CASROOT} environment variable and - # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file - # already reliably identify all requisite OpenCASCADE paths. Failure to - # patch this file results in src_configure() failures resembling: - # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES) - sed -i \ - -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \ - -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \ - -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \ - OCP/FindOpenCascade.cmake || die - - # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed - # as an absolute path both here and below to minimize eclass issues. - CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -B "${S}/OCP.build" - -DPYTHON_EXECUTABLE="${PYTHON}" - -Wno-dev - ) - - CMAKE_USE_DIR="${S}/OCP" cmake_src_configure -} - -src_compile() { - CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile -} - -# OCP currently ships no test suite, so we synthesize a crude import unit test. -src_test() { - PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \ - 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ' -} - -src_install() { - python_moduleinto . - python_domodule "${S}/OCP.build/"OCP*.so -} diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild index 064952018..8a97782bd 100644 --- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild +++ b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) # OCP uses "python-single-r1" only because VTK uses "python-single-r1". inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs @@ -18,7 +18,9 @@ HOMEPAGE="https://github.com/CadQuery/OCP" SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz" LICENSE="Apache-2.0" -KEYWORDS="~amd64 ~x86" +# Hard masking due to opencascade slot 0/7.5 having been removed from ::gentoo in ff9032e688571dde15e9d36cebedf5a247ded1b8 +#KEYWORDS="~amd64 ~x86" +KEYWORDS="" SLOT="0" REQUIRED_USE="${PYTHON_REQUIRED_USE}" diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest index e5aef7ccf..4bccc9e86 100644 --- a/dev-python/cadquery-pywrap/Manifest +++ b/dev-python/cadquery-pywrap/Manifest @@ -1,2 +1 @@ -DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872 DIST cadquery-pywrap-7.5.3_rc20220113.tar.gz 5584755 BLAKE2B d6585d33eddc34c719f9694322d209969698d6e5c67288a95ad841efbc2347d2cb162d8f3443a4e3373d70b97423485d1535c60713e4cb8ace413d114b852083 SHA512 f0d984b6fa6df3151d9cb612560a5266f98d286b9ab283c4647095dda3da1c54fb102babee4d2db574b695604332bc7576740406907995940eb60635afb614b8 diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild deleted file mode 100644 index 3217b8774..000000000 --- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit llvm distutils-r1 - -DESCRIPTION="C++ binding generator based on libclang and pybind11" -HOMEPAGE="https://github.com/CadQuery/pywrap" - -#FIXME: Uncomment on bumping to the next stable release. -# MY_PN=occt -# MY_PV=$(ver_cut 1-2) -# MY_P="${MY_PN}${MY_PV}" -# SRC_URI="https://github.com/CadQuery/pywrap/archive/refs/tags/${MY_P}.tar.gz" - -# The official pywrap 7.4.0 tarball is broken, but pywrap 7.5.2 has yet to be -# officially released. We instead package a commit known to work as expected. -MY_COMMIT="f8869e5a47fd3e3e1d31e7ab89b46c158f7487bf" -SRC_URI="https://github.com/CadQuery/pywrap/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -KEYWORDS="~amd64 ~x86" -SLOT="0" - -# Dependencies are intentionally listed in "setup.py" order. -RDEPEND=" - dev-python/click[${PYTHON_USEDEP}] - dev-python/logzero[${PYTHON_USEDEP}] - dev-python/path[${PYTHON_USEDEP}] - dev-python/clang-python[${PYTHON_USEDEP}] - dev-python/cymbal[${PYTHON_USEDEP}] - dev-python/toml[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - >=dev-python/joblib-1.0.0[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/toposort[${PYTHON_USEDEP}] - dev-python/pyparsing[${PYTHON_USEDEP}] - dev-python/pybind11[${PYTHON_USEDEP}] - dev-python/schema[${PYTHON_USEDEP}] - sci-libs/vtk -" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/pywrap-${MY_COMMIT}" - -src_prepare() { - # Relax Jinja version requirements. See also upstream pull request: - # https://github.com/CadQuery/pywrap/pull/34 - sed -i -e "s~'jinja2==\\(.*\\)',~'jinja2>=\\1,<4',~" setup.py || die - sed -i \ - -e 's~^\({%- macro super(cls,classes,typedefs\)\() -%}\)$~\1=[]\2~' \ - bindgen/macros.j2 || die - - #FIXME: Submit an upstream issue. This violates PEP 440 standards. - # Sanitize the "bindgen" version to avoid Gentoo QA notices. - sed -i -e 's~\(version=\)"0.1dev"~\1"'$(ver_rs 3 '')'"~' setup.py || die - - # Replace conda- with Gentoo-specific prefix dirnames. - sed -i -e "s~\\bgetenv('CONDA_PREFIX')~'${EPREFIX}/usr'~" bindgen/*.py || - die - - # Reduce all hardcoded header includes to noops. - sed -i -e 's~rv\.append(Path(prefix).*~True~' bindgen/utils.py || die - - distutils-r1_src_prepare -} diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild index 3197a52ea..7a3b772f3 100644 --- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild +++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit llvm distutils-r1 diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest index 380c3e6ae..2b4ddbec1 100644 --- a/dev-python/cadquery/Manifest +++ b/dev-python/cadquery/Manifest @@ -1,2 +1 @@ -DIST cadquery-2.2_rc20210804.tar.gz 2832275 BLAKE2B b1b25130a9eb73e4913c6e9fc8d1fafd689bc9d216adee6d7fcc6fd80805b9351e87839fae3d6bf7e0a1ccf147e5b4a9afe8f6afc0e01c1b3a287e2671870c8d SHA512 0c5b16da24deba2267b204e5f51f707fffab9a238b27af84a500b8a98aa190be24be75d7bc2d1e282c04aea7116eb404ed4520515d53ae5a64aebafc647aa4a3 DIST cadquery-2.2_rc20220506.tar.gz 2872821 BLAKE2B a48b4279a6e24166842c3f7c43e0ff3552f22f8821fa203fce30b76110423c375019228b1a458b0020ebfd23a052545ae0d90e3246619a2e53dbe8f411449f3d SHA512 65bd62268f920d1fa170921033c4e4f451e1bdf7e4d1cef457bf34c4466a076de57f40d38ed7fb1d8f207b45447d6763a52880d9d49426372b06fefd536e7c17 diff --git a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild deleted file mode 100644 index e31f8d37c..000000000 --- a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_SINGLE_IMPL=1 -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 - -DESCRIPTION="Python parametric CAD scripting framework based on OCCT" -HOMEPAGE="https://cadquery.readthedocs.io" - -# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but -# CadQuery 2.2 has yet to be officially released. We instead package a commit -# known to work as expected with OCCT 7.5.2. -MY_COMMIT="9b657093c30147293034068dd9d58ec2b728e61a" - -#FIXME: Uncomment on bumping to the next stable release. -# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz" -SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its -# Anaconda focus, "setup.py" currently fails to list dependencies. -BDEPEND=" - test? ( - $(python_gen_cond_dep ' - dev-python/pytest[${PYTHON_USEDEP}] - dev-python/docutils[${PYTHON_USEDEP}] - dev-python/path[${PYTHON_USEDEP}] - ') - ) -" -RDEPEND=" - >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}] - $(python_gen_cond_dep ' - >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}] - dev-python/ezdxf[${PYTHON_USEDEP}] - dev-python/ipython[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - dev-python/nptyping[${PYTHON_USEDEP}] - sci-libs/nlopt[python,${PYTHON_USEDEP}] - ') -" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}-${MY_COMMIT}" - -distutils_enable_tests pytest - -#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints". -# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild index a40a5c69a..29edf6601 100644 --- a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild +++ b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild @@ -5,7 +5,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools DISTUTILS_SINGLE_IMPL=1 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -23,7 +23,9 @@ SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P LICENSE="Apache-2.0" SLOT="0" -KEYWORDS="~amd64 ~x86" +# Hard masking since package depends on dev-python/cadquery-ocp, which depends on sci-libs/opencascade, which is no longer available from ::gentoo in the required slot. +KEYWORDS="" +#KEYWORDS="~amd64 ~x86" # Dependencies are intentionally listed in "conda/meta.yml" order. Due to its # Anaconda focus, "setup.py" currently fails to list dependencies. diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild index 015dd2910..03fd9123d 100644 --- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild +++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -24,7 +24,7 @@ KEYWORDS="~amd64 ~x86" # pytest-filter-subpackage>=0.1 RESTRICT="test" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" RDEPEND=" >=dev-python/astropy-4.0.6[${PYTHON_USEDEP}] diff --git a/dev-python/cligj/cligj-0.7.2.ebuild b/dev-python/cligj/cligj-0.7.2.ebuild index c90584b75..28e7f5510 100644 --- a/dev-python/cligj/cligj-0.7.2.ebuild +++ b/dev-python/cligj/cligj-0.7.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/colorcet/Manifest b/dev-python/colorcet/Manifest index 0bb308038..9692f6be6 100644 --- a/dev-python/colorcet/Manifest +++ b/dev-python/colorcet/Manifest @@ -1 +1,2 @@ DIST colorcet-2.0.6.tar.gz 2924576 BLAKE2B 7354047b9cad133d7376d9ad19a6c09f6aa0c70e5cf0b5df6405064fdea2013df97e3beda7bba2d2483134ce3c3d63287dd911d2c2c9ed52b932eb0069dfb3a0 SHA512 b447e21a8922f0df94fd73791b8794467cc1a6a576367f073693450121fe936837da558e9ce79b930db64bcbc910f0528d84dd90eaf8ffe68b5546ac81a37813 +DIST colorcet-3.0.1.tar.gz 3036207 BLAKE2B fabdd32dafc1828d50236ec93aa78e46aa125fe3564e732c2ece203cb71578d2d23303ccb2d069c938f513bd7df6a35f692b74b0c692546544f9e04fc28e9cae SHA512 92ede4947ef3af8b8cc3a4822c0e738cc8f0730fafb9f58a4a2c9bd3cda9c1e6ed254b9eec92f0306de95643eccd644b8ad955bc079ad20c00ee62e5f611431e diff --git a/dev-python/colorcet/colorcet-2.0.6.ebuild b/dev-python/colorcet/colorcet-2.0.6.ebuild index c8024aa51..ba5c3db0a 100644 --- a/dev-python/colorcet/colorcet-2.0.6.ebuild +++ b/dev-python/colorcet/colorcet-2.0.6.ebuild @@ -1,12 +1,13 @@ -# 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 # Portage incorrectly claims "DISTUTILS_USE_SETUPTOOLS value is probably # incorrect" for this package. It isn't. This package imports from neither # "distutils", "packaging", "pkg_resources", nor "setuptools" at runtime. -PYTHON_COMPAT=( python3_{7..9} pypy3 ) +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -17,6 +18,9 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" +# Reported upstream: +# https://github.com/holoviz/colorcet/issues/103 +RESTRICT="test" DEPEND=" >=dev-python/param-1.7.0[${PYTHON_USEDEP}] diff --git a/dev-python/colorcet/colorcet-3.0.1.ebuild b/dev-python/colorcet/colorcet-3.0.1.ebuild new file mode 100644 index 000000000..25182e5d2 --- /dev/null +++ b/dev-python/colorcet/colorcet-3.0.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# Portage incorrectly claims "DISTUTILS_USE_SETUPTOOLS value is probably +# incorrect" for this package. It isn't. This package imports from neither +# "distutils", "packaging", "pkg_resources", nor "setuptools" at runtime. +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Collection of perceptually uniform colormaps" +HOMEPAGE="https://holoviz.org" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=dev-python/param-1.7.0[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest diff --git a/dev-python/connection_pool/Manifest b/dev-python/connection_pool/Manifest new file mode 100644 index 000000000..3e0ede4f4 --- /dev/null +++ b/dev-python/connection_pool/Manifest @@ -0,0 +1 @@ +DIST connection_pool-0.0.3.tar.gz 3795 BLAKE2B 6a391b739f2727c69abad3ad95635aef7fa542f86b0f4c8a440ae28dee1af80d3af022733685f8e671ed3be479db291b2f763424b746c0918faf991c4b830981 SHA512 a628608f4b57156b2f3f036ccbc620d9ba457f5958d907fa8749dd8df83a167654efd04f411e20436cf1958d9cf6b3f49bf0a11703bfc8d85332d5fc93b13183 diff --git a/dev-python/connection_pool/connection_pool-0.0.3.ebuild b/dev-python/connection_pool/connection_pool-0.0.3.ebuild new file mode 100644 index 000000000..96d3c1f62 --- /dev/null +++ b/dev-python/connection_pool/connection_pool-0.0.3.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2021 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 pypi + +DESCRIPTION="Thread safe connection pool" +HOMEPAGE="https://github.com/zhouyl/ConnectionPool" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" diff --git a/dev-python/connection_pool/metadata.xml b/dev-python/connection_pool/metadata.xml new file mode 100644 index 000000000..efc2a5c9e --- /dev/null +++ b/dev-python/connection_pool/metadata.xml @@ -0,0 +1,12 @@ +<?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">zhouyl/ConnectionPool</remote-id> + <remote-id type="pypi">connection_pool</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild index a16fcd44c..bada7bbe6 100644 --- a/dev-python/cymbal/cymbal-1.0.0.ebuild +++ b/dev-python/cymbal/cymbal-1.0.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest index 041d6cab7..58b4b1500 100644 --- a/dev-python/dandi-schema/Manifest +++ b/dev-python/dandi-schema/Manifest @@ -1,5 +1,4 @@ -DIST dandi-schema-0.4.3.tar.gz 51831 BLAKE2B 177a0ec148c1e823abdaa2b7e60d971c17a7f49bc72b69b16989e32ed014cf6df6378530be7fa142ca49662134a169b21903e9c49d9849ee944dfa9462fe6c3a SHA512 3d6c8f8cf86c933a04017f34a3832d642cf4ee27fd3edf6cf57ceab2e0ad6a1b82c245e4e27283913db941f86877996256604d345c1ee798acca2981ee046b5e -DIST dandi-schema-0.5.1.tar.gz 55945 BLAKE2B b9af1b34c7e4ce07b2fdac1d74dd746684f9e5e4667890931bbf2cb2421a01690eaed5114f2d077c46304f1298475739acef5a256430cac470ceb9fc1884e182 SHA512 699e9fb6626dd87576f29b908cd259748a6ebbd94391d8c5ba821273496323a3b4b9e88ee337809abc65c9aaeadca8aee4d986c173b055914c4ca67ddfd88804 -DIST dandi-schema-0.5.3.tar.gz 56222 BLAKE2B 3b23c93330f621a5a050c9e5b597fd8b9046a66465c16f26b5216d443547a0c8d07a491213cde90c411f5cda6f6c6b2a23d1c0f4b2d7a1e7336c55e5768d3338 SHA512 bf0d434ac6d8e5584ba9f31dd179e5402c13c89257bc87c2d34b03483e9ab85d9b616391a40c64ad853e6774f950ecc58d3f3fde29305586d5faa387dc5b3e80 -DIST dandi-schema-0.6.0.tar.gz 57102 BLAKE2B eb4ef024ef87e234c4c9e741fa2e70920aa13e0ab661aa179553b81ae8d28853274102b49532fc542368ebb43be9779a96434134e35b7c3380609511bed5ce8c SHA512 e2846e3e573264b83e95d92e7d2f2e4177721f32228beb63c701280312611bc668d1042248f4c65ed8f07b8c80991c398a4d29969513f235b4d37369cae0ddcd -DIST dandi-schema-0.7.1.tar.gz 57312 BLAKE2B 5aa77c4c98633f82511a964f0b202b44acdb63e162cff62785f44fab64fdf97c04f10b10b3c1329ea7176d7ee1b12eeabd64d467d9646550b1db14b2fcc36a2b SHA512 04e0bf6caa9183cdac021430869be884ba8db207e7056a145ecac11858e9ecf051212cee10f5b4d501ca513838edc112dde014e256ab2256729c810d0c2c6cdf +DIST dandi-schema-0.5.1.gh.tar.gz 55945 BLAKE2B b9af1b34c7e4ce07b2fdac1d74dd746684f9e5e4667890931bbf2cb2421a01690eaed5114f2d077c46304f1298475739acef5a256430cac470ceb9fc1884e182 SHA512 699e9fb6626dd87576f29b908cd259748a6ebbd94391d8c5ba821273496323a3b4b9e88ee337809abc65c9aaeadca8aee4d986c173b055914c4ca67ddfd88804 +DIST dandi-schema-0.6.0.gh.tar.gz 57102 BLAKE2B eb4ef024ef87e234c4c9e741fa2e70920aa13e0ab661aa179553b81ae8d28853274102b49532fc542368ebb43be9779a96434134e35b7c3380609511bed5ce8c SHA512 e2846e3e573264b83e95d92e7d2f2e4177721f32228beb63c701280312611bc668d1042248f4c65ed8f07b8c80991c398a4d29969513f235b4d37369cae0ddcd +DIST dandi-schema-0.7.1.gh.tar.gz 57312 BLAKE2B 5aa77c4c98633f82511a964f0b202b44acdb63e162cff62785f44fab64fdf97c04f10b10b3c1329ea7176d7ee1b12eeabd64d467d9646550b1db14b2fcc36a2b SHA512 04e0bf6caa9183cdac021430869be884ba8db207e7056a145ecac11858e9ecf051212cee10f5b4d501ca513838edc112dde014e256ab2256729c810d0c2c6cdf +DIST dandi-schema-0.8.2.gh.tar.gz 57936 BLAKE2B 2ba355137196b805214e6c9321dd0b8dd9f5f1a39cf732aa3733b51a90f043d39a003e46620e1ec4bf77654cf21a7a45e9d888321b2ceb59f33a52c75db11597 SHA512 b792b5bdc6c51dc63ab796997e3b61cbb3ae3b0dbc5d1c55c51e1c879d1a694e3fc6a89640ac26909399bc63a2a3480c7ef630952cac44a3bb5a27d7fe11d09e diff --git a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild deleted file mode 100644 index cf3c8a34f..000000000 --- a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Schemata for DANDI archive project" -HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] - dev-python/python-email-validator[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${PN}-0.3.4-coverage.patch" - "${FILESDIR}/${PN}-0.3.4-versioningit.patch" -) - -src_configure() { - echo "__version__ = '${PV}'" >> dandischema/_version.py -} - -distutils_enable_tests pytest - -python_test() { - export DANDI_TESTS_NONETWORK=1 - pushd dandischema || die - epytest tests - popd -} diff --git a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild index 19a906634..c0ac63b6b 100644 --- a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild +++ b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Schemata for DANDI archive project" HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="Apache-2.0" SLOT="0" diff --git a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild index 19a906634..c0ac63b6b 100644 --- a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild +++ b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Schemata for DANDI archive project" HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="Apache-2.0" SLOT="0" diff --git a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild index 19a906634..c0ac63b6b 100644 --- a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild +++ b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Schemata for DANDI archive project" HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="Apache-2.0" SLOT="0" diff --git a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild index 19a906634..c0ac63b6b 100644 --- a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild +++ b/dev-python/dandi-schema/dandi-schema-0.8.2.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Schemata for DANDI archive project" HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="Apache-2.0" SLOT="0" diff --git a/dev-python/datrie/datrie-0.8.2.ebuild b/dev-python/datrie/datrie-0.8.2-r1.ebuild index d3046bf8d..6c05c8216 100644 --- a/dev-python/datrie/datrie-0.8.2.ebuild +++ b/dev-python/datrie/datrie-0.8.2-r1.ebuild @@ -1,15 +1,16 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{9..11} ) +# Fails to compile with pep517 +#DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Implements a topological sort algorithm" HOMEPAGE="https://github.com/pytries/datrie" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="LGPL-2+" SLOT="0" diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild index 1ae0a527a..d417f89d8 100644 --- a/dev-python/delegator/delegator-0.1.1.ebuild +++ b/dev-python/delegator/delegator-0.1.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/dev-python/delegator/metadata.xml b/dev-python/delegator/metadata.xml index aaa27d18e..33a95485e 100644 --- a/dev-python/delegator/metadata.xml +++ b/dev-python/delegator/metadata.xml @@ -9,13 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> - <longdescription lang="en"> - The num2words library converts numbers like 42 to words like forty-two. - It supports multiple languages (see the list below for full list of - languages) and can even generate ordinal numbers like forty-second - (although this last feature is a bit buggy for some languages at the moment). - </longdescription> <upstream> - <remote-id type="github">savoirefairelinux/num2words</remote-id> + <remote-id type="github">amitt001/delegator</remote-id> + <remote-id type="pypi">delegator.py</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp b/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp Binary files differnew file mode 100644 index 000000000..d281f7480 --- /dev/null +++ b/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp diff --git a/dev-python/distinctipy/Manifest b/dev-python/distinctipy/Manifest new file mode 100644 index 000000000..b6e69e178 --- /dev/null +++ b/dev-python/distinctipy/Manifest @@ -0,0 +1 @@ +DIST distinctipy-1.2.2.gh.tar.gz 8215214 BLAKE2B c25f34f1b0000751fe22e73845922f31bc3cb1a03a673df608cfb8dda9493765c3694bc151a7318d6702f4ed6d151d9336e75828599ee0cb568d3eaf808786ab SHA512 52ec8189a699fe4dd10e3e3d43f50551ce8825835c4605a7f674db022b766a4a9f1714e6ba312bec8f2f0ce87a4d9d038b784f68c0aae603e2011908529010ec diff --git a/dev-python/distinctipy/distinctipy-1.2.2.ebuild b/dev-python/distinctipy/distinctipy-1.2.2.ebuild new file mode 100644 index 000000000..cd4c407d8 --- /dev/null +++ b/dev-python/distinctipy/distinctipy-1.2.2.ebuild @@ -0,0 +1,34 @@ +# Copyright 2021-2023 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="Lightweight package for generating visually distinct colours" +HOMEPAGE=" + https://distinctipy.readthedocs.io/en/latest/ + https://github.com/alan-turing-institute/distinctipy +" +# PyPI archive does not include tests: +# https://github.com/alan-turing-institute/distinctipy/issues/29 +SRC_URI="https://github.com/alan-turing-institute/distinctipy/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest + +# Requires networking: +EPYTEST_DESELECT=( + tests/test_examples.py::test_compare_clusters + tests/test_examples.py::test_simulate_clusters +) diff --git a/dev-python/distinctipy/metadata.xml b/dev-python/distinctipy/metadata.xml new file mode 100644 index 000000000..eb8a425e8 --- /dev/null +++ b/dev-python/distinctipy/metadata.xml @@ -0,0 +1,16 @@ +<?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> + <upstream> + <remote-id type="github">alan-turing-institute/distinctipy</remote-id> + <remote-id type="pypi">distinctipy</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dpctl/Manifest b/dev-python/dpctl/Manifest new file mode 100644 index 000000000..20d7c42f5 --- /dev/null +++ b/dev-python/dpctl/Manifest @@ -0,0 +1 @@ +DIST dpctl-0.14.1_rc2.gh.tar.gz 409028 BLAKE2B 481be08bb6a7b1a439580d600b0e14036f10793e568314f9373ffa46daad7d3e43d33fc66c3c48ec7e3de71e9d0a7256cdfdd984c38fa7f1694dcc0227dae93f SHA512 91ab20a51893e3afc9e140ab9dfd1aa19b24e58227a001faefb9ceba6ffc4aa235214663c7456e977acf556796be097eabacc9b01b94eb42e8c70677a2f2dd9d diff --git a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild new file mode 100644 index 000000000..65526b110 --- /dev/null +++ b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild @@ -0,0 +1,69 @@ +# 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="Data Parallel Control " +HOMEPAGE="https://github.com/IntelPython/dpctl" +SRC_URI="https://github.com/IntelPython/dpctl/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN}-${PV//_rc/dev}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/scikit-build[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-python/versioneer[${PYTHON_USEDEP}] + dev-util/cmake + dev-vcs/git + sys-devel/DPC++ +" + +DEPEND=" + dev-libs/level-zero + dev-libs/opencl-icd-loader + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + sci-libs/oneDAL + sys-devel/DPC++:0/6 +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-0.14.0-find-opencl.patch" + "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-level-zero.patch" + "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-pybind.patch" + #"${FILESDIR}/${PN}-0.14.1_rc2-include-tuple.patch" +) + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + + # Build system reads version from git tag + git init -q || die + git config --global user.email "larry@gentoo.org" || die + git config --global user.name "Larry the Cow" || die + git add . || die + git commit -qm "init" || die + git tag -a "${PV}" -m "${PN} version ${PV}" || die + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch new file mode 100644 index 000000000..b7dab5c75 --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.13.0-dont-fetch-pybind.patch @@ -0,0 +1,21 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 23ae1dd..e144e90 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -26,15 +26,7 @@ install(FILES ${_dpctl_capi_headers} + # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR + include(GNUInstallDirs) + +-# Fetch pybind11 +-include(FetchContent) +- +-FetchContent_Declare( +- pybind11 +- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.9.2.tar.gz +- URL_HASH SHA256=6bd528c4dbe2276635dc787b6b1f2e5316cf6b49ee3e150264e455a0d68d19c1 +-) +-FetchContent_MakeAvailable(pybind11) ++include(/usr/share/cmake/pybind11/pybind11Config.cmake) + + add_subdirectory(dpctl) + diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch new file mode 100644 index 000000000..ac0301886 --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-level-zero.patch @@ -0,0 +1,82 @@ +diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake +index 2929c33..731f054 100644 +--- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake ++++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake +@@ -26,76 +26,10 @@ + + function(get_level_zero_headers) + +- if(EXISTS level-zero) +- # Update the checkout +- execute_process( +- COMMAND ${GIT_EXECUTABLE} fetch +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not update Level Zero sources." +- ) +- endif() +- else() +- # Clone the Level Zero git repo +- execute_process( +- COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not clone Level Zero sources from github.com/oneapi-src/level-zero." +- ) +- endif() +- endif() +- +- # Use git describe to get latest tag name +- execute_process( +- COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0 +- RESULT_VARIABLE result +- OUTPUT_VARIABLE latest_tag +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not get the name for the latest release." +- ) +- endif() +- +- # Use git describe to get latest tag name +- execute_process( +- COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag} +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not checkout the latest release." +- ) +- endif() +- + # Populate the path to the headers + find_path(LEVEL_ZERO_INCLUDE_DIR + NAMES zet_api.h +- PATHS ${CMAKE_BINARY_DIR}/level-zero/include ++ PATHS /usr/include/level_zero + NO_DEFAULT_PATH + NO_CMAKE_ENVIRONMENT_PATH + NO_CMAKE_PATH diff --git a/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch new file mode 100644 index 000000000..b2b8c5d81 --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.0-dont-fetch-pybind.patch @@ -0,0 +1,21 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index da138c1..ecab139 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -28,15 +28,7 @@ install(FILES ${_dpctl_capi_headers} + # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR + include(GNUInstallDirs) + +-# Fetch pybind11 +-include(FetchContent) +- +-FetchContent_Declare( +- pybind11 +- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.1.tar.gz +- URL_HASH SHA256=111014b516b625083bef701df7880f78c2243835abdb263065b6b59b960b6bad +-) +-FetchContent_MakeAvailable(pybind11) ++include(/usr/share/cmake/pybind11/pybind11Config.cmake) + + add_subdirectory(dpctl) + diff --git a/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch new file mode 100644 index 000000000..3841816ee --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch @@ -0,0 +1,13 @@ +diff --git a/libsyclinterface/cmake/modules/FindIntelSycl.cmake b/libsyclinterface/cmake/modules/FindIntelSycl.cmake +index 84e8946..ccc2591 100644 +--- a/libsyclinterface/cmake/modules/FindIntelSycl.cmake ++++ b/libsyclinterface/cmake/modules/FindIntelSycl.cmake +@@ -134,7 +134,7 @@ if(${clangxx_result} MATCHES "0") + find_file( + IntelSycl_OPENCL_LIBRARY + NAMES "libOpenCL.so" +- PATHS ${IntelSycl_LIBRARY_DIR} ++ PATHS /usr/lib64 + ) + endif() + diff --git a/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch b/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch new file mode 100644 index 000000000..44b950cb6 --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.0-include-tuple.patch @@ -0,0 +1,47 @@ +From d0d3e6f1a9ffbac91f24cc06abce6dcad6509a6b Mon Sep 17 00:00:00 2001 +From: Julien Jerphanion <git@jjerphan.xyz> +Date: Tue, 6 Dec 2022 10:24:26 +0100 +Subject: [PATCH 1/2] MAINT Include tuple in 'utils/strided_iters.hpp' + +This include directive seems to have been forgotten and it is impossible +for me to compile dpctl without it. +--- + dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp +index c24ed54941..595ad3f4a7 100644 +--- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp ++++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp +@@ -30,6 +30,7 @@ + #include <array> + #include <numeric> // std::iota + #include <vector> ++#include <tuple> + + /* An N-dimensional array can be stored in a single + * contiguous chunk of memory by contiguously laying + +From f75ccd8c8aeaae92f0cb03874f93be5e7a63a6a7 Mon Sep 17 00:00:00 2001 +From: Julien Jerphanion <git@jjerphan.xyz> +Date: Tue, 6 Dec 2022 14:45:40 +0100 +Subject: [PATCH 2/2] Make clang-format happy + +--- + dpctl/tensor/libtensor/include/utils/strided_iters.hpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp +index 595ad3f4a7..0abd7f4f2a 100644 +--- a/dpctl/tensor/libtensor/include/utils/strided_iters.hpp ++++ b/dpctl/tensor/libtensor/include/utils/strided_iters.hpp +@@ -29,8 +29,8 @@ + #include <algorithm> // sort + #include <array> + #include <numeric> // std::iota +-#include <vector> + #include <tuple> ++#include <vector> + + /* An N-dimensional array can be stored in a single + * contiguous chunk of memory by contiguously laying diff --git a/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch new file mode 100644 index 000000000..a7a4adf8b --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch @@ -0,0 +1,82 @@ +diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake +index fe109fc..55595e9 100644 +--- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake ++++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake +@@ -26,76 +26,10 @@ + + function(get_level_zero_headers) + +- if(EXISTS level-zero) +- # Update the checkout +- execute_process( +- COMMAND ${GIT_EXECUTABLE} fetch +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not update Level Zero sources. Return code: ${result}" +- ) +- endif() +- else() +- # Clone the Level Zero git repo +- execute_process( +- COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not clone Level Zero sources from github.com/oneapi-src/level-zero. Return code: ${result}" +- ) +- endif() +- endif() +- +- # Use git describe to get latest tag name +- execute_process( +- COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0 +- RESULT_VARIABLE result +- OUTPUT_VARIABLE latest_tag +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not get the name for the latest release. Return code: ${result}" +- ) +- endif() +- +- # Use git describe to get latest tag name +- execute_process( +- COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag} +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not checkout the latest release. Return code: ${result}" +- ) +- endif() +- + # Populate the path to the headers + find_path(LEVEL_ZERO_INCLUDE_DIR + NAMES zet_api.h +- PATHS ${CMAKE_BINARY_DIR}/level-zero/include ++ PATHS /usr/include/level_zero + NO_DEFAULT_PATH + NO_CMAKE_ENVIRONMENT_PATH + NO_CMAKE_PATH diff --git a/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch new file mode 100644 index 000000000..d56dc27b3 --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch @@ -0,0 +1,21 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index d97ca9a..3914bd9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -32,15 +32,7 @@ install(FILES ${_dpctl_capi_headers} + # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR + include(GNUInstallDirs) + +-# Fetch pybind11 +-include(FetchContent) +- +-FetchContent_Declare( +- pybind11 +- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.2.tar.gz +- URL_HASH SHA256=93bd1e625e43e03028a3ea7389bba5d3f9f2596abc074b068e70f4ef9b1314ae +-) +-FetchContent_MakeAvailable(pybind11) ++include(/usr/share/cmake/pybind11/pybind11Config.cmake) + + add_subdirectory(dpctl) + diff --git a/dev-python/dpctl/metadata.xml b/dev-python/dpctl/metadata.xml new file mode 100644 index 000000000..06d339ee1 --- /dev/null +++ b/dev-python/dpctl/metadata.xml @@ -0,0 +1,12 @@ +<?