diff options
Diffstat (limited to 'sci-biology')
44 files changed, 391 insertions, 468 deletions
diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild index 49f2b6d9f..096349f5a 100644 --- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild +++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.6.ebuild @@ -16,7 +16,7 @@ KEYWORDS="~amd64" RDEPEND=" >=sci-biology/bioperl-1.4 >=sci-biology/velvet-0.7.5.1 - dev-lang/perl[ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh + dev-lang/perl[perl_features_ithreads]" # actually >=5.8 but make sure 5.16 is recognized as > 5.8, heh src_install(){ dobin VelvetOptimiser.pl diff --git a/sci-biology/afni-datasets/Manifest b/sci-biology/afni-datasets/Manifest new file mode 100644 index 000000000..99d2de1a8 --- /dev/null +++ b/sci-biology/afni-datasets/Manifest @@ -0,0 +1 @@ +DIST afni-datasets-20240503.tar.gz 57863597 BLAKE2B 07508c1d7b7d162a8116887ead440e3dd728ec53c19eb5b6c6662dfcc7c51ed13b1e9fdce2289410c1225010329b6ab3f9917d45f48a906571ba9c83747470f4 SHA512 5636ab403335c0ed8b34c00d89b38344654cda783fd928af632dd72f7cb51803b35caa60bc0561b8a1684870670d2977f3471ef6083676db33f172b41adb47f5 diff --git a/sci-biology/afni-datasets/afni-datasets-20240503.ebuild b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild new file mode 100644 index 000000000..4d554a633 --- /dev/null +++ b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_P="afni_atlases_dist_2024_0503" + +DESCRIPTION="Datasets for using and testing sci-biology/afni" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI="https://afni.nimh.nih.gov/pub/dist/atlases/${MY_P}.tgz -> ${P}.tar.gz" + +S="${WORKDIR}/${MY_P}" +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_install() { + insinto /usr/share/${PN} + doins -r * +} diff --git a/sci-biology/afni-datasets/metadata.xml b/sci-biology/afni-datasets/metadata.xml new file mode 100644 index 000000000..cb6710311 --- /dev/null +++ b/sci-biology/afni-datasets/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>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest index d1e783ff1..cc0d96468 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,4 +1,6 @@ -DIST afni-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8 DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6 +DIST afni-24.1.15.gh.tar.gz 53136605 BLAKE2B aab19b572b3d3f32e4d91414c127a8ef5cfd5cef04cb55836060298340c3d0e6cf0ec2f5f324590ce432e920842358007858a278198b37b47e6eeb8f318855b3 SHA512 ca8e3d26a32feea0118e4219c5915f8541bf5194f0db8e4b51637fb79a08c15d1772bc75499b71a47af5cac831bbd484efb3fce848d499f51ef002f9f52a6e10 +DIST afni-24.1.16.gh.tar.gz 53139168 BLAKE2B dff31b9b6e89cd2c62e2ab8cb1b7d1ed28e7bc3bbeb586ae7218ccc276237b0632d06c65928469560684871b8fd25dc382e5bdffcc4c5181c5b9855565398df8 SHA512 c507bc8d3bbad8b61daef3321e48bd88c2f020c940c61a7c3ff4dafe1d2823dad5c87b96080716ab6c59d5312b7fa33c8289426f3fcc4938d3ef049df54134b3 DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2 DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5 +DIST nifti-f24bec503f1a5d501c0413c1bb8aa3d6e04aebda.tar.gz 451555 BLAKE2B d83e8e265d996bb041fa7c712e4f67f6ab3c4e7e7b9713f5d5a0e045b11c2c5c34a193a0d6f69594d37ff1ac09bb295f9be6b04a7a29711cfad8d27167c15058 SHA512 8a4707edfd11112bdb0c359223bb39c6e1d9281234759ebf65bffe34b52a0530053b2e9368c36a77b788194113db5ac66ddf44204036983fffda3d81699e1d5b diff --git a/sci-biology/afni/afni-24.0.08.ebuild b/sci-biology/afni/afni-24.0.08-r3.ebuild index 75ff5b6b6..12d6c8f87 100644 --- a/sci-biology/afni/afni-24.0.08.ebuild +++ b/sci-biology/afni/afni-24.0.08-r3.