commit: bb32520915a3f84ea64263e505ad9c560153a1b5 Author: Michael Schubert <mschu.dev <AT> gmail <DOT> com> AuthorDate: Sat Jul 13 10:18:51 2024 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Wed Oct 30 08:03:04 2024 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb325209
sci-libs/rdkit: version bump 2024.03.4 Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com> Closes: https://github.com/gentoo/sci/pull/1288 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../files/rdkit-2021.09.4-find-rapidjson.patch | 22 ------------ .../files/rdkit-2024.03.4-find-rapidjson.patch | 40 ++++++++++++++++++++++ sci-libs/rdkit/metadata.xml | 4 --- ...kit-2021.09.4.ebuild => rdkit-2024.03.4.ebuild} | 12 +++---- 4 files changed, 46 insertions(+), 32 deletions(-) diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch deleted file mode 100644 index 94a209e0f..000000000 --- a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt -index 8027444..6a8c715 100644 ---- a/Code/GraphMol/MolInterchange/CMakeLists.txt -+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt -@@ -1,16 +1,5 @@ - --if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") -- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"; -- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" -- "badd12c511e081fec6c89c43a7027bce") -- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf -- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz -- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) --else() -- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") --endif() -- --include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) -+include_directories(/usr/include/rapidjson) - - - rdkit_library(MolInterchange diff --git a/sci-libs/rdkit/files/rdkit-2024.03.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2024.03.4-find-rapidjson.patch new file mode 100644 index 000000000..42d7c5663 --- /dev/null +++ b/sci-libs/rdkit/files/rdkit-2024.03.4-find-rapidjson.patch @@ -0,0 +1,40 @@ +diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt +index 0c1e9a0de..e6f4fe753 100644 +--- a/Code/GraphMol/MolInterchange/CMakeLists.txt ++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt +@@ -1,24 +1,5 @@ + +-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") +- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"; +- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" +- "badd12c511e081fec6c89c43a7027bce") +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf +- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz +- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) +- # comment out a line which causes a compilation error on some platforms +- # (based on the change which has already been applied to the RapidJSON master branch, see +- # https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414) +- file(READ ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h RAPIDJSON_DOCUMENT_H) +- string(REGEX REPLACE +- "( *)(GenericStringRef& operator=\\(const GenericStringRef& rhs\\) { s = rhs\\.s. length = rhs\\.length. })" "\\1//\\2" +- RAPIDJSON_DOCUMENT_H "${RAPIDJSON_DOCUMENT_H}") +- file(WRITE ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h