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">IntelPython/dpctl</remote-id> + <remote-id type="pypi">dpctl</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dpnp/Manifest b/dev-python/dpnp/Manifest new file mode 100644 index 000000000..0286f1b8e --- /dev/null +++ b/dev-python/dpnp/Manifest @@ -0,0 +1 @@ +DIST dpnp-0.11.1_rc1.gh.tar.gz 495726 BLAKE2B 13e9696195abd21f41b1a8e6f235f840cd22a4eb1b67f7bbedfdc775f0cb7832157af51309b1d8a5f2d1cde78250c70730a2794f11b01f8bd572e7a1e29f2b47 SHA512 ef58591aaed330123b78268c7b0b04222efc8e688e1bfe2426e13836fe23ae84572f3337d7084525a6dd5e5fcf91dd68c501643b922ebebc7f0fb94115f92749 diff --git a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild new file mode 100644 index 000000000..5443b2dfd --- /dev/null +++ b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild @@ -0,0 +1,65 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +# Breaks library installation +#DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Data Parallel Extension for NumPy" +HOMEPAGE="https://github.com/IntelPython/dpnp" +SRC_URI="https://github.com/IntelPython/dpnp/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN}-${PV//_rc/dev}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-util/cmake + sys-devel/DPC++ +" + +RDEPEND=" + dev-cpp/tbb + dev-python/dpctl[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl + sys-devel/DPC++:= +" +DEPEND="${RDEPEND} + sys-devel/oneDPL +" + +PATCHES=( + "${FILESDIR}/${P}-fix-compile.patch" +) + +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="${ESYSROOT}/usr/lib/llvm/intel" + export DPL_ROOT="${ESYSROOT}/usr/include/include/oneapi/dpl" + # Parallel build broken + export MAKEOPTS="-j1" + + distutils-r1_python_prepare_all +} + +python_compile() { + export BUILD_DIR_LIBS="${BUILD_DIR}/lib/dpnp" + distutils-r1_python_compile +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/lib" + elog $PYTHONPATH + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch new file mode 100644 index 000000000..deaa95d0b --- /dev/null +++ b/dev-python/dpnp/files/dpnp-0.10.0-fix-compile.patch @@ -0,0 +1,97 @@ +diff --git a/0.build.sh b/0.build.sh +index c089b1d..3bb0739 100755 +--- a/0.build.sh ++++ b/0.build.sh +@@ -10,14 +10,14 @@ python setup.py clean + DPLROOT=/opt/intel/oneapi/dpl/latest python setup.py build_clib + + # inplace build +-CC=dpcpp python setup.py build_ext --inplace ++CC=${CC} python setup.py build_ext --inplace + + # development build. Root privileges needed + # python setup.py develop + + echo + echo =========example3============== +-dpcpp -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3 ++${CXX} -g -fPIC dpnp/backend/examples/example3.cpp -Idpnp -Idpnp/backend/include -Ldpnp -Wl,-rpath='$ORIGIN'/dpnp -ldpnp_backend_c -o example3 + # LD_DEBUG=libs,bindings,symbols ./example3 + ./example3 + +diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt +index 81f073c..bcc4ecc 100644 +--- a/dpnp/backend/CMakeLists.txt ++++ b/dpnp/backend/CMakeLists.txt +@@ -88,24 +88,6 @@ if (CMAKE_VERSION VERSION_EQUAL 3.19.1) + ) + endif() + +-if(UNIX) +- set(CMAKE_CXX_COMPILER "dpcpp") +- # add_compile_options(-fPIC) +-elseif(WIN32) +- set(CMAKE_CXX_COMPILER "dpcpp") +- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link") +- # set(CMAKE_LINKER "lld-link") +- # include (Platform/Windows-Clang) +- # set(CMAKE_LINKER "dpcpp") +- # set(CMAKE_AR "llvm-ar") +- # set(CMAKE_RANLIB "llvm-ranlib") +- # set(CMAKE_CXX_FLAGS "/EHsc") +- +- add_compile_options(/EHsc) # /Ox /W3 /GL /DNDEBUG /MD /EHsc +-else() +- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case") +-endif() +- + # set language version + set(CMAKE_CXX_STANDARD 17) + set(CMAKE_CXX_STANDARD_REQUIRED ON) +@@ -280,6 +262,7 @@ endif() + # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION}) + + install(TARGETS dpnp_backend_c ++ DESTINATION ${DPNP_INSTALL_PREFIX} + PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE + ) + +diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py +index dc9f322..35432fa 100644 +--- a/utils/command_build_clib.py ++++ b/utils/command_build_clib.py +@@ -60,8 +60,8 @@ else: + Set compiler for the project + """ + # default variables (for Linux) +-_project_compiler = "dpcpp" +-_project_linker = "dpcpp" ++_project_compiler = os.environ.get("CXX") ++_project_linker = os.environ.get("CXX") + _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel"] + _project_cmplr_flag_sycl = ["-fsycl"] + _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"] +@@ -113,8 +113,8 @@ except ImportError: + + # other OS specific + if IS_WIN: +- _project_compiler = "dpcpp" +- _project_linker = "lld-link" ++ _project_compiler = os.environ.get("CXX") ++ _project_linker = os.environ.get("CXX") + _project_cmplr_flag_sycl = [] + _project_cmplr_flag_stdcpp_static = [] + _project_cmplr_flag_compatibility = [] +diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py +index 0ef0e24..84f2469 100644 +--- a/utils/command_build_cmake_clib.py ++++ b/utils/command_build_cmake_clib.py +@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib): + "-S" + backend_directory, + "-B" + abs_build_temp_path, + "-DCMAKE_BUILD_TYPE=" + config, +- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments ++ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments + "-DDPNP_INSTALL_STRUCTURED=OFF", + # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory, + "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists, diff --git a/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch new file mode 100644 index 000000000..2ccc0a6b8 --- /dev/null +++ b/dev-python/dpnp/files/dpnp-0.11.0-fix-compile.patch @@ -0,0 +1,80 @@ +diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt +index 409a29f..11d21f1 100644 +--- a/dpnp/backend/CMakeLists.txt ++++ b/dpnp/backend/CMakeLists.txt +@@ -98,30 +98,7 @@ string(CONCAT COMMON_LINK_FLAGS + "-fsycl " + "-fsycl-device-code-split=per_kernel " + ) +-if(UNIX) +- set(CMAKE_CXX_COMPILER "dpcpp") +- # add_compile_options(-fPIC) +-elseif(WIN32) +- set(CMAKE_CXX_COMPILER "dpcpp") +- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link") +- # set(CMAKE_LINKER "lld-link") +- # include (Platform/Windows-Clang) +- # set(CMAKE_LINKER "dpcpp") +- # set(CMAKE_AR "llvm-ar") +- # set(CMAKE_RANLIB "llvm-ranlib") +- # set(CMAKE_CXX_FLAGS "/EHsc") + +- string(APPEND COMMON_COMPILER_FLAGS +- "/EHsc " +-# "/Ox " +-# "/W3 " +-# "/GL " +-# "/DNDEBUG " +-# "/MD " +- ) +-else() +- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case") +-endif() + + # set language version + set(CMAKE_CXX_STANDARD 17) +@@ -327,6 +304,7 @@ endif() + # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION}) + + install(TARGETS dpnp_backend_c ++ DESTINATION ${DPNP_INSTALL_PREFIX} + PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE + ) + +diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py +index 3d1177b..d8fbdac 100644 +--- a/utils/command_build_clib.py ++++ b/utils/command_build_clib.py +@@ -61,8 +61,8 @@ else: + Set compiler for the project + """ + # default variables (for Linux) +-_project_compiler = "dpcpp" +-_project_linker = "dpcpp" ++_project_compiler = os.environ.get("CXX") ++_project_linker = os.environ.get("CXX") + _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func"] + _project_cmplr_flag_sycl = ["-fsycl"] + _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"] +@@ -114,7 +114,7 @@ except ImportError: + + # other OS specific + if IS_WIN: +- _project_compiler = "dpcpp" ++ _project_compiler = os.environ.get("CXX") + _project_linker = "lld-link" + _project_cmplr_flag_sycl = [] + _project_cmplr_flag_stdcpp_static = [] +diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py +index 0ef0e24..84f2469 100644 +--- a/utils/command_build_cmake_clib.py ++++ b/utils/command_build_cmake_clib.py +@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib): + "-S" + backend_directory, + "-B" + abs_build_temp_path, + "-DCMAKE_BUILD_TYPE=" + config, +- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments ++ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments + "-DDPNP_INSTALL_STRUCTURED=OFF", + # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory, + "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists, diff --git a/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch new file mode 100644 index 000000000..25c0d3484 --- /dev/null +++ b/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch @@ -0,0 +1,71 @@ +diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt +index baee709..3202662 100644 +--- a/dpnp/backend/CMakeLists.txt ++++ b/dpnp/backend/CMakeLists.txt +@@ -99,30 +99,6 @@ string(CONCAT COMMON_LINK_FLAGS + "-fsycl " + "-fsycl-device-code-split=per_kernel " + ) +-if(UNIX) +- set(CMAKE_CXX_COMPILER "icpx") +- # add_compile_options(-fPIC) +-elseif(WIN32) +- set(CMAKE_CXX_COMPILER "icx") +- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link") +- # set(CMAKE_LINKER "lld-link") +- # include (Platform/Windows-Clang) +- # set(CMAKE_LINKER "dpcpp") +- # set(CMAKE_AR "llvm-ar") +- # set(CMAKE_RANLIB "llvm-ranlib") +- # set(CMAKE_CXX_FLAGS "/EHsc") +- +- string(APPEND COMMON_COMPILE_FLAGS +- "/EHsc " +-# "/Ox " +-# "/W3 " +-# "/GL " +-# "/DNDEBUG " +-# "/MD " +- ) +-else() +- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case") +-endif() + + # set language version + set(CMAKE_CXX_STANDARD 17) +@@ -334,6 +310,7 @@ endif() + # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION}) + + install(TARGETS dpnp_backend_c ++ DESTINATION ${DPNP_INSTALL_PREFIX} + PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE + ) + +diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py +index d16bab3..7fd2afa 100644 +--- a/utils/command_build_clib.py ++++ b/utils/command_build_clib.py +@@ -61,8 +61,8 @@ else: + Set compiler for the project + """ + # default variables (for Linux) +-_project_compiler = "icpx" +-_project_linker = "icpx" ++_project_compiler = os.environ.get("CXX") ++_project_linker = os.environ.get("CXX") + _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func", "-fno-finite-math-only"] + _project_cmplr_flag_sycl = ["-fsycl"] + _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"] +diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py +index 0ef0e24..84f2469 100644 +--- a/utils/command_build_cmake_clib.py ++++ b/utils/command_build_cmake_clib.py +@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib): + "-S" + backend_directory, + "-B" + abs_build_temp_path, + "-DCMAKE_BUILD_TYPE=" + config, +- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments ++ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments + "-DDPNP_INSTALL_STRUCTURED=OFF", + # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory, + "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists, diff --git a/dev-python/dpnp/metadata.xml b/dev-python/dpnp/metadata.xml new file mode 100644 index 000000000..868959c89 --- /dev/null +++ b/dev-python/dpnp/metadata.xml @@ -0,0 +1,12 @@ +<?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">IntelPython/dpnp</remote-id> + <remote-id type="pypi">dpnp</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/extension-helpers/Manifest b/dev-python/extension-helpers/Manifest index b80cb117c..1e59aebf1 100644 --- a/dev-python/extension-helpers/Manifest +++ b/dev-python/extension-helpers/Manifest @@ -1 +1,2 @@ DIST extension-helpers-0.1.tar.gz 24306 BLAKE2B 8fa5134bd26f4c5b9a66694d1c057c969607bfe9a05d5c470cdccda87bbff329174916bccc390ff80fdce72af5b764d0b3a7c34b632c01e33e3c84f913c6527b SHA512 d8394f5f0de28dfa2c204b918a39b5f3b990057bfdb7a21907b0b9ae3bacd5b95c5f25b32a08a50606fbae35b93629dcfe1fee512c6aa4f4e7c08c22bcfd3fbb +DIST extension-helpers-1.0.0.tar.gz 23463 BLAKE2B 0b1edffabc112120ac85c6445255986145143da9552221390a0827516a20e2877cad47e5968f6c7d293550db566574f86c877758d6233e51ca0762c3ff2e9327 SHA512 30234591100e5e8b7bda4392d72421911773a3aabb40c003367e8b335edcea3285f79fd962edd3d09b96ed7b4b936a97086376dfff50b18df85b55c612d61f8d diff --git a/dev-python/extension-helpers/extension-helpers-0.1.ebuild b/dev-python/extension-helpers/extension-helpers-0.1.ebuild index 8119b0206..976e33986 100644 --- a/dev-python/extension-helpers/extension-helpers-0.1.ebuild +++ b/dev-python/extension-helpers/extension-helpers-0.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild b/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild new file mode 100644 index 000000000..4532642fa --- /dev/null +++ b/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Utilities for building and installing packages in the Astropy ecosystem" +HOMEPAGE="https://github.com/astropy/astropy-helpers" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-doctestplus>=0.2.0 +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +distutils_enable_tests pytest +distutils_enable_sphinx docs dev-python/sphinx-astropy diff --git a/dev-python/extension-helpers/metadata.xml b/dev-python/extension-helpers/metadata.xml index 4f4367037..9f1bfe0c4 100644 --- a/dev-python/extension-helpers/metadata.xml +++ b/dev-python/extension-helpers/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astropy-helpers</remote-id> + <remote-id type="pypi">extension-helpers</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ezdxf/ezdxf-0.16.5.ebuild b/dev-python/ezdxf/ezdxf-0.16.5.ebuild index 43bf7c371..27c8ff04b 100644 --- a/dev-python/ezdxf/ezdxf-0.16.5.ebuild +++ b/dev-python/ezdxf/ezdxf-0.16.5.ebuild @@ -4,7 +4,7 @@ EAPI=8 #FIXME: Upstream explicitly supports "pypy3", but Gentoo dependencies do not. -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest index 2140ef1a5..bed2fa4ce 100644 --- a/dev-python/fiona/Manifest +++ b/dev-python/fiona/Manifest @@ -1,2 +1 @@ -DIST fiona-1.8.21.tar.gz 270166 BLAKE2B 752957f3cc3ed6a35713536e90cdbc542d73de9718e878a449f71c9b9a2150b4ead90ff5d9ce254a6adcfcf7deb61b4483e7cf5bfee12997e581fd0a3ffc767e SHA512 c77cedae67fb7e2b6b6a84aeef39ce5424ccb38b13774f7c2e9bd5934836a6abe6759eeea1d4a8cfc83c5111442f2028d18dd79af209e11618789de2149e7885 - +DIST fiona-1.9.0.gh.tar.gz 290797 BLAKE2B 1cd2a4a26d23d057433889937b4fecefb1e1585dc6b507e297ef3bab8cf72f734bc080bab8487d58c636312bca1330960f78fc2916d27c9a7247df087818c9b3 SHA512 f59d148cfc4f1cab6d89660146522920fab8b6fb1120ad8f3d3e8349d5fa823860984f8fd331e2fc3183a4a186a165508db8dcbcbdf4b943a7dad82d8d51d866 diff --git a/dev-python/fiona/fiona-1.8.21.ebuild b/dev-python/fiona/fiona-1.9.0.ebuild index 51ded0d37..7bc415b14 100644 --- a/dev-python/fiona/fiona-1.8.21.ebuild +++ b/dev-python/fiona/fiona-1.9.0.ebuild @@ -1,15 +1,16 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 DESCRIPTION="API for reading/writing vector geospatial data" HOMEPAGE="https://github.com/Toblerity/fiona" -SRC_URI="https://github.com/Toblerity/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/Toblerity/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/Fiona-${PV}" LICENSE="BSD" SLOT="0" @@ -21,7 +22,6 @@ RDEPEND=" dev-python/click-plugins[${PYTHON_USEDEP}] dev-python/cligj[${PYTHON_USEDEP}] dev-python/munch[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] dev-python/certifi[${PYTHON_USEDEP}] " @@ -33,8 +33,6 @@ BDEPEND=" ) " -S="${WORKDIR}/Fiona-${PV}" - distutils_enable_tests pytest python_test() { diff --git a/dev-python/fscacher/fscacher-0.1.4.ebuild b/dev-python/fscacher/fscacher-0.1.4.ebuild index 3f55c8604..b15c37615 100644 --- a/dev-python/fscacher/fscacher-0.1.4.ebuild +++ b/dev-python/fscacher/fscacher-0.1.4.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Cache results of operations on heavy file trees" diff --git a/dev-python/fscacher/fscacher-0.2.0.ebuild b/dev-python/fscacher/fscacher-0.2.0.ebuild index bb632800e..8bb00f6f4 100644 --- a/dev-python/fscacher/fscacher-0.2.0.ebuild +++ b/dev-python/fscacher/fscacher-0.2.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Cache results of operations on heavy file trees" diff --git a/dev-python/fslpy/fslpy-3.10.0.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild index 7140be033..d25cfb22f 100644 --- a/dev-python/fslpy/fslpy-3.10.0.ebuild +++ b/dev-python/fslpy/fslpy-3.10.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 virtualx @@ -29,7 +29,7 @@ RDEPEND=" " distutils_enable_tests pytest -distutils_enable_sphinx doc dev-python/sphinx_rtd_theme +distutils_enable_sphinx doc dev-python/sphinx-rtd-theme python_prepare_all() { # Do not depend on coverage diff --git a/dev-python/gammapy/Manifest b/dev-python/gammapy/Manifest index 4645ef4fd..6cd1ed25d 100644 --- a/dev-python/gammapy/Manifest +++ b/dev-python/gammapy/Manifest @@ -1 +1 @@ -DIST gammapy-0.18.2.tar.gz 2077004 BLAKE2B 1dd22566d92d73bb9ef5f0cca455096caa014353a570dfa111c22db174dd52ebe93752347fc37d086a6f16b567227a45a18f2212f5078639793593c0fa77ec39 SHA512 b500756a90eb29fd3c275166b6d980249b2db48fd007f25a43a53d5d63a9e1e53fb16e4a4707313616ece2abdfa3e8d339e99f8f4c2f0bb9b3bd9287c86ce958 +DIST gammapy-1.0.tar.gz 3548471 BLAKE2B c6f66a5fe3158d42fefbae3e14a659d2d637b935cede97e0dfefad32d0aa39a3d5ece23b19e95436deb1299e60b472c7ed01bd5c9c4c1e009618d8dead8b1951 SHA512 acf8f7940b910cdd1277a876e14fde9e962c40d7742610dd8c37b7769b132485bb0aa6fadbd0f68af37858c110985d34679e6f3f4fe52c28a11bd4d56dcf3699 diff --git a/dev-python/gammapy/gammapy-0.18.2.ebuild b/dev-python/gammapy/gammapy-1.0.ebuild index c26732aed..ab50e7a85 100644 --- a/dev-python/gammapy/gammapy-0.18.2.ebuild +++ b/dev-python/gammapy/gammapy-1.0.ebuild @@ -1,16 +1,15 @@ # Copyright 1999-2021 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_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 optfeature +inherit distutils-r1 pypi optfeature DESCRIPTION="A Python package for gamma-ray astronomy" HOMEPAGE="https://github.com/gammapy/gammapy" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/gammapy/metadata.xml b/dev-python/gammapy/metadata.xml index a9f88e7d8..f4a01e639 100644 --- a/dev-python/gammapy/metadata.xml +++ b/dev-python/gammapy/metadata.xml @@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies. </longdescription> <upstream> <remote-id type="github">gammapy/gammapy</remote-id> + <remote-id type="pypi">gammapy</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest index c541ed559..23cd9b3d5 100644 --- a/dev-python/geopandas/Manifest +++ b/dev-python/geopandas/Manifest @@ -1 +1 @@ -DIST geopandas-0.10.2.tar.gz 6317604 BLAKE2B 5eb0d84c11eda99b43bc15b179a971c5e56fb36d40c771b523161dd6ddac4faee4bac483ccd1bdb9f10f73dfd2adf6d72703cc180359cd68383bfba9410f4f5b SHA512 339660c423955b9f110eb390c3d1dc88eeb1ed74fa300870ae277d312e9b2e6733463bc45b445c73a9f8b6dee82d82f203c7b75c0a4aad7e36e43e5c7ec78f42 +DIST geopandas-0.12.2.gh.tar.gz 6360014 BLAKE2B ded0b7fdff88f91ad02f690013b92b4fd7378742fbe01473a0351164df526fe4ca7cbfb1097b79311d2f6c3fa4301199cf7862befe970e4b6fa6a0d8c1317c38 SHA512 6470bf45360bb6486607870ee643f295a8823ce3109b777ec9d1eb576bc11c717d3dc40777481748ffe8d17a6d9869245efff5298bea274ec108ca9d0b1502ba diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.12.2.ebuild index e63aaa1bc..10edebed5 100644 --- a/dev-python/geopandas/geopandas-0.10.2.ebuild +++ b/dev-python/geopandas/geopandas-0.12.2.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_PEP517="setuptools" -inherit distutils-r1 +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 optfeature DESCRIPTION="Python tools for geographic data" -HOMEPAGE="https://github.com/geopandas/geopandas" -SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +HOMEPAGE="https://github.com/geopandas/geopandas https://pypi.org/project/geopandas/" +SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" @@ -32,3 +32,9 @@ python_test() { epytest ${deselect[@]/#/--deselect } } + +pkg_postinst() { + optfeature "plotting" dev-python/matplotlib + optfeature "spatial indexes and spatial joins" sci-libs/rtree + optfeature "geocoding" sci-geosciences/geopy +} diff --git a/dev-python/geopandas/metadata.xml b/dev-python/geopandas/metadata.xml index a9b62a0d8..a102c7148 100644 --- a/dev-python/geopandas/metadata.xml +++ b/dev-python/geopandas/metadata.xml @@ -1,19 +1,19 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - GeoPandas is a project to add support for geographic data to pandas - objects. It currently implements GeoSeries and GeoDataFrame types - which are subclasses of pandas.Series and pandas.DataFrame - respectively. GeoPandas objects can act on shapely geometry objects - and perform geometric operations. -</longdescription> - <upstream> - <remote-id type="github">geopandas/geopandas</remote-id> - <remote-id type="pypi">geopandas</remote-id> - </upstream> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + GeoPandas is a project to add support for geographic data to pandas + objects. It currently implements GeoSeries and GeoDataFrame types + which are subclasses of pandas.Series and pandas.DataFrame + respectively. GeoPandas objects can act on shapely geometry objects + and perform geometric operations. + </longdescription> + <upstream> + <remote-id type="github">geopandas/geopandas</remote-id> + <remote-id type="pypi">geopandas</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/gffpandas/Manifest b/dev-python/gffpandas/Manifest index 8d84e74c6..1a3ae3b5f 100644 --- a/dev-python/gffpandas/Manifest +++ b/dev-python/gffpandas/Manifest @@ -1 +1 @@ -DIST gffpandas-1.2.0.tar.gz 32040 BLAKE2B 66f53357876d417997366cdcbacd778f2b17e7df113d21f2a836b082719f549ede5e06a9a6c46e9c5bee2d86946871e68ab1f9b7af0defcaa8a55ae8ef93b274 SHA512 feb67ea93a078547103c1c6b8f32bd6bbd69ab669b93b90aa5f48bc0ebc25ea23e35130976bf1a89ff5e92fdbd054c4df98cc961278c7caaf28b48c202a662d7 +DIST gffpandas-1.2.0.gh.tar.gz 32040 BLAKE2B 66f53357876d417997366cdcbacd778f2b17e7df113d21f2a836b082719f549ede5e06a9a6c46e9c5bee2d86946871e68ab1f9b7af0defcaa8a55ae8ef93b274 SHA512 feb67ea93a078547103c1c6b8f32bd6bbd69ab669b93b90aa5f48bc0ebc25ea23e35130976bf1a89ff5e92fdbd054c4df98cc961278c7caaf28b48c202a662d7 diff --git a/dev-python/gffpandas/gffpandas-1.2.0.ebuild b/dev-python/gffpandas/gffpandas-1.2.0.ebuild index 12ec9927c..e0fe2f621 100644 --- a/dev-python/gffpandas/gffpandas-1.2.0.ebuild +++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild @@ -1,16 +1,16 @@ -# Copyright 2021 Gentoo Authors +# Copyright 2021-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Python library to Filter and sort GFF3 annotations" HOMEPAGE="https://github.com/foerstner-lab/gffpandas https://gffpandas.readthedocs.io/en/latest/" -SRC_URI="https://github.com/foerstner-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/foerstner-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="ISC" SLOT="0" @@ -19,7 +19,7 @@ KEYWORDS="~amd64 ~x86" RDEPEND="dev-python/pandas[${PYTHON_USEDEP}]" distutils_enable_tests pytest -distutils_enable_sphinx docs/source dev-python/sphinx_rtd_theme +distutils_enable_sphinx docs/source dev-python/sphinx-rtd-theme python_prepare_all() { # Do not depend on pytest-runner diff --git a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild index 785646336..88e1a333a 100644 --- a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild +++ b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/google-cloud-storage/Manifest b/dev-python/google-cloud-storage/Manifest new file mode 100644 index 000000000..6bd5af5b0 --- /dev/null +++ b/dev-python/google-cloud-storage/Manifest @@ -0,0 +1 @@ +DIST google-cloud-storage-2.7.0.tar.gz 5490914 BLAKE2B 582fcf9a84bedcff41de2b26558ccae96474cbbe91c86bbe6bf53ff6a2fe38d7eb8dbe396fccd36ad252f171ed7eda45974ca9e7867e3ee9542c85570a951aef SHA512 89c4208781735bb0e8b0978202877af324154d5233d7abafd1b2b14b4bb381c18572cfdc791e42577ad929f3c4ded0857d9bd9f4eb52a93ed74e8884d797b365 diff --git a/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild b/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild new file mode 100644 index 000000000..403f75dee --- /dev/null +++ b/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild @@ -0,0 +1,25 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Google Cloud Storage API client library" +HOMEPAGE="https://github.com/googleapis/python-storage" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/google-auth[${PYTHON_USEDEP}] + dev-python/google-api-core[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/google-cloud-storage/metadata.xml b/dev-python/google-cloud-storage/metadata.xml new file mode 100644 index 000000000..d67c6b09f --- /dev/null +++ b/dev-python/google-cloud-storage/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://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">googleapis/python-storage</remote-id> + <remote-id type="pypi">google-cloud-storage</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/grabbit/grabbit-0.2.6.ebuild b/dev-python/grabbit/grabbit-0.2.6.ebuild index 93e08ccf4..c7e710a70 100644 --- a/dev-python/grabbit/grabbit-0.2.6.ebuild +++ b/dev-python/grabbit/grabbit-0.2.6.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/gwcs/Manifest b/dev-python/gwcs/Manifest index 4c4dc60c1..91b72eae3 100644 --- a/dev-python/gwcs/Manifest +++ b/dev-python/gwcs/Manifest @@ -1 +1,2 @@ DIST gwcs-0.16.1.tar.gz 171068 BLAKE2B 0406a7b8545b56d7811b8326c148f0d413dd6ae38f90c9e50d984fd9a35d2f130d61821a237acc2bec2746e012d199f4ed08231299520de46ffa1554fe4d860b SHA512 2414f1c40be632e7b7cdb6657f54869a2aa8aefce6074ff0e6c5c277fd6c125d72c42b76e9344f100367f810bfcd5dc49b4e6ec6318b08a975799a918debb9cc +DIST gwcs-0.18.3.tar.gz 184361 BLAKE2B a4afcf3d6281f65f1ff6733bb83f82ba089fc56d2a21c2d6f5fd8370ef518b97376ebe718a9e4f9fa34ae80fc66baecf9e32835bb18f1737bf3f47e972e31118 SHA512 51aac4dd1f3b835b274f265cf26d4f9cf757435bb8355d43a31b7eba665991c233b46f9e0a87d22985c04fdabc0455958b99f37aeb55a04a9c0b4901d5069891 diff --git a/dev-python/gwcs/gwcs-0.16.1.ebuild b/dev-python/gwcs/gwcs-0.16.1.ebuild index 373410501..cef67f6ea 100644 --- a/dev-python/gwcs/gwcs-0.16.1.ebuild +++ b/dev-python/gwcs/gwcs-0.16.1.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_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..10} ) inherit distutils-r1 @@ -14,8 +14,11 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" +# Tests do not pass, reported upstream: +# https://github.com/spacetelescope/gwcs/issues/437 +RESTRICT=test -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}] +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}] test? ( dev-python/pytest-doctestplus[${PYTHON_USEDEP}] ) diff --git a/dev-python/gwcs/gwcs-0.18.3-r1.ebuild b/dev-python/gwcs/gwcs-0.18.3-r1.ebuild new file mode 100644 index 000000000..eef5aeb36 --- /dev/null +++ b/dev-python/gwcs/gwcs-0.18.3-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Generalized World Coordinate System" +HOMEPAGE="https://gwcs.readthedocs.io/en/latest/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Tests do not pass, reported upstream: +# https://github.com/spacetelescope/gwcs/issues/437 +RESTRICT=test + +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + ) +" + +RDEPEND=" + dev-python/asdf[${PYTHON_USEDEP}] + >=dev-python/astropy-4.1[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" + +# TODO: package stsci-rtd-theme +#distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/sphinx-automodapi dev-python/sphinx_rtd_theme +distutils_enable_tests pytest + +python_test() { + # discovers things in docs dir if we do not + # explicitly set it to run on the tests dir + epytest gwcs/tests +} diff --git a/dev-python/gwcs/metadata.xml b/dev-python/gwcs/metadata.xml index 4f4367037..d7b713ef5 100644 --- a/dev-python/gwcs/metadata.xml +++ b/dev-python/gwcs/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">gwcs</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/hdbscan/Manifest b/dev-python/hdbscan/Manifest new file mode 100644 index 000000000..b162353da --- /dev/null +++ b/dev-python/hdbscan/Manifest @@ -0,0 +1,2 @@ +DIST hdbscan-0.8.26.tar.gz 10776639 BLAKE2B 7f1cb7b479746e3ff262cce90d48cca42dccabc131a60300ae5448455260eb27387ab2eeeee19257930ee646d06df80fa2997cf1819da18178c5522a8a27a30c SHA512 7337f4246511d22e8e11308e7776aad6929f26674daecc1e174b01673782837815a40820a6565406315b1ae14ed059c4945810ac997abfde9e24abda352de622 +DIST hdbscan-0.8.29.tar.gz 11666106 BLAKE2B de324386d7d2178f74ea958fa75e5eccb9dcdeba3d85cecce1150930e2d687caecbc79469de6ad62806c5bd860962bba57f27323c69f3abc6b0d4694a553656d SHA512 fd349c1c6c09f0288a9a2501eb7794fb03139c11261a835d90f1c9cd80955a4d8d075ff3864ddb9cfcbc204a3d0662011074bdb29b66b72d5469f76bc4f7ecca diff --git a/dev-python/hdbscan/hdbscan-0.8.26.ebuild b/dev-python/hdbscan/hdbscan-0.8.26.ebuild new file mode 100644 index 000000000..91e83eb87 --- /dev/null +++ b/dev-python/hdbscan/hdbscan-0.8.26.ebuild @@ -0,0 +1,33 @@ +# Copyright 2021-2023 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="A high performance implementation of HDBSCAN clustering." +HOMEPAGE="https://github.com/scikit-learn-contrib/hdbscan" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="test" +# Tests fail, reported to upstream +# https://github.com/scikit-learn-contrib/hdbscan/issues/501 + +DEPEND="" +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" +BDEPEND="" + +distutils_enable_tests pytest diff --git a/dev-python/hdbscan/hdbscan-0.8.29.ebuild b/dev-python/hdbscan/hdbscan-0.8.29.ebuild new file mode 100644 index 000000000..e13b6da0e --- /dev/null +++ b/dev-python/hdbscan/hdbscan-0.8.29.ebuild @@ -0,0 +1,33 @@ +# Copyright 2021-2023 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="A high performance implementation of HDBSCAN clustering." +HOMEPAGE="https://github.com/scikit-learn-contrib/hdbscan" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Reported upstream: +# https://github.com/scikit-learn-contrib/hdbscan/issues/501 +RESTRICT="test" + +DEPEND="" +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" +BDEPEND="" + +distutils_enable_tests pytest diff --git a/dev-python/hdbscan/metadata.xml b/dev-python/hdbscan/metadata.xml new file mode 100644 index 000000000..3e9aab1c5 --- /dev/null +++ b/dev-python/hdbscan/metadata.xml @@ -0,0 +1,29 @@ +<?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"> + HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications with + Noise. Performs DBSCAN over varying epsilon values and integrates the result + to find a clustering that gives the best stability over epsilon. This allows + HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more + robust to parameter selection. + + In practice this means that HDBSCAN returns a good clustering straight away + with little or no parameter tuning -- and the primary parameter, minimum + cluster size, is intuitive and easy to select. HDBSCAN is ideal for + exploratory data analysis; it's a fast and robust algorithm that you can + trust to return meaningful clusters (if there are any). + </longdescription> + <upstream> + <remote-id type="github">scikit-learn-contrib/hdbscan</remote-id> + <remote-id type="pypi">hdbscan</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/hdf5storage/Manifest b/dev-python/hdf5storage/Manifest index dee5fa709..caea5df39 100644 --- a/dev-python/hdf5storage/Manifest +++ b/dev-python/hdf5storage/Manifest @@ -1,2 +1 @@ -DIST hdf5storage-0.1.17.tar.gz 91008 BLAKE2B 7956573a1b9531146f5e5509788a9894317e77afcc4c12faf9ba197744bc4a1e2cc28e063bb51f94bcebbc26d876edefdc2f113dbf4ad26d559d77cefcf8cc1d SHA512 5a0781ac93bfc486025022c04aa6d7253910194b2d4b5e00d2a396a5865e1eccb6bde1565c66dde5a9798d16441461c539586a7a67f039ca960bce1cdcb8bbd9 -DIST hdf5storage-0.1.18.tar.gz 91599 BLAKE2B 822dde832ab5abb0def1d6b478e6b02cbe5597b009a3be9c76f1d0583f44aa28bfc0cedb10eadac6619daabc08d4642815779e1380e69d601e8e55500cba595e SHA512 5c8df3768b3fca0cd600acff65b96faf29e517e2375ed2dd7c1a516f30929ec21c70a6c9dc8b17271d5643ea94ffa01e8ed9963a2fa161e2af14aab57851b59e +DIST hdf5storage-0.1.19.tar.gz 92294 BLAKE2B b4379e9c6b69af1c205072d0d8b29f6322c3271cc1f5e56ab81a4ec3c09db9f9ac107b912e4d74772253ade269db589ed4ac140cde6cfd95346de7fcdc6dc752 SHA512 0ea4068be1af2521bba3fba3b0b020c0faff64be487644c46350ef19f4f3997593af90438db5b0d9b80ac303ff99755a0f59504ad34cfa27f1bc8c7881f024ce diff --git a/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild deleted file mode 100644 index 22f9151e0..000000000 --- a/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files" -HOMEPAGE="https://github.com/frejanordsiek/hdf5storage" - -SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" -KEYWORDS="~amd64 ~x86" - -LICENSE="BSD" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -distutils_enable_tests nose diff --git a/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild index 22f9151e0..ab64fefbc 100644 --- a/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild +++ b/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild @@ -2,14 +2,15 @@ # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files" HOMEPAGE="https://github.com/frejanordsiek/hdf5storage" -SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64 ~x86" LICENSE="BSD" @@ -21,4 +22,4 @@ RDEPEND=" " DEPEND="${RDEPEND}" -distutils_enable_tests nose +distutils_enable_tests pytest diff --git a/dev-python/hdf5storage/hdf5storage-9999.ebuild b/dev-python/hdf5storage/hdf5storage-9999.ebuild index 3a6391eb0..1bcf35a57 100644 --- a/dev-python/hdf5storage/hdf5storage-9999.ebuild +++ b/dev-python/hdf5storage/hdf5storage-9999.ebuild @@ -2,7 +2,8 @@ # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -28,4 +29,4 @@ RDEPEND=" " DEPEND="${RDEPEND}" -distutils_enable_tests nose +distutils_enable_tests pytest diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest index 683f37a69..a8bb51f14 100644 --- a/dev-python/hdmf/Manifest +++ b/dev-python/hdmf/Manifest @@ -1,2 +1,4 @@ -DIST hdmf-3.1.1.tar.gz 292419 BLAKE2B eed1b1c282f022f7e1bd3af63c3078563a74895bf177244841ee0cabd3ab391e2d7a48c9a111a909f5982bf1a1c9b44f1b82fd710f9729681bcada396d3c3d7b SHA512 41776932b1150126a162e9f87072d6626a28bb3f0e05f75337e4f6529c27005ca9db932fdff0c45bb16cbebf68388c7cbf575bbd17950c29c300702a37afacf0 -DIST hdmf-3.3.2.tar.gz 312991 BLAKE2B 6765f1543e73746fd07279104d70ccf069795140781375427b14586d4ab0d433f7769051436618791db7d2eb09cf4515d983c0232c76aa8a67bacd65b9e9bc2a SHA512 b769216b048df8f9fb220c38053d2f1c7976b0ad9cfcac5f36656fcf5cabfab25f910c9a1fec7fbb20ad919bf4c791751e92e485e02b3e26314e7f396e45549b +DIST hdmf-3.4.7.tar.gz 319714 BLAKE2B 189b7629b818371bea002f4c340149e5807a5da9e2b27301574b74c50eda575b711ffbffac997ee2c2d25c30c926ada13d84319e054bf796e5bd74516d84be21 SHA512 c5b6b9dfeace0ea140bcd2cf822f9b45007ea7acefd6eca950b4b023731e31b8ebc592da0e3633e41a41e377a33565f6f5c04a88852a190816c95e89b49efa02 +DIST hdmf-3.5.0.tar.gz 324330 BLAKE2B 256fd974230fb750c5329fbf2cece0f151b6d7366aea26ffd08bafff0601ba6fde789dc906f4de5dbb1a02e9a0d21965a17eda76083df03d3a3afdacf9a7ba70 SHA512 8e1244f70c75f01d18d2d09b6c481efcab59bd02e69392f3da46d2e4541073fccaa9606907cee1ca0873221011e9ce8040668f2affd2ef4ee98fd35bd6356ff4 +DIST hdmf-3.5.1.tar.gz 324778 BLAKE2B b82d2389466be8e8b4acd843beaafe69b731a38045abab0a741fb7a6143e8ed8f60d570603629c7485f7f7a261047bcc9e21ebeb61802e6d81b35aa276d09af0 SHA512 1545f0c1c6b2bac66437941e631adaa45a42c18436ed68d5ee21a7cafe950a85e2843a4b2258b3f5c0ece5fd6d3ef6f0fd596a83bacd208750bfb5b78a1d5815 +DIST hdmf-3.5.2.tar.gz 567466 BLAKE2B 99872885aec1b0aff30dfde17cc3c2f5f30e9da7f3ac5aa77dad203fe795ad6c207bdafd6d19548bf8c3f901a1ec8655b048d9ba41be11eaca3a7c55e6de2825 SHA512 47f8de397fe3defe814db3da7f2bf7ec3814bf3a1d9389c6fe823e229ddea441c97122e41a11883f1c7b5968a841d8fdd0c7314e9d82d4e5ea43a713a40afbfa diff --git a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch deleted file mode 100644 index 58822989d..000000000 --- a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- a/setup.py 2022-01-31 02:48:24.645837186 -0500 -+++ b/setup.py 2022-01-31 02:49:55.066949247 -0500 -@@ -12,12 +12,12 @@ - schema_dir = 'common/hdmf-common-schema/common' - - reqs = [ -- 'h5py>=2.10,<4', -- 'numpy>=1.16,<1.22', -- 'scipy>=1.1,<2', -- 'pandas>=1.0.5,<2', -- 'ruamel.yaml>=0.16,<1', -- 'jsonschema>=2.6.0,<4', -+ 'h5py', -+ 'numpy', -+ 'scipy', -+ 'pandas', -+ 'ruamel.yaml', -+ 'jsonschema', - 'setuptools', - ] - diff --git a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch new file mode 100644 index 000000000..544bf8f4b --- /dev/null +++ b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch @@ -0,0 +1,170 @@ +From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <oruebel@lbl.gov> +Date: Wed, 18 Jan 2023 16:05:57 -0800 +Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to + clsoe links + +--- + src/hdmf/backends/hdf5/h5tools.py | 13 +++++++++---- + 1 file changed, 9 insertions(+), 4 deletions(-) + +diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py +index ba8946c60..acf2061ad 100644 +--- a/src/hdmf/backends/hdf5/h5tools.py ++++ b/src/hdmf/backends/hdf5/h5tools.py +@@ -746,10 +746,15 @@ def close_linked_files(self): + not, which prevents the linked-to file from being deleted or truncated. Use this method to close all opened, + linked-to files. + """ +- for obj in self.