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) DISTUTILS_USE_PEP517=setuptools inherit cmake distutils-r1 toolchain-funcs @@ -12,35 +12,37 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" -DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" SRC_URI=" https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz " -SLOT="0" +S="${WORKDIR}/afni-AFNI_${PV}" + LICENSE="GPL-3+" +SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="test whirlgif" RESTRICT="!test? ( test )" RDEPEND=" + dev-build/ninja + dev-libs/expat dev-libs/glib:2 dev-libs/libf2c - dev-libs/expat - dev-build/ninja media-libs/freeglut media-libs/glu media-libs/netpbm media-libs/qhull media-video/mpeg-tools + sci-biology/afni-datasets sci-libs/gsl sci-libs/gts sys-devel/llvm:* sys-libs/libomp - dev-libs/libpthread-stubs virtual/jpeg-compat:62 x11-libs/libGLw x11-libs/libXft @@ -58,8 +60,6 @@ DEPEND=" #Update jpeg-compat to virtual/jpeg:0 # look for xmhtlm -S="${WORKDIR}/afni-AFNI_${PV}" - #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die src_prepare() { tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die @@ -72,8 +72,9 @@ src_configure() { if use !whirlgif; then eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake export CFLAGS="-pthread ${CFLAGS}" - export GIT_REPO_VERSION=3.0.1.1 local mycmakeargs=( -DLIBDIR=/usr/$(get_libdir) -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) @@ -112,4 +113,13 @@ src_install() { popd cd "${D}" rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo } diff --git a/sci-biology/afni/afni-24.0.04.ebuild b/sci-biology/afni/afni-24.1.15.ebuild index c00ef846f..12d6c8f87 100644 --- a/sci-biology/afni/afni-24.0.04.ebuild +++ b/sci-biology/afni/afni-24.1.15.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) +PYTHON_COMPAT=( python3_{10..13} ) DISTUTILS_USE_PEP517=setuptools inherit cmake distutils-r1 toolchain-funcs @@ -12,35 +12,37 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" -DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" SRC_URI=" https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz " -SLOT="0" +S="${WORKDIR}/afni-AFNI_${PV}" + LICENSE="GPL-3+" +SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="test whirlgif" RESTRICT="!test? ( test )" RDEPEND=" + dev-build/ninja + dev-libs/expat dev-libs/glib:2 dev-libs/libf2c - dev-libs/expat - dev-build/ninja media-libs/freeglut media-libs/glu media-libs/netpbm media-libs/qhull media-video/mpeg-tools + sci-biology/afni-datasets sci-libs/gsl sci-libs/gts sys-devel/llvm:* sys-libs/libomp - dev-libs/libpthread-stubs virtual/jpeg-compat:62 x11-libs/libGLw x11-libs/libXft @@ -54,9 +56,11 @@ DEPEND=" ${RDEPEND} app-shells/tcsh " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm -S="${WORKDIR}/afni-AFNI_${PV}" - + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die src_prepare() { tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die @@ -66,10 +70,11 @@ src_prepare() { src_configure() { if use !whirlgif; then - eapply "${FILESDIR}/${P}-whirlgif.patch" + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake export CFLAGS="-pthread ${CFLAGS}" - export GIT_REPO_VERSION=3.0.1.1 local mycmakeargs=( -DLIBDIR=/usr/$(get_libdir) -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) @@ -108,4 +113,13 @@ src_install() { popd cd "${D}" rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo } diff --git a/sci-biology/afni/afni-24.1.16.ebuild b/sci-biology/afni/afni-24.1.16.ebuild new file mode 100644 index 000000000..0759d30a0 --- /dev/null +++ b/sci-biology/afni/afni-24.1.16.ebuild @@ -0,0 +1,127 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="f24bec503f1a5d501c0413c1bb8aa3d6e04aebda" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +S="${WORKDIR}/afni-AFNI_${PV}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-build/ninja + dev-libs/expat + dev-libs/glib:2 + dev-libs/libf2c + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-biology/afni-datasets + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + +PATCHES=("${FILESDIR}/afni-24.1.16-niftiio.patch") + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + # We need a name without the hash to reference in patches + mv "${WORKDIR}/nifti_clib-${NIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github" + mv "${WORKDIR}/gifti_clib-${GIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github" + cmake_src_prepare +} + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" + fi + # Fix AFNI version, no better way seemed to work + sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake + export CFLAGS="-pthread ${CFLAGS}" + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode + doenvd "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni new file mode 100644 index 000000000..dbf463f47 --- /dev/null +++ b/sci-biology/afni/files/97afni @@ -0,0 +1 @@ +export AFNI_ATLAS_PATH=/usr/share/afni-datasets diff --git a/sci-biology/afni/files/afni-24.1.16-niftiio.patch b/sci-biology/afni/files/afni-24.1.16-niftiio.patch new file mode 100644 index 000000000..a4eb35435 --- /dev/null +++ b/sci-biology/afni/files/afni-24.1.16-niftiio.patch @@ -0,0 +1,27 @@ +From 05dbcd2659fa6177b221a2686300036e4ae435d6 Mon Sep 17 00:00:00 2001 +From: Yaroslav Halchenko <debian@onerussian.com> +Date: Mon, 3 Jun 2024 19:28:21 -0400 +Subject: [PATCH] Announce niftiio as PRIVATE for linking to prevent + propagating linking against it + +I am just a messanger from the cmake-wise @leej3 at +https://github.com/afni/afni/issues/639#issuecomment-2145703256 + +Supposedly closes #639 +--- + src/nifti/nifticdf/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/nifti/nifticdf/CMakeLists.txt b/src/nifti/nifticdf/CMakeLists.txt +index 473be7e3be..01b18a14d8 100644 +--- a/nifti_clib_from_github/nifticdf/CMakeLists.txt ++++ b/nifti_clib_from_github/nifticdf/CMakeLists.txt +@@ -8,7 +8,7 @@ set_target_properties( + "${CMAKE_CURRENT_LIST_DIR}/nifticdf.h" + ) + target_compile_options(${NIFTI_CDFLIB_NAME} PRIVATE "-D__COMPILE_UNUSED_FUNCTIONS__") +-target_link_libraries(${NIFTI_CDFLIB_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}niftiio) ++target_link_libraries(${NIFTI_CDFLIB_NAME} PRIVATE ${NIFTI_PACKAGE_PREFIX}niftiio) + get_lib_version_vars("nifticdf_version.h" NIFTICDF_VERSION NIFTICDF_MAJOR_VERSION) + if(BUILD_SHARED_LIBS) + set_target_properties(${NIFTI_CDFLIB_NAME} diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest index 90147dff7..69572ef1e 100644 --- a/sci-biology/bx-python/Manifest +++ b/sci-biology/bx-python/Manifest @@ -1,2 +1 @@ -DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea -DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc +DIST bx-python-0.12.0.gh.tar.gz 1660806 BLAKE2B 0eddb9b9a93520319d275001067a3518015483605cf4d096729ec92e14c0eb35f2ceb34db964216dd3c6687351a7415c46061960b1f66a7564c90efeba3a587b SHA512 821b33841dd2935485669f6c112277d404475b1cd778deb3eaa1194f3b21594335a219d9345e279e7afc3adb1e347e71e60f0029712fc58e95d1e70f9e8fbb55 diff --git a/sci-biology/bx-python/bx-python-0.12.0.ebuild b/sci-biology/bx-python/bx-python-0.12.0.ebuild new file mode 100644 index 000000000..1a00b0395 --- /dev/null +++ b/sci-biology/bx-python/bx-python-0.12.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://github.com/bxlab/bx-python" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# doctests have external deps +PATCHES=( + "${FILESDIR}/no-doctest.patch" +) + +distutils_enable_tests pytest + +# https://github.com/bxlab/bx-python/issues/101 +EPYTEST_DESELECT=( + lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo + lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer +) + +python_test() { + cd "${BUILD_DIR}/build" || die + ln -s "${S}/pytest.ini" . || die + ln -s "${S}/test_data" . || die + epytest +} diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild deleted file mode 100644 index 6cffba1be..000000000 --- a/sci-biology/bx-python/bx-python-0.8.9.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild deleted file mode 100644 index 6cffba1be..000000000 --- a/sci-biology/bx-python/bx-python-0.9.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild deleted file mode 100644 index b29975b58..000000000 --- a/sci-biology/bx-python/bx-python-9999.