__open_links: +- if obj: +- obj.file.close() +- self.__open_links = [] ++ # Make sure ++ try: ++ for obj in self.__open_links: ++ if obj: ++ obj.file.close() ++ except AttributeError: # In case that self.__open_links does not exist on delete ++ pass ++ finally: ++ self.__open_links = [] + + @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the GroupBuilder object representing the HDF5 file'}, + {'name': 'link_data', 'type': bool, + +From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <oruebel@lbl.gov> +Date: Wed, 18 Jan 2023 17:32:20 -0800 +Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error + +--- + src/hdmf/backends/hdf5/h5tools.py | 19 +++++++++++++++---- + 1 file changed, 15 insertions(+), 4 deletions(-) + +diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py +index acf2061ad..75044a64a 100644 +--- a/src/hdmf/backends/hdf5/h5tools.py ++++ b/src/hdmf/backends/hdf5/h5tools.py +@@ -736,8 +736,15 @@ def close(self, close_links=True): + """ + if close_links: + self.close_linked_files() +- if self.__file is not None: +- self.__file.close() ++ try: ++ if self.__file is not None: ++ self.__file.close() ++ except AttributeError: ++ # Do not do anything in case that self._file does not exist. This ++ # may happen in case that an error occurs before HDF5IO has been fully ++ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises ++ # and error before self.__file has been created ++ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__file") + + def close_linked_files(self): + """Close all opened, linked-to files. +@@ -751,8 +758,12 @@ def close_linked_files(self): + for obj in self.__open_links: + if obj: + obj.file.close() +- except AttributeError: # In case that self.__open_links does not exist on delete +- pass ++ except AttributeError: ++ # Do not do anything in case that self.__open_links does not exist. This ++ # may happen in case that an error occurs before HDF5IO has been fully ++ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises ++ # and error before self.__open_links has been created. ++ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__open_links.") + finally: + self.__open_links = [] + + +From a43e65d13726936aa2ab49169e265a42c5a1be7f Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <oruebel@lbl.gov> +Date: Wed, 18 Jan 2023 17:32:55 -0800 +Subject: [PATCH 3/5] Add unit test for case where HDF5IO.close is called + before HDF5IO.__init__ is complete + +--- + tests/unit/test_io_hdf5_h5tools.py | 34 ++++++++++++++++++++++++++++++ + 1 file changed, 34 insertions(+) + +diff --git a/tests/unit/test_io_hdf5_h5tools.py b/tests/unit/test_io_hdf5_h5tools.py +index 8c03e72f8..0f2f81e31 100644 +--- a/tests/unit/test_io_hdf5_h5tools.py ++++ b/tests/unit/test_io_hdf5_h5tools.py +@@ -826,6 +826,40 @@ def test_constructor(self): + self.assertEqual(io.manager, self.manager) + self.assertEqual(io.source, self.path) + ++ def test_delete_with_incomplete_construction_missing_file(self): ++ """ ++ Here we test what happens when close is called before HDF5IO.__init__ has ++ bee completed. In this case self.__file is missing ++ """ ++ class MyHDF5IO(HDF5IO): ++ def __init__(self): ++ raise ValueError("test error") ++ with self.assertWarnsWith(warn_type=UserWarning, ++ exc_msg="HDF5IO was not fully initialized before close. Missing self.__file"): ++ try: ++ with MyHDF5IO() as _: ++ pass ++ except ValueError: ++ pass ++ ++ def test_delete_with_incomplete_construction_missing_open_files(self): ++ """ ++ Here we test what happens when close is called before HDF5IO.__init__ has ++ bee completed. In this case self.__open_file is missing ++ """ ++ ++ class MyHDF5IO(HDF5IO): ++ def __init__(self): ++ raise ValueError("test error") ++ ++ with self.assertWarnsWith(warn_type=UserWarning, ++ exc_msg="HDF5IO was not fully initialized before close. Missing self.__open_links."): ++ try: ++ with MyHDF5IO() as _: ++ pass ++ except ValueError: ++ pass ++ + def test_set_file_mismatch(self): + self.file_obj = File(get_temp_filepath(), 'w') + err_msg = ("You argued %s as this object's path, but supplied a file with filename: %s" + +From f79b3a26bdfaee22b8d24bd3094c93be77e5595f Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <oruebel@lbl.gov> +Date: Thu, 19 Jan 2023 13:54:33 -0800 +Subject: [PATCH 5/5] Move init of __file and __openlink up to prevent warning + during close + +--- + src/hdmf/backends/hdf5/h5tools.py | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py +index 75044a64a..44b9c612c 100644 +--- a/src/hdmf/backends/hdf5/h5tools.py ++++ b/src/hdmf/backends/hdf5/h5tools.py +@@ -55,6 +55,9 @@ def __init__(self, **kwargs): + path, manager, mode, comm, file_obj, driver = popargs('path', 'manager', 'mode', 'comm', 'file', 'driver', + kwargs) + ++ self.__open_links = [] # keep track of other files opened from links in this file ++ self.__file = None # This will be set below, but set to None first in case an error occurs and we need to close ++ + if path is None and file_obj is None: + raise ValueError("You must supply either a path or a file.") + +@@ -89,7 +92,6 @@ def __init__(self, **kwargs): + self.__dci_queue = HDF5IODataChunkIteratorQueue() # a queue of DataChunkIterators that need to be exhausted + ObjectMapper.no_convert(Dataset) + self._written_builders = WriteStatusTracker() # track which builders were written (or read) by this IO object +- self.__open_links = [] # keep track of other files opened from links in this file + + @property + def comm(self): diff --git a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild b/dev-python/hdmf/hdmf-3.4.7.ebuild index 1bec3913c..883b5b95b 100644 --- a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild +++ b/dev-python/hdmf/hdmf-3.4.7.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="The Hierarchical Data Modeling Framework" @@ -25,8 +25,4 @@ RDEPEND=" " BDEPEND="" -PATCHES=( - "${FILESDIR}/${P}-versions.patch" -) - distutils_enable_tests pytest diff --git a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild new file mode 100644 index 000000000..053831f8d --- /dev/null +++ b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +MY_PV="${PV//_p*/}" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="The Hierarchical Data Modeling Framework" +HOMEPAGE="https://github.com/hdmf-dev/hdmf" +SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${MY_PV}/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="" + +PATCHES=( + "${FILESDIR}/${MY_P}-open_links.patch" +) + +distutils_enable_tests pytest + +S="${WORKDIR}/${MY_P}" diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild b/dev-python/hdmf/hdmf-3.5.1.ebuild index 866b5e553..883b5b95b 100644 --- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild +++ b/dev-python/hdmf/hdmf-3.5.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=rdepend +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="The Hierarchical Data Modeling Framework" @@ -26,13 +26,3 @@ RDEPEND=" BDEPEND="" distutils_enable_tests pytest - -# Known to upstream: -# https://github.com/hdmf-dev/hdmf/issues/687 -EPYTEST_DESELECT=( - tests/unit/utils_test/test_labelleddict.py::TestLabelledDict::test_set_key_attr -) - -PATCHES=( - "${FILESDIR}/${P}-versions.patch" -) diff --git a/dev-python/hdmf/hdmf-3.5.2.ebuild b/dev-python/hdmf/hdmf-3.5.2.ebuild new file mode 100644 index 000000000..ee978516e --- /dev/null +++ b/dev-python/hdmf/hdmf-3.5.2.ebuild @@ -0,0 +1,29 @@ +# 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} ) +inherit distutils-r1 pypi + +DESCRIPTION="The Hierarchical Data Modeling Framework" +HOMEPAGE="https://github.com/hdmf-dev/hdmf" +SRC_URI="$(pypi_sdist_url hdmf)" +#SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="" + +distutils_enable_tests pytest diff --git a/dev-python/heudiconv/Manifest b/dev-python/heudiconv/Manifest new file mode 100644 index 000000000..55669a6ad --- /dev/null +++ b/dev-python/heudiconv/Manifest @@ -0,0 +1 @@ +DIST heudiconv-0.11.6.tar.gz 9070519 BLAKE2B df6c66080bbaa89f74490f136674eabd64e9b2844ae7daef82ef4b4ef8c42ed16d3ae3b790534cc13ec121e63de8486838eb7e7becbcdbffff2df6e8bd2bd54c SHA512 c4d1f0caaed9713360ad2614bc276f2cc0e356c54b1b37c8912d762db429313c75d0f081886cb6ea0b8fd171bc5fc5a338fd3b670a8b10a3fbed0c6f9dfb7477 diff --git a/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch b/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch new file mode 100644 index 000000000..23be6d000 --- /dev/null +++ b/dev-python/heudiconv/files/heudiconv-0.11.6-gitenv.patch @@ -0,0 +1,24 @@ +From 0c30781248e0c1f2d437e0dfd923a74d7e647411 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Wed, 1 Feb 2023 21:34:58 -0500 +Subject: [PATCH] Setting git author and email in test environment + +--- + heudiconv/tests/conftest.py | 3 +++ + 1 file changed, 3 insertions(+) + create mode 100644 heudiconv/tests/conftest.py + +diff --git /dev/null b/heudiconv/tests/conftest.py +new file mode 100644 +index 00000000..f4f47d16 +--- /dev/null ++++ b/heudiconv/tests/conftest.py +@@ -0,0 +1,8 @@ ++import os ++import pytest ++@pytest.fixture(autouse=True, scope="session") ++def git_env(): ++ os.environ["GIT_AUTHOR_EMAIL"] = "maxm@example.com" ++ os.environ["GIT_AUTHOR_NAME"] = "Max Mustermann" ++ os.environ["GIT_COMMITTER_EMAIL"] = "maxm@example.com" ++ os.environ["GIT_COMMITTER_NAME"] = "Max Mustermann" diff --git a/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild b/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild new file mode 100644 index 000000000..847424235 --- /dev/null +++ b/dev-python/heudiconv/heudiconv-0.11.6-r1.ebuild @@ -0,0 +1,42 @@ +# 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 ) +inherit distutils-r1 + +DESCRIPTION="Flexible DICOM conversion to structured directory layouts" +HOMEPAGE=" + https://github.com/nipy/heudiconv + https://heudiconv.readthedocs.io/en/latest/ +" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/versioningit[${PYTHON_USEDEP}] + sci-biology/dcm2niix + sci-biology/dcmstack[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-libs/nipype[${PYTHON_USEDEP}] + sci-libs/pydicom[${PYTHON_USEDEP}] + " +BDEPEND=" + test? ( + dev-python/six[${PYTHON_USEDEP}] + ) +" + +# Patch sumbitted upstream, check if removal possible in next release: +# https://github.com/nipy/heudiconv/pull/631 +PATCHES=( + "${FILESDIR}/${P}-gitenv.patch" +) + +distutils_enable_tests pytest diff --git a/dev-python/heudiconv/metadata.xml b/dev-python/heudiconv/metadata.xml new file mode 100644 index 000000000..a98cbf459 --- /dev/null +++ b/dev-python/heudiconv/metadata.xml @@ -0,0 +1,16 @@ +<?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> + <upstream> + <remote-id type="pypi">heudiconv</remote-id> + <remote-id type="github">nipy/heudiconv</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/holoviews/Manifest b/dev-python/holoviews/Manifest index 94e17efc1..806b0513d 100644 --- a/dev-python/holoviews/Manifest +++ b/dev-python/holoviews/Manifest @@ -1 +1,2 @@ DIST holoviews-1.14.2.tar.gz 6929549 BLAKE2B 72746a846ea7628b45e61b892ea940df4b2d7886efda054eedb859caac5dc3b66ed1c0aa9a4df8766905e35a973f6ee9226558cf6fb68394d17fe7c2f77982b2 SHA512 473a344f36c6ab1abc0847df46f4dc015fe225b9285a86152a78e13402770d5e7fdbd51aef21ff5cc53fbab89898237a260bea86dadef91ccb30bbce9344daf0 +DIST holoviews-1.15.3.tar.gz 6905214 BLAKE2B 60bb7008dd5af474295245eb0dbce240cfb4dcaf4122bc6073561e829c506b670201ac7d2b7ae1eea640929eb0993148c22c1a3e8d8ccb8e00582a2fbd3e696b SHA512 b1d4b64503511c61ede67d6d45472acde1afb854e19f7a30acb35d7fab2400ffe1e43db7b6e85eefe542b8353982af9cb41d505412bb0674cb20926c24f76494 diff --git a/dev-python/holoviews/holoviews-1.14.2.ebuild b/dev-python/holoviews/holoviews-1.14.2.ebuild index 505133d78..4c8af05d9 100644 --- a/dev-python/holoviews/holoviews-1.14.2.ebuild +++ b/dev-python/holoviews/holoviews-1.14.2.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..10} ) # HoloViews imports from "distutils" at runtime. DISTUTILS_USE_SETUPTOOLS=rdepend diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild b/dev-python/holoviews/holoviews-1.15.3.ebuild new file mode 100644 index 000000000..425290441 --- /dev/null +++ b/dev-python/holoviews/holoviews-1.15.3.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) + +# HoloViews imports from "distutils" at runtime. +DISTUTILS_USE_SETUPTOOLS=rdepend + +inherit distutils-r1 + +DESCRIPTION="Make data analysis and visualization seamless and simple" +HOMEPAGE="https://holoviews.org" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Reported upstream: +# https://github.com/holoviz/holoviews/issues/5592 +RESTRICT="test" + +DEPEND=" + >=dev-python/param-1.9.3[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/bokeh[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nbconvert[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] + sci-visualization/dash[${PYTHON_USEDEP}] + ) +" +RDEPEND="${DEPEND} + dev-python/colorcet[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + >=dev-python/numpy-1.0.0[${PYTHON_USEDEP}] + >=dev-python/panel-0.8.0[${PYTHON_USEDEP}] + >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild index 5dfb4bc6b..29c57f90a 100644 --- a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild +++ b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild @@ -1,14 +1,15 @@ -# 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} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="python frontend for the fast ripser tda tool" -HOMEPAGE="https://ripser.scikit-tda.org/" +HOMEPAGE="https://ripser.scikit-tda.org/ https://github.com/sofiatolaosebikan/hopcroftkarp" COMMIT="2846e1dd3265d95d2bddb0cf4190b830cbb4efe6" SRC_URI="https://github.com/sofiatolaosebikan/hopcroftkarp/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}"/${PN}-${COMMIT} diff --git a/dev-python/interleave/interleave-0.2.0.ebuild b/dev-python/interleave/interleave-0.2.0.ebuild index c8a9c9ca1..7dbb9d5c9 100644 --- a/dev-python/interleave/interleave-0.2.0.ebuild +++ b/dev-python/interleave/interleave-0.2.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10}) +PYTHON_COMPAT=( python3_10) inherit distutils-r1 diff --git a/dev-python/kmapper/Manifest b/dev-python/kmapper/Manifest index 61c31630b..0eeec60f6 100644 --- a/dev-python/kmapper/Manifest +++ b/dev-python/kmapper/Manifest @@ -1,2 +1 @@ -DIST kmapper-1.4.1.tar.gz 100655 BLAKE2B 7321266be9fea509da054a481328178bd5bb5403b60f09b64ece4ef1fa54713a5f9b292553b87385464b52e82407461659575d7bd5d2b6038b69d500b934da77 SHA512 dc760c7b3c838d44f4b96ba744f03482e4495bb4341380aa4448c57a1292c6d8d95a9e7fb8bd9171a26e56677e578c1a8002fd429166fe87a60a8313fada7e4a -DIST kmapper-2.0.1.tar.gz 6686101 BLAKE2B 8afa79a2479370c335debb4cee7375b0d47b0e79d02649ff53681d006e2a80cd6175f8aeb3c3a6fa0ac32d0cf30ba8217d348f6158b9ee1bc7c683d0a5b4290e SHA512 751f02ee3f5a55eb74b55b0a9204e54d05c9af2a816f8070082a73d4213c1fb7842e41e3e27316d69efaa2cf3e2f9b2d967870905ace8d9e9a3e67f9ea181ed2 +DIST kmapper-2.0.1.gh.tar.gz 6686101 BLAKE2B 8afa79a2479370c335debb4cee7375b0d47b0e79d02649ff53681d006e2a80cd6175f8aeb3c3a6fa0ac32d0cf30ba8217d348f6158b9ee1bc7c683d0a5b4290e SHA512 751f02ee3f5a55eb74b55b0a9204e54d05c9af2a816f8070082a73d4213c1fb7842e41e3e27316d69efaa2cf3e2f9b2d967870905ace8d9e9a3e67f9ea181ed2 diff --git a/dev-python/kmapper/kmapper-1.4.1.ebuild b/dev-python/kmapper/kmapper-1.4.1.ebuild deleted file mode 100644 index 763a962de..000000000 --- a/dev-python/kmapper/kmapper-1.4.1.ebuild +++ /dev/null @@ -1,41 +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 implementation of Mapper algorithm for Topological Data Analysis" -HOMEPAGE="https://kepler-mapper.scikit-tda.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="${PYTHON_DEPS} - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/markupsafe[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/plotly[${PYTHON_USEDEP}] - dev-python/python-igraph[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" -BDEPEND=" - test? ( - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/ipywidgets[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_prepare_all() { - rm "${S}"/test/test_plotly.py || die - distutils-r1_python_prepare_all -} diff --git a/dev-python/kmapper/kmapper-2.0.1.ebuild b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild index 2099fa4db..c8bdf2b00 100644 --- a/dev-python/kmapper/kmapper-2.0.1.ebuild +++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild @@ -1,15 +1,16 @@ # Copyright 1999-2021 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_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Python implementation of Mapper algorithm for Topological Data Analysis" HOMEPAGE="https://kepler-mapper.scikit-tda.org" -SRC_URI="https://github.com/scikit-tda/kepler-mapper/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/scikit-tda/kepler-mapper/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" S="${WORKDIR}"/kepler-mapper-${PV} LICENSE="MIT" diff --git a/dev-python/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml index 006b418f5..4dee7702f 100644 --- a/dev-python/kmapper/metadata.xml +++ b/dev-python/kmapper/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="github">scikit-tda/kepler-mapper</remote-id> + <remote-id type="pypi">kmapper</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/latexify_py/latexify_py-0.2.0.ebuild b/dev-python/latexify_py/latexify_py-0.2.0.ebuild index 5079c5ef3..bd42c3cf3 100644 --- a/dev-python/latexify_py/latexify_py-0.2.0.ebuild +++ b/dev-python/latexify_py/latexify_py-0.2.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..11} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=hatchling inherit distutils-r1 diff --git a/dev-python/lazy_ops/Manifest b/dev-python/lazy_ops/Manifest new file mode 100644 index 000000000..b5b4cce5e --- /dev/null +++ b/dev-python/lazy_ops/Manifest @@ -0,0 +1 @@ +DIST lazy_ops-0.2.0.tar.gz 5284 BLAKE2B ba8747ba9028103fad7e0cab5eb53ebfefca5e886dcd39a499c8c8c6c8c466dcdb85438fc012f32cff7b98e486fe8154ef4e3c08241c3c9c738f0a399a6f91af SHA512 b0c7e49d37553f56f491d7e7aaeee8e6e18d44f6f34f7148ed98a596573dc26523e9cbc7bb6dce04bae99dbe59cecd35759173985fc203d7e59dfa61592e6955 diff --git a/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild new file mode 100644 index 000000000..a873e6b85 --- /dev/null +++ b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Lazy transposing and slicing of h5py and Zarr data" +HOMEPAGE="https://github.com/catalystneuro/lazy_ops" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# There are no source archive with tests available: +# https://github.com/catalystneuro/lazy_ops/issues/29 +RESTRICT="test" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/lazy_ops/metadata.xml b/dev-python/lazy_ops/metadata.xml new file mode 100644 index 000000000..d5101128a --- /dev/null +++ b/dev-python/lazy_ops/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">catalystneuro/lazy_ops</remote-id> + <remote-id type="pypi">lazy_ops</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch new file mode 100644 index 000000000..d35979ebc --- /dev/null +++ b/dev-python/llvmlite/files/llvmlite-0.39.1-allow-py3.11.patch @@ -0,0 +1,13 @@ +diff --git a/setup.py b/setup.py +index 02b1604..a45c9b8 100644 +--- a/setup.py ++++ b/setup.py +@@ -33,7 +33,7 @@ except ImportError: + + + min_python_version = "3.7" +-max_python_version = "3.11" # exclusive ++max_python_version = "3.12" # exclusive + + + def _guard_py_ver(): diff --git a/dev-python/llvmlite/llvmlite-0.39.1.ebuild b/dev-python/llvmlite/llvmlite-0.39.1.ebuild index a2c3a6750..7302c93dd 100644 --- a/dev-python/llvmlite/llvmlite-0.39.1.ebuild +++ b/dev-python/llvmlite/llvmlite-0.39.1.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 llvm DESCRIPTION="Python wrapper around the llvm C++ library" @@ -16,7 +17,7 @@ SLOT="0" KEYWORDS="~amd64 ~arm ~arm64 ~x86" IUSE="examples" -LLVM_MAX_SLOT=13 +LLVM_MAX_SLOT=15 RDEPEND=" sys-devel/llvm:${LLVM_MAX_SLOT} @@ -24,7 +25,10 @@ RDEPEND=" " DEPEND="${RDEPEND}" -PATCHES=( "${FILESDIR}/${P}-llvm12.patch" ) +PATCHES=( + "${FILESDIR}/${P}-llvm12.patch" + "${FILESDIR}/${P}-allow-py3.11.patch" +) src_prepare() { sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die diff --git a/dev-python/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild index 717426899..59f029e95 100644 --- a/dev-python/logzero/logzero-1.7.0.ebuild +++ b/dev-python/logzero/logzero-1.7.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} pypy3 ) +PYTHON_COMPAT=( python3_10 pypy3 ) inherit distutils-r1 diff --git a/dev-python/looseversion/Manifest b/dev-python/looseversion/Manifest new file mode 100644 index 000000000..1fe929b12 --- /dev/null +++ b/dev-python/looseversion/Manifest @@ -0,0 +1,2 @@ +DIST looseversion-1.0.2.gh.tar.gz 8144 BLAKE2B 1c3b76c6f77499ac39863897771bbc2246e5d1ad47e3ae4f0c21d4bb6a717270ebe6550ea53b188740ed74bf5a7fef31d743486f0ee54ddb9758d2806374dbdf SHA512 d166c49a1788fe6453d4187af62a860f9c66ce7b71ec924ad3a6d19101d9619394bb81e17e52054b5a8e693051ca40c4269e415f4af513d35212eab678837569 +DIST looseversion-1.0.3.tar.gz 6874 BLAKE2B ce0cc5af699c7db85f180ba0e4b465411d15a1bd4f669fc34ede985f0ceca63a01d9ab7755b722018770633342bfe6eeeb59b98026616641aca1a522acd47f7b SHA512 262f6b33516020bf38878cdf0dfcd3e51507d20f40a348a8fcd8ba66c2eaef564738c275297c3efe8daf9ff5efc5b7dffa8d76f77626c3eefdac7b097db27f78 diff --git a/dev-python/looseversion/looseversion-1.0.2.ebuild b/dev-python/looseversion/looseversion-1.0.2.ebuild new file mode 100644 index 000000000..0150e69f5 --- /dev/null +++ b/dev-python/looseversion/looseversion-1.0.2.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="A backwards/forwards-compatible fork of distutils' LooseVersion" +HOMEPAGE="https://github.com/effigies/looseversion" +SRC_URI="https://github.com/effigies/looseversion/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="PSF-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RDEPEND="" +BEPEND="" + +distutils_enable_tests pytest + +python_test() { + epytest tests.py +} diff --git a/dev-python/looseversion/looseversion-1.0.3.ebuild b/dev-python/looseversion/looseversion-1.0.3.ebuild new file mode 100644 index 000000000..aa8ebcc32 --- /dev/null +++ b/dev-python/looseversion/looseversion-1.0.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=flit +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="A backwards/forwards-compatible fork of distutils' LooseVersion" +HOMEPAGE="https://github.com/effigies/looseversion" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="PSF-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RDEPEND="" +BEPEND="" + +distutils_enable_tests pytest + +python_test() { + epytest tests.py +} diff --git a/dev-python/looseversion/metadata.xml b/dev-python/looseversion/metadata.xml new file mode 100644 index 000000000..20b71d2b7 --- /dev/null +++ b/dev-python/looseversion/metadata.xml @@ -0,0 +1,25 @@ +<?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"> + A backwards/forwards-compatible fork of distutils.version.LooseVersion, for times + when PEP-440 isn't what you need. The goal of this package is to be a drop-in + replacement for the original LooseVersion. It implements an identical interface + and comparison logic to LooseVersion. The only major change is that a + looseversion.LooseVersion is comparable to a distutils.version.LooseVersion, + which means tools should not need to worry whether all dependencies that use + LooseVersion have migrated. + </longdescription> + <upstream> + <remote-id type="github">effigies/looseversion</remote-id> + <remote-id type="pypi">looseversion</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/matlabengine/Manifest b/dev-python/matlabengine/Manifest new file mode 100644 index 000000000..8704c974e --- /dev/null +++ b/dev-python/matlabengine/Manifest @@ -0,0 +1 @@ +DIST matlabengine-9.13.7.tar.gz 18796 BLAKE2B ccc5dae8fb9bc7a7cf240021f6066d4779d86d266b76cad3a610ed1fb455e1eefbef00cc5b1fe425f1f4f033dcb7721c2d1d3856c026fba13d2155604bfbf81f SHA512 b8d5d4d99f657fd24226f2accab676340a34739464fd289f1ca1c2db28a22f4b1288dfe160e8e193926e5db3e4fda0fcbbbf67b67f9a509910429e023b9cc3fb diff --git a/dev-python/matlabengine/matlabengine-9.13.7.ebuild b/dev-python/matlabengine/matlabengine-9.13.7.ebuild new file mode 100644 index 000000000..d65b1c0e5 --- /dev/null +++ b/dev-python/matlabengine/matlabengine-9.13.7.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) # No 3.11 according to setup.py +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="A module to call MATLAB from Python" +HOMEPAGE="https://github.com/mathworks/matlab-engine-for-python" + +LICENSE="MathWorks" +SLOT="0" +KEYWORDS="-* ~amd64" + +RESTRICT="bindist mirror" diff --git a/dev-python/matlabengine/metadata.xml b/dev-python/matlabengine/metadata.xml new file mode 100644 index 000000000..83a61da06 --- /dev/null +++ b/dev-python/matlabengine/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">matlabengine</remote-id> + <remote-id type="github">mathworks/matlab-engine-for-python</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/meshpy/meshpy-2020.1.ebuild b/dev-python/meshpy/meshpy-2020.1.ebuild index 191589690..78ee45fbc 100644 --- a/dev-python/meshpy/meshpy-2020.1.ebuild +++ b/dev-python/meshpy/meshpy-2020.1.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_IN_SOURCE_BUILD=1 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/mkl-service/Manifest b/dev-python/mkl-service/Manifest new file mode 100644 index 000000000..f0b775c11 --- /dev/null +++ b/dev-python/mkl-service/Manifest @@ -0,0 +1 @@ +DIST mkl-service-2.4.0.gh.tar.gz 18705 BLAKE2B 12896adba1c001a581ff10a18cf11b3b87344687807307ae7ee002583281ac8072730b9496ce94c48d8d9ded5ae815c432e1944715091043c222bd93e2728ed8 SHA512 fc33b0a3670fcac5564c020ee870a800b113b93f344eddf63874303347c7151b7f00052adf5a9544ff7557892aefb6088ee9c53cce043536f4456bd9903dc232 diff --git a/dev-python/mkl-service/metadata.xml b/dev-python/mkl-service/metadata.xml new file mode 100644 index 000000000..813808eb0 --- /dev/null +++ b/dev-python/mkl-service/metadata.xml @@ -0,0 +1,12 @@ +<?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">IntelPython/mkl-service</remote-id> + <remote-id type="pypi">mkl-service</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl-service/mkl-service-2.4.0.ebuild b/dev-python/mkl-service/mkl-service-2.4.0.ebuild new file mode 100644 index 000000000..decfc57bb --- /dev/null +++ b/dev-python/mkl-service/mkl-service-2.4.0.ebuild @@ -0,0 +1,38 @@ +# 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 hooks for Intel Math Kernel Library runtime control settings" +HOMEPAGE="https://github.com/IntelPython/mkl-service" +SRC_URI="https://github.com/IntelPython/mkl-service/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/mkl_fft/Manifest b/dev-python/mkl_fft/Manifest new file mode 100644 index 000000000..24960cd58 --- /dev/null +++ b/dev-python/mkl_fft/Manifest @@ -0,0 +1 @@ +DIST mkl_fft-1.3.1.gh.tar.gz 41796 BLAKE2B 880c5fef47e8f489c51c7ae69516ca073fe49583a1a11c16289d5313161190d0f4fe2be43defe51b26c6d1f5a4df8c40da8fe65c10911f40483e0400d177f859 SHA512 5d9bb76a5d5dfcf93a05fe6e1ebc267ba7011370ef40e84d6e017e90db301cedb1fb202b1f0851133537fa8bf09260bc9b3f5eb497efc049d6153a4de088854f diff --git a/dev-python/mkl_fft/metadata.xml b/dev-python/mkl_fft/metadata.xml new file mode 100644 index 000000000..95348817f --- /dev/null +++ b/dev-python/mkl_fft/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">IntelPython/mkl_fft</remote-id> + <remote-id type="pypi">mkl-fft</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild new file mode 100644 index 000000000..9b9c72d41 --- /dev/null +++ b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild @@ -0,0 +1,39 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="NumPy-based Python interface to Intel MKL FFT functionality" +HOMEPAGE="https://github.com/IntelPython/mkl_fft" +SRC_URI="https://github.com/IntelPython/mkl_fft/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +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="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/mkl_random/Manifest b/dev-python/mkl_random/Manifest new file mode 100644 index 000000000..a826880d4 --- /dev/null +++ b/dev-python/mkl_random/Manifest @@ -0,0 +1 @@ +DIST mkl_random-1.2.2.gh.tar.gz 80274 BLAKE2B f59091c2bdb4b0136e218e3a1341d1852aa9fcec097dc435330f9b175a71aefc1d7fe7fb56411f562f4f56bbff52fa46dec3506a36f73fecd91646b7b1ac56d4 SHA512 dd691fb9873cf54e4f488a20de9c85993536bbeaedb7fbd731e9c021e3b40992f45a01268f3166ce08e766b9374745ac2ee81e99eb013c7406d40d365241cb31 diff --git a/dev-python/mkl_random/metadata.xml b/dev-python/mkl_random/metadata.xml new file mode 100644 index 000000000..394347ca5 --- /dev/null +++ b/dev-python/mkl_random/metadata.xml @@ -0,0 +1,12 @@ +<?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">IntelPython/mkl_random</remote-id> + <remote-id type="pypi">mkl-random</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl_random/mkl_random-1.2.2.ebuild b/dev-python/mkl_random/mkl_random-1.2.2.ebuild new file mode 100644 index 000000000..7bd845de9 --- /dev/null +++ b/dev-python/mkl_random/mkl_random-1.2.2.ebuild @@ -0,0 +1,41 @@ +# 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 interface to Intel Math Kernel Library's random number generation" +HOMEPAGE="https://github.com/IntelPython/mkl_random" +SRC_URI="https://github.com/IntelPython/mkl_random/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +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="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + export C_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/" + export CPLUS_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/mkl_umath/Manifest b/dev-python/mkl_umath/Manifest new file mode 100644 index 000000000..6e1df7796 --- /dev/null +++ b/dev-python/mkl_umath/Manifest @@ -0,0 +1 @@ +DIST mkl_umath-0.1.1.gh.tar.gz 47263 BLAKE2B cb336ad38853298152ebef56e20dac5c6154352a1e443097db27c21ef3099b1ce93ba14a8a9d93ec163aecd0bef2ad8bbff436ae3f4f35ff1029ac6c34a808f5 SHA512 7e545c294d879ca602d2527945b9bb6782cf4e01c44cbde617c3ffcf8d639e428fecc3c9427b4089d70dbc8ae723630a8148917df18109b9c1727a25ad651775 diff --git a/dev-python/mkl_umath/metadata.xml b/dev-python/mkl_umath/metadata.xml new file mode 100644 index 000000000..f23ce9644 --- /dev/null +++ b/dev-python/mkl_umath/metadata.xml @@ -0,0 +1,12 @@ +<?