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -EGIT_REPO_URI="https://github.com/bxlab/bx-python" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/files/no-doctest.patch b/sci-biology/bx-python/files/no-doctest.patch new file mode 100644 index 000000000..d0c2b2e62 --- /dev/null +++ b/sci-biology/bx-python/files/no-doctest.patch @@ -0,0 +1,9 @@ +diff --git a/pytest.ini b/pytest.ini +index e77e08f..4184247 100644 +--- a/pytest.ini ++++ b/pytest.ini +@@ -1,4 +1,3 @@ + [pytest] +-addopts = --doctest-cython --doctest-modules + python_files = *_tests.py + testpaths = lib script_tests/ diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index f1fc4360e..2ead27d78 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -5,10 +5,6 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <upstream> <remote-id type="github">bxlab/bx-python</remote-id> <remote-id type="pypi">bx-python</remote-id> diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 49bf65452..56c76a408 100644 --- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -7,7 +7,7 @@ inherit toolchain-funcs DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage" HOMEPAGE="https://codonw.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz +SRC_URI="https://downloads.sourceforge.net/${PN}/CodonWSourceCode_${PV//./_}.tar.gz https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" LICENSE="GPL-2" diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild index cd91cf192..6e5d6e779 100644 --- a/sci-biology/fsl/fsl-6.0.4.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -151,8 +151,8 @@ src_compile() { # define the default build system to match upstream official standard # -> individual projects may overwrite the '-std=' flag - export ANSI_CFLAGS="-std=c99" - export ANSI_CXXFLAGS="-std=c++98" + export ANSI_CFLAGS="-std=c11" + export ANSI_CXXFLAGS="-std=c++11" export USERLDFLAGS="${LDFLAGS}" export USERCFLAGS="${CFLAGS}" diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest index e8b006cbf..ca30cec83 100644 --- a/sci-biology/gffutils/Manifest +++ b/sci-biology/gffutils/Manifest @@ -1 +1 @@ -DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb +DIST gffutils-0.13.gh.tar.gz 1644910 BLAKE2B c8c4bc5d8a51e2e63d359bed8953730dc2d64ab04a96021fbaa891443f77c259886bcb81bab59eff622f23aeaed77c30bd1635b03761607ec562fa52d92ebea7 SHA512 617f84aeaa4d16b140083012c6b3656d5ea44a9a0619f8516e51379f92e9be85dff42e31c9ac2c3a77d7e3715f43c0106cd534317cc6ff4b6257fce56a1b635f diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild deleted file mode 100644 index 8ee8fd4b5..000000000 --- a/sci-biology/gffutils/gffutils-0.11.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) - -inherit distutils-r1 - -DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" -SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -# Nose tests no longer supported, migration on next release -#RESTRICT="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/argh[${PYTHON_USEDEP}] - dev-python/argcomplete[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - sci-biology/pybedtools[${PYTHON_USEDEP}] - sci-biology/pyfaidx[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -python_prepare_all() { - if use test; then - sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die - fi - distutils-r1_python_prepare_all -} - -python_test() { - distutils_install_for_testing - nosetests -v -x --with-doctest -a '!slow' || die -} diff --git a/sci-biology/gffutils/gffutils-0.13.ebuild b/sci-biology/gffutils/gffutils-0.13.ebuild new file mode 100644 index 000000000..fbd90b6d9 --- /dev/null +++ b/sci-biology/gffutils/gffutils-0.13.