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">IntelPython/mkl_umath</remote-id> + <remote-id type="pypi">mkl-umath</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild new file mode 100644 index 000000000..1210fdfd8 --- /dev/null +++ b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild @@ -0,0 +1,37 @@ +# 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="Package implementing NumPy's UFuncs based on SVML and MKL VML" +HOMEPAGE="https://github.com/IntelPython/mkl_umath" +SRC_URI="https://github.com/IntelPython/mkl_umath/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +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="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/multimethod/multimethod-1.8.ebuild b/dev-python/multimethod/multimethod-1.8.ebuild index 4d3c7837c..595a728a4 100644 --- a/dev-python/multimethod/multimethod-1.8.ebuild +++ b/dev-python/multimethod/multimethod-1.8.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/neo/Manifest b/dev-python/neo/Manifest new file mode 100644 index 000000000..e3b133b9e --- /dev/null +++ b/dev-python/neo/Manifest @@ -0,0 +1,2 @@ +DIST neo-0.11.0.tar.gz 9411608 BLAKE2B 9257fd8ff9eea8ec80b0a4eb701b63a9db10d51e6f145b704eb5e9a394dd13a5c6e567cb3469fa4d86f538637f80e9c660823d358bb7ddfd651291dc5df73450 SHA512 dab4832317c8dc6a794ffc9fb118124734fa2428c0527eb9c86bc3d35195a34bdb162bc0a44a3604cb8067fff7263ab5b106c0f9871007a093e7185df5ba9993 +DIST neo-0.11.1.tar.gz 3906151 BLAKE2B 26b60c715d6f3ec017cdb909c1f54b1509db4862f0630ab6d60b4b07153d5cb8512fbf16dd9039d1998b08e0f9e828bb271d4f482cc2d34a5d17a010ef4d203b SHA512 1f93a9eea020ee40f792f038bef76e053ff4f6e05951f78afa70bf4009bac3da8222be57c2cee88ae5e7539c5c8978cf50bf52cce787dbacafe6d5450d5e1aa7 diff --git a/dev-python/neo/metadata.xml b/dev-python/neo/metadata.xml new file mode 100644 index 000000000..5a50da2a7 --- /dev/null +++ b/dev-python/neo/metadata.xml @@ -0,0 +1,23 @@ +<?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"> + Neo is a Python package for working with electrophysiology data in Python, + together with support for reading a wide range of neurophysiology file + formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, + Plexon, Tdt, and support for writing to a subset of these formats plus + non-proprietary formats including HDF5. + </longdescription> + <upstream> + <remote-id type="github">NeuralEnsemble/python-neo</remote-id> + <remote-id type="pypi">neo</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/neo/neo-0.11.0.ebuild b/dev-python/neo/neo-0.11.0.ebuild new file mode 100644 index 000000000..c66b2b951 --- /dev/null +++ b/dev-python/neo/neo-0.11.0.ebuild @@ -0,0 +1,62 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +MY_PN="python-neo" + +DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python" +HOMEPAGE="https://github.com/NeuralEnsemble/python-neo" +SRC_URI="https://github.com/NeuralEnsemble/python-neo/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/quantities[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + ${RDEPEND} + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/datalad[${PYTHON_USEDEP}] + ) +" +# Testing deps also need: +# igor +# pyedflib https://github.com/holgern/pyedflib +# klusta +# nixio +# sonpy +# ipython + +S="${WORKDIR}/${MY_PN}-${PV}" + +distutils_enable_tests pytest + +EPYTEST_DESELECT=( + neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset +) + +# Reported upstream +# https://github.com/NeuralEnsemble/python-neo/issues/1037 +python_test() { + local EPYTEST_IGNORE=( + neo/test/iotest/* + neo/test/rawiotest/* + ) + epytest +} diff --git a/dev-python/neo/neo-0.11.1.ebuild b/dev-python/neo/neo-0.11.1.ebuild new file mode 100644 index 000000000..c7a36d0e3 --- /dev/null +++ b/dev-python/neo/neo-0.11.1.ebuild @@ -0,0 +1,55 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python" +HOMEPAGE="https://github.com/NeuralEnsemble/python-neo" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +#SRC_URI="https://github.com/NeuralEnsemble/python-neo/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/quantities[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + ${RDEPEND} + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/datalad[${PYTHON_USEDEP}] + ) +" +# Testing deps also need: +# igor +# pyedflib https://github.com/holgern/pyedflib +# klusta +# nixio +# sonpy +# ipython + +distutils_enable_tests pytest + +# Reported upstream +# https://github.com/NeuralEnsemble/python-neo/issues/1037 +python_test() { + local EPYTEST_IGNORE=( + neo/test/iotest/* + neo/test/rawiotest/* + ) + epytest +} diff --git a/dev-python/num2words/metadata.xml b/dev-python/num2words/metadata.xml index aaa27d18e..f3e4e8fcd 100644 --- a/dev-python/num2words/metadata.xml +++ b/dev-python/num2words/metadata.xml @@ -16,6 +16,7 @@ (although this last feature is a bit buggy for some languages at the moment). </longdescription> <upstream> - <remote-id type="github">savoirefairelinux/num2words</remote-id> + <remote-id type="github">savoirfairelinux/num2words</remote-id> + <remote-id type="pypi">num2words</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/num2words/num2words-0.5.10.ebuild b/dev-python/num2words/num2words-0.5.10.ebuild index e846480bd..78a73cb5e 100644 --- a/dev-python/num2words/num2words-0.5.10.ebuild +++ b/dev-python/num2words/num2words-0.5.10.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/dev-python/numba-dpex/Manifest b/dev-python/numba-dpex/Manifest new file mode 100644 index 000000000..5286ff524 --- /dev/null +++ b/dev-python/numba-dpex/Manifest @@ -0,0 +1 @@ +DIST numba-dpex-0.20.0_rc3.gh.tar.gz 237831 BLAKE2B 69e1f133f6f015139d37258eac039380a14b139acaee010f66af233e34702f9f5d8a27070c34a917c0c3f40950070c948c609f6d8e40d429e55e1d83c9569f8c SHA512 3f381c0719ca6fad380b1f3729ec77caa47bb3e097d842e8fab1b82627e1f9b5d6905b3eb9682d80977ac745335a7bab20849b883f12fdc77f1ffb3ab9a706e8 diff --git a/dev-python/numba-dpex/metadata.xml b/dev-python/numba-dpex/metadata.xml new file mode 100644 index 000000000..c98aa52a0 --- /dev/null +++ b/dev-python/numba-dpex/metadata.xml @@ -0,0 +1,12 @@ +<?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">IntelPython/numba-dpex</remote-id> + <remote-id type="pypi">numba-dpex</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild b/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild new file mode 100644 index 000000000..a3b63bf1f --- /dev/null +++ b/dev-python/numba-dpex/numba-dpex-0.20.0_rc3.ebuild @@ -0,0 +1,41 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Data Parallel Extension for Numba" +HOMEPAGE="https://github.com/IntelPython/numba-dpex" +SRC_URI="https://github.com/IntelPython/numba-dpex/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN}-${PV//_rc/dev}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/dpctl[${PYTHON_USEDEP}] + dev-python/dpnp[${PYTHON_USEDEP}] + dev-python/numba[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +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" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest index ded0ae03c..7f3f072b4 100644 --- a/dev-python/numba/Manifest +++ b/dev-python/numba/Manifest @@ -1 +1,2 @@ DIST numba-0.56.3.tar.gz 2492552 BLAKE2B a8a3070ef6ca709594f308c751700a8c2cae1077c15b12291632a2022ca47460af245f02253555f4dfd4a93ef179c262baa36127b135158e48d60783f2ee0bb4 SHA512 42a1d9007ff89a58a79a80743e883e013a7a53b5035e1754b4c9f1ec715834a036eee32bff42ab0aa89132a7b6cb15decd9e918a9e49c42ce5a024e10ece3169 +DIST numba-0.56.4.gh.tar.gz 2492671 BLAKE2B c4669d15861bfea3d0fd187df9d2d4264a4b0c440fd5d46203f0494f3282ec89116fa31763550ce9593694bf2b264d6b086d206ced4aacb653d0910d2baa15d3 SHA512 15ed581cb34be30711e64e54289a29d845ceb841f8341bbbdac4d4cb7fa7cebfd4409cac7f0e0f5b1164c9bd142897b90761529ef3ad1c198a00d16ada38942e diff --git a/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch b/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch new file mode 100644 index 000000000..07c1b5d88 --- /dev/null +++ b/dev-python/numba/files/numba-0.56.4-allow-py3.11.patch @@ -0,0 +1,13 @@ +diff --git a/setup.py b/setup.py +index 68feca4..1d254ec 100644 +--- a/setup.py ++++ b/setup.py +@@ -20,7 +20,7 @@ except ImportError: + + + min_python_version = "3.7" +-max_python_version = "3.11" # exclusive ++max_python_version = "3.12" # exclusive + min_numpy_build_version = "1.11" + min_numpy_run_version = "1.18" + max_numpy_run_version = "1.24" diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml index 43b02aeec..63bc398e0 100644 --- a/dev-python/numba/metadata.xml +++ b/dev-python/numba/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="github">numba/numba</remote-id> + <remote-id type="pypi">numba</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/numba/numba-0.56.3.ebuild b/dev-python/numba/numba-0.56.3.ebuild index 9644fdf54..85fb09a85 100644 --- a/dev-python/numba/numba-0.56.3.ebuild +++ b/dev-python/numba/numba-0.56.3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=setuptools inherit optfeature multiprocessing distutils-r1 @@ -31,7 +31,7 @@ BDEPEND=" " distutils_enable_tests unittest -distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme +distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx-rtd-theme PATCHES=( "${FILESDIR}/${PN}-0.52.0-skip_tests.patch" diff --git a/dev-python/numba/numba-0.56.4.ebuild b/dev-python/numba/numba-0.56.4.ebuild new file mode 100644 index 000000000..3fcfd4a94 --- /dev/null +++ b/dev-python/numba/numba-0.56.4.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# py3.11 fails to compile: +# error: ‘CFrame’ does not name a type; did you mean ‘_frame’? +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit optfeature multiprocessing distutils-r1 + +DESCRIPTION="NumPy aware dynamic Python compiler using LLVM" +HOMEPAGE="https://numba.pydata.org/ + https://github.com/numba" +SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~arm64 ~x86" +IUSE="openmp threads" + +RDEPEND=" + >=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}] + <=dev-python/llvmlite-0.40.0 + >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] + <dev-python/numpy-1.24[${PYTHON_USEDEP}] + threads? ( >=dev-cpp/tbb-2021.1 <dev-cpp/tbb-2021.6 ) +" +BDEPEND=" + dev-python/pip[${PYTHON_USEDEP}] + dev-python/versioneer[${PYTHON_USEDEP}] +" + +distutils_enable_tests unittest +distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx-rtd-theme + +PATCHES=( + "${FILESDIR}/${PN}-0.52.0-skip_tests.patch" + "${FILESDIR}/${PN}-0.56.4-allow-py3.11.patch" +) + +pkg_setup() { + if ! use openmp; then + export NUMBA_DISABLE_OPENMP=1 || die + else + unset NUMBA_DISABLE_OPENMP || die + fi + if ! use threads; then + export NUMBA_DISABLE_TBB=1 || die + else + unset NUMBA_DISABLE_TBB || die + export TBBROOT="${EPREFIX}/usr" || die + fi +} + +python_prepare_all() { + # This conf.py only works in a git repo + if use doc; then + git init -q || die + git config user.email "larry@gentoo.org" || die + git config user.name "Larry the Cow" || die + git add . || die + git commit -m "init" || die + fi + distutils-r1_python_prepare_all +} + +python_compile() { + # FIXME: parallel python building fails. See Portage bug #614464 and + # gentoo/sci issue #1080. + export MAKEOPTS=-j1 || die + distutils-r1_python_compile +} + +# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests +python_test() { + ${EPYTHON} setup.py build_ext --inplace || die \ + "${EPYTHON} failed to build_ext" + ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \ + "${EPYTHON} failed unittests" +} + +pkg_postinst() { + optfeature "compile cuda code" dev-util/nvidia-cuda-sdk +} diff --git a/dev-python/numcodecs/numcodecs-0.10.0.ebuild b/dev-python/numcodecs/numcodecs-0.10.0.ebuild index 7219b5b7b..b2030d332 100644 --- a/dev-python/numcodecs/numcodecs-0.10.0.ebuild +++ b/dev-python/numcodecs/numcodecs-0.10.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Data storage buffer compression and transformation codecs" diff --git a/dev-python/numcodecs/numcodecs-0.9.0.ebuild b/dev-python/numcodecs/numcodecs-0.9.0.ebuild index 7219b5b7b..b2030d332 100644 --- a/dev-python/numcodecs/numcodecs-0.9.0.ebuild +++ b/dev-python/numcodecs/numcodecs-0.9.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Data storage buffer compression and transformation codecs" diff --git a/dev-python/numcodecs/numcodecs-0.9.1.ebuild b/dev-python/numcodecs/numcodecs-0.9.1.ebuild index 7219b5b7b..b2030d332 100644 --- a/dev-python/numcodecs/numcodecs-0.9.1.ebuild +++ b/dev-python/numcodecs/numcodecs-0.9.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Data storage buffer compression and transformation codecs" diff --git a/dev-python/numpy/Manifest b/dev-python/numpy/Manifest new file mode 100644 index 000000000..fdd711d83 --- /dev/null +++ b/dev-python/numpy/Manifest @@ -0,0 +1,4 @@ +DIST numpy-1.23.5.tar.gz 10731755 BLAKE2B d2ed6d359a51343a1618f64604e4d5c030115caa63f2aadf2fc150775630e40fbebaad28f5657faae1365264fd45bc9efb00854bf9cd393b7628c96d6fc87db9 SHA512 8f3ece76dbe79bc887275332d25f851ade2087de3026de5fb7ed793590b3e7d274f590357296e152373b4e9a245d4d563393ba7198bca6d44631b941acb89c2c +DIST numpy-html-1.23.5.zip 27964271 BLAKE2B 0aa26d7c39f2d6b119e404dfb9642967770881ee0d640157a9ed11d16f21cd43109bed3c08f89fda457ec470292d945e2bf8b2dab56e4b36192d5e8eb3757b44 SHA512 218a2e893816af767c7cedd1f2256e05f68e59491c29277c95de653a206aaff35c5fe3bc6afd6d6d5ea7957748ec565593eb30d004e36e94c894ea4a6884902a +DIST numpy-ref-1.23.5.pdf 7715485 BLAKE2B 7fbb0ce29e86fc7cd4932a6a9f0221b579b6cae695231edfebf863e5b4c2920796d802ccf9ae3e05b331964ac7c4f51099578d91b6b7fb357c6de2110a5f7cba SHA512 6036c6a36f332b83f371c7530a6ba6f354b1334d667d2a52993a1e52aa9d94d524e216f768928a006c717ed4b4131879f6e491a294ecfd3a0d1b0f9f937a887a +DIST numpy-user-1.23.5.pdf 4123384 BLAKE2B d4587c9f979e1ef4734768598d6e106f2b4b0c8222f901a6c4caf0920e41622201252c5bd172b16346e0357138b5ff27c59e56c851be5ae3b7712624bd9cc5b4 SHA512 58e1ab96d2cfbd96df205c86f0a1a09e204349f70d21df7f8481c21ded8b46f4b9ede3216d5cce6c2b9bfc0aacbecdfa198bdb2d4c258a0dd4acb6e3ba421f9c diff --git a/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch b/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch new file mode 100644 index 000000000..d87a16a4b --- /dev/null +++ b/dev-python/numpy/files/numpy-1.22.0-no-hardcode-blasv2.patch @@ -0,0 +1,50 @@ +Originally added in: https://gitweb.gentoo.org/repo/gentoo.git/commit/dev-python/numpy/files?id=e5ce90a04e79f6413604e96e4803cb95ada7c859 +https://bugs.gentoo.org/567938 +--- a/numpy/distutils/system_info.py ++++ b/numpy/distutils/system_info.py +@@ -505,33 +505,7 @@ def get_info(name, notfound_action=0): + 'blas_armpl': blas_armpl_info, + 'lapack_armpl': lapack_armpl_info, + 'fftw3_armpl': fftw3_armpl_info, +- 'atlas': atlas_info, # use lapack_opt or blas_opt instead +- 'atlas_threads': atlas_threads_info, # ditto +- 'atlas_blas': atlas_blas_info, +- 'atlas_blas_threads': atlas_blas_threads_info, +- 'lapack_atlas': lapack_atlas_info, # use lapack_opt instead +- 'lapack_atlas_threads': lapack_atlas_threads_info, # ditto +- 'atlas_3_10': atlas_3_10_info, # use lapack_opt or blas_opt instead +- 'atlas_3_10_threads': atlas_3_10_threads_info, # ditto +- 'atlas_3_10_blas': atlas_3_10_blas_info, +- 'atlas_3_10_blas_threads': atlas_3_10_blas_threads_info, +- 'lapack_atlas_3_10': lapack_atlas_3_10_info, # use lapack_opt instead +- 'lapack_atlas_3_10_threads': lapack_atlas_3_10_threads_info, # ditto +- 'flame': flame_info, # use lapack_opt instead +- 'mkl': mkl_info, +- # openblas which may or may not have embedded lapack +- 'openblas': openblas_info, # use blas_opt instead +- # openblas with embedded lapack +- 'openblas_lapack': openblas_lapack_info, # use blas_opt instead +- 'openblas_clapack': openblas_clapack_info, # use blas_opt instead +- 'blis': blis_info, # use blas_opt instead +- 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead +- 'blas_mkl': blas_mkl_info, # use blas_opt instead + 'accelerate': accelerate_info, # use blas_opt instead +- 'openblas64_': openblas64__info, +- 'openblas64__lapack': openblas64__lapack_info, +- 'openblas_ilp64': openblas_ilp64_info, +- 'openblas_ilp64_lapack': openblas_ilp64_lapack_info, + 'x11': x11_info, + 'fft_opt': fft_opt_info, + 'fftw': fftw_info, +@@ -951,10 +925,7 @@ class system_info: + return [b for b in [a.strip() for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): +- if hasattr(self, '_lib_names'): +- return self.get_libs(key, default=self._lib_names) +- else: +- return self.get_libs(key, '') ++ return self.get_libs(key, '') + + def library_extensions(self): + c = customized_ccompiler() diff --git a/dev-python/numpy/metadata.xml b/dev-python/numpy/metadata.xml new file mode 100644 index 000000000..26b229a9c --- /dev/null +++ b/dev-python/numpy/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="project"> + <email>python@gentoo.org</email> + <name>Python</name> + </maintainer> + <longdescription lang="en"> + NumPy is a general-purpose array-processing Python package designed to + efficiently manipulate large multi-dimensional arrays of arbitrary + records without sacrificing too much speed for small multi-dimensional + arrays. There are also basic facilities for discrete fourier transform, + basic linear algebra and random number generation. + It is the successor of Numeric and numarray. + </longdescription> + <upstream> + <remote-id type="github">numpy/numpy</remote-id> + <remote-id type="pypi">numpy</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/numpy/numpy-1.23.5.ebuild b/dev-python/numpy/numpy-1.23.5.ebuild new file mode 100644 index 000000000..51be775b9 --- /dev/null +++ b/dev-python/numpy/numpy-1.23.5.ebuild @@ -0,0 +1,187 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_REQ_USE="threads(+)" + +FORTRAN_NEEDED=lapack + +inherit distutils-r1 flag-o-matic fortran-2 toolchain-funcs + +DOC_PV=${PV} +# For when docs aren't ready yet, set to last version +#DOC_PV=1.23.0 +DESCRIPTION="Fast array and numerical python library" +HOMEPAGE=" + https://numpy.org/ + https://github.com/numpy/numpy/ + https://pypi.org/project/numpy/ +" +SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-html.zip -> numpy-html-${DOC_PV}.zip + https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-ref.pdf -> numpy-ref-${DOC_PV}.pdf + https://numpy.org/doc/$(ver_cut 1-2 ${DOC_PV})/numpy-user.pdf -> numpy-user-${DOC_PV}.pdf + ) +" +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha amd64 arm arm64 hppa ~ia64 ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~x64-solaris ~x86-solaris" +IUSE="doc lapack" + +RDEPEND=" + lapack? ( + >=virtual/cblas-3.8 + >=virtual/lapack-3.8 + ) +" +BDEPEND=" + ${RDEPEND} + >=dev-python/cython-0.29.30[${PYTHON_USEDEP}] + lapack? ( + virtual/pkgconfig + ) + doc? ( + app-arch/unzip + ) + test? ( + >=dev-python/hypothesis-5.8.0[${PYTHON_USEDEP}] + >=dev-python/pytz-2019.3[${PYTHON_USEDEP}] + >=dev-python/cffi-1.14.0[${PYTHON_USEDEP}] + ) +" + +PATCHES=( + "${FILESDIR}"/numpy-1.22.0-no-hardcode-blasv2.patch +) + +distutils_enable_tests pytest + +src_unpack() { + default + if use doc; then + unzip -qo "${DISTDIR}"/numpy-html-${DOC_PV}.zip -d html || die + fi +} + +python_prepare_all() { + # Allow use with setuptools 60.x + # See numpy-1.22.1-revert-setuptools-upper-bound.patch for details + export SETUPTOOLS_USE_DISTUTILS=stdlib + + if use lapack; then + local incdir="${EPREFIX}"/usr/include + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF || die + [blas] + include_dirs = ${incdir} + library_dirs = ${libdir} + blas_libs = cblas,blas + [lapack] + library_dirs = ${libdir} + lapack_libs = lapack + EOF + else + export {ATLAS,PTATLAS,BLAS,LAPACK,MKL}=None + fi + + export CC="$(tc-getCC) ${CFLAGS}" + + append-flags -fno-strict-aliasing + + # See progress in http://projects.scipy.org/scipy/numpy/ticket/573 + # with the subtle difference that we don't want to break Darwin where + # -shared is not a valid linker argument + if [[ ${CHOST} != *-darwin* ]]; then + append-ldflags -shared + fi + + # only one fortran to link with: + # linking with cblas and lapack library will force + # autodetecting and linking to all available fortran compilers + append-fflags -fPIC + if use lapack; then + NUMPY_FCONFIG="config_fc --noopt --noarch" + # workaround bug 335908 + [[ $(tc-getFC) == *gfortran* ]] && NUMPY_FCONFIG+=" --fcompiler=gnu95" + fi + + # don't version f2py, we will handle it. + sed -i -e '/f2py_exe/s: + os\.path.*$::' numpy/f2py/setup.py || die + + distutils-r1_python_prepare_all +} + +python_compile() { + export MAKEOPTS=-j1 #660754 + + distutils-r1_python_compile ${NUMPY_FCONFIG} +} + +python_test() { + local EPYTEST_DESELECT=( + # very disk- and memory-hungry + numpy/lib/tests/test_io.py::test_large_zip + + # precision problems + numpy/core/tests/test_umath_accuracy.py::TestAccuracy::test_validate_transcendentals + + # runs the whole test suite recursively, that's just crazy + numpy/core/tests/test_mem_policy.py::test_new_policy + + # very slow, unlikely to be practically useful + numpy/typing/tests/test_typing.py + ) + + if use arm && [[ $(uname -m || echo "unknown") == "armv8l" ]] ; then + # Degenerate case. arm32 chroot on arm64. + # bug #774108 + EPYTEST_DESELECT+=( + numpy/core/tests/test_cpu_features.py::Test_ARM_Features::test_features + ) + fi + + if use x86 ; then + EPYTEST_DESELECT+=( + # https://github.com/numpy/numpy/issues/18388 + numpy/core/tests/test_umath.py::TestRemainder::test_float_remainder_overflow + # https://github.com/numpy/numpy/issues/18387 + numpy/random/tests/test_generator_mt19937.py::TestRandomDist::test_pareto + # more precision problems + numpy/core/tests/test_einsum.py::TestEinsum::test_einsum_sums_int16 + ) + fi + if use arm || use x86 ; then + EPYTEST_DESELECT+=( + # too large for 32-bit platforms + numpy/core/tests/test_ufunc.py::TestUfunc::test_identityless_reduction_huge_array + ) + fi + + distutils_install_for_testing --single-version-externally-managed \ + --record "${TMPDIR}/record.txt" ${NUMPY_FCONFIG} + + cd "${TEST_DIR}/lib" || die + epytest -k "not _fuzz" +} + +python_install() { + # https://github.com/numpy/numpy/issues/16005 + local mydistutilsargs=( build_src ) + distutils-r1_python_install ${NUMPY_FCONFIG} + python_optimize +} + +python_install_all() { + local DOCS=( LICENSE.txt README.md THANKS.txt ) + + if use doc; then + local HTML_DOCS=( "${WORKDIR}"/html/. ) + DOCS+=( "${DISTDIR}"/${PN}-{user,ref}-${DOC_PV}.pdf ) + fi + + distutils-r1_python_install_all +} diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest index a414f7e1f..78267d7a8 100644 --- a/dev-python/nwbinspector/Manifest +++ b/dev-python/nwbinspector/Manifest @@ -1,4 +1,3 @@ -DIST nwbinspector-0.3.9.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e -DIST nwbinspector-0.4.12.tar.gz 455926 BLAKE2B 4bb8b493367593fdd575535e574b8494980a60a6ed1983a08f895c106e03e25ad6cd76b6c72cfcc42a34778d5059c90940bc9907dc9d87569df79aeae1698135 SHA512 60bb799beaff61612e7993069a34f62e0b6053dc3e820474f33c020c02f8c7b11bed0bca7e2bb335edfd60b06159be90b1a50dfcd497f6a3fb0916dc49cf17b7 -DIST nwbinspector-0.4.14.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa +DIST nwbinspector-0.4.14.gh.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa DIST nwbinspector-0.4.19.gh.tar.gz 570101 BLAKE2B f3950a8e24225fe490a6454ab5cd429bcb741eeee9cf12591089508600d283b4242ef70427e116960d16367e16c6d5a5869cfcedd829500ce920387d8ebca916 SHA512 3ecd7d1db1d53c0ec5db986a211e56b4818c165a376d15e7a79ede9c8ca45560b6f302e3c9b1e960153d632bfa759660be4e44540399e272be3728d76fd52a7c +DIST nwbinspector-0.4.26.gh.tar.gz 575576 BLAKE2B 5ec888fc578dd0225b346426b93193f1a08cf92fa9c11e7653773c6bd74603c9e3456514209b3e2a12cf9d868f6004b64700c98212f3837b4b77096dff23ea72 SHA512 901df8422aa3b8666f01e9a6389c22f7caca30007494cb8680ee228bb58a9192f4f35a2426f38f068df5e938fe192db6db4d5626d00ca96e766114dd301efce3 diff --git a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild deleted file mode 100644 index e248266d4..000000000 --- a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" -HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector" -SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="" -RDEPEND=" - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/natsort[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] -" -BDEPEND="" - -distutils_enable_tests pytest diff --git a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild index a2b20f5af..5f5bc2045 100644 --- a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild +++ b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild @@ -1,15 +1,15 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2022-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector" -SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild index f18fc135f..a80527994 100644 --- a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild +++ b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild @@ -1,10 +1,10 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2022-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" diff --git a/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild index a2b20f5af..46f158e0e 100644 --- a/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild +++ b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild @@ -1,15 +1,15 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2022-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector" -SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" @@ -20,6 +20,7 @@ RESTRICT="!test? ( test )" DEPEND="" RDEPEND=" dev-python/click[${PYTHON_USEDEP}] + dev-python/isodate[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/natsort[${PYTHON_USEDEP}] dev-python/pynwb[${PYTHON_USEDEP}] @@ -29,11 +30,3 @@ RDEPEND=" BDEPEND="" distutils_enable_tests pytest - -python_test() { - local EPYTEST_IGNORE=( - tests/test_inspector.py - tests/unit_tests/test_time_series.py - ) - epytest -} diff --git a/dev-python/panel/Manifest b/dev-python/panel/Manifest index dacf388f1..5bd9272be 100644 --- a/dev-python/panel/Manifest +++ b/dev-python/panel/Manifest @@ -1 +1,3 @@ DIST panel-0.11.0.tar.gz 9682808 BLAKE2B 2f953aaa9e791433d254219ad3cf9efdd486164e713f41a3539628a6c87f5b7b800ebd166537d021799ce74dddd3bc259343e6ec4161d0d87393864502215a00 SHA512 6fa2e04dd758583db851fa7d36592b7fb10ad2838b1f51fb53cb9ead4b5504a975ca040525f3f210ff0a67e8ce579195d980570b2d7616308cc126c61a9e9f59 +DIST panel-0.14.1.tar.gz 20052944 BLAKE2B 225c42562f7b5922380eca6f58da38ef228dbcb46ada930f7e0423fe2ce0d81d23d026b3f375a5bd46b521f6e49293f861cf92bc4d5044414818e0e1f787b0de SHA512 4d730a4555fffcb543b22900a17ad377eadb36a890ecc6cf873726da12c067d1cfeaf9626a0e4559b5c08e5646abb5c5cc0f28201341d9989f2c8fb345f8ecbd +DIST panel-0.14.2.tar.gz 20352366 BLAKE2B 429a2da7e92cc1b0f3a42fc120eddc4a8a54e3805c1ca249aad7c243cef0092959e62a13b0f9c64c4765a6d2533b6519a90640e85d4d512a257df40fff1a4522 SHA512 c611e4bc592edeca5920441102cf7baea336016b9f90778c05fc61c57a4b8b48c80e16c182daa1763440be10c6a0ffabb80699bf6aaa96e03566b4ac55b56f4b diff --git a/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch new file mode 100644 index 000000000..387cfb61b --- /dev/null +++ b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch @@ -0,0 +1,47 @@ +Subject: Prevent Panel from violating network sandboxing. + + * By default, "setup.py" invokes "npm" to rebuild Node.js packages bundled with Panel. + * Without this patch we get `error: HTTPSConnectionPool` + * A `sed` fix of the `_build_paneljs()` line will break the syntax. + * Using the `PANEL_LITE_BUILD` variable might do the trick instead of a patch, but thus far it didn't +Author: Horea Christian <gentoo@chymera.eu> +diff --git a/setup.py b/setup.py +index d2541dfb..8cfbf933 100644 +--- a/setup.py ++++ b/setup.py +@@ -54,8 +54,6 @@ class CustomDevelopCommand(develop): + """Custom installation for development mode.""" + + def run(self): +- if not PANEL_LITE_BUILD: +- _build_paneljs() + develop.run(self) + + +@@ -63,8 +61,6 @@ class CustomInstallCommand(install): + """Custom installation for install mode.""" + + def run(self): +- if not PANEL_LITE_BUILD: +- _build_paneljs() + install.run(self) + + +@@ -72,8 +68,6 @@ class CustomSdistCommand(sdist): + """Custom installation for sdist mode.""" + + def run(self): +- if not PANEL_LITE_BUILD: +- _build_paneljs() + sdist.run(self) + + +@@ -92,8 +86,6 @@ try: + + def run(self): + """Do nothing so the command intentionally fails.""" +- if not PANEL_LITE_BUILD: +- _build_paneljs() + bdist_wheel.run(self) + + _COMMANDS['bdist_wheel'] = CustomBdistWheelCommand diff --git a/dev-python/panel/panel-0.11.0.ebuild b/dev-python/panel/panel-0.11.0.ebuild index 594377dcd..072c763ad 100644 --- a/dev-python/panel/panel-0.11.0.ebuild +++ b/dev-python/panel/panel-0.11.0.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..10} ) # Panel imports from "distutils" at runtime. DISTUTILS_USE_SETUPTOOLS=rdepend diff --git a/dev-python/panel/panel-0.14.1.ebuild b/dev-python/panel/panel-0.14.1.ebuild new file mode 100644 index 000000000..aa535f46f --- /dev/null +++ b/dev-python/panel/panel-0.14.1.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) + +# Panel imports from "distutils" at runtime. +DISTUTILS_USE_SETUPTOOLS=rdepend + +inherit distutils-r1 + +DESCRIPTION="High-level app and dashboarding solution for Python" +HOMEPAGE="https://panel.holoviz.org" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that +# away below. Our patched Panel thus requires Bokeh only at runtime. +DEPEND=" + >=dev-python/param-1.10.0[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND} + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + >=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}] + >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] + >=net-libs/nodejs-15.11.0 +" + +PATCHES=( "${FILESDIR}/${P}-disable_lite_build.patch" ) + +src_prepare() { + # Install Jupyter configuration files to "/etc" rather than "/usr/etc". + sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die + + default_src_prepare +} + +pkg_postinst() { + panel_pkg_postinst() { + PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')" + elog "Node.js packages bundled with Panel under ${EPYTHON} may be" + elog "desynchronized from Bokeh and require manual rebuilding with:" + elog " sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\"" + elog + } + + python_foreach_impl panel_pkg_postinst +} diff --git a/dev-python/panel/panel-0.14.2.ebuild b/dev-python/panel/panel-0.14.2.ebuild new file mode 100644 index 000000000..866110947 --- /dev/null +++ b/dev-python/panel/panel-0.14.2.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) + +# Panel imports from "distutils" at runtime. +DISTUTILS_USE_SETUPTOOLS=rdepend + +inherit distutils-r1 + +DESCRIPTION="High-level app and dashboarding solution for Python" +HOMEPAGE="https://panel.holoviz.org" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that +# away below. Our patched Panel thus requires Bokeh only at runtime. +DEPEND=" + >=dev-python/param-1.10.0[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND} + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + >=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}] + >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] + >=net-libs/nodejs-15.11.0 +" + +PATCHES=( "${FILESDIR}/${PN}-0.14.1-disable_lite_build.patch" ) + +# This does not work, need to patch.. +#export PANEL_LITE_BUILD=1 + +src_prepare() { + # Install Jupyter configuration files to "/etc" rather than "/usr/etc". + sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die + + default_src_prepare +} + +# This also does not work, still need patch :( +#src_compile() { +# export PANEL_LITE_BUILD=1 +# distutils-r1_src_compile +#} + +pkg_postinst() { + panel_pkg_postinst() { + PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')" + elog "Node.js packages bundled with Panel under ${EPYTHON} may be" + elog "desynchronized from Bokeh and require manual rebuilding with:" + elog " sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\"" + elog + } + + python_foreach_impl panel_pkg_postinst +} diff --git a/dev-python/param/Manifest b/dev-python/param/Manifest index bec3c8061..d26e110b2 100644 --- a/dev-python/param/Manifest +++ b/dev-python/param/Manifest @@ -1 +1,2 @@ -DIST param-1.10.1.tar.gz 74216 BLAKE2B 98486a386b31f400647fa3da3d280867935a0e5c493de4b31dccfa7c5650a3b55e2590e09cbf15097d700e54dbdd33fda12ead4489ed745977ec0065b27735da SHA512 8f4693651b1abd12126248e1508b0bed7796a1a4d33cd0ed05cc1e176d1216f9bc504f8637220a92585e7682f2d0ad2600a5b24427702536d4ef679971e9c4a7 +DIST param-1.10.1.gh.tar.gz 132562 BLAKE2B ec4f8f6fada02aa91049cc665efddc75ab289a4f86cbd8951d9720c8174b5236415df884e630ede57b76d01da62b477a5db50b97cb46d04d46e37503ec0410a0 SHA512 ca035325829bbb9fdcfadc8fabac8d5a690e38b0942d30d8963f14259f0dc8ebeeba84723904aae8804898f6ea6d5cfa97d2a1103db29f0d6d3355577abe8d14 +DIST param-1.12.3.gh.tar.gz 460593 BLAKE2B 45e004f4df4d70ceb3d5ff654e260d2fdb28cd47c904408ccda86233502464907bc2e709840b060189a81242f348d3cd6e3f021a157be67962365f93a0b08327 SHA512 c7181dfb7ccffaab7521744566d601470678dc35a2ecd9b55fc5adda73a7cd4998f583f4a7b5930a5c811913cd5a9f2152fbc270a541b749c32b0901985cead2 diff --git a/dev-python/param/param-1.10.1.ebuild b/dev-python/param/param-1.10.1.ebuild index 3be942fe3..8e8ec8053 100644 --- a/dev-python/param/param-1.10.1.ebuild +++ b/dev-python/param/param-1.10.1.ebuild @@ -1,16 +1,22 @@ -# 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} pypy3 ) +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters" HOMEPAGE="https://param.holoviz.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +# Pypi sources do not include tests +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" KEYWORDS="~amd64 ~x86" SLOT="0" + +# Some tests require nose: +#distutils_enable_tests unittest diff --git a/dev-python/param/param-1.12.3.ebuild b/dev-python/param/param-1.12.3.ebuild new file mode 100644 index 000000000..9ce9e3762 --- /dev/null +++ b/dev-python/param/param-1.12.3.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters" +HOMEPAGE="https://param.holoviz.org" +# Pypi sources do not include tests, reported upstream: +# https://github.com/holoviz/param/issues/678 +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" +SLOT="0" + +distutils_enable_tests pytest diff --git a/dev-python/persim/metadata.xml b/dev-python/persim/metadata.xml index 2f2c0b51c..ea34f9f89 100644 --- a/dev-python/persim/metadata.xml +++ b/dev-python/persim/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">persim</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/persim/persim-0.1.3.ebuild b/dev-python/persim/persim-0.1.3.ebuild index 722ae4d39..e8aad47df 100644 --- a/dev-python/persim/persim-0.1.3.ebuild +++ b/dev-python/persim/persim-0.1.3.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -24,3 +25,13 @@ RDEPEND="${PYTHON_DEPS} " distutils_enable_tests pytest + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/scikit-tda/persim/issues/64 + test/test_persim.py::test_integer_diagrams + test/test_persim.py::TestEmpty::test_empyt_diagram_list + test/test_persim.py::TestTransforms::test_lists_of_lists + test/test_persim.py::TestTransforms::test_n_pixels + test/test_persim.py::TestTransforms::test_multiple_diagrams +) diff --git a/dev-python/persim/persim-0.2.0.ebuild b/dev-python/persim/persim-0.2.0.ebuild index 8ca453bf9..792839a0b 100644 --- a/dev-python/persim/persim-0.2.0.ebuild +++ b/dev-python/persim/persim-0.2.0.ebuild @@ -1,9 +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} ) +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -24,3 +25,20 @@ RDEPEND="${PYTHON_DEPS} " distutils_enable_tests pytest + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/scikit-tda/persim/issues/65 + test/test_persim.py::test_integer_diagrams + test/test_persim.py::TestEmpty::test_empyt_diagram_list + test/test_persim.py::TestTransforms::test_lists_of_lists + test/test_persim.py::TestTransforms::test_n_pixels + test/test_persim.py::TestTransforms::test_multiple_diagrams + test/test_persistence_imager.py::test_empty_diagram_list + test/test_persistence_imager.py::test_fit_diagram + test/test_persistence_imager.py::test_fit_diagram_list + test/test_persistence_imager.py::test_mixed_pairs + test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists + test/test_persistence_imager.py::TestTransformOutput::test_n_pixels + test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams +) diff --git a/dev-python/persim/persim-0.3.0.ebuild b/dev-python/persim/persim-0.3.0.ebuild index 6e1d989aa..91b9514ad 100644 --- a/dev-python/persim/persim-0.3.0.ebuild +++ b/dev-python/persim/persim-0.3.0.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -26,3 +27,21 @@ RDEPEND="${PYTHON_DEPS} BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )" distutils_enable_tests pytest + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/scikit-tda/persim/issues/66 + test/test_landscapes.py::TestPersLandscapeExact::test_exact_critical_pairs + test/test_persim.py::test_integer_diagrams + test/test_persim.py::TestEmpty::test_empyt_diagram_list + test/test_persim.py::TestTransforms::test_lists_of_lists + test/test_persim.py::TestTransforms::test_n_pixels + test/test_persim.py::TestTransforms::test_multiple_diagrams + test/test_persistence_imager.py::test_empty_diagram_list + test/test_persistence_imager.py::test_fit_diagram + test/test_persistence_imager.py::test_fit_diagram_list + test/test_persistence_imager.py::test_mixed_pairs + test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists + test/test_persistence_imager.py::TestTransformOutput::test_n_pixels + test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams +) diff --git a/dev-python/persim/persim-0.3.1.ebuild b/dev-python/persim/persim-0.3.1.ebuild index 6e1d989aa..78b86d6ea 100644 --- a/dev-python/persim/persim-0.3.1.ebuild +++ b/dev-python/persim/persim-0.3.1.ebuild @@ -1,21 +1,21 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Distances and representations of persistence diagrams" HOMEPAGE="https://persim.scikit-tda.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="${PYTHON_DEPS} +RDEPEND=" dev-python/hopcroftkarp[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] @@ -26,3 +26,21 @@ RDEPEND="${PYTHON_DEPS} BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )" distutils_enable_tests pytest + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/scikit-tda/persim/issues/66 + test/test_landscapes.py::TestPersLandscapeExact::test_exact_critical_pairs + test/test_persim.py::test_integer_diagrams + test/test_persim.py::TestEmpty::test_empyt_diagram_list + test/test_persim.py::TestTransforms::test_lists_of_lists + test/test_persim.py::TestTransforms::test_n_pixels + test/test_persim.py::TestTransforms::test_multiple_diagrams + test/test_persistence_imager.py::test_empty_diagram_list + test/test_persistence_imager.py::test_fit_diagram + test/test_persistence_imager.py::test_fit_diagram_list + test/test_persistence_imager.py::test_mixed_pairs + test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists + test/test_persistence_imager.py::TestTransformOutput::test_n_pixels + test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams +) diff --git a/dev-python/photutils/Manifest b/dev-python/photutils/Manifest index bbd7ab4a7..00cdad6e8 100644 --- a/dev-python/photutils/Manifest +++ b/dev-python/photutils/Manifest @@ -1 +1 @@ -DIST photutils-1.0.1.tar.gz 995604 BLAKE2B 552e66cfb20db193da97da570dfd6116eb6674b38c1510393c35e6929a7b9717ee75ecf06cfe874a628b6e096a57bd68ebc79a3f52c5ef94ef384e03e2543784 SHA512 3abcace35fde3b8c4de99c56afe813db50bde87bf1aeda65b1b37edf7c9409420f3aa62bd6b98ae4f381542c1fd3aff100b19220f6a7210f2a0c06f8a039f1b5 +DIST photutils-1.6.0.tar.gz 1062334 BLAKE2B dd694299ab52e561f3ba419bd3f2329d73017cefd2ab84dcd278dd93b290fb45457ccc6b9bd0cac769f0bce9a4e3ddd15c097a8345fc5a63af52b5c9aa577f4c SHA512 6d7e20f032f7417cedaaf29692b790a597b1a0e8a2d4e25605c2e598e6908de7e1a76e075f02cb1f281df586d9e6d45d0d61bc16eb3996c41568c9d1478725ed diff --git a/dev-python/photutils/metadata.xml b/dev-python/photutils/metadata.xml index 5c3d380b2..8069e65c7 100644 --- a/dev-python/photutils/metadata.xml +++ b/dev-python/photutils/metadata.xml @@ -12,5 +12,6 @@ centroid and shape parameters, and performing photometry. </longdescription> <upstream> <remote-id type="github">astropy/photutils</remote-id> + <remote-id type="pypi">photutils</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/photutils/photutils-1.0.1.ebuild b/dev-python/photutils/photutils-1.6.0.ebuild index ac34ff93a..b2ea8d831 100644 --- a/dev-python/photutils/photutils-1.0.1.ebuild +++ b/dev-python/photutils/photutils-1.6.0.ebuild @@ -1,15 +1,15 @@ # Copyright 1999-2021 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} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Affiliated package for image photometry utilities" HOMEPAGE="https://github.com/astropy/photutils" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest index b2c8e3956..7d88bcad7 100644 --- a/dev-python/probeinterface/Manifest +++ b/dev-python/probeinterface/Manifest @@ -1,3 +1,3 @@ DIST probeinterface-0.2.11.gh.tar.gz 194474 BLAKE2B 806d1d83a47fdd3a3196386d08ac5cee7f8561547be819fe814f67265e5b1e31e35107a047ed5c5ae533123b318ab6dca4b37ec8ddb6d30431644402b499b5d2 SHA512 a7e12fba55b952dea3b062dde37178b02259424ec82f788bb210a94cf7fb48d325045f2451c3e764b68563948fe81b60d1d378827a15ae5470931b120b2bc10d DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2 -DIST probeinterface-0.2.5.gh.tar.gz 154572 BLAKE2B fdd339fdeec0c71f404fb96665b7d92db29d15f84163924d4508cbe17bf88b4a95e0296c48cf8f878034ed0ce3b249e750363ad32385b2e9d3e83900a760bebe SHA512 fdf170e1e4057445b0c8701105c7e6283258b460b1250e992f9896d6d3a0feacf3eb7dc6f8b35b77f591e1654930bd20d548758ea01b5d4cdb15a57dac24c4f9 +DIST probeinterface-0.2.16.gh.tar.gz 302386 BLAKE2B e2124774f2f50779f1dc67b682085d87691c935909ab81591f005abd756c0925837b97e97bf651e2a84e2276f57bf6fd1df6de6289431b16227dc9caa6cea51c SHA512 7c38534dbcab837df1289074db054e31c0768bceefafeb6d70051f88a6ac289d664d77cd6c456f40e7c52a7b60a09e80a4a4fe5e8f491121157b0bbb4d5c1f84 diff --git a/dev-python/probeinterface/probeinterface-0.2.11.ebuild b/dev-python/probeinterface/probeinterface-0.2.11.ebuild index d7751fe0d..15579b701 100644 --- a/dev-python/probeinterface/probeinterface-0.2.11.ebuild +++ b/dev-python/probeinterface/probeinterface-0.2.11.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Python package to handle probe layout, geometry and wiring to device" diff --git a/dev-python/probeinterface/probeinterface-0.2.14.ebuild b/dev-python/probeinterface/probeinterface-0.2.14.ebuild index ac66253b4..d3827a5e9 100644 --- a/dev-python/probeinterface/probeinterface-0.2.14.ebuild +++ b/dev-python/probeinterface/probeinterface-0.2.14.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Python package to handle probe layout, geometry and wiring to device" diff --git a/dev-python/probeinterface/probeinterface-0.2.5.ebuild b/dev-python/probeinterface/probeinterface-0.2.16.ebuild index d7751fe0d..d3827a5e9 100644 --- a/dev-python/probeinterface/probeinterface-0.2.5.ebuild +++ b/dev-python/probeinterface/probeinterface-0.2.16.ebuild @@ -4,12 +4,14 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Python package to handle probe layout, geometry and wiring to device" HOMEPAGE="https://github.com/SpikeInterface/probeinterface" SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145 +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/dev-python/py2bit/Manifest b/dev-python/py2bit/Manifest index 4b58d5605..afd79913c 100644 --- a/dev-python/py2bit/Manifest +++ b/dev-python/py2bit/Manifest @@ -1 +1,2 @@ DIST py2bit-0.3.0.tar.gz 16059 BLAKE2B b66621b91db8c0370933d1531c25e3e9d2cf34cc453e085f5acf92175f16bc4a87368d5b97f4ad1f6b0aeb715ac91e02f752f27d660e733cbcf9788f7fb9ff0b SHA512 914ee4490605a005c5c83e914e5d469dcb860a76cf52dd2337086954d9a37f21addca7a581eb8ff612b77f7969334057de4ab5d5ce2c6e15fb88e56abd36e193 +DIST py2bit-0.3.1.tar.gz 16771 BLAKE2B 044f6c638bc001694a5ee1c0924bebfeccd26616dbeb7f7a692df71dde6937851227d8a4263c9f0c4e44a34d53900340bdf95818aa2c9c699d26b36a75e64158 SHA512 e9cb16e6f617f5f9c4a324abc949562da8aa0b4792e7011148103462ec49f3f38ab29a2c1821a374ec99726c292de2888de506966510a10211ee24295e9f775c diff --git a/dev-python/py2bit/py2bit-0.3.0.ebuild b/dev-python/py2bit/py2bit-0.3.0.ebuild index 7c6c27ef2..4b1c29658 100644 --- a/dev-python/py2bit/py2bit-0.3.0.ebuild +++ b/dev-python/py2bit/py2bit-0.3.0.ebuild @@ -1,9 +1,10 @@ -# 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} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -23,3 +24,9 @@ SLOT="0" DEPEND="sci-libs/lib2bit" RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest "py2bitTest/test.py" +} diff --git a/dev-python/py2bit/py2bit-0.3.1.ebuild b/dev-python/py2bit/py2bit-0.3.1.ebuild new file mode 100644 index 000000000..4b1c29658 --- /dev/null +++ b/dev-python/py2bit/py2bit-0.3.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2023 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 library for accessing 2bit files" +HOMEPAGE="https://github.com/dpryan79/py2bit" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/py2bit" +else + SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="sci-libs/lib2bit" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest "py2bitTest/test.py" +} diff --git a/dev-python/py2bit/py2bit-9999.ebuild b/dev-python/py2bit/py2bit-9999.ebuild index 7c6c27ef2..4b1c29658 100644 --- a/dev-python/py2bit/py2bit-9999.ebuild +++ b/dev-python/py2bit/py2bit-9999.ebuild @@ -1,9 +1,10 @@ -# 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} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -23,3 +24,9 @@ SLOT="0" DEPEND="sci-libs/lib2bit" RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest "py2bitTest/test.py" +} diff --git a/dev-python/pyBigWig/Manifest b/dev-python/pyBigWig/Manifest index 96d66a343..b27a43a9b 100644 --- a/dev-python/pyBigWig/Manifest +++ b/dev-python/pyBigWig/Manifest @@ -1 +1,2 @@ DIST pyBigWig-0.3.17.tar.gz 65490 BLAKE2B 5ae3ad5792357ae36082022aa34548fb7ad105909eccc27305064f8f948714f462e1d239c3af7f9b75b84f5658bcb03231d7d1d3b0ebc8025c96d2e7835f1bfb SHA512 b52fec3a85984708660dd454f5569900a5cce7804d02e719bddbdc7ed2f9f4ab1131e55b0a01ae977b18bb0bbd079e13ec887d5df108d8abfebdd04ad56e503f +DIST pyBigWig-0.3.18.tar.gz 66478 BLAKE2B 0d2e20bed5f59fb8c79026f453c4d5c3e4f9b663e96614b3ef8cbb939357c8895edfa92184da018efdd40e14bbf357f13cc32f898d9cf89419382e7be89b01c8 SHA512 e782f059a8c47043498b2c4b1c0b63f3a1863d03f641c469995536bded220714c61fe0a2f1dbe5841152fe54d0d43b544e14ec4999447d4d808e01b452fa5e88 diff --git a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild index eaa5d5375..acaca2306 100644 --- a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild +++ b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild @@ -1,9 +1,10 @@ -# 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} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="quick access to and creation of bigWig files" diff --git a/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild new file mode 100644 index 000000000..acaca2306 --- /dev/null +++ b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2023 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="quick access to and creation of bigWig files" +HOMEPAGE="https://github.com/dpryan79/pyBigWig" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig" +else + SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="sci-biology/libBigWig" +RDEPEND="${DEPEND}" diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild index eaa5d5375..acaca2306 100644 --- a/dev-python/pyBigWig/pyBigWig-9999.ebuild +++ b/dev-python/pyBigWig/pyBigWig-9999.ebuild @@ -1,9 +1,10 @@ -# 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} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="quick access to and creation of bigWig files" diff --git a/dev-python/pyarrow/Manifest b/dev-python/pyarrow/Manifest new file mode 100644 index 000000000..6832ef69d --- /dev/null +++ b/dev-python/pyarrow/Manifest @@ -0,0 +1 @@ +DIST apache-arrow-11.0.0.tar.gz 19956186 BLAKE2B dff0faecbde9e2d19f092fd0c48a7ac7a401da6dbfd17f30af1b35c9e3fd3e1ba5611311f5bcb08383368de195cff783a178a9397a63a1c4f740a81349f8b8d3 SHA512 46df4fb5a703d38d0a74fde9838e9f9702b24b442cb225517516c335a5ab18955699000bf0b2fc7d1698ada6d2e890ba3860933b6280f5160b0fce8a07484d0e diff --git a/dev-python/pyarrow/metadata.xml b/dev-python/pyarrow/metadata.xml new file mode 100644 index 000000000..6c72ac84b --- /dev/null +++ b/dev-python/pyarrow/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>xgreenlandforwyy@gmail.com</email> + <name>Yiyang Wu</name> + </maintainer> + <use> + <flag name='dataset'>Build the arrow dataset modules</flag> + <flag name='parquet'>Enables read/write parquet data format</flag> + </use> +</pkgmetadata> diff --git a/dev-python/pyarrow/pyarrow-11.0.0.ebuild b/dev-python/pyarrow/pyarrow-11.0.0.ebuild new file mode 100644 index 000000000..857592359 --- /dev/null +++ b/dev-python/pyarrow/pyarrow-11.0.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2023 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 multiprocessing + +DESCRIPTION="Python library for Apache Arrow" +SRC_URI="mirror://apache/arrow/arrow-${PV}/apache-arrow-${PV}.tar.gz" +HOMEPAGE="https://arrow.apache.org/" + +IUSE="+parquet +dataset" +REQUIRED_USE="dataset? ( parquet )" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" +S="${WORKDIR}/apache-arrow-${PV}/python" +RESTRICT="test" # tests seems not working + +BDEPEND="dev-util/cmake" +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + ~dev-libs/apache-arrow-${PV}[csv,parquet?] +" +DEPEND="${RDEPEND}" + +src_compile() { + export PYARROW_WITH_PARQUET=$(usex parquet "ON" "") + export PYARROW_WITH_DATASET=$(usex dataset "ON" "") + local jobs=$(makeopts_jobs "${MAKEOPTS}" INF) + export PYARROW_PARALLEL="${jobs}" + export PYARROW_BUILD_VERBOSE="1" + export PYARROW_BUNDLE_ARROW_CPP_HEADERS=0 + export PYARROW_CMAKE_GENERATOR=Ninja + distutils-r1_src_compile +} diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild index f73f2dd4b..f983beb99 100644 --- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild +++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="PEP 561 type stubs generator for pybind11 modules" diff --git a/dev-python/pyct/pyct-0.4.8.ebuild b/dev-python/pyct/pyct-0.4.8.ebuild index f40dc6d49..6201e2cf2 100644 --- a/dev-python/pyct/pyct-0.4.8.ebuild +++ b/dev-python/pyct/pyct-0.4.8.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} pypy3 ) +PYTHON_COMPAT=( python3_{10..11} pypy3 ) # HoloViews imports from "distutils" at runtime. DISTUTILS_USE_SETUPTOOLS=rdepend diff --git a/dev-python/pyerfa/metadata.xml b/dev-python/pyerfa/metadata.xml index 4f4367037..5615e25d7 100644 --- a/dev-python/pyerfa/metadata.xml +++ b/dev-python/pyerfa/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">liberfa/pyerfa</remote-id> + <remote-id type="pypi">pyerfa</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild index 2e5bdf3e0..b52026473 100644 --- a/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild +++ b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild @@ -3,30 +3,30 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Python bindings for ERFA" HOMEPAGE="https://github.com/liberfa/pyerfa/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" # ImportError: cannot import name 'ufunc' from 'erfa' -#RESTRICT="test" +RESTRICT="test" RDEPEND=" sci-astronomy/erfa:0= >=dev-python/numpy-1.17[${PYTHON_USEDEP}] " BDEPEND="${RDEPEND} - dev-python/setuptools_scm[${PYTHON_USEDEP}] + dev-python/setuptools-scm[${PYTHON_USEDEP}] test? ( dev-python/pytest-doctestplus[${PYTHON_USEDEP}] )" distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/sphinx-astropy +#distutils_enable_sphinx docs dev-python/sphinx-astropy diff --git a/dev-python/pynndescent/pynndescent-0.5.6.ebuild b/dev-python/pynndescent/pynndescent-0.5.6.ebuild index 1e9eb00e4..241b0b746 100644 --- a/dev-python/pynndescent/pynndescent-0.5.6.ebuild +++ b/dev-python/pynndescent/pynndescent-0.5.6.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/pynrrd/pynrrd-0.4.2.ebuild b/dev-python/pynrrd/pynrrd-0.4.2.ebuild index aa922e6ed..f25908cb3 100644 --- a/dev-python/pynrrd/pynrrd-0.4.2.ebuild +++ b/dev-python/pynrrd/pynrrd-0.4.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/pynrrd/pynrrd-0.4.3.ebuild b/dev-python/pynrrd/pynrrd-0.4.3.ebuild index aa922e6ed..f25908cb3 100644 --- a/dev-python/pynrrd/pynrrd-0.4.3.ebuild +++ b/dev-python/pynrrd/pynrrd-0.4.3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest index 3a1d1f7a9..808263ac7 100644 --- a/dev-python/pynwb/Manifest +++ b/dev-python/pynwb/Manifest @@ -1,3 +1,3 @@ -DIST pynwb-2.0.1.tar.gz 452718 BLAKE2B d29347d748bd37bdf9326e0f9cc88b84742714ba78e6b0c56a923a4dd723c94e69ab3f325b5a5c66aef3ef819228abd64704268240fbdd369dac41b25e226b43 SHA512 897fa3bce93e733222a94bf9f043ed39c606c29f392f932a21c1004eebc1866d4caf50905a8e59baca87744af04d93e9957a7efb7e775422af5022787c4d086e DIST pynwb-2.1.0.tar.gz 459375 BLAKE2B 3645c4cac9a9c8e8726d6a6bf38d1fa8946237c7496fde76162ee5dec66de4d0c86241a7f076d44ce857c8b411a33e9e52af47c1c5e74cf4eb84da484950c61c SHA512 11d5b23809de1e5b13baf4d02420200baf215aa99237b8e747a9d401830bef5356306eb7f9a464be36e88e64e8c50018606102b126daa450a7ee624c5babb025 DIST pynwb-2.2.0.tar.gz 582890 BLAKE2B 7bc5774ddeb2144266af5457640d8721c9976d17dbfa9ce2b1027fdc736ca185935eb0f908aa7f4ad6c42df0c1e64f18221db6203f194f65493e9c61694a6ee0 SHA512 49e50be6be1856330abc87cc6621f94f7bddfd742bc024cddf31f4d693d8bce68e23839ae9a0dd76602a70b44b9e46019e05840c7840c4fccf5c9ffb6b4bfd57 +DIST pynwb-2.3.1.tar.gz 617910 BLAKE2B 6f8a965ff077523d043dd20b34ab1c69387b434a2a489a2a9dab718270fe7484cd88df4acce17da2aa513c56afbc75022fed132d157a0c804c6ced84a0bd627b SHA512 795a20b52d7734d2b1d4ba7da0df75d0e8cdbac4f8911a0a8977fd8890751d8c10b58858f2740a73557dc0d8ffa95530437544b71f4bf14ec0cc9e99213afda0 diff --git a/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch b/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch new file mode 100644 index 000000000..bf496b900 --- /dev/null +++ b/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch @@ -0,0 +1,54 @@ +From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001 +From: rly <rly@lbl.gov> +Date: Fri, 24 Mar 2023 10:17:13 -0700 +Subject: [PATCH] Fix deprecation warning with pkg_resources + +--- + src/pynwb/__init__.py | 14 +++++++++++--- + tests/back_compat/test_import_structure.py | 1 - + 2 files changed, 11 insertions(+), 4 deletions(-) + +diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py +index 2df273d43..023cda237 100644 +--- a/src/pynwb/__init__.py ++++ b/src/pynwb/__init__.py +@@ -15,16 +15,24 @@ + import hdmf.common + + CORE_NAMESPACE = 'core' +-__core_ns_file_name = 'nwb.namespace.yaml' + + from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace # noqa E402 + from .validate import validate # noqa: F401, E402 + + + def __get_resources(): +- from pkg_resources import resource_filename ++ try: ++ from importlib.resources import files ++ except ImportError: ++ # TODO: Remove when python 3.9 becomes the new minimum ++ from importlib_resources import files ++ ++ __location_of_this_file = files(__name__) ++ __core_ns_file_name = 'nwb.namespace.yaml' ++ __schema_dir = 'nwb-schema/core' ++ + ret = dict() +- ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name) ++ ret['namespace_path'] = str(__location_of_this_file / __schema_dir / __core_ns_file_name) + return ret + + +diff --git a/tests/back_compat/test_import_structure.py b/tests/back_compat/test_import_structure.py +index dba11a48a..e5f931f5d 100644 +--- a/tests/back_compat/test_import_structure.py ++++ b/tests/back_compat/test_import_structure.py +@@ -34,7 +34,6 @@ def test_outer_import_structure(self): + "__TYPE_MAP", + "__builtins__", + "__cached__", +- "__core_ns_file_name", + "__doc__", + "__file__", + "__get_resources", diff --git a/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch new file mode 100644 index 000000000..bf496b900 --- /dev/null +++ b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch @@ -0,0 +1,54 @@ +From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001 +From: rly <rly@lbl.gov> +Date: Fri, 24 Mar 2023 10:17:13 -0700 +Subject: [PATCH] Fix deprecation warning with pkg_resources + +--- + src/pynwb/__init__.py | 14 +++++++++++--- + tests/back_compat/test_import_structure.py | 1 - + 2 files changed, 11 insertions(+), 4 deletions(-) + +diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py +index 2df273d43..023cda237 100644 +--- a/src/pynwb/__init__.py ++++ b/src/pynwb/__init__.py +@@ -15,16 +15,24 @@ + import hdmf.common + + CORE_NAMESPACE = 'core' +-__core_ns_file_name = 'nwb.namespace.yaml' + + from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace # noqa E402 + from .validate import validate # noqa: F401, E402 + + + def __get_resources(): +- from pkg_resources import resource_filename ++ try: ++ from importlib.resources import files ++ except ImportError: ++ # TODO: Remove when python 3.9 becomes the new minimum ++ from importlib_resources import files ++ ++ __location_of_this_file = files(__name__) ++ __core_ns_file_name = 'nwb.namespace.yaml' ++ __schema_dir = 'nwb-schema/core' ++ + ret = dict() +- ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name) ++ ret['namespace_path'] = str(__location_of_this_file / __schema_dir / __core_ns_file_name) + return ret + + +diff --git a/tests/back_compat/test_import_structure.py b/tests/back_compat/test_import_structure.py +index dba11a48a..e5f931f5d 100644 +--- a/tests/back_compat/test_import_structure.py ++++ b/tests/back_compat/test_import_structure.py +@@ -34,7 +34,6 @@ def test_outer_import_structure(self): + "__TYPE_MAP", + "__builtins__", + "__cached__", +- "__core_ns_file_name", + "__doc__", + "__file__", + "__get_resources", diff --git a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch new file mode 100644 index 000000000..e672f243b --- /dev/null +++ b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch @@ -0,0 +1,13 @@ +diff --git a/src/pynwb/ophys.py b/src/pynwb/ophys.py +index b09267ff6..e3d9f8f6d 100644 +--- a/src/pynwb/ophys.py ++++ b/src/pynwb/ophys.py +@@ -192,7 +192,7 @@ def __init__(self, **kwargs): + args_to_set = popargs_to_dict(keys_to_set, kwargs) + super().__init__(**kwargs) + +- if args_to_set["binning"] < 0: ++ if args_to_set["binning"] is not None and args_to_set["binning"] < 0: + raise ValueError(f"Binning value must be >= 0: {args_to_set['binning']}") + if isinstance(args_to_set["binning"], int): + args_to_set["binning"] = np.uint(args_to_set["binning"]) diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild b/dev-python/pynwb/pynwb-2.0.1.ebuild deleted file mode 100644 index 3fe21370f..000000000 --- a/dev-python/pynwb/pynwb-2.0.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " -HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-libs/hdf5[ros3(-)] - <dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - " -BDEPEND="" - -EPYTEST_DESELECT=( - # Reported upsream: - # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425 - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore - tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache - tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns -) - -distutils_enable_tests pytest diff --git a/dev-python/pynwb/pynwb-2.1.0-r1.ebuild b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild index c24dae23a..e95649217 100644 --- a/dev-python/pynwb/pynwb-2.1.0-r1.ebuild +++ b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " @@ -16,7 +16,7 @@ LICENSE="BSD" KEYWORDS="~amd64 ~x86" RDEPEND=" - sci-libs/hdf5[ros3(-)] + >=sci-libs/hdf5-1.12.2 >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] dev-python/h5py[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] diff --git a/dev-python/pynwb/pynwb-2.2.0.ebuild b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild index 6ea595a8f..52fab7a63 100644 --- a/dev-python/pynwb/pynwb-2.2.0.ebuild +++ b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " @@ -16,7 +16,7 @@ LICENSE="BSD" KEYWORDS="~amd64 ~x86" RDEPEND=" - sci-libs/hdf5[ros3(-)] + >=sci-libs/hdf5-1.12.2 >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] dev-python/h5py[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild new file mode 100644 index 000000000..585dcc37d --- /dev/null +++ b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild @@ -0,0 +1,51 @@ +# 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} ) +inherit distutils-r1 pypi + +DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " +HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" +SRC_URI="$(pypi_sdist_url pynwb)" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + >=sci-libs/hdf5-1.12.2 + >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + " +BDEPEND="" + +# Remove both in next release +PATCHES=( + "${FILESDIR}/${P}-typing.patch" + "${FILESDIR}/${P}-pkg_resources.patch" + ) + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1580 + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns +) + +distutils_enable_tests pytest diff --git a/dev-python/pynwb/pynwb-2.3.1.ebuild b/dev-python/pynwb/pynwb-2.3.1.ebuild new file mode 100644 index 000000000..cce90c5d1 --- /dev/null +++ b/dev-python/pynwb/pynwb-2.3.1.ebuild @@ -0,0 +1,50 @@ +# 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} ) +inherit distutils-r1 pypi + +DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " +HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" +SRC_URI="$(pypi_sdist_url pynwb)" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + >=sci-libs/hdf5-1.12.2 + >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + " +BDEPEND="" + +# Remove in next release +PATCHES=( + "${FILESDIR}/${P}-typing.patch" + ) + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1580 + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns +) + +distutils_enable_tests pytest diff --git a/dev-python/pyout/files/pyout-0.7.2-blessed.patch b/dev-python/pyout/files/pyout-0.7.2-blessed.patch new file mode 100644 index 000000000..89e189916 --- /dev/null +++ b/dev-python/pyout/files/pyout-0.7.2-blessed.patch @@ -0,0 +1,140 @@ +From 0f7c6d6f2abb304c9c473afb504cb03d17fef036 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Sat, 7 Jan 2023 21:49:32 -0500 +Subject: [PATCH 1/2] Accepting either bless* library + +--- + pyout/field.py | 7 ++++++- + pyout/tabular.py | 9 +++++++-- + pyout/tests/terminal.py | 9 +++++++-- + pyout/tests/test_interface.py | 7 ++++++- + pyout/tests/test_tabular.py | 7 ++++++- + 5 files changed, 32 insertions(+), 7 deletions(-) + +diff --git a/pyout/field.py b/pyout/field.py +index 5105081..99c310f 100644 +--- a/pyout/field.py ++++ b/pyout/field.py +@@ -495,7 +495,12 @@ class TermProcessors(StyleProcessors): + + Parameters + ---------- +- term : blessings.Terminal ++ term : blessed.Terminal or blessings.Terminal ++ ++ Notes ++ ----- ++ * Eventually we may want to retire blessings: ++ https://github.com/pyout/pyout/issues/136 + """ + + def __init__(self, term): +diff --git a/pyout/tabular.py b/pyout/tabular.py +index 2a776a1..0d4797a 100644 +--- a/pyout/tabular.py ++++ b/pyout/tabular.py +@@ -7,7 +7,12 @@ + from logging import getLogger + import os + +-from blessings import Terminal ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ from blessed import Terminal ++except ImportError: ++ from blessings import Terminal + + from pyout import interface + from pyout.field import TermProcessors +@@ -16,7 +21,7 @@ + + + class TerminalStream(interface.Stream): +- """Stream interface implementation using blessings.Terminal. ++ """Stream interface implementation using blessed/blessings.Terminal. + """ + + def __init__(self, stream=None, interactive=None): +diff --git a/pyout/tests/terminal.py b/pyout/tests/terminal.py +index 53aabd7..2d8857c 100644 +--- a/pyout/tests/terminal.py ++++ b/pyout/tests/terminal.py +@@ -6,12 +6,17 @@ + from functools import partial + import re + +-import blessings ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ import blessed as bls ++except ImportError: ++ import blessings as bls + + from pyout.tests.utils import assert_contains + + +-class Terminal(blessings.Terminal): ++class Terminal(bls.Terminal): + + def __init__(self, *args, **kwargs): + super(Terminal, self).__init__( +diff --git a/pyout/tests/test_interface.py b/pyout/tests/test_interface.py +index 5205ef3..8348323 100644 +--- a/pyout/tests/test_interface.py ++++ b/pyout/tests/test_interface.py +@@ -1,6 +1,11 @@ + import pytest + +-pytest.importorskip("blessings") ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ pytest.importorskip("blessed") ++except pytest.skip.Exception: ++ pytest.importorskip("blessings") + + import inspect + +diff --git a/pyout/tests/test_tabular.py b/pyout/tests/test_tabular.py +index 2044e92..a1d35e5 100644 +--- a/pyout/tests/test_tabular.py ++++ b/pyout/tests/test_tabular.py +@@ -1,7 +1,12 @@ + # -*- coding: utf-8 -*- + import pytest + +-pytest.importorskip("blessings") ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ pytest.importorskip("blessed") ++except pytest.skip.Exception: ++ pytest.importorskip("blessings") + + from collections import Counter + from collections import OrderedDict + +From 5f6691c114578217a124d2ac1b24468993178e27 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Sat, 7 Jan 2023 23:48:37 -0500 +Subject: [PATCH 2/2] Preferring blessings + +--- + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index b376c2e..43005e7 100644 +--- a/setup.py ++++ b/setup.py +@@ -2,7 +2,7 @@ + + requires = { + "core": [ +- "blessings; sys_platform != 'win32'", ++ "blessed; sys_platform != 'win32'", + "jsonschema>=3.0.0", + ], + "tests": ["pytest", "pytest-timeout"], diff --git a/dev-python/pyout/pyout-0.7.2.ebuild b/dev-python/pyout/pyout-0.7.1-r1.ebuild index 6cf80ec85..9cd796883 100644 --- a/dev-python/pyout/pyout-0.7.2.ebuild +++ b/dev-python/pyout/pyout-0.7.1-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Terminal styling for structured data" @@ -13,10 +13,11 @@ SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}. SLOT="0" LICENSE="MIT" KEYWORDS="~amd64 ~x86" +RESTRICT="test" RDEPEND=" dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/blessings[${PYTHON_USEDEP}] + dev-python/blessed[${PYTHON_USEDEP}] " DEPEND=" test? ( @@ -26,6 +27,10 @@ DEPEND=" distutils_enable_tests pytest + +PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" ) + + python_prepare_all() { sed -i -e '/pytest-runner/d' setup.py || die distutils-r1_python_prepare_all diff --git a/dev-python/pyout/pyout-0.7.1.ebuild b/dev-python/pyout/pyout-0.7.2-r1.ebuild index 6cf80ec85..7e262b158 100644 --- a/dev-python/pyout/pyout-0.7.1.ebuild +++ b/dev-python/pyout/pyout-0.7.2-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Terminal styling for structured data" @@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86" RDEPEND=" dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/blessings[${PYTHON_USEDEP}] + dev-python/blessed[${PYTHON_USEDEP}] " DEPEND=" test? ( @@ -26,6 +26,8 @@ DEPEND=" distutils_enable_tests pytest +PATCHES=( "${FILESDIR}/${P}-blessed.patch" ) + python_prepare_all() { sed -i -e '/pytest-runner/d' setup.py || die distutils-r1_python_prepare_all diff --git a/dev-python/pysolar/Manifest b/dev-python/pysolar/Manifest index e8d002718..d353c6cbd 100644 --- a/dev-python/pysolar/Manifest +++ b/dev-python/pysolar/Manifest @@ -1 +1 @@ -DIST pysolar-0.8.tar.gz 1574747 BLAKE2B 7343cbed9c7e80deb1ee54406ceb96daebef76495d1595c44467aa5a025d161e730f3356a3c1b11ce27a1c96d1d47bd97a2f3e95b8864f6009b2fb3a14a1a722 SHA512 ca9d168c1fd5142998d07a18d3dde812ed38c667f1226fc62deb1fb148669039f6c5707bfed9aeea4bef8fbe962235495705e41043d7e381413caf55f9abba99 +DIST pysolar-0.10.tar.gz 1569021 BLAKE2B f1f30b32030e6dda00635257b6d2cbc5d75bf8122f27db2db6c0471339b73f4123627b116008c262a7547b5ca7a0664318ad90a92d6d4fc0b53d65de708cde29 SHA512 bccb41874bb6f344a64db694b8ed81137ddaa7c0df9b6011192c3ce3acb4b8f4d934e70000d91ced005936c5e1751043a80ad96b5d262ebf1d96ee061326e114 diff --git a/dev-python/pysolar/pysolar-0.8.ebuild b/dev-python/pysolar/pysolar-0.10.ebuild index 65027edb9..0e11e7967 100644 --- a/dev-python/pysolar/pysolar-0.8.ebuild +++ b/dev-python/pysolar/pysolar-0.10.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools AUTHOR=pingswept @@ -17,13 +18,16 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" +# Still depends on nose +RESTRICT="test" + RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/pytz[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] " -distutils_enable_tests nose +distutils_enable_tests pytest python_prepare_all() { sed \ diff --git a/dev-python/pytest-doctestplus/Manifest b/dev-python/pytest-doctestplus/Manifest index 4a1e50d88..47318a5ee 100644 --- a/dev-python/pytest-doctestplus/Manifest +++ b/dev-python/pytest-doctestplus/Manifest @@ -1 +1,2 @@ DIST pytest-doctestplus-0.11.2.tar.gz 34943 BLAKE2B a45779ff3d65e1b920282f400d67b618f620a9a905da69edff96db799f30e1b93562e69bd567a49629194b962a080b1f675619b0c6995227a1391c3d0e74be20 SHA512 fed49a551be78f51db60161ccfa592e461719cca76e2a48e3267e8a22dbec60d02d8fbb757a88cb5cf4dc22143e27d3d20f25b51855be835254c72fd8260abbd +DIST pytest-doctestplus-0.12.1.tar.gz 36434 BLAKE2B 95baa9f6185423fdd3e61ec0c269de54a4cf3298f2db90087b1413608663e4200e48158240cf565c8cc267244fbf8d60a0a5241b3b8f1fa8c1187e34824b17ae SHA512 46b999abd5632fa5c5743900b8b78ee7b6be742959daeb85296ebdf820d7533cff0a78d1c8aed7f5d5a15436998b2f7fe3e571133be14fce056276900493fef9 diff --git a/dev-python/pytest-doctestplus/metadata.xml b/dev-python/pytest-doctestplus/metadata.xml index 4f4367037..33e3f0e33 100644 --- a/dev-python/pytest-doctestplus/metadata.xml +++ b/dev-python/pytest-doctestplus/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">pytest-doctestplus</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild index 17b19cbb0..c9149842e 100644 --- a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild +++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild new file mode 100644 index 000000000..89f6c46eb --- /dev/null +++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Pytest plugin with advanced doctest features" +HOMEPAGE="https://astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] +" + +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/numpy[${PYTHON_USEDEP}] + ) +" + +# Skip the remote tests +EPYTEST_DESELECT=( + tests/test_doctestplus.py::test_remote_data_url + tests/test_doctestplus.py::test_remote_data_float_cmp + tests/test_doctestplus.py::test_remote_data_ignore_whitespace + tests/test_doctestplus.py::test_remote_data_ellipsis + tests/test_doctestplus.py::test_remote_data_requires + tests/test_doctestplus.py::test_remote_data_ignore_warnings +) + +distutils_enable_tests pytest diff --git a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild index f2d829835..b5fdf845b 100644 --- a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild +++ b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/python-igraph/Manifest b/dev-python/python-igraph/Manifest index 45cb90874..a0620dd02 100644 --- a/dev-python/python-igraph/Manifest +++ b/dev-python/python-igraph/Manifest @@ -1,2 +1 @@ -DIST igraph-0.9.11.tar.gz 3728842 BLAKE2B 7ddac705757a98c3c9dbbfdc841f078c8766aa9baedf0df693163920c47419da481c4bc54a0b7adc103885e2e75c77832faaa38f954d9596114fa700492a89e2 SHA512 a85e02144d33eb02ce0fe594cf91d5fc852af36d11c6da26d714f1e66bb116a9732945db43939e18f704ac725a9011358b3b89073ba81b0f4bf6440dc727f90e -DIST python-igraph-0.9.0.tar.gz 3366754 BLAKE2B baab83753bea4ee880564fe189b246c2ce0647a74ea1a41299062c3a2e203ec155abe1a3680c228d62a28e7bbf263e60e4529f151094b916ce4a1cae9f360705 SHA512 bd6071fc20c6c8f65034c71be6083e66367eb3047f376eb603e590da3606338fbd9890a2a74b8e0547fba2900c353f952683ea69b4d996f5643e84ee1c450b03 +DIST python-igraph-0.10.4.tar.gz 4209850 BLAKE2B 2f3b75569ea93d08b50c4af7331a1e072d1ded66a6437d52ca054ee2603f60cbbec9371107d8c6eeda5a8215b0fa5ee6eac420dbda9247ab2246d70b01d25aa5 SHA512 675388c3a9a346534c66ec96f4a427b34e88e15a1d401af4f283ee7f1f17fad85bd1636a85af58b6d1969238b40e0314d7b6db4b84723e0eb1f3afbc660f0300 diff --git a/dev-python/python-igraph/metadata.xml b/dev-python/python-igraph/metadata.xml index e97c4322a..4a86617fb 100644 --- a/dev-python/python-igraph/metadata.xml +++ b/dev-python/python-igraph/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">python-igraph</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/python-igraph/python-igraph-0.9.11.ebuild b/dev-python/python-igraph/python-igraph-0.10.4.ebuild index 4d2a6ee5f..f0096ae23 100644 --- a/dev-python/python-igraph/python-igraph-0.9.11.ebuild +++ b/dev-python/python-igraph/python-igraph-0.10.4.ebuild @@ -3,24 +3,22 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 -MY_PN="${PN#python-}" -MY_P="${MY_PN}-${PV}" - DESCRIPTION="Python interface for igraph" HOMEPAGE="https://igraph.org" -SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" -S="${WORKDIR}/${MY_P}" +SRC_URI="mirror://pypi/i/igraph/igraph-${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/igraph-${PV}" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" RDEPEND=" - >=dev-libs/igraph-0.9.0 + >=dev-libs/igraph-$(ver_cut 1-2) >=dev-python/texttable-1.6.2[${PYTHON_USEDEP}] " DEPEND="${RDEPEND}" diff --git a/dev-python/python-igraph/python-igraph-0.9.0.ebuild b/dev-python/python-igraph/python-igraph-0.9.0.ebuild deleted file mode 100644 index cec61215e..000000000 --- a/dev-python/python-igraph/python-igraph-0.9.0.ebuild +++ /dev/null @@ -1,46 +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="Python interface for igraph" -HOMEPAGE="https://igraph.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="${PYTHON_DEPS} - dev-libs/igraph - dev-python/texttable[${PYTHON_USEDEP}] - dev-python/pycairo[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" -BDEPEND=" - test? ( - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/ipywidgets[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_prepare_all() { - # fix the igraph include path - cd src || die - find -type f -name "*.h" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die - find -type f -name "*.c" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die - cd .. || die - - distutils-r1_python_prepare_all -} - -python_compile() { - distutils-r1_python_compile --use-pkg-config -} diff --git a/dev-python/pytorch-lightning/Manifest b/dev-python/pytorch-lightning/Manifest index f9f1f6b1d..2876dd7d6 100644 --- a/dev-python/pytorch-lightning/Manifest +++ b/dev-python/pytorch-lightning/Manifest @@ -1 +1 @@ -DIST pytorch-lightning-1.5.8.tar.gz 444592 BLAKE2B 7fa8e230811381a0aea43f4d098f9d833350183cfe10ea2f51aa6c4a8c9835ed979d103572b352c2831361d5802caf66a674da0fccf948ba9b14cdb7d77d325e SHA512 e9c08b5614f8041e2511977b0e42be5d209efbf20a80ae8067bf7ac4dedd5d30908a33542fb3f1601814dba769ffeb545ba8a66ff368ff038e8fdc5f630dc808 +DIST pytorch-lightning-1.8.6.tar.gz 576205 BLAKE2B a8a2d0a14d331303f45319f3aa840f4bc0a21e6c6ac3bac8e7d72f92947126f64e06da36a62eed6ff0c33caae935905348ccb1379b53ee73cd35e569973d6551 SHA512 85e6474637f5d237c22cf0775ee8d6f56c000c3c0376af2087b68d0c4311608d35d02e856ef1dddca1c481e531ee0fb246357b91f5c185637a740c80a0152510 diff --git a/dev-python/pytorch-lightning/metadata.xml b/dev-python/pytorch-lightning/metadata.xml index 2e30eb3db..df24db4ac 100644 --- a/dev-python/pytorch-lightning/metadata.xml +++ b/dev-python/pytorch-lightning/metadata.xml @@ -6,7 +6,7 @@ <name>Science Project</name> </maintainer> <upstream> - <remote-id type="github">PyTorchLightning/pytorch-lightning</remote-id> + <remote-id type="github">Lightning-AI/lightning</remote-id> <remote-id type="pypi">pytorch-lightning</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild deleted file mode 100644 index cf51f4e9b..000000000 --- a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 - -DESCRIPTION="Lightweight PyTorch wrapper for ML researchers" -HOMEPAGE="https://github.com/PyTorchLightning/pytorch-lightning" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - sci-libs/pytorch[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/future[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/fsspec[${PYTHON_USEDEP}] - sci-visualization/tensorboard[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - dev-python/ratelimit[${PYTHON_USEDEP}] -" diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild new file mode 100644 index 000000000..c50848555 --- /dev/null +++ b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_SINGLE_IMPL=1 +inherit distutils-r1 + +DESCRIPTION="Lightweight PyTorch wrapper for ML researchers" +HOMEPAGE="https://github.com/Lightning-AI/lightning" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/fsspec[${PYTHON_USEDEP}] + sci-visualization/tensorboard[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/ratelimit[${PYTHON_USEDEP}] + ') +" diff --git a/dev-python/pyvista/pyvista-0.33.2.ebuild b/dev-python/pyvista/pyvista-0.33.2.ebuild index c8b5a59dc..ed4a21a4e 100644 --- a/dev-python/pyvista/pyvista-0.33.2.ebuild +++ b/dev-python/pyvista/pyvista-0.33.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..10} ) DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1" inherit distutils-r1 diff --git a/dev-python/pyviz_comms/Manifest b/dev-python/pyviz_comms/Manifest index 315e51357..9f4d81ce1 100644 --- a/dev-python/pyviz_comms/Manifest +++ b/dev-python/pyviz_comms/Manifest @@ -1 +1,2 @@ DIST pyviz_comms-2.0.1.tar.gz 125046 BLAKE2B d0913fb873396ddb11db2781cb65cd4b2a9dd22ce496af58a656a2c17c4d0ca1af1351a618b293c5eca964dc7f32840c577a831139a0e5e9cd7667886c97aa2c SHA512 da913ee537588cd7e643c034f14b141e28699ddddb1dcd89053b3b9482bc330582f381e4257cd07546049da67f20b1f25cf9ffb4d11c9ef457bd4915781a751c +DIST pyviz_comms-2.2.0.tar.gz 31910 BLAKE2B 42175d8750e9cb8dea4888970028898a9ee1e34b2ca5c895d2a1db40d9eec2f7eb86aec41090431b723ffcfdd0411016c04015e286d467a4c9d89eb710e7e08c SHA512 de6dba5b5d93a9a496b6895f4bf884dd80afd4124e1519bbd243b7672827f04f51d353f3941678be3780a250640e03b0c4ea0a3f87b8b9892980845bdca07439 diff --git a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild index df1d2bfe2..8526bd511 100644 --- a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild +++ b/dev-python/pyviz_comms/pyviz_comms-2.0.1.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 @@ -16,3 +16,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" RDEPEND="dev-python/param[${PYTHON_USEDEP}]" + +# Tarballs do not include tests, reported upstream: +# https://github.com/holoviz/pyviz_comms/issues/104 +#distutils_enable_tests pytest diff --git a/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild new file mode 100644 index 000000000..8526bd511 --- /dev/null +++ b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Bidirectional communication for the HoloViz ecosystem" +HOMEPAGE="https://holoviz.org" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/param[${PYTHON_USEDEP}]" + +# Tarballs do not include tests, reported upstream: +# https://github.com/holoviz/pyviz_comms/issues/104 +#distutils_enable_tests pytest diff --git a/dev-python/pyvote/pyvote-0.1.ebuild b/dev-python/pyvote/pyvote-0.1.ebuild index b7ef458e2..95d95cb1b 100644 --- a/dev-python/pyvote/pyvote-0.1.ebuild +++ b/dev-python/pyvote/pyvote-0.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/pyzo/Manifest b/dev-python/pyzo/Manifest index 53069b179..781107b6f 100644 --- a/dev-python/pyzo/Manifest +++ b/dev-python/pyzo/Manifest @@ -1 +1 @@ -DIST pyzo-4.11.2.tar.gz 5340033 BLAKE2B 0c5c89deac947878ab84e7744dd21ca1092e6a9448573ad85067a20861f7823727623eb45a4c3f598e0bb2056bdf153d6818daed29ec8485313bebe8fccac32f SHA512 f96e4db48b414c5d6c2d9cb723e1bef2c4e0bc461c35710b1d7bf533c935734c5a17824ade59894f273624c80823b6283f131b972cbbe7cef3d0d20ff206f7db +DIST pyzo-4.12.7.gh.tar.gz 2280468 BLAKE2B c71e29730c677cc0e75a16a10f752b26dd5675ab978493e98049a3cb6ff51449e554c22d9b171ade7e96d8908fcf4b09842c9107d09cbfee2b4e488a3ef3ed28 SHA512 974e4166227afb42ffb950f0abd8733264e57fbf5cb1c23fc72f76a41940be5cf7cc9bc39bc93353ce392aaf204a420853e62313c139814771fff92729dbe032 diff --git a/dev-python/pyzo/pyzo-4.11.2.ebuild b/dev-python/pyzo/pyzo-4.12.7.ebuild index 772793be5..f65ebcc7d 100644 --- a/dev-python/pyzo/pyzo-4.11.2.ebuild +++ b/dev-python/pyzo/pyzo-4.12.7.ebuild @@ -3,13 +3,14 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 virtualx desktop xdg DESCRIPTION="The Python IDE for scientific computing" HOMEPAGE="https://pyzo.org/" -SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD-2" SLOT="0" @@ -17,12 +18,14 @@ KEYWORDS="~amd64" # For some reason this requires network access # Qt: Session management error: Could not open network socket +PROPERTIES="test_network" RESTRICT="test" RDEPEND=" dev-python/QtPy[${PYTHON_USEDEP}] " BDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] test? ( dev-python/visvis[${PYTHON_USEDEP}] ) @@ -42,8 +45,8 @@ python_prepare_all() { distutils-r1_python_prepare_all } -src_test() { - virtx python_foreach_impl python_test +python_test() { + virtx epytest } python_install() { diff --git a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild index 7ae9776c7..c2aa347f1 100644 --- a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild +++ b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild index 3567cdb42..5074a1566 100644 --- a/dev-python/rasterstats/rasterstats-0.16.0.ebuild +++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/regions/Manifest b/dev-python/regions/Manifest index e3051705f..7e2e2f89a 100644 --- a/dev-python/regions/Manifest +++ b/dev-python/regions/Manifest @@ -1 +1 @@ -DIST regions-0.4.tar.gz 1108822 BLAKE2B 7b2de2815c0a7a4e4d75aa08443520c8baf50772a0d2d892e6922d6223c32f4a05089acd464cdfba8a8737984de982b472329c800c9254f5d9ed3d8e649287d2 SHA512 571ab06c40a9abf0ebe5665b0efe7d09b0f2a9c6295fcd56f30ab25bfa506bfd80b89f7e88e83a5dbe68e084bb94e374abb01ecc043cd564a2b9cb78f6057acf +DIST regions-0.7.tar.gz 666091 BLAKE2B 7fd8cc1c9c34b236301c0493e11b99a3d2177e31c15c3ef43f38053eec653f8a68b84c4e0568395e38c940e987fcdf3a52a06e012a387a741de0cb46ec1995e8 SHA512 0e86b1cda4e479e29c00d151079788630a5b434f3d721d21ee81b4abcb03ea959e04351d61f48bfc19713dc938396fc9383c00998ba947f50fbbf9477db7d760 diff --git a/dev-python/regions/metadata.xml b/dev-python/regions/metadata.xml index a9f88e7d8..b0d9fd489 100644 --- a/dev-python/regions/metadata.xml +++ b/dev-python/regions/metadata.xml @@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies. </longdescription> <upstream> <remote-id type="github">gammapy/gammapy</remote-id> + <remote-id type="pypi">regions</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/regions/regions-0.4.ebuild b/dev-python/regions/regions-0.7.ebuild index eccec0eda..ef412a153 100644 --- a/dev-python/regions/regions-0.4.ebuild +++ b/dev-python/regions/regions-0.7.ebuild @@ -1,16 +1,15 @@ # Copyright 1999-2021 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_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Astropy affilated package for region handling" HOMEPAGE="https://github.com/astropy/regions" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild index 2daccec83..62ad23af9 100644 --- a/dev-python/reproject/reproject-0.8.ebuild +++ b/dev-python/reproject/reproject-0.8.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -24,7 +24,7 @@ KEYWORDS="~amd64 ~x86" # pytest-filter-subpackage>=0.1 RESTRICT="test" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" RDEPEND=" >=dev-python/astropy-3.2[${PYTHON_USEDEP}] diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml index 9656580bb..228d0e4bf 100644 --- a/dev-python/repsep_utils/metadata.xml +++ b/dev-python/repsep_utils/metadata.xml @@ -6,12 +6,12 @@ <name>Horea Christian</name> </maintainer> <longdescription lang="en"> - Utilities for compiling and developing RepSeP-style articles, such as the - reference implementation. The package contains generic boilerplate code for - PythonTeX-interaction, as used by all RepSeP-style articles, as well as an - executable file allowing single-script execution for development and - debugging purposes. - </longdescription> + Utilities for compiling and developing RepSeP-style articles, such as the + reference implementation. The package contains generic boilerplate code for + PythonTeX-interaction, as used by all RepSeP-style articles, as well as an + executable file allowing single-script execution for development and + debugging purposes. + </longdescription> <upstream> <remote-id type="github">TheChymera/repsep_utils</remote-id> </upstream> diff --git a/dev-python/reretry/Manifest b/dev-python/reretry/Manifest new file mode 100644 index 000000000..af408dac3 --- /dev/null +++ b/dev-python/reretry/Manifest @@ -0,0 +1 @@ +DIST reretry-0.11.8.gh.tar.gz 6629 BLAKE2B eb13ecce1ca29ce29932566e08b57a05d3f2426f41633b33b1c51eed1c4d880c5520adda4e5386ac13d064f7ff6bdc3831ce612c64c8dd24e63164a55907ae3b SHA512 e499e64cc06af8e1bb7e9fdd857c02305dcb76fd3205de128d389332a94493696c85a705efaf1e9ac0110b94a1cd443a44d49856f26b31a7eba8ad317f7deba4 diff --git a/dev-python/reretry/metadata.xml b/dev-python/reretry/metadata.xml new file mode 100644 index 000000000..64af0841d --- /dev/null +++ b/dev-python/reretry/metadata.xml @@ -0,0 +1,12 @@ +<?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">leshchenko1979/reretry</remote-id> + <remote-id type="pypi">reretry</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/reretry/reretry-0.11.8.ebuild b/dev-python/reretry/reretry-0.11.8.ebuild new file mode 100644 index 000000000..64da7215b --- /dev/null +++ b/dev-python/reretry/reretry-0.11.8.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2021 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="An easy-to-use but functional retry decorator in python" +HOMEPAGE="https://github.com/leshchenko1979/reretry" +SRC_URI="https://github.com/leshchenko1979/reretry/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + test? ( + dev-python/pytest-asyncio[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/ripser/Manifest b/dev-python/ripser/Manifest index 2a8f78db2..4f2515c0a 100644 --- a/dev-python/ripser/Manifest +++ b/dev-python/ripser/Manifest @@ -1 +1 @@ -DIST ripser-0.6.0.tar.gz 71420 BLAKE2B 28c34ccda4bcf5762d4ccf782aa0a1c6fe5e24fc6b84721da7ffb1475c9132b19115e7eb981ef966714f6fab2d745e2ca17f637489d1913d2fb14f82c9ed041b SHA512 1e091130c9a88eda6e29365c6616a2e12d93c9b65bda7eb5d21673f73940c24ab671ce88e716743a36bcc77ade673a49513f5e6840aa6a1810b7e17d8de741ee +DIST ripser-0.6.4.tar.gz 74642 BLAKE2B a6d7a39671415a86978ae4514f1f915f13ec791f246e632d3974553b53c398b971989e25b3cca2027a910831404c478994e646ed6e03010350b1e95438d7fc10 SHA512 b3fc216e75c807666e24d9f797a96296f2e1ffbddf3bba499220dab385690cdb6f47138cb55977eb68678dfbff9d750d7f1c4bcd8ea9267a940c9949a8dae360 diff --git a/dev-python/ripser/metadata.xml b/dev-python/ripser/metadata.xml index 2f2c0b51c..f983c3d4c 100644 --- a/dev-python/ripser/metadata.xml +++ b/dev-python/ripser/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">ripser</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ripser/ripser-0.6.0.ebuild b/dev-python/ripser/ripser-0.6.4.ebuild index 5317a7208..e0ea6f24b 100644 --- a/dev-python/ripser/ripser-0.6.0.ebuild +++ b/dev-python/ripser/ripser-0.6.4.ebuild @@ -1,22 +1,21 @@ # Copyright 1999-2020 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_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="python frontend for the fast ripser tda tool" HOMEPAGE="https://ripser.scikit-tda.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND="${PYTHON_DEPS} +RDEPEND=" dev-python/cython[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/persim[${PYTHON_USEDEP}] diff --git a/dev-python/schema/schema-0.7.4.ebuild b/dev-python/schema/schema-0.7.4.ebuild index 05e8712bb..d8c8b0c2a 100644 --- a/dev-python/schema/schema-0.7.4.ebuild +++ b/dev-python/schema/schema-0.7.4.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} pypy3 ) +PYTHON_COMPAT=( python3_10 pypy3 ) inherit distutils-r1 diff --git a/dev-python/scooby/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild index 19d343eca..b876c3425 100644 --- a/dev-python/scooby/scooby-0.5.7.ebuild +++ b/dev-python/scooby/scooby-0.5.7.ebuild @@ -3,7 +3,7 @@ EAPI=7 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/smart-open/Manifest b/dev-python/smart-open/Manifest new file mode 100644 index 000000000..37703129f --- /dev/null +++ b/dev-python/smart-open/Manifest @@ -0,0 +1 @@ +DIST smart-open-6.3.0.gh.tar.gz 131300 BLAKE2B 816b2e42fca7783891eefbe767ac28423c533fe726707bf40be2b53107d7c928e74dec904db79542f7b0d41100f5aada78598478c9bc6ca23d3dbe2341575ad4 SHA512 78a63b22fc00b1ab9b60161ab0ea79d7c760539f1c69386cba1c9844099b597dc8a8a77940e019f126cb989ae63c3f2418493f4e8e86f6605662d7f2904108e4 diff --git a/dev-python/smart-open/metadata.xml b/dev-python/smart-open/metadata.xml new file mode 100644 index 000000000..6c86761f0 --- /dev/null +++ b/dev-python/smart-open/metadata.xml @@ -0,0 +1,12 @@ +<?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">RaRe-Technologies/smart_open</remote-id> + <remote-id type="pypi">smart-open</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/smart-open/smart-open-6.3.0.ebuild b/dev-python/smart-open/smart-open-6.3.0.ebuild new file mode 100644 index 000000000..b585f1d4b --- /dev/null +++ b/dev-python/smart-open/smart-open-6.3.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2021 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="Utils for streaming large files (S3, HDFS, gzip, bz2...) " +HOMEPAGE="https://github.com/RaRe-Technologies/smart_open" +SRC_URI="https://github.com/RaRe-Technologies/smart_open/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN//-/_}-${PV}" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/boto3[${PYTHON_USEDEP}] + dev-python/google-cloud-storage[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/paramiko[${PYTHON_USEDEP}] +" + +BDEPEND=" + test? ( + dev-python/moto[${PYTHON_USEDEP}] + dev-python/responses[${PYTHON_USEDEP}] + dev-python/pytest-rerunfailures[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest index d82883f77..fbef82cf7 100644 --- a/dev-python/snakemake/Manifest +++ b/dev-python/snakemake/Manifest @@ -1 +1 @@ -DIST snakemake-5.32.2.tar.gz 7010842 BLAKE2B 70526d55ae058d4658c9486cad993fd626308c2ae21cc8e4a484c4f0916d5835ab27b6205e500b13303cae13f659bd542442b1e9a255b7f7f4b7cb4878694a17 SHA512 aa9c53f451bcf454209df25c5bbc795c4d67f27d1b3fe641ce9b788ee1350826e0a4d92514a50fbce58e5a3a462cca9c4015a58646a36a6a3f043381cc5b929d +DIST snakemake-7.24.2.gh.tar.gz 8849295 BLAKE2B 3ea9149ef8dbba080063cd2038ec75c42332ec3024f4ddeca0e3b2feb73d536f96484622fd9f45c51682c329cf575f3745048529e62b56f14afbea9e97b80ebe SHA512 f12e8c864a55940adbba04f3f88522e1a46739d73e77baf9b9b462cd1256336733d0591b8bc7d331231d30852ea29f2ac305745774cee78c1b6e46c4699b08a8 diff --git a/dev-python/snakemake/snakemake-5.32.2.ebuild b/dev-python/snakemake/snakemake-7.24.2.ebuild index 59d2f061a..fb9895514 100644 --- a/dev-python/snakemake/snakemake-5.32.2.ebuild +++ b/dev-python/snakemake/snakemake-7.24.2.ebuild @@ -1,47 +1,55 @@ # Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Make-like task language" HOMEPAGE="https://snakemake.readthedocs.io" -SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" -# missing test dep google.cloud +# cannot import name '_helpers' from 'google.cloud' RESTRICT="test" -BDEPEND="test? ( - dev-python/requests-mock[${PYTHON_USEDEP}] - dev-python/google-api-python-client[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/pygments[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/oauth2client[${PYTHON_USEDEP}] - net-libs/google-cloud-cpp -)" +BDEPEND=" + dev-python/tomli[${PYTHON_USEDEP}] + test? ( + dev-python/requests-mock[${PYTHON_USEDEP}] + dev-python/google-api-python-client[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pygments[${PYTHON_USEDEP}] + dev-python/pygraphviz[${PYTHON_USEDEP}] + net-libs/google-cloud-cpp + ) +" RDEPEND=" dev-python/appdirs[${PYTHON_USEDEP}] dev-python/ConfigArgParse[${PYTHON_USEDEP}] + dev-python/connection_pool[${PYTHON_USEDEP}] dev-python/datrie[${PYTHON_USEDEP}] dev-python/docutils[${PYTHON_USEDEP}] dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/humanfriendly[${PYTHON_USEDEP}] + dev-python/jinja[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/nbformat[${PYTHON_USEDEP}] dev-python/psutil[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/ratelimit[${PYTHON_USEDEP}] dev-python/requests[${PYTHON_USEDEP}] + dev-python/reretry[${PYTHON_USEDEP}] + dev-python/smart-open[${PYTHON_USEDEP}] + dev-python/stopit[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + dev-python/throttler[${PYTHON_USEDEP}] dev-python/toposort[${PYTHON_USEDEP}] dev-python/wrapt[${PYTHON_USEDEP}] sci-mathematics/pulp[${PYTHON_USEDEP}] @@ -50,7 +58,8 @@ RDEPEND=" distutils_enable_sphinx docs \ dev-python/sphinxcontrib-napoleon \ dev-python/sphinx-argparse \ - dev-python/sphinx_rtd_theme \ + dev-python/sphinx-rtd-theme \ dev-python/docutils \ - dev-python/recommonmark + dev-python/recommonmark \ + dev-python/myst-parser distutils_enable_tests pytest diff --git a/dev-python/snuggs/snuggs-1.4.7.ebuild b/dev-python/snuggs/snuggs-1.4.7.ebuild index ebae883ff..be3395de7 100644 --- a/dev-python/snuggs/snuggs-1.4.7.ebuild +++ b/dev-python/snuggs/snuggs-1.4.7.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/specutils/Manifest b/dev-python/specutils/Manifest index a612bb26f..9ee9c42c5 100644 --- a/dev-python/specutils/Manifest +++ b/dev-python/specutils/Manifest @@ -1 +1 @@ -DIST specutils-1.1.1.tar.gz 508922 BLAKE2B fb7eafae5ccdd1b7e73d2bf45c5e9b490ddfbae35cb583a1db5ba9bae7fa9e568f6064929395ddcba9a31ead5552d6e59c5b2da1c4684af09f5080fc5c43a284 SHA512 f20c7a3f3c8bd59d0fd3532ca3c52bea651c726d3d5ee7570d840babee73f83bbaeb6a18cd370393d739835358a768771b232ce81df211efee32b795fd61cddc +DIST specutils-1.9.1.tar.gz 665564 BLAKE2B 733bfecfdc61a03f85bc7f7588724eac869db66e135c4ef22993c3b1d537b67ef6ca784d03a0182741684282c4a7385642352f20d3fce948f0b26a4e950ba82f SHA512 f06e878539173b3c8a9220fd87f8deff15db744c3d267405afb1a43f98c181440c160c5396c636d2f6e2ed4373055537e6274e4a65e5f4e82f9163a446a6d450 diff --git a/dev-python/specutils/metadata.xml b/dev-python/specutils/metadata.xml index d8e354751..1055c50cb 100644 --- a/dev-python/specutils/metadata.xml +++ b/dev-python/specutils/metadata.xml @@ -12,5 +12,6 @@ into a class with special handling of 1D spectra. </longdescription> <upstream> <remote-id type="github">astropy/specutils</remote-id> + <remote-id type="pypi">specutils</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/specutils/specutils-1.1.1.ebuild b/dev-python/specutils/specutils-1.9.1.ebuild index 24f1d3118..c77a1078d 100644 --- a/dev-python/specutils/specutils-1.1.1.ebuild +++ b/dev-python/specutils/specutils-1.9.1.ebuild @@ -1,16 +1,15 @@ # Copyright 1999-2021 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_SETUPTOOLS=rdepend +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Package for spectroscopic astronomical data" HOMEPAGE="https://github.com/astropy/specutils" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild index 4210a094b..2660d4912 100644 --- a/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild +++ b/dev-python/sphinx-argparse/sphinx-argparse-0.3.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..11} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=poetry inherit distutils-r1 diff --git a/dev-python/sphinx-astropy/Manifest b/dev-python/sphinx-astropy/Manifest index 26a909677..1084d6cfa 100644 --- a/dev-python/sphinx-astropy/Manifest +++ b/dev-python/sphinx-astropy/Manifest @@ -1 +1,2 @@ DIST sphinx-astropy-1.7.0.tar.gz 18266 BLAKE2B 363733c5a3e5974cdf0f62f879babc9a28617ff61d15292649acd189798e24611c2d84e69af5dc05b89241f395cc997233f966bdf8e8a84ccfe235f873d533c2 SHA512 4b9af1528805c5017695be6ad9d0b789437da4ea01080190d5c0e44a76d927098864002cfd2a59529924a8d2844e26d2e7635fb3f0417ed90502e7e47d0239d3 +DIST sphinx-astropy-1.8.0.tar.gz 18310 BLAKE2B 0d13ba59b2ffcb792e66e58d2a87057b79da811d38e6fd101b074b0edbf5ad6d76e79300f5863521b0bbb1b40921ba6773f8d37c32d68dd36078cb2d0497e2ff SHA512 f02fe8d3ed58ffeff190492c07e2df91a2bd5bcc8e82c6685002e543585a5fc1294ebd46821b7dc0a364540f3a45adacf1b90261b7da95657bc99dcd6130f4d5 diff --git a/dev-python/sphinx-astropy/metadata.xml b/dev-python/sphinx-astropy/metadata.xml index 4f4367037..8d01c3b18 100644 --- a/dev-python/sphinx-astropy/metadata.xml +++ b/dev-python/sphinx-astropy/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">sphinx-astropy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild index be4395414..cf6e3a5c5 100644 --- a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild +++ b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild new file mode 100644 index 000000000..89d58fc6b --- /dev/null +++ b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Sphinx extensions and configuration specific to the Astropy project" +HOMEPAGE="https://www.astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# Requires access to the internet +RESTRICT="test" + +RDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}] + dev-python/numpydoc[${PYTHON_USEDEP}] + >=dev-python/sphinx-1.7[${PYTHON_USEDEP}] + dev-python/sphinx-automodapi[${PYTHON_USEDEP}] + dev-python/sphinx-gallery[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/sphinx-automodapi/metadata.xml b/dev-python/sphinx-automodapi/metadata.xml index 4f4367037..092a8c5e9 100644 --- a/dev-python/sphinx-automodapi/metadata.xml +++ b/dev-python/sphinx-automodapi/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">sphinx-automodapi</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild index f98b972ae..e64b9a0e0 100644 --- a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild +++ b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild @@ -3,13 +3,14 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Sphinx extension for auto-generating API documentation for entire modules" -HOMEPAGE="https://astropy.