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="GFF and GTF file manipulation and interconversion" +HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" +SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/argh[${PYTHON_USEDEP}] + dev-python/argcomplete[${PYTHON_USEDEP}] + dev-python/pyfaidx[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +# https://github.com/daler/gffutils/issues/233 + cli not installed yet +EPYTEST_DESELECT=( + gffutils/test/test_biopython_integration.py::test_roundtrip + gffutils/test/test_cli.py::test_issue_224 +) + +distutils_enable_tests pytest diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml index c9fe23ced..dc2c60220 100644 --- a/sci-biology/gffutils/metadata.xml +++ b/sci-biology/gffutils/metadata.xml @@ -5,10 +5,6 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <upstream> <remote-id type="github">daler/gffutils</remote-id> </upstream> diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest index 4c5068f0a..c8a1eba20 100644 --- a/sci-biology/imagej/Manifest +++ b/sci-biology/imagej/Manifest @@ -1,3 +1,3 @@ -DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3 DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9 -DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615 +DIST imagej-1.54i.gh.tar.gz 5826446 BLAKE2B 05a21929a29e7c4109a91714d0d4d2763f9fe5d83500d334a717d7050765d50c08119b8a7bb54b9290ccf4f82a75cfb392fdf2ee269ee0b05e0f7447aa7c2d1b SHA512 13a0ec252328f972570ccbd85881b64cff25b03f92eb5f68bb6b1b00d7530ba31cd2ff617c462aa428158027f042ea1d18682f3e0deb4d0728ae56965ed5f8e8 +DIST imagej.png 14480 BLAKE2B a507afad5be462cf7a6e693b7930e40abc10877d137d1adeea7938c2b95fecef1b73eb401dc32670ccee6d83a5ecdfc4b6487ed908820bfaa09bec39400cd576 SHA512 87a2bbc17353488a17adb446f2199fb75292ba3bdf00cb97c0508107ee56c12f282bebd8d6618bf6e12ebbcfca7a12bf24057803aeb570edefa992d975b386f5 diff --git a/sci-biology/imagej/imagej-1.54h-r1.ebuild b/sci-biology/imagej/imagej-1.54i-r1.ebuild index 0252d6613..f95167bcd 100644 --- a/sci-biology/imagej/imagej-1.54h-r1.ebuild +++ b/sci-biology/imagej/imagej-1.54i-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -11,12 +11,12 @@ IJ_PV="154" #plugins now available for 154 DESCRIPTION="Image Processing and Analysis in Java" HOMEPAGE=" - https://imagej.nih.gov/ij/ + https://imagej.net/software/imagej/ https://github.com/imagej " SRC_URI=" - https://imagej.nih.gov/ij/images/ImageJ.png + https://imagej.net/media/icons/imagej.png plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" # plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins @@ -50,12 +50,11 @@ DEPEND=" " BDEPEND=" - dev-java/ant-core app-arch/unzip " src_prepare() { - cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die if [[ ${PV} == 9999 ]]; then if use plugins ; then diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild index 0252d6613..f95167bcd 100644 --- a/sci-biology/imagej/imagej-9999.ebuild +++ b/sci-biology/imagej/imagej-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -11,12 +11,12 @@ IJ_PV="154" #plugins now available for 154 DESCRIPTION="Image Processing and Analysis in Java" HOMEPAGE=" - https://imagej.nih.gov/ij/ + https://imagej.net/software/imagej/ https://github.com/imagej " SRC_URI=" - https://imagej.nih.gov/ij/images/ImageJ.png + https://imagej.net/media/icons/imagej.png plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" # plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins @@ -50,12 +50,11 @@ DEPEND=" " BDEPEND=" - dev-java/ant-core app-arch/unzip " src_prepare() { - cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + cp "${DISTDIR}"/imagej.png "${WORKDIR}/${PN}.png" || die if [[ ${PV} == 9999 ]]; then if use plugins ; then diff --git a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild index 5d89c0822..42fc0b62d 100644 --- a/sci-biology/mrfast/mrfast-2.6.0.1.ebuild +++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild @@ -7,7 +7,7 @@ inherit flag-o-matic toolchain-funcs DESCRIPTION="Micro Read Fast Alignment Search Tool" HOMEPAGE="http://mrfast.