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://www.astropy.org/" LICENSE="BSD" SLOT="0" diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild index 7680d8206..0a962fd5e 100644 --- a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild +++ b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild @@ -1,15 +1,16 @@ # Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Allow a different format in dosctrings for better clarity" HOMEPAGE="https://sphinxcontrib-napoleon.readthedocs.io/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/spikeinterface/Manifest b/dev-python/spikeinterface/Manifest new file mode 100644 index 000000000..28ed71b4c --- /dev/null +++ b/dev-python/spikeinterface/Manifest @@ -0,0 +1,2 @@ +DIST spikeinterface-0.96.1.tar.gz 1596455 BLAKE2B 52b5d4f0b435433396e7d06b9a2ed83646280ebefb1f62f179f068a060f43898a822e41bf1500ec53087ad5410ee060806f415988606b0197d13d7a671a5603a SHA512 12de90a8d27e900489d36d0ca14edaac3d1abab1a29f0c41ff1d1648fbf11be09c6c01cb0bd1cc4e1d00a81303fab5ffcb4de596ae69be9508e0503edab768ef +DIST spikeinterface-0.97.0.tar.gz 6735715 BLAKE2B c11bee4306f8d96ae5cd09cf1b852e267c1db6caa13565f6364cd65ee36fe62c04589e8e0657517003ed1dd6d76d25f60bef226820403111db4ed7717e8a20cd SHA512 befdf3382de6aad2ef2c72e3bbdf64fbee1c1f72f83610ca8bba2f8693992c84b515f8c000dc6b3609825347b0bcd85b026747633e90777d7fdd30dc0ae0ef13 diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml new file mode 100644 index 000000000..f91c7a26c --- /dev/null +++ b/dev-python/spikeinterface/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="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> + <use> + <flag name="extractors">support for all extractors</flag> + <flag name="full">support for all optional processing features</flag> + </use> + <upstream> + <remote-id type="github">SpikeInterface/spikeinterface</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild new file mode 100644 index 000000000..6dae8d191 --- /dev/null +++ b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild @@ -0,0 +1,93 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." +HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" +SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="extractors full test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + extractors? ( + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) + full? ( + dev-python/distinctipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + ) +" +# Also wants: +# # Extractors: +# MEArec +# pyedflib +# sonpy +# dev-python/hdf5storage (in ::science, masked) + +distutils_enable_tests pytest + +# Test failures reported upstream: +# https://github.com/SpikeInterface/spikeinterface/issues/307 +python_test() { + # Network sandboxing, mostly (?) + local EPYTEST_DESELECT=( + spikeinterface/core/tests/test_datasets.py::test_download_dataset + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid + spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters + spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity + spikeinterface/exporters/tests/test_report.py::test_export_report + spikeinterface/extractors/tests/test_neoextractors.py + spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict + spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity + spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run + spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks + spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks + spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks + spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline + spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates + spikeinterface/widgets/tests/test_widgets.py::TestWidgets + ) + # Reported upstream: + # https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998 + EPYTEST_DESELECT+=( + spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs + ) + local EPYTEST_IGNORE=( + spikeinterface/widgets/_legacy_mpl_widgets/tests/* + ) + epytest +} diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild new file mode 100644 index 000000000..5c4e65481 --- /dev/null +++ b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." +HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" +SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="extractors full test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + extractors? ( + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) + full? ( + dev-python/distinctipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + ) +" +# Also wants: +# # Extractors: +# MEArec +# pyedflib +# sonpy +# dev-python/hdf5storage (in ::science, masked) + +distutils_enable_tests pytest + +# Test failures reported upstream: +# https://github.com/SpikeInterface/spikeinterface/issues/307 +python_test() { + # Network sandboxing, mostly (?) + local EPYTEST_DESELECT=( + spikeinterface/core/tests/test_datasets.py::test_download_dataset + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid + spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters + spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity + spikeinterface/exporters/tests/test_report.py::test_export_report + spikeinterface/extractors/tests/test_neoextractors.py + spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict + spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity + spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run + spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks + spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks + spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks + spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline + spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates + spikeinterface/widgets/tests/test_widgets.py::TestWidgets + ) + # Reported upstream: + # https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998 + EPYTEST_DESELECT+=( + spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs + ) + local EPYTEST_IGNORE=( + spikeinterface/widgets/_legacy_mpl_widgets/tests/* + ) + epytest +} diff --git a/dev-python/stopit/Manifest b/dev-python/stopit/Manifest new file mode 100644 index 000000000..8509ce69f --- /dev/null +++ b/dev-python/stopit/Manifest @@ -0,0 +1 @@ +DIST stopit-1.1.2.tar.gz 18281 BLAKE2B 500c4c60f7a1ae65231f546c28c6406bb1b01c48b43ac97757b87db1c6cfe460b9fb96543a46ec4ff36640e6aa758dbea543f75628bf7bf237e1f76acd54e62e SHA512 5ddf93c12ac19e2a2bf52a22838de13da1cf50f1a4d2ef8958dc3ddccd1884b7edaa629edc29121071ba231bfc1e3188bfa089da6e8fc994364c134f0c7aa0c8 diff --git a/sci-biology/blasr/metadata.xml b/dev-python/stopit/metadata.xml index 8417d1580..21d0546f4 100644 --- a/sci-biology/blasr/metadata.xml +++ b/dev-python/stopit/metadata.xml @@ -2,7 +2,10 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">stopit</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/stopit/stopit-1.1.2.ebuild b/dev-python/stopit/stopit-1.1.2.ebuild new file mode 100644 index 000000000..64d63502a --- /dev/null +++ b/dev-python/stopit/stopit-1.1.2.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2021 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 pypi + +DESCRIPTION="Timeout control decorator and context managers" +HOMEPAGE="https://pypi.org/project/stopit" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" diff --git a/dev-python/texext/Manifest b/dev-python/texext/Manifest index acfea3010..3300b31c6 100644 --- a/dev-python/texext/Manifest +++ b/dev-python/texext/Manifest @@ -1 +1 @@ -DIST texext-0.6.6.tar.gz 38121 BLAKE2B 655ac678ecf1de5f7fa34148bff93c4ba8a28253117afccc197da3e44592024a6ec523452c2e02697275f4061ae2452beae74e9d3fa305eb1faddffb33c992ac SHA512 117a74c85fc36af8921a145e387b560e3c6c115090f777539178021cafac0075077fc81c62d18fa2bbee0b0f59e256274a9526f2a688d00a99ecbda2ac944ccd +DIST texext-0.6.7.gh.tar.gz 42823 BLAKE2B 224cb700f5ee74de75c41d8248a1cbb494f773f8124638974fbabdbffcd2bf72237c55b15e12ea8e5a5086dab02fde798efe5f3519befddb1a4535ed233414a3 SHA512 abdc57f9fd38b3d6e261347a3ba2d7d7400d8b7bd79c2763a40cc34aa72a079fe55dae1fc0117f2da604331a449b2d9168f320a6ecc2f13c62a6615c000523f8 diff --git a/dev-python/texext/texext-0.6.6.ebuild b/dev-python/texext/texext-0.6.7.ebuild index 15d6a83d1..fdeb2350a 100644 --- a/dev-python/texext/texext-0.6.6.ebuild +++ b/dev-python/texext/texext-0.6.7.ebuild @@ -1,15 +1,15 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) +EAPI=8 +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Sphinx extensions for working with LaTeX math" HOMEPAGE="https://github.com/matthew-brett/texext" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +SRC_URI="https://github.com/matthew-brett/texext/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/throttler/Manifest b/dev-python/throttler/Manifest new file mode 100644 index 000000000..fcd07b799 --- /dev/null +++ b/dev-python/throttler/Manifest @@ -0,0 +1 @@ +DIST throttler-1.2.2.gh.tar.gz 8874 BLAKE2B f4f62059483551d2516e0d744ce4de4de1d83c5d169583944f2fba390acc2f6aadd5f212158de2c59b85356d71396a02404051e9206dfffec25be95ae983686a SHA512 a45cba0400e2e6225bcc396d1a216e781be9264345c215aa0c9e009d463bb80fca449ef0cc6a67657c443f9624e0864644cd5187351e815292894176dd6f13bb diff --git a/dev-python/throttler/metadata.xml b/dev-python/throttler/metadata.xml new file mode 100644 index 000000000..dff8139fd --- /dev/null +++ b/dev-python/throttler/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">uburuntu/throttler</remote-id> + <remote-id type="pypi">throttler</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/throttler/throttler-1.2.2.ebuild b/dev-python/throttler/throttler-1.2.2.ebuild new file mode 100644 index 000000000..0d0d62a16 --- /dev/null +++ b/dev-python/throttler/throttler-1.2.2.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Easy throttling with asyncio support" +HOMEPAGE="https://github.com/uburuntu/throttler" +SRC_URI="https://github.com/uburuntu/throttler/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + test? ( + dev-python/pytest-asyncio[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/traits/Manifest b/dev-python/traits/Manifest index 4c0fe0428..8e8de91b3 100644 --- a/dev-python/traits/Manifest +++ b/dev-python/traits/Manifest @@ -1,2 +1,3 @@ -DIST traits-6.0.0.tar.gz 441607 BLAKE2B d8f28e8ccdca8d65a4abb71210f6fe36d6fd2eb07ce5e8f1d374a64cf44e9ce95a318274c68b6791c91f2e105c4f9385e4a743d33434b608ce1d939693958e33 SHA512 b89f844b18c97e2fd2239fc74253e83f255aa231a3d02207a5acf27da7686c32c57cb7c36ffb92a59f7bfa4d98a5e1a95ae2b70e34aa4577a7ae82c8c6756e1e DIST traits-6.1.1.tar.gz 567019 BLAKE2B 4b6ed46c87b1fda2a2001299106b5aacafbe8b148ba0564c4f39b67a8de76f6713366c8b00841db254a26c87a7b2b73b6935ecade770d92ad972aa8a0425cecf SHA512 7f7e9f11d4861c02164ae1ce595888859c8ce23213290cfc3ac11df100d33beeeea4c7def6799b70ef2d090b3f7bd98407f3605affff0867914d0fe0164dd50f +DIST traits-6.3.2.tar.gz 9517139 BLAKE2B 9c6209a24fd07def86699174a66e2e0b3332670d974a75ead9486187c37e1c2c25b2a0c47e5444a03577931411ce6938b3b9ba195261a46c86d660c5abe9b502 SHA512 792004d88d2a00a1e9ba03974d58ec692b620f3c45aaf3bd82f93396818df8663a86903d43806c877230a66c5c8fee4d68268ed9355c166af00b5d060ba14c7d +DIST traits-6.4.1.tar.gz 9527016 BLAKE2B 12036eeb845cc3014b0cba9984e1c1686a6720630678d440a2059c47916c08284b1f823ca566dcb6c1c86594ebec5400bb2a8c44d43d765a25d00e157fbbda74 SHA512 04b936195d57320c02fee9f0d5e7dbcfee28add422c151bd4aaa6d1c58c59f8de7fe54b4df039bb2023ffc9dae9570bba52210cd015ce462e0f736e9439327e5 diff --git a/dev-python/traits/traits-6.1.1.ebuild b/dev-python/traits/traits-6.1.1.ebuild index 677be0b9e..7282ebfa8 100644 --- a/dev-python/traits/traits-6.1.1.ebuild +++ b/dev-python/traits/traits-6.1.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -16,10 +16,12 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" +# Reported upstream: https://github.com/enthought/traits/issues/1731 +RESTRICT="test" RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" -distutils_enable_tests nose +distutils_enable_tests unittest # ToDo: Fix doc building: # AttributeError: 'NoDefaultSpecified' object has no attribute '__name__' #distutils_enable_sphinx docs/source --no-autodoc diff --git a/dev-python/traits/traits-6.0.0.ebuild b/dev-python/traits/traits-6.3.2.ebuild index 0d6ffae85..3d81493f5 100644 --- a/dev-python/traits/traits-6.0.0.ebuild +++ b/dev-python/traits/traits-6.3.2.ebuild @@ -1,43 +1,35 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python" -HOMEPAGE="https://docs.enthought.com/traits/ +HOMEPAGE=" + https://docs.enthought.com/traits/ https://github.com/enthought/traits - https://pypi.org/project/traits/" +" SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/nose[${PYTHON_USEDEP}] - ${RDEPEND} - )" +distutils_enable_tests unittest +# ToDo: Fix doc building: +# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__' +#distutils_enable_sphinx docs/source --no-autodoc python_prepare_all() { sed -i -e "s/'-O3'//g" setup.py || die distutils-r1_python_prepare_all } -python_compile() { - python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" - distutils-r1_python_compile -} - python_test() { cd "${BUILD_DIR}"/lib || die ${EPYTHON} -m unittest discover || die diff --git a/dev-python/traits/traits-6.4.1.ebuild b/dev-python/traits/traits-6.4.1.ebuild new file mode 100644 index 000000000..3d81493f5 --- /dev/null +++ b/dev-python/traits/traits-6.4.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python" +HOMEPAGE=" + https://docs.enthought.com/traits/ + https://github.com/enthought/traits +" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" + +distutils_enable_tests unittest +# ToDo: Fix doc building: +# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__' +#distutils_enable_sphinx docs/source --no-autodoc + +python_prepare_all() { + sed -i -e "s/'-O3'//g" setup.py || die + distutils-r1_python_prepare_all +} + +python_test() { + cd "${BUILD_DIR}"/lib || die + ${EPYTHON} -m unittest discover || die +} diff --git a/dev-python/transforms3d/transforms3d-0.3.1.ebuild b/dev-python/transforms3d/transforms3d-0.3.1.ebuild index ed719c6a5..661d78acb 100644 --- a/dev-python/transforms3d/transforms3d-0.3.1.ebuild +++ b/dev-python/transforms3d/transforms3d-0.3.1.ebuild @@ -1,23 +1,22 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=no +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Functions for 3D coordinate transformations" -HOMEPAGE="https://matthew-brett.github.io/transforms3d" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://matthew-brett.github.io/transforms3d/" LICENSE="BSD-2" KEYWORDS="~amd64 ~x86" SLOT="0" -BDEPEND="test? ( dev-python/numpy[${PYTHON_USEDEP}] )" -RDEPEND=">=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" +RDEPEND=" + >=dev-python/numpy-1.5.1[${PYTHON_USEDEP}] +" -distutils_enable_tests nose +distutils_enable_tests pytest diff --git a/dev-python/tridesclous/Manifest b/dev-python/tridesclous/Manifest new file mode 100644 index 000000000..4bcef3213 --- /dev/null +++ b/dev-python/tridesclous/Manifest @@ -0,0 +1,2 @@ +DIST tridesclous-1.6.4.tar.gz 571689 BLAKE2B c941c159a0aed2f69dd098b5a7073898f305aa04c4db4753fc7de135cf87866fe8857a89b2d1248e3a2dada09229195f2dad557c0c110ac2f061dfe39c8aa257 SHA512 29182af03dc9219c422e37000ceb40787db89408f66b94201bbb2226f97ef251140eafa28a77554aaa1539978c46eece0156d2941c8156212499f544cf42740c +DIST tridesclous-1.6.6.gh.tar.gz 11798502 BLAKE2B af9eb4d4e899f2a065d37e6daaae9ad04209b3d10c250957985ef3603e5d5727947dafff75adf5bb892a4ccbbf2f575f682bd601afcf36bda48f5f7a2af6ab26 SHA512 b101a8a8c2e95b7eb51b7d24d2708a30421be63d48d5a7047dfa2be3ce0f15ce02ce518d5516d5fae3d040cb0d2037a49afd34fdbd03bc641dc42014d8861d0d diff --git a/dev-python/tridesclous/metadata.xml b/dev-python/tridesclous/metadata.xml new file mode 100644 index 000000000..819340cd1 --- /dev/null +++ b/dev-python/tridesclous/metadata.xml @@ -0,0 +1,16 @@ +<?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> + <upstream> + <remote-id type="github">tridesclous/tridesclous</remote-id> + <remote-id type="pypi">tridesclous</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/tridesclous/tridesclous-1.6.4.ebuild b/dev-python/tridesclous/tridesclous-1.6.4.ebuild new file mode 100644 index 000000000..a65c30298 --- /dev/null +++ b/dev-python/tridesclous/tridesclous-1.6.4.ebuild @@ -0,0 +1,101 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="offline/online spike sorting" +HOMEPAGE="https://github.com/tridesclous/tridesclous" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="gui test" + +RDEPEND=" + <dev-python/numpy-1.24.0[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + dev-python/hdbscan[${PYTHON_USEDEP}] + dev-python/loky[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numba + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + gui? ( + dev-python/PyQt5[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +# Network sandboxing, this is sadly more than half the test suite :( +EPYTEST_DESELECT=( + tridesclous/tests/test_cleancluster.py::test_auto_split + tridesclous/tests/test_cleancluster.py::test_trash_not_aligned + tridesclous/tests/test_cleancluster.py::test_auto_merge + tridesclous/tests/test_cleancluster.py::test_trash_low_extremum + tridesclous/tests/test_cleancluster.py::test_trash_small_cluster + tridesclous/tests/test_cluster.py::test_sawchaincut + tridesclous/tests/test_cluster.py::test_pruningshears + tridesclous/tests/test_decomposition.py::test_all_decomposition + tridesclous/tests/test_export.py::test_export + tridesclous/tests/test_export.py::test_export_catalogue_spikes + tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor + tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_signals + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms + tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d + tridesclous/tests/test_metrics.py::test_all_metrics + tridesclous/tests/test_metrics.py::test_cluster_ratio + tridesclous/tests/test_peeler.py::test_peeler_geometry + tridesclous/tests/test_peeler.py::test_peeler_geometry_cl + tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue + tridesclous/tests/test_peeler.py::test_peeler_several_chunksize + tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor + tridesclous/tests/test_peeler.py::test_export_spikes + tridesclous/tests/test_report.py::test_summary_catalogue_clusters + tridesclous/tests/test_report.py::test_summary_noise + tridesclous/tests/test_report.py::test_summary_after_peeler_clusters + tridesclous/tests/test_report.py::test_generate_report + tridesclous/tests/test_autoparams.py::test_get_auto_params + tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue + tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude + tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection + tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps + tridesclous/tests/test_dataio.py::test_DataIO + tridesclous/tests/test_dataio.py::test_DataIO_probes + tridesclous/tests/test_datasets.py::test_download_dataset + tridesclous/tests/test_datasets.py::test_get_dataset + tridesclous/tests/test_datasource.py::test_RawDataSource + tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator + tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines + tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks + tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry + tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines + tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width + tridesclous/tests/test_tools.py::test_fix_prb_file_py2 +) + +python_test() { + local EPYTEST_IGNORE=( + tridesclous/online/tests/* + ) + if use !gui ; then + local EPYTEST_IGNORE+=( + tridesclous/gui/* + ) + fi + epytest +} diff --git a/dev-python/tridesclous/tridesclous-1.6.6.ebuild b/dev-python/tridesclous/tridesclous-1.6.6.ebuild new file mode 100644 index 000000000..13697e657 --- /dev/null +++ b/dev-python/tridesclous/tridesclous-1.6.6.ebuild @@ -0,0 +1,101 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="offline/online spike sorting" +HOMEPAGE="https://github.com/tridesclous/tridesclous" +SRC_URI="https://github.com/tridesclous/tridesclous/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="gui test" + +RDEPEND=" + <dev-python/numpy-1.24.0[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + dev-python/hdbscan[${PYTHON_USEDEP}] + dev-python/loky[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numba + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + gui? ( + dev-python/PyQt5[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +# Network sandboxing, this is sadly more than half the test suite :( +EPYTEST_DESELECT=( + tridesclous/tests/test_cleancluster.py::test_auto_split + tridesclous/tests/test_cleancluster.py::test_trash_not_aligned + tridesclous/tests/test_cleancluster.py::test_auto_merge + tridesclous/tests/test_cleancluster.py::test_trash_low_extremum + tridesclous/tests/test_cleancluster.py::test_trash_small_cluster + tridesclous/tests/test_cluster.py::test_sawchaincut + tridesclous/tests/test_cluster.py::test_pruningshears + tridesclous/tests/test_decomposition.py::test_all_decomposition + tridesclous/tests/test_export.py::test_export + tridesclous/tests/test_export.py::test_export_catalogue_spikes + tridesclous/tests/test_jobtools.py::test_run_parallel_signalprocessor + tridesclous/tests/test_matplotlibplot.py::test_plot_probe_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_signals + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms_with_geometry + tridesclous/tests/test_matplotlibplot.py::test_plot_waveforms + tridesclous/tests/test_matplotlibplot.py::test_plot_features_scatter_2d + tridesclous/tests/test_metrics.py::test_all_metrics + tridesclous/tests/test_metrics.py::test_cluster_ratio + tridesclous/tests/test_peeler.py::test_peeler_geometry + tridesclous/tests/test_peeler.py::test_peeler_geometry_cl + tridesclous/tests/test_peeler.py::test_peeler_empty_catalogue + tridesclous/tests/test_peeler.py::test_peeler_several_chunksize + tridesclous/tests/test_peeler.py::test_peeler_with_and_without_preprocessor + tridesclous/tests/test_peeler.py::test_export_spikes + tridesclous/tests/test_report.py::test_summary_catalogue_clusters + tridesclous/tests/test_report.py::test_summary_noise + tridesclous/tests/test_report.py::test_summary_after_peeler_clusters + tridesclous/tests/test_report.py::test_generate_report + tridesclous/tests/test_autoparams.py::test_get_auto_params + tridesclous/tests/test_catalogueconstructor.py::test_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_make_catalogue + tridesclous/tests/test_catalogueconstructor.py::test_ratio_amplitude + tridesclous/tests/test_catalogueconstructor.py::test_create_savepoint_catalogue_constructor + tridesclous/tests/test_catalogueconstructor.py::test_feature_with_lda_selection + tridesclous/tests/test_cataloguetools.py::test_apply_all_catalogue_steps + tridesclous/tests/test_dataio.py::test_DataIO + tridesclous/tests/test_dataio.py::test_DataIO_probes + tridesclous/tests/test_datasets.py::test_download_dataset + tridesclous/tests/test_datasets.py::test_get_dataset + tridesclous/tests/test_datasource.py::test_RawDataSource + tridesclous/tests/test_datasource.py::test_NeoRawIOAggregator + tridesclous/tests/test_peakdetector.py::test_compare_offline_online_engines + tridesclous/tests/test_peakdetector.py::test_detect_geometrical_peaks + tridesclous/tests/test_peakdetector.py::test_peak_sign_symetry + tridesclous/tests/test_signalpreprocessor.py::test_compare_offline_online_engines + tridesclous/tests/test_signalpreprocessor.py::test_auto_pad_width + tridesclous/tests/test_tools.py::test_fix_prb_file_py2 +) + +python_test() { + local EPYTEST_IGNORE=( + tridesclous/online/tests/* + ) + if use !gui ; then + local EPYTEST_IGNORE+=( + tridesclous/gui/* + ) + fi + epytest +} diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild index 3c32b1184..f597d0175 100644 --- a/dev-python/typish/typish-1.9.3.ebuild +++ b/dev-python/typish/typish-1.9.3.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Functionality for types" diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild b/dev-python/umap-learn/umap-learn-0.5.2.ebuild index f0dc3dab5..45b45b7f1 100644 --- a/dev-python/umap-learn/umap-learn-0.5.2.ebuild +++ b/dev-python/umap-learn/umap-learn-0.5.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/visvis/Manifest b/dev-python/visvis/Manifest index 10c6f487a..5b433e036 100644 --- a/dev-python/visvis/Manifest +++ b/dev-python/visvis/Manifest @@ -1 +1,2 @@ DIST visvis-1.13.0.tar.gz 5095145 BLAKE2B 4c47002902d7ee15f4ccc684b53daec09657422d9e53438a0e91d11ea17b76fd8e413b6caab8fee63752116247b526454bc7830751db1d3bb6d12adab914cc1a SHA512 a2272250060e418c7b78acb51599bf5d440d6d20ffe41d5fbfb3b68f6486b6d9312300dfa94697ff23bdadb2e79a871dc75bf0ba53be3267107d392236693d6a +DIST visvis-1.14.0.tar.gz 4892032 BLAKE2B 564e328d4265676bec35798149ff1283b7289fe04e946ca78b6068ae6f70d1dff809a4ec19b94b1d49a9c3ac7f0b186996070736d3eb4ba4897feac7d03edb6a SHA512 d056ec8a83ac9cee4cbb05806145287fa9dab8064fbc910463255d4510f082ca29f393c309c7b649c6d625f1c368bf5ef28f44de1ebb30ccd1d5650fadb76a81 diff --git a/dev-python/visvis/metadata.xml b/dev-python/visvis/metadata.xml index ae9640ffb..7eac38327 100644 --- a/dev-python/visvis/metadata.xml +++ b/dev-python/visvis/metadata.xml @@ -5,4 +5,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">visvis</remote-id> + <remote-id type="github">almarklein/visvis</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild index 05eb0e162..68d53d30e 100644 --- a/dev-python/visvis/visvis-1.13.0.ebuild +++ b/dev-python/visvis/visvis-1.13.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_SETUPTOOLS=no -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/visvis/visvis-1.14.0.ebuild b/dev-python/visvis/visvis-1.14.0.ebuild new file mode 100644 index 000000000..1f210c0b4 --- /dev/null +++ b/dev-python/visvis/visvis-1.14.0.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2021 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 pypi + +DESCRIPTION="An object oriented approach to visualization of 1D to 4D data" +HOMEPAGE="https://github.com/almarklein/visvis" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/imageio[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/wraps/wraps-0.1.0-r1.ebuild b/dev-python/wraps/wraps-0.1.0-r1.ebuild index 8474019e7..4f51a06f2 100644 --- a/dev-python/wraps/wraps-0.1.0-r1.ebuild +++ b/dev-python/wraps/wraps-0.1.0-r1.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=poetry -PYTHON_COMPAT=( python3_{8..11} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/dev-python/wraps/wraps-0.2.0.ebuild b/dev-python/wraps/wraps-0.2.0.ebuild index f3b37bb5c..0e4ec817c 100644 --- a/dev-python/wraps/wraps-0.2.0.ebuild +++ b/dev-python/wraps/wraps-0.2.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=poetry -PYTHON_COMPAT=( python3_{8..11} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/dev-python/xgboost/xgboost-1.6.2.ebuild b/dev-python/xgboost/xgboost-1.6.2.ebuild index e429f5741..645522c9c 100644 --- a/dev-python/xgboost/xgboost-1.6.2.ebuild +++ b/dev-python/xgboost/xgboost-1.6.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..11} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 diff --git a/dev-python/zarr/zarr-2.11.1.ebuild b/dev-python/zarr/zarr-2.11.1.ebuild index 8cb175408..fb138aad0 100644 --- a/dev-python/zarr/zarr-2.11.1.ebuild +++ b/dev-python/zarr/zarr-2.11.1.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.11.3.ebuild index 1fa4e9af9..aecd66ba9 100644 --- a/dev-python/zarr/zarr-2.11.3.ebuild +++ b/dev-python/zarr/zarr-2.11.3.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -59,4 +59,4 @@ EPYTEST_DESELECT=( ) distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme +distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme diff --git a/dev-python/zarr/zarr-2.12.0.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild index 1fa4e9af9..aecd66ba9 100644 --- a/dev-python/zarr/zarr-2.12.0.ebuild +++ b/dev-python/zarr/zarr-2.12.0.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -59,4 +59,4 @@ EPYTEST_DESELECT=( ) distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme +distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme diff --git a/dev-python/zarr_checksum/Manifest b/dev-python/zarr_checksum/Manifest new file mode 100644 index 000000000..ec799eebf --- /dev/null +++ b/dev-python/zarr_checksum/Manifest @@ -0,0 +1 @@ +DIST zarr_checksum-0.2.8.tar.gz 11824 BLAKE2B b26b6e1b9559e6572c95fb3700afada3c9040dfa1d26f736dcf6edfe4272c2e513f209286e24d7690de9fa2789297075469258f65edc8a2999fa2c4eee58f3ee SHA512 5c79611568decc8b9a353002e96c6ca73ec2c378debcba11f89feecb62089a78a4c3a8f4948971dd1a120a476dba7f357b23ba0b6edcf93d3f44dbb7c531feb5 diff --git a/sci-biology/mouse-brain-atlases/metadata.xml b/dev-python/zarr_checksum/metadata.xml index 16fcf156a..57bdec31a 100644 --- a/sci-biology/mouse-brain-atlases/metadata.xml +++ b/dev-python/zarr_checksum/metadata.xml @@ -9,7 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> - <use> - <flag name="hires">Also install high-resolution atlases.</flag> - </use> + <upstream> + <remote-id type="github">dandi/zarr_checksum</remote-id> + <remote-id type="pypi">zarr_checksum</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild new file mode 100644 index 000000000..47c21433e --- /dev/null +++ b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=poetry + +inherit distutils-r1 pypi + +DESCRIPTION="Calculatine zarr checksums from local or cloud storage" +HOMEPAGE="https://github.com/dandi/zarr_checksum" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/boto3[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest index d58fa0e76..a9f6d958f 100644 --- a/dev-vcs/dandi-cli/Manifest +++ b/dev-vcs/dandi-cli/Manifest @@ -1,4 +1,5 @@ -DIST dandi-0.45.1.tar.gz 321362 BLAKE2B d07296be6bd4237fea4aa83c0b087de45234157aa6aa457f8d44f56b514a4deca11226831182b84c19a72b398183b3b181beb3946c7f8cce2d842ac80f0b57e2 SHA512 07d97420651bbd82d8d4146322ff80873489bd49869834ace9986f1ddc1880be5ff6bd1d625d8b4607a90de8007aeba152e8161af05c25a804cb18c7a0c78e29 DIST dandi-0.46.6.tar.gz 218868 BLAKE2B 7900c153172aa9669d0eae6bc2293ef51d1640b2fdd4e40eb887b1aba555d61617f95fb76601f1e81aeb9e0a54901c711bfb3c95eb478853490b29a0c1ee20e7 SHA512 db04e261205be716d6a098fbb63760411d3869c692df78954b50b649228747e0c18a9a32d3a9b0a5f21f55432e6a6cadad2142ee99168d02f02cfe51bf7eef93 -DIST dandi-cli-0.38.0.gh.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054 -DIST dandi-cli-0.39.4.gh.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b +DIST dandi-0.48.0.tar.gz 228206 BLAKE2B 5cef713220839751b873170223bead06effddedf4b0d98d7de134fb87d64a4cc49521dd26d6a90777d331e77649c271466af9e30fd2511d72a3e505b5a904fbe SHA512 2e6686169105299f39f66d32542ce0e2d9d9fd9035f306c537771218ef8ced9832e6ea7911259623112604d83675aa52322410078eb7d00b6f83ec77a2cbc2c6 +DIST dandi-0.49.0.tar.gz 227445 BLAKE2B d698327fa12fa4dc1d3b1816181c8eb99eed1ac57a8ea9d5fddf96b9b8267313993053f39deeddfc3f4f3123a609d82b79dba69bb4decf30a2cd9903daa1effd SHA512 f3174a16fe1ddea894fad3ed8fdafca3b7664bdb110b5a8e3e3305f08705afa1ef985729aafea95ffdd59b1073fa9bb284ae00856291f4bd80bc9afd8e7f1bc8 +DIST dandi-0.50.0.tar.gz 236960 BLAKE2B b36f890e7d7de77ed2202d54516c897fb293ca5b360849199a0cd5fbe61ff07056b328eb3454f72b974a53ddef24ede5180c7f32b32b663c4bbe77f513301fa3 SHA512 91beb1b2330ab425a7cb4f744e2f11c3e5ab5f631903b05b676be898dba4ca16c42c2f9abb21b45858b50bb00c181fab341303846c9ccf416ddcd88c19136ffa +DIST dandi-0.51.0.tar.gz 233955 BLAKE2B 500a6290cba32f413610879357c0ee525d877575c4ad520818a556ae7f58f90c2aec88387dbb0ca78e7906b48673c2c2d3c9c457833727fb312e5ca6d75ce088 SHA512 e77fa803dd2707df8cab2318377a71c28abb8bdc6e2d086cb43daf24512f361e533d249dabd88bfc6c0de06e6332606ac2f3c57482ae9717fedb66da4e2e8d89 diff --git a/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild index 581257bdb..963aacdd4 100644 --- a/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild +++ b/dev-vcs/dandi-cli/dandi-cli-0.46.6.ebuild @@ -1,19 +1,19 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_{10..10} ) -inherit distutils-r1 +inherit distutils-r1 pypi MY_PN="dandi" MY_P="${MY_PN}-${PV}" DESCRIPTION="DANDI command line client to facilitate common operations" HOMEPAGE="https://github.com/dandi/dandi-cli" -SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" +SRC_URI="$(pypi_sdist_url dandi)" LICENSE="Apache-2.0" SLOT="0" diff --git a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild index 0453e2f00..963aacdd4 100644 --- a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild +++ b/dev-vcs/dandi-cli/dandi-cli-0.48.0.ebuild @@ -1,20 +1,19 @@ -# Copyright 1999-2022 Gentoo Authors +# 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_{8..10} ) +PYTHON_COMPAT=( python3_{10..10} ) -inherit distutils-r1 +inherit distutils-r1 pypi MY_PN="dandi" MY_P="${MY_PN}-${PV}" DESCRIPTION="DANDI command line client to facilitate common operations" HOMEPAGE="https://github.com/dandi/dandi-cli" -#SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" -SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" +SRC_URI="$(pypi_sdist_url dandi)" LICENSE="Apache-2.0" SLOT="0" diff --git a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.49.0.ebuild index a83a0b219..8bbba64e8 100644 --- a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild +++ b/dev-vcs/dandi-cli/dandi-cli-0.49.0.ebuild @@ -1,16 +1,19 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..10} ) -inherit distutils-r1 +inherit distutils-r1 pypi + +MY_PN="dandi" +MY_P="${MY_PN}-${PV}" DESCRIPTION="DANDI command line client to facilitate common operations" HOMEPAGE="https://github.com/dandi/dandi-cli" -SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +SRC_URI="$(pypi_sdist_url dandi)" LICENSE="Apache-2.0" SLOT="0" @@ -18,10 +21,11 @@ KEYWORDS="~amd64" IUSE="test etelemetry" RDEPEND=" + =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}] + >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/click[${PYTHON_USEDEP}] dev-python/click-didyoumean[${PYTHON_USEDEP}] - ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] dev-python/fasteners[${PYTHON_USEDEP}] dev-python/fscacher[${PYTHON_USEDEP}] dev-python/humanize[${PYTHON_USEDEP}] @@ -32,7 +36,6 @@ RDEPEND=" dev-python/nwbinspector[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] dev-python/pycryptodome[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] dev-python/pynwb[${PYTHON_USEDEP}] dev-python/pyout[${PYTHON_USEDEP}] dev-python/python-dateutil[${PYTHON_USEDEP}] @@ -42,6 +45,7 @@ RDEPEND=" dev-python/tenacity[${PYTHON_USEDEP}] dev-python/wheel[${PYTHON_USEDEP}] dev-python/zarr[${PYTHON_USEDEP}] + dev-python/zarr_checksum[${PYTHON_USEDEP}] " BDEPEND=" @@ -56,22 +60,10 @@ BDEPEND=" # Upstream might be amenable to dropping opencv: # https://github.com/dandi/dandi-cli/issues/944 -# Some tests require deep copy with git history -# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299 -EPYTEST_DESELECT=( - "dandi/tests/test_utils.py::test_get_instance_dandi_with_api" - "dandi/tests/test_utils.py::test_get_instance_url" - "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old" - "dandi/tests/test_utils.py::test_get_instance_bad_cli_version" -) +S="${WORKDIR}/${MY_P}" distutils_enable_tests pytest -PATCHES=( - "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch" - "${FILESDIR}/${PN}-0.37.0-pep517.patch" -) - src_prepare() { if use etelemetry; then default diff --git a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.50.0.ebuild index 1842cbb5e..8bbba64e8 100644 --- a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild +++ b/dev-vcs/dandi-cli/dandi-cli-0.50.0.ebuild @@ -1,16 +1,19 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..10} ) -inherit distutils-r1 +inherit distutils-r1 pypi + +MY_PN="dandi" +MY_P="${MY_PN}-${PV}" DESCRIPTION="DANDI command line client to facilitate common operations" HOMEPAGE="https://github.com/dandi/dandi-cli" -SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +SRC_URI="$(pypi_sdist_url dandi)" LICENSE="Apache-2.0" SLOT="0" @@ -18,10 +21,11 @@ KEYWORDS="~amd64" IUSE="test etelemetry" RDEPEND=" + =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}] + >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/click[${PYTHON_USEDEP}] dev-python/click-didyoumean[${PYTHON_USEDEP}] - ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] dev-python/fasteners[${PYTHON_USEDEP}] dev-python/fscacher[${PYTHON_USEDEP}] dev-python/humanize[${PYTHON_USEDEP}] @@ -29,9 +33,9 @@ RDEPEND=" dev-python/joblib[${PYTHON_USEDEP}] dev-python/keyring[${PYTHON_USEDEP}] dev-python/keyrings-alt[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] dev-python/pycryptodome[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] dev-python/pynwb[${PYTHON_USEDEP}] dev-python/pyout[${PYTHON_USEDEP}] dev-python/python-dateutil[${PYTHON_USEDEP}] @@ -41,9 +45,10 @@ RDEPEND=" dev-python/tenacity[${PYTHON_USEDEP}] dev-python/wheel[${PYTHON_USEDEP}] dev-python/zarr[${PYTHON_USEDEP}] + dev-python/zarr_checksum[${PYTHON_USEDEP}] " -DEPEND=" +BDEPEND=" test? ( dev-python/anys[${PYTHON_USEDEP}] dev-python/responses[${PYTHON_USEDEP}] @@ -55,22 +60,10 @@ DEPEND=" # Upstream might be amenable to dropping opencv: # https://github.com/dandi/dandi-cli/issues/944 -# Some tests require deep copy with git history -# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299 -EPYTEST_DESELECT=( - "dandi/tests/test_utils.py::test_get_instance_dandi_with_api" - "dandi/tests/test_utils.py::test_get_instance_url" - "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old" - "dandi/tests/test_utils.py::test_get_instance_bad_cli_version" -) +S="${WORKDIR}/${MY_P}" distutils_enable_tests pytest -PATCHES=( - "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch" - "${FILESDIR}/${PN}-0.37.0-pep517.patch" -) - src_prepare() { if use etelemetry; then default diff --git a/dev-vcs/dandi-cli/dandi-cli-0.51.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.51.0.ebuild new file mode 100644 index 000000000..e4da9cb75 --- /dev/null +++ b/dev-vcs/dandi-cli/dandi-cli-0.51.0.ebuild @@ -0,0 +1,80 @@ +# 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..10} ) + +inherit distutils-r1 pypi + +MY_PN="dandi" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="DANDI command line client to facilitate common operations" +HOMEPAGE="https://github.com/dandi/dandi-cli" +SRC_URI="$(pypi_sdist_url dandi)" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test etelemetry" + +RDEPEND=" + =dev-python/dandi-schema-0.8*[${PYTHON_USEDEP}] + >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] + dev-python/appdirs[${PYTHON_USEDEP}] + dev-python/click-didyoumean[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + dev-python/fscacher[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/interleave[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/keyrings-alt[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pycryptodome[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyout[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/semantic_version[${PYTHON_USEDEP}] + dev-python/tenacity[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + dev-python/zarr_checksum[${PYTHON_USEDEP}] +" + +BDEPEND=" + test? ( + dev-python/anys[${PYTHON_USEDEP}] + dev-python/responses[${PYTHON_USEDEP}] + dev-python/pyfakefs[${PYTHON_USEDEP}] + dev-python/pytest-mock[${PYTHON_USEDEP}] + media-libs/opencv[ffmpeg,${PYTHON_USEDEP}] + ) +" +# Upstream might be amenable to dropping opencv: +# https://github.com/dandi/dandi-cli/issues/944 + +S="${WORKDIR}/${MY_P}" + +distutils_enable_tests pytest + +src_prepare() { + if use etelemetry; then + default + else + eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch" + default + sed -i "/etelemetry/d" setup.cfg + fi +} + +python_test() { + export DANDI_TESTS_NONETWORK=1 + epytest +} diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest index 521f7a0be..92f325b66 100644 --- a/dev-vcs/datalad/Manifest +++ b/dev-vcs/datalad/Manifest @@ -1,4 +1,2 @@ -DIST datalad-0.16.1.tar.gz 1472447 BLAKE2B b62f2fb37d0bc5cdaa8fd36f1bdea1beab4b4c071ba32c45b1ba5f2036788e4dc4767b406b20c0e0ccf3a5e02fbcb77b73ac9d8f254d02d6004ce909a94bffb5 SHA512 7236e635f8c9b9fbc9f82776d325dce1585d9a99d767b66f2877fb935d788c36335562ae8679821dea1b433f5d122f687e0c6b2098d8e388b8f8f6134751cc5b -DIST datalad-0.17.0.tar.gz 1510529 BLAKE2B 797a4d15139a88d20f03d1b81cf8b19088cf91925852a0a0d2079b3a64debfaa4945c31f21cc701ac507b00c1eabe10eb57653d8cbef1914d2c7babc48324458 SHA512 fea35a574f13b4957149f87553c80eceaebde064921e5fa28960b088e6d8f38a2eb2cbf797c9e031bd696bdca1400c2baa4c3e94c2b78bf8c1349a752928b09c -DIST datalad-0.17.2.tar.gz 1512123 BLAKE2B 83f1d437f6a2d300c169710fd12c8e126e5ab89aee9f0ccda48325c13c26a7e895fc11d33e61a266d7e4f5ac976244950851080055639b679819f659286c3c57 SHA512 7eceaea6bd0f0e251f194d8c1846e5abfff46174c536a42c1c0f891ca06f9688f8d291dec706f4ca51128d6588ceaf28039d80e63ebc5a15417bca3c74f0d866 -DIST datalad-0.17.7.tar.gz 1534265 BLAKE2B daeee7a6ca66ac632b085ce1fed2a702f3189da195d50b3fe5bc63c568c2f6633dbcc6da91883f64dd8d2391d8cfdef9bdbcd28091b098fc9edde6ca743767c1 SHA512 b01442bdd672e6ab0ebfe7fc71721437e117df0ddbe68558b8c21d4f5d387de807870250eac83630e52d2bb5ecf69686b5679c2a1458edb13b7e2a940c4e1330 +DIST datalad-0.18.0.tar.gz 1425155 BLAKE2B 8d7cbf7f56b1de82c74fa823b2d4512112f1b4c4be106cac433c8db696b2e7f77da758c0bb62b7cb9fe0fbb08d49431dda2818d08d5c60b5052154895c335b33 SHA512 0df8276edc3872c73fee7286ea4e578648a6fb2a630fa49a4f8945e0d6ff88353d9b11d29d942c0ce22ed17a8223e71f99d8b519a6a8afbc2ac9e6da89d95ee5 +DIST datalad-0.18.1.tar.gz 1425820 BLAKE2B 574e864feb500062f829dfea3f9c8c51f9ad2e0e68e70966c2a5ea315fafffb259de9a0f57427c0aae1ee93c24ec9a3a91ef42637d109d912cf5b6c41ac07b11 SHA512 19f011428fe66d9f21410ae33276133f26cf2b1a367c23a83c56ab48a0e038837ba18163e12ab2d74eba7d0ec9ce2e660a21494ddba0da3a2df6da2c043c4aad diff --git a/dev-vcs/datalad/datalad-0.16.1-r1.ebuild b/dev-vcs/datalad/datalad-0.16.1-r1.ebuild deleted file mode 100644 index d1592fbf6..000000000 --- a/dev-vcs/datalad/datalad-0.16.1-r1.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Keep code, data, containers under control with git and git-annex" -HOMEPAGE="https://github.com/datalad/datalad" -SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test +downloaders +metadata +publish misc" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-arch/p7zip - dev-python/annexremote[${PYTHON_USEDEP}] - dev-vcs/git-annex - dev-python/appdirs[${PYTHON_USEDEP}] - >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] - dev-python/distro[${PYTHON_USEDEP}] - dev-python/iso8601[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - app-arch/patool[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/wrapt[${PYTHON_USEDEP}] - downloaders? ( - dev-python/boto[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings-alt[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - ) - metadata? ( - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/whoosh[${PYTHON_USEDEP}] - ) - misc? ( - dev-python/argcomplete[${PYTHON_USEDEP}] - dev-python/pyperclip[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - ) - publish? ( - dev-vcs/python-gitlab[${PYTHON_USEDEP}] - dev-python/PyGithub[${PYTHON_USEDEP}] - ) -" -BDEPEND=" - dev-python/packaging[${PYTHON_USEDEP}] - test? ( - ${RDEPEND} - dev-python/beautifulsoup4[${PYTHON_USEDEP}] - dev-python/httpretty[${PYTHON_USEDEP}] - dev-python/vcrpy[${PYTHON_USEDEP}] - ) -" - -# Noticed by upstream: -# https://github.com/datalad/datalad/issues/6623 -PATCHES=( "${FILESDIR}/${P}-input.patch" ) - -distutils_enable_tests nose - -python_test() { - export DATALAD_TESTS_NONETWORK=1 - ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die - # Full test suite takes for ever: - # ${EPYTHON} -m nose -s -v datalad || die -} diff --git a/dev-vcs/datalad/datalad-0.17.0-r1.ebuild b/dev-vcs/datalad/datalad-0.17.0-r1.ebuild deleted file mode 100644 index 8e2de55bb..000000000 --- a/dev-vcs/datalad/datalad-0.17.0-r1.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Keep code, data, containers under control with git and git-annex" -HOMEPAGE="https://github.com/datalad/datalad" -SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test +downloaders +metadata +publish misc" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-arch/p7zip - app-arch/patool[${PYTHON_USEDEP}] - dev-vcs/git-annex - dev-python/annexremote[${PYTHON_USEDEP}] - >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] - dev-python/distro[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/iso8601[${PYTHON_USEDEP}] - dev-python/platformdirs[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/wraps[${PYTHON_USEDEP}] - downloaders? ( - dev-python/boto[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings-alt[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - ) - metadata? ( - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/whoosh[${PYTHON_USEDEP}] - ) - misc? ( - dev-python/argcomplete[${PYTHON_USEDEP}] - dev-python/pyperclip[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - ) - publish? ( - dev-vcs/python-gitlab[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/beautifulsoup4[${PYTHON_USEDEP}] - dev-python/httpretty[${PYTHON_USEDEP}] - dev-python/nose[${PYTHON_USEDEP}] - dev-python/vcrpy[${PYTHON_USEDEP}] - ) -" - -# Noticed by upstream: -# https://github.com/datalad/datalad/issues/6623 -PATCHES=( "${FILESDIR}/${PN}-0.17.0-skip.patch" ) - -EPYTEST_DESELECT=( - # Reported upstream: https://github.com/datalad/datalad/issues/6870 - datalad/tests/test_misc.py::test_test - datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper -) - -distutils_enable_tests pytest - -python_test() { - local -x DATALAD_TESTS_NONETWORK=1 - #export DATALAD_TESTS_NONETWORK=1 - epytest -k "not turtle and not slow and not usecase" - #epytest -k "not turtle" - #${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die - # Full test suite takes for ever: - # ${EPYTHON} -m nose -s -v datalad || die -} diff --git a/dev-vcs/datalad/datalad-0.17.7.ebuild b/dev-vcs/datalad/datalad-0.18.0.ebuild index fc8276b00..69b1a5cb5 100644 --- a/dev-vcs/datalad/datalad-0.17.7.ebuild +++ b/dev-vcs/datalad/datalad-0.18.0.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Keep code, data, containers under control with git and git-annex" @@ -18,18 +18,19 @@ IUSE="test +downloaders +metadata +publish misc" RESTRICT="!test? ( test )" RDEPEND=" + >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] app-arch/p7zip app-arch/patool[${PYTHON_USEDEP}] - dev-vcs/git-annex dev-python/annexremote[${PYTHON_USEDEP}] - >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] dev-python/distro[${PYTHON_USEDEP}] dev-python/fasteners[${PYTHON_USEDEP}] dev-python/humanize[${PYTHON_USEDEP}] dev-python/iso8601[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] dev-python/platformdirs[${PYTHON_USEDEP}] dev-python/tqdm[${PYTHON_USEDEP}] dev-python/wraps[${PYTHON_USEDEP}] + dev-vcs/git-annex downloaders? ( dev-python/boto[${PYTHON_USEDEP}] dev-python/keyring[${PYTHON_USEDEP}] @@ -50,28 +51,20 @@ RDEPEND=" dev-vcs/python-gitlab[${PYTHON_USEDEP}] ) " -BEPEND=" +BDEPEND=" dev-python/packaging[${PYTHON_USEDEP}] test? ( ${RDEPEND} dev-python/beautifulsoup4[${PYTHON_USEDEP}] dev-python/httpretty[${PYTHON_USEDEP}] dev-python/mypy[${PYTHON_USEDEP}] - dev-python/nose[${PYTHON_USEDEP}] dev-python/vcrpy[${PYTHON_USEDEP}] ) " -# also wants base RDEPEND: -# looseversion # Also wants test dep: # dev-python/types-requests # dev-python/types-python-dateutil -EPYTEST_DESELECT=( - # Reported upstream: https://github.com/datalad/datalad/issues/6870 - datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper -) - distutils_enable_tests pytest python_test() { diff --git a/dev-vcs/datalad/datalad-0.17.2-r1.ebuild b/dev-vcs/datalad/datalad-0.18.1.ebuild index c06056657..69b1a5cb5 100644 --- a/dev-vcs/datalad/datalad-0.17.2-r1.ebuild +++ b/dev-vcs/datalad/datalad-0.18.1.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Keep code, data, containers under control with git and git-annex" @@ -18,18 +18,19 @@ IUSE="test +downloaders +metadata +publish misc" RESTRICT="!test? ( test )" RDEPEND=" + >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] app-arch/p7zip app-arch/patool[${PYTHON_USEDEP}] - dev-vcs/git-annex dev-python/annexremote[${PYTHON_USEDEP}] - >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] dev-python/distro[${PYTHON_USEDEP}] dev-python/fasteners[${PYTHON_USEDEP}] dev-python/humanize[${PYTHON_USEDEP}] dev-python/iso8601[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] dev-python/platformdirs[${PYTHON_USEDEP}] dev-python/tqdm[${PYTHON_USEDEP}] dev-python/wraps[${PYTHON_USEDEP}] + dev-vcs/git-annex downloaders? ( dev-python/boto[${PYTHON_USEDEP}] dev-python/keyring[${PYTHON_USEDEP}] @@ -56,16 +57,13 @@ BDEPEND=" ${RDEPEND} dev-python/beautifulsoup4[${PYTHON_USEDEP}] dev-python/httpretty[${PYTHON_USEDEP}] - dev-python/nose[${PYTHON_USEDEP}] + dev-python/mypy[${PYTHON_USEDEP}] dev-python/vcrpy[${PYTHON_USEDEP}] ) " - -EPYTEST_DESELECT=( - # Reported upstream: https://github.com/datalad/datalad/issues/6870 - datalad/distributed/tests/test_ria_basics.py::test_version_check - datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper -) +# Also wants test dep: +# dev-python/types-requests +# dev-python/types-python-dateutil distutils_enable_tests pytest diff --git a/dev-vcs/datalad/files/datalad-0.16.1-input.patch b/dev-vcs/datalad/files/datalad-0.16.1-input.patch deleted file mode 100644 index 97d16e70a..000000000 --- a/dev-vcs/datalad/files/datalad-0.16.1-input.patch +++ /dev/null @@ -1,131 +0,0 @@ -diff --git a/datalad/local/tests/test_gitcredential.py b/datalad/local/tests/test_gitcredential.py -index 09387a70d..6dc0e0be4 100644 ---- a/datalad/local/tests/test_gitcredential.py -+++ b/datalad/local/tests/test_gitcredential.py -@@ -70,89 +70,6 @@ def test_gitcredential_interface(path): - assert_false(cred['password']) - - --@with_tempfile --def test_datalad_credential_helper(path): -- -- ds = Dataset(path).create() -- -- # tell git to use git-credential-datalad -- ds.config.add('credential.helper', 'datalad', where='local') -- ds.config.add('datalad.credentials.githelper.noninteractive', 'true', -- where='global') -- -- from datalad.downloaders.providers import Providers -- -- url1 = "https://datalad-test.org/some" -- url2 = "https://datalad-test.org/other" -- provider_name = "datalad-test.org" -- -- # `Providers` code is old and only considers a dataset root based on PWD -- # for config lookup. contextmanager below can be removed once the -- # provider/credential system is redesigned. -- with chpwd(ds.path): -- -- gitcred = GitCredentialInterface(url=url1, repo=ds) -- -- # There's nothing set up yet, helper should return empty -- gitcred.fill() -- eq_(gitcred['username'], '') -- eq_(gitcred['password'], '') -- -- # store new credentials -- # Note, that `Providers.enter_new()` currently uses user-level config -- # files for storage only. TODO: make that an option! -- # To not mess with existing ones, fail if it already exists: -- -- cfg_file = Path(Providers._get_providers_dirs()['user']) \ -- / f"{provider_name}.cfg" -- assert_false(cfg_file.exists()) -- -- # Make sure we clean up -- from datalad.tests import _TEMP_PATHS_GENERATED -- _TEMP_PATHS_GENERATED.append(str(cfg_file)) -- -- # Give credentials to git and ask it to store them: -- gitcred = GitCredentialInterface(url=url1, username="dl-user", -- password="dl-pwd", repo=ds) -- gitcred.approve() -- -- assert_true(cfg_file.exists()) -- providers = Providers.from_config_files() -- p1 = providers.get_provider(url=url1, only_nondefault=True) -- assert_is_instance(p1.credential, UserPassword) -- eq_(p1.credential.get('user'), 'dl-user') -- eq_(p1.credential.get('password'), 'dl-pwd') -- -- # default regex should be host only, so matching url2, too -- p2 = providers.get_provider(url=url2, only_nondefault=True) -- assert_is_instance(p1.credential, UserPassword) -- eq_(p1.credential.get('user'), 'dl-user') -- eq_(p1.credential.get('password'), 'dl-pwd') -- -- # git, too, should now find it for both URLs -- gitcred = GitCredentialInterface(url=url1, repo=ds) -- gitcred.fill() -- eq_(gitcred['username'], 'dl-user') -- eq_(gitcred['password'], 'dl-pwd') -- -- gitcred = GitCredentialInterface(url=url2, repo=ds) -- gitcred.fill() -- eq_(gitcred['username'], 'dl-user') -- eq_(gitcred['password'], 'dl-pwd') -- -- # Rejection must not currently lead to deleting anything, since we would -- # delete too broadly. -- gitcred.reject() -- assert_true(cfg_file.exists()) -- gitcred = GitCredentialInterface(url=url1, repo=ds) -- gitcred.fill() -- eq_(gitcred['username'], 'dl-user') -- eq_(gitcred['password'], 'dl-pwd') -- dlcred = UserPassword(name=provider_name) -- eq_(dlcred.get('user'), 'dl-user') -- eq_(dlcred.get('password'), 'dl-pwd') -- -- - @with_tempfile - def test_credential_cycle(path): - ---- a/datalad/distribution/tests/test_siblings.py 2022-10-24 16:06:18.740935265 -0400 -+++ b/datalad/distribution/tests/test_siblings.py 2022-10-24 16:08:43.054322297 -0400 -@@ -9,6 +9,8 @@ - - """ - -+from nose import SkipTest -+ - from datalad.support.path import ( - basename, - join as opj, -@@ -504,6 +504,7 @@ - @with_tempfile(mkdir=True) - @serve_path_via_http - def test_as_common_datasource(testbed, viapath, viaurl, remotepath, url): -+ raise SkipTest("Known to fail in Portage environment.") - ds = Dataset(remotepath).create() - (ds.pathobj / 'testfile').write_text('likemagic') - (ds.pathobj / 'testfile2').write_text('likemagic2') ---- a/datalad/local/tests/test_add_archive_content.py -+++ b/datalad/local/tests/test_add_archive_content.py -@@ -13,6 +13,7 @@ - __docformat__ = 'restructuredtext' - - import os -+from nose import SkipTest - from glob import glob - from os import unlink - from os.path import ( -@@ -514,6 +515,7 @@ - assert_false(lexists(self.ds.pathobj / '1.tar')) - - def test_add_archive_leading_dir(self): -+ raise SkipTest("Known to fail in Portage environment.") - import os - os.mkdir(self.ds.pathobj / 'sub') - f123 = Path('sub') / '123.tar' diff --git a/dev-vcs/datalad/files/datalad-0.16.1-tests.patch b/dev-vcs/datalad/files/datalad-0.16.1-tests.patch deleted file mode 100644 index e6231b7f1..000000000 --- a/dev-vcs/datalad/files/datalad-0.16.1-tests.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/datalad-0.16.1/datalad/distribution/tests/test_siblings.py 2022-10-24 16:06:18.740935265 -0400 -+++ b/datalad-0.16.1/datalad/distribution/tests/test_siblings.py 2022-10-24 16:08:43.054322297 -0400 -@@ -504,6 +504,7 @@ - @with_tempfile(mkdir=True) - @serve_path_via_http - def test_as_common_datasource(testbed, viapath, viaurl, remotepath, url): -+ raise SkipTest("Known to fail in Portage environment.") - ds = Dataset(remotepath).create() - (ds.pathobj / 'testfile').write_text('likemagic') - (ds.pathobj / 'testfile2').write_text('likemagic2') diff --git a/dev-vcs/datalad/files/datalad-0.17.0-skip.patch b/dev-vcs/datalad/files/datalad-0.17.0-skip.patch deleted file mode 100644 index 33b2d6f63..000000000 --- a/dev-vcs/datalad/files/datalad-0.17.0-skip.patch +++ /dev/null @@ -1,162 +0,0 @@ ---- a/datalad/tests/utils_pytest.py 2022-07-08 01:32:06.000000000 -0400 -+++ b/datalad/tests/utils_pytest.py 2022-07-21 05:07:09.341386460 -0400 -@@ -209,7 +209,7 @@ - try: - imp = __import__(module) - except Exception as exc: -- pytest.skip("Module %s fails to load" % module) -+ pytest.skip("Module %s fails to load" % module, allow_module_level=True) - - - def skip_if_scrapy_without_selector(): -@@ -220,7 +220,9 @@ - except ImportError: - pytest.skip( - "scrapy misses Selector (too old? version: %s)" -- % getattr(scrapy, '__version__')) -+ % getattr(scrapy, '__version__'), -+ allow_module_level=True, -+ ) - - - def skip_if_url_is_not_available(url, regex=None): -@@ -231,9 +233,11 @@ - try: - content = providers.fetch(url) - if regex and re.search(regex, content): -- pytest.skip("%s matched %r -- skipping the test" % (url, regex)) -+ pytest.skip("%s matched %r -- skipping the test" % (url, regex), -+ allow_module_level=True, -+ ) - except DownloadError: -- pytest.skip("%s failed to download" % url) -+ pytest.skip("%s failed to download" % url, allow_module_level=True) - - - def check_not_generatorfunction(func): -@@ -252,7 +256,9 @@ - - def check_and_raise(): - if dl_cfg.get('datalad.tests.nonetwork'): -- pytest.skip("Skipping since no network settings") -+ pytest.skip("Skipping since no network settings", -+ allow_module_level=True, -+ ) - - if func: - @wraps(func) -@@ -273,7 +279,7 @@ - - def check_and_raise(): - if on_windows: -- pytest.skip("Skipping on Windows") -+ pytest.skip("Skipping on Windows", allow_module_level=True) - - if func: - @wraps(func) -@@ -296,7 +302,9 @@ - - def check_and_raise(): - if hasattr(os, "geteuid") and os.geteuid() == 0: -- pytest.skip("Skipping: test assumptions fail under root") -+ pytest.skip("Skipping: test assumptions fail under root", -+ allow_module_level=True, -+ ) - - if func: - @wraps(func) -@@ -333,7 +341,9 @@ - def _wrap_skip_if(*args, **kwargs): - if cond: - if method == 'raise': -- pytest.skip(msg if msg else "condition was True") -+ pytest.skip(msg if msg else "condition was True", -+ allow_module_level=True, -+ ) - elif method == 'pass': - print(msg if msg else "condition was True") - return -@@ -375,7 +385,7 @@ - @skip_ssh - def _wrap_skip_nomultiplex_ssh(*args, **kwargs): - if SSHManager is not MultiplexSSHManager: -- pytest.skip("SSH without multiplexing is used") -+ pytest.skip("SSH without multiplexing is used", allow_module_level=True) - return func(*args, **kwargs) - return _wrap_skip_nomultiplex_ssh - -@@ -784,7 +794,7 @@ - port = queue.get(timeout=300) - except multiprocessing.queues.Empty as e: - if self.use_ssl: -- pytest.skip('No working SSL support') -+ pytest.skip('No working SSL support', allow_module_level=True) - else: - raise - self.url = 'http{}://{}:{}/'.format( -@@ -822,7 +832,7 @@ - #except requests.exceptions.SSLError as e: - except Exception as e: - self.stop() -- pytest.skip('No working HTTPS setup') -+ pytest.skip('No working HTTPS setup', allow_module_level=True) - # now verify that the stdlib tooling also works - # if this fails, check datalad/tests/ca/prov.sh - # for info on deploying a datalad-root.crt -@@ -843,7 +853,7 @@ - #except URLError as e: - except Exception as e: - self.stop() -- pytest.skip('No working HTTPS setup') -+ pytest.skip('No working HTTPS setup', allow_module_level=True) - - def stop(self): - """Stop serving `path`. -@@ -911,7 +921,7 @@ - @attr('without_http_proxy') - def _wrap_without_http_proxy(*args, **kwargs): - if on_windows: -- pytest.skip('Unclear why this is not working on windows') -+ pytest.skip('Unclear why this is not working on windows', allow_module_level=True) - # Such tests don't require real network so if http_proxy settings were - # provided, we remove them from the env for the duration of this run - env = os.environ.copy() -@@ -1246,7 +1256,9 @@ - assert(testrepos_uris) - else: - if not testrepos_uris: -- pytest.skip("No non-networked repos to test on") -+ pytest.skip("No non-networked repos to test on", -+ allow_module_level=True, -+ ) - - fake_dates = dl_cfg.get("datalad.fake-dates") - ntested = 0 -@@ -1298,7 +1310,7 @@ - # https://git-annex.branchable.com/bugs/Recent_hang_with_rsync_remote_with_older_systems___40__Xenial__44___Jessie__41__/ - if external_versions['cmd:system-ssh'] < '7.4' and \ - '8.20200522' < external_versions['cmd:annex'] < '8.20200720': -- pytest.skip("Test known to hang") -+ pytest.skip("Test known to hang", allow_module_level=True) - - sr_path, repo_path = args[-2:] - fn_args = args[:-2] -@@ -2089,7 +2101,7 @@ - _TESTS_ADJUSTED_TMPDIR = _check() - - if _TESTS_ADJUSTED_TMPDIR: -- pytest.skip("Test incompatible with adjusted branch default") -+ pytest.skip("Test incompatible with adjusted branch default", allow_module_level=True) - return func(*args, **kwargs) - return _wrap_skip_if_adjusted_branch - -@@ -2134,7 +2146,9 @@ - - if port is None: - pytest.skip("port for {} could not be determined: {}" -- .format(host, err)) -+ .format(host, err), -+ allow_module_level=True, -+ ) - return port - diff --git a/eclass/intel-sdp-r1.eclass b/eclass/intel-sdp-r1.eclass deleted file mode 100644 index 9d902395f..000000000 --- a/eclass/intel-sdp-r1.eclass +++ /dev/null @@ -1,571 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -# @ECLASS: intel-sdp-r1.eclass -# @MAINTAINER: -# Justin Lecher <jlec@gentoo.org> -# David Seifert <soap@gentoo.org> -# Sci Team <sci@gentoo.org> -# @BLURB: Handling of Intel's Software Development Products package management - -MULTILIB_COMPAT=( abi_x86_{32,64} ) - -inherit check-reqs eutils multilib-build - -EXPORT_FUNCTIONS src_unpack src_install pkg_postinst pkg_postrm pkg_pretend - -if [[ ! ${_INTEL_SDP_R1_ECLASS_} ]]; then - -case "${EAPI}" in - 7) ;; - *) die "EAPI=${EAPI} is not supported" ;; -esac - -# @ECLASS-VARIABLE: INTEL_DIST_NAME -# @DESCRIPTION: -# The package name to download from Intel. -# To determine its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. parallel_studio_xe -# -# Must be defined before inheriting the eclass. -: ${INTEL_DIST_NAME:=parallel_studio_xe} - -# @ECLASS-VARIABLE: INTEL_DIST_PV -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package download version from Intel. -# To determine its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. 2016_update1 -# -# Must be defined before inheriting the eclass. - -# @ECLASS-VARIABLE: INTEL_DIST_TARX -# @DESCRIPTION: -# The package distfile suffix. -# To determine its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. tgz -# -# Must be defined before inheriting the eclass. -: ${INTEL_DIST_TARX:=tgz} - -# @ECLASS-VARIABLE: INTEL_SUBDIR -# @DESCRIPTION: -# The package sub-directory (without version numbers) where it will end-up in /opt/intel -# -# e.g. compilers_and_libraries -# -# To determine its value, you have to do a raw install from the Intel tarball. -: ${INTEL_SUBDIR:=compilers_and_libraries} - -# @ECLASS-VARIABLE: INTEL_SKIP_LICENSE -# @DEFAULT_UNSET -# @DESCRIPTION: -# Possibility to skip the mandatory check for licenses. Only set this if there -# is really no fix. - -# @ECLASS-VARIABLE: INTEL_RPMS_DIR -# @DESCRIPTION: -# Main subdirectory which contains the rpms to extract. -: ${INTEL_RPMS_DIR:=rpm} - -# @ECLASS-VARIABLE: INTEL_DIST_BIN_RPMS -# @DESCRIPTION: -# Functional name of rpm without any version/arch tag. -# Has to be a bash array -# -# e.g. ("icc-l-all-devel") -# -# if the rpm is located in a directory other than INTEL_RPMS_DIR you can -# specify the full path -# -# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli") -[[ ${INTEL_DIST_BIN_RPMS[@]} ]] || INTEL_DIST_BIN_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_AMD64_RPMS -# @DESCRIPTION: -# AMD64 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS. -# Has to be a bash array. -[[ ${INTEL_DIST_AMD64_RPMS[@]} ]] || INTEL_DIST_AMD64_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_X86_RPMS -# @DESCRIPTION: -# X86 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS. -# Has to be a bash array. -[[ ${INTEL_DIST_X86_RPMS[@]} ]] || INTEL_DIST_X86_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_DAT_RPMS -# @DESCRIPTION: -# Functional name of rpm of common data which are arch free -# without any version tag. Has to be a bash array. -# -# e.g. ("openmp-l-all-devel") -# -# if the rpm is located in a directory different to INTEL_RPMS_DIR you can -# specify the full path -# -# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli-common") -[[ ${INTEL_DIST_DAT_RPMS[@]} ]] || INTEL_DIST_DAT_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_SPLIT_ARCH -# @DESCRIPTION: -# Set to "true" if arches are to be fetched separately, instead of using -# the combined tarball. -: ${INTEL_DIST_SPLIT_ARCH:=false} - -# @FUNCTION: _isdp_path_exists -# @INTERNAL -# @USAGE: [-a|-o] <paths> -# @DESCRIPTION: -# Check if the specified paths exist. Works for all types of paths -# (files/dirs/etc...). The -a and -o flags control the requirements -# of the paths. They correspond to "and" and "or" logic. So the -a -# flag means all the paths must exist while the -o flag means at least -# one of the paths must exist. The default behavior is "and". If no -# paths are specified, then the return value is "false". -_isdp_path_exists() { - local opt=$1 - [[ ${opt} == -[ao] ]] && shift || opt="-a" - - # no paths -> return false - # same behavior as: [[ -e "" ]] - [[ $# -eq 0 ]] && return 1 - - local p r=0 - for p in "$@" ; do - [[ -e ${p} ]] - : $(( r += $? )) - done - - case ${opt} in - -a) return $(( r != 0 )) ;; - -o) return $(( r == $# )) ;; - esac - eerror "path_exists has been removed. Please see the following post" - eerror "for a replacement snippet:" - eerror "https://blogs.gentoo.org/mgorny/2018/08/09/inlining-path_exists/" - die "path_exists is banned" -} - -# @FUNCTION: _isdp_get-sdp-year -# @INTERNAL -# @DESCRIPTION: -# Gets the year component from INTEL_DIST_PV -_isdp_get-sdp-year() { - local _intel_sdp_year - _intel_sdp_year=${INTEL_DIST_PV} - _intel_sdp_year=${_intel_sdp_year%_sp*} - _intel_sdp_year=${_intel_sdp_year%_update*} - echo "${_intel_sdp_year}" -} - -# @FUNCTION: isdp_get-sdp-dir -# @DESCRIPTION: -# Gets the full rootless path to the installation directory -# -# e.g. opt/intel/compilers_and_libraries_2016.1.150 -# opt/intel/vtune_amplifier_2018.2.0.551022 -isdp_get-sdp-dir() { - local _intel_sdp_dir="opt/intel/${INTEL_SUBDIR}_$(_isdp_get-sdp-year).$(ver_cut 3-)" - echo "${_intel_sdp_dir}" -} - -# @FUNCTION: isdp_get-sdp-edir -# @DESCRIPTION: -# Gets the full rooted/prefixed path to the installation directory -# -# e.g. /opt/intel/compilers_and_libraries_2016.1.150 -isdp_get-sdp-edir() { - local _intel_sdp_edir="${EPREFIX%/}/$(isdp_get-sdp-dir)" - echo "${_intel_sdp_edir}" -} - -SRC_URI="${INTEL_DIST_NAME}_${INTEL_DIST_PV}.${INTEL_DIST_TARX}" -LICENSE="Intel-SDP" -# TODO: Proper slotting -# Future work, #394411 -SLOT="0" - -RESTRICT="bindist mirror fetch" - -RDEPEND="" -DEPEND="app-arch/rpm2targz" - -S="${WORKDIR}" - -QA_PREBUILT="$(isdp_get-sdp-dir)/*" - -# @FUNCTION: isdp_convert2intel-arch -# @USAGE: <arch> -# @DESCRIPTION: -# Convert between portage arch (e.g. amd64, x86) and intel installed arch -# nomenclature (e.g. intel64, ia32) -isdp_convert2intel-arch() { - debug-print-function ${FUNCNAME} "${@}" - - case $1 in - *amd64*|abi_x86_64) - echo "intel64" - ;; - *x86*) - echo "ia32" - ;; - *) - die "Abi \'$1\' is unsupported" - ;; - esac -} - -# @FUNCTION: isdp_get-native-abi-arch -# @DESCRIPTION: -# Determine the the intel arch string of the native ABI -isdp_get-native-abi-arch() { - debug-print-function ${FUNCNAME} "${@}" - - use amd64 && echo "$(isdp_convert2intel-arch abi_x86_64)" - use x86 && echo "$(isdp_convert2intel-arch abi_x86_32)" -} - -# @FUNCTION: isdp_get-sdp-installed-arches -# @DESCRIPTION: -# Returns a space separated list of the arch suffixes used in directory -# names for enabled ABIs. Intel uses "ia32" for x86 and "intel64" for -# amd64. The result would be "ia32 intel64" if both ABIs were enabled. -isdp_get-sdp-installed-arches() { - local arch=() - use abi_x86_64 && arch+=($(isdp_convert2intel-arch abi_x86_64)) - use abi_x86_32 && arch+=($(isdp_convert2intel-arch abi_x86_32)) - echo "${arch[*]}" -} - -# @FUNCTION: _isdp_generate-list-install-rpms -# @INTERNAL -# @DESCRIPTION: -# Generates the list of fully expanded RPMs to be extracted. -_isdp_generate-list-install-rpms() { - debug-print-function ${FUNCNAME} "${@}" - - # Expand components into full RPM filenames - expand_component_into_full_rpm() { - local deref_var="${1}[@]" - local p rpm_prefix expanded_full_rpms=() - - for p in "${!deref_var}"; do - # check if a directory is prefixed - if [[ "${p}" == "${p##*/}" ]]; then - rpm_prefix="${INTEL_RPMS_DIR}/intel-" - else - rpm_prefix="" - fi - expanded_full_rpms+=( "${rpm_prefix}${p}" ) - done - echo ${expanded_full_rpms[*]} - } - - local vars_to_expand=("INTEL_DIST_BIN_RPMS" "INTEL_DIST_DAT_RPMS") - if use abi_x86_32; then - vars_to_expand+=("INTEL_DIST_X86_RPMS") - fi - if use abi_x86_64; then - vars_to_expand+=("INTEL_DIST_AMD64_RPMS") - fi - - local i fully_expanded_intel_rpms=() - for ((i=0; i<${#vars_to_expand[@]}; i++)); do - fully_expanded_intel_rpms+=($(expand_component_into_full_rpm "${vars_to_expand[i]}")) - done |