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest index 3585038a3..cf36e2eb5 100644 --- a/sci-biology/multiqc/Manifest +++ b/sci-biology/multiqc/Manifest @@ -1 +1 @@ -DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354 +DIST multiqc-1.23.gh.tar.gz 5639815 BLAKE2B 1cd02d82d5a1856470777cdd5db48fbf2d86a37e713fa32118edb608703c9fbf1d23af6254a0ed15c47f2c073999a58c53a5a67c6df9a6bfc61cb773fc857bae SHA512 f7d910122ec34373dfa2d60dd7436ec66494980daf7e46729fbae90481bcceb1318c5dbafc64725dca2079deb5fe66834371813aa4dda7e9bf676dff5a043995 diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild deleted file mode 100644 index 187f06c22..000000000 --- a/sci-biology/multiqc/multiqc-1.19.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{10..11} ) - -inherit pypi distutils-r1 - -DESCRIPTION="Aggregate bioinformatics results across many samples into a single report" -HOMEPAGE="https://multiqc.info/" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~amd64-linux" - -RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/click[${PYTHON_USEDEP}] - dev-python/coloredlogs[${PYTHON_USEDEP}] - dev-python/future[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/lzstring[${PYTHON_USEDEP}] - dev-python/markdown[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/rich[${PYTHON_USEDEP}] - dev-python/rich-click[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/spectra[${PYTHON_USEDEP}] - dev-python/importlib-metadata[$PYTHON_USEDEP] - dev-python/humanize[$PYTHON_USEDEP] - dev-python/pyaml-env[$PYTHON_USEDEP]" - -# pypi tarball does not include tests -RESTRICT="test" -#distutils_enable_tests pytest diff --git a/sci-biology/multiqc/multiqc-1.23.ebuild b/sci-biology/multiqc/multiqc-1.23.ebuild new file mode 100644 index 000000000..bf45065aa --- /dev/null +++ b/sci-biology/multiqc/multiqc-1.23.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 + +DESCRIPTION="Aggregate bioinformatics results across many samples into a single report" +HOMEPAGE="https://multiqc.info/" +SRC_URI="https://github.com/MultiQC/MultiQC/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}"/MultiQC-${PV} + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/click[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/importlib-metadata[${PYTHON_USEDEP}] + >=dev-python/jinja-3.0.0[${PYTHON_USEDEP}] + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + >=dev-python/pillow-10[${PYTHON_USEDEP}] + >=dev-python/plotly-5.18[${PYTHON_USEDEP}] + >=dev-python/pyyaml-4[${PYTHON_USEDEP}] + dev-python/pyaml-env[${PYTHON_USEDEP}] + >=dev-python/rich-10[${PYTHON_USEDEP}] + dev-python/rich-click[${PYTHON_USEDEP}] + dev-python/coloredlogs[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + >=dev-python/spectra-0.0.10[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.7.1[${PYTHON_USEDEP}] + dev-python/typeguard[${PYTHON_USEDEP}]" +# dev-python/kaleido[${PYTHON_USEDEP}] # tested and is optional + +RESTRICT="test" # no items collected +#distutils_enable_tests pytest diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest index 1963b7225..35c461b92 100644 --- a/sci-biology/neuroconv/Manifest +++ b/sci-biology/neuroconv/Manifest @@ -1,2 +1 @@ -DIST neuroconv-0.2.4.gh.tar.gz 757136 BLAKE2B a3a21b3a00667bde4461d91ade514891c8710f309413b100e1cccfd2684dfcbf9b21feaf4f58b3c5ff845aa08e69bf47467b411926eeb7d3b2862753302b1d9b SHA512 293038feae2704442b81ba0f012d775ba96d7bdffb6aaacaaebd09ca2f8b39e91ef4ea69c972abf060f0f9ab8cb76fedb77dda67455fa992edd52f0e6e504b0d -DIST neuroconv-0.4.6.gh.tar.gz 1000357 BLAKE2B 24fc43a4c7c1cb588b5af49c1da2348f775506efd0c36b838b7882cf4a03520dac6e0fe6fd17310c17ae84371d3eeb8e3aec4b16fc3b07c10bec2e3c46e51dff SHA512 eeccc6900b6ae9f053f67503a93c4040033afc8b056b8869ad562f7cd2dd802cce2b7a467b5ccaa20fe84a188697821c328043b6177302d1913a30a5a789ae15 +DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild deleted file mode 100644 index c554ce791..000000000 --- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 2021-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="Create NWB files from proprietary formats." -HOMEPAGE="https://github.com/catalystneuro/neuroconv" -SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+ecephys +icephys +ophys" - -RDEPEND=" - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/hdmf[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/psutil[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-vcs/dandi-cli[${PYTHON_USEDEP}] - ecephys? ( - dev-python/spikeinterface[${PYTHON_USEDEP}] - ) - icephys? ( - dev-python/neo[${PYTHON_USEDEP}] - ) - ophys? ( - sci-biology/roiextractors[${PYTHON_USEDEP}] - ) -" -BDEPEND=" - test? ( - dev-python/parameterized[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_test() { - # Additional tests require complex data getting infrastructure, ophys tests still have issues: - # https://github.com/catalystneuro/neuroconv/issues/305 - local my_tests=( "tests/test_minimal" ) - use ecephys && my_tests+=( "tests/test_ecephys" ) - #use ophys && my_tests+=( "tests/test_ophys" ) - epytest ${my_tests[*]// /|} -} diff --git a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild index 1676aa6b7..b21c2fd8e 100644 --- a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild +++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild @@ -17,20 +17,21 @@ KEYWORDS="~amd64" IUSE="+ecephys +icephys +ophys" RDEPEND=" + dev-python/docstring-parser[${PYTHON_USEDEP}] dev-python/h5py[${PYTHON_USEDEP}] - dev-python/hdmf[${PYTHON_USEDEP}] dev-python/hdmf-zarr[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/nwbinspector[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] dev-python/parse[${PYTHON_USEDEP}] dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] dev-python/pynwb[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] ecephys? ( dev-python/spikeinterface[${PYTHON_USEDEP}] ) @@ -49,6 +50,12 @@ BDEPEND=" distutils_enable_tests pytest +# Reported upstream: +# https://github.com/catalystneuro/neuroconv/issues/785 +EPYTEST_DESELECT=( + tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface +) + python_test() { # Additional tests require complex data getting infrastructure, ophys tests still have issues: # https://github.com/catalystneuro/neuroconv/issues/305 diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index 3064c0ba5..92c788f28 100644 --- a/sci-biology/nilearn/nilearn-0.8.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -27,7 +27,7 @@ BDEPEND=" RDEPEND=" >=dev-python/joblib-0.12[${PYTHON_USEDEP}] >=dev-python/numpy-1.16[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}] + >=dev-python/scikit-learn-0.21[${PYTHON_USEDEP}] >=dev-python/scipy-1.2[${PYTHON_USEDEP}] >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}] >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}] diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild index 425e79444..4dbe5101e 100644 --- a/sci-biology/nilearn/nilearn-0.9.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -25,7 +25,7 @@ RDEPEND=" >=dev-python/requests-2[${PYTHON_USEDEP}] >=dev-python/scipy-1.5[${PYTHON_USEDEP}] >=sci-libs/nibabel-3[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}] + >=dev-python/scikit-learn-0.22[${PYTHON_USEDEP}] " PATCHES=( "${FILESDIR}/${P}-tests.patch" ) diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild index bae672851..bc15bb8f4 100644 --- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild +++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild @@ -5,7 +5,7 @@ EAPI=7 DESCRIPTION="Primers design for standard PCR, bisulphite PCR and Real-time PCR" HOMEPAGE="http://perlprimer.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.bz2" LICENSE="GPL-2" SLOT="0" diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest deleted file mode 100644 index a952ac4b8..000000000 --- a/sci-biology/pybedtools/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe -DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18 diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml deleted file mode 100644 index b80afba97..000000000 --- a/sci-biology/pybedtools/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="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">daler/pybedtools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild deleted file mode 100644 index bc02bda6f..000000000 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# 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="Use BED and GFF files from python using BEDtools" -HOMEPAGE="https://daler.github.io/pybedtools" -SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/bedtools - sci-biology/pysam[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] -" - -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" - -# TODO: fix docs building -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -# even if pybedtools is installed -#distutils_enable_sphinx docs/source -distutils_enable_tests pytest - -python_test() { - # Requires network - local EPYTEST_DESELECT=( - test/test_helpers.py::test_chromsizes - ) - cd "${T}" || die - epytest --pyargs pybedtools -} diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild deleted file mode 100644 index bc02bda6f..000000000 --- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# 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="Use BED and GFF files from python using BEDtools" -HOMEPAGE="https://daler.github.io/pybedtools" -SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/bedtools - sci-biology/pysam[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] -" - -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" - -# TODO: fix docs building -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -# even if pybedtools is installed -#distutils_enable_sphinx docs/source -distutils_enable_tests pytest - -python_test() { - # Requires network - local EPYTEST_DESELECT=( - test/test_helpers.py::test_chromsizes - ) - cd "${T}" || die - epytest --pyargs pybedtools -} diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest deleted file mode 100644 index 0bb3b35f4..000000000 --- a/sci-biology/pyfaidx/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pyfaidx-0.5.9.2.tar.gz 93438 BLAKE2B 3d3d225907f8bd04fdf4b20d608d02cd0e5a723f2a73df24b732992f139102e2a9042c37c5a73f762256fd007dd7e14bace910c0961e60870926c2ce1dca3ac3 SHA512 57b94421d6858fa2bd7b867b386d47d53d3afd75878b08e6e32fb7d8f4942f2a051e0123e6c4b4395abe656d639fa4f47afadbd8c4b2cbc001c5113cbbf96af4 -DIST pyfaidx-0.7.2.1.tar.gz 102951 BLAKE2B d8c76bb9f817a7f4a0f3aa58ef20344c1d5aa5e99a181f1171145264baab4603d772d7c37f8286654442ee0f6bf3b62f8d94d6e0495a65f54495e084403c0b92 SHA512 20833c2e11f942aa69b524170a0203ca4d035d058d1d8029c2fab50c4b60a4e947cbbdc0dc954e4ecdefbf07d095f861a86dbebdfdac4bdbecf65a691226e25c diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml deleted file mode 100644 index 47cc39d79..000000000 --- a/sci-biology/pyfaidx/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="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">pyfaidx</remote-id> - <remote-id type="github">mdshw5/pyfaidx</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild deleted file mode 100644 index bec223f6c..000000000 --- a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# 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_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Efficient pythonic random access to fasta subsequences" -HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx" -SRC_URI="https://github.com/mdshw5/pyfaidx/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -REPEND="dev-python/six[${PYTHON_USEDEP}]" - -#distutils_enable_tests nose diff --git a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild deleted file mode 100644 index 14f557869..000000000 --- a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# 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="Efficient pythonic random access to fasta subsequences" -HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -# Test issues reported upstream: -# https://github.com/mdshw5/pyfaidx/issues/208 -RESTRICT="test" - -REPEND="dev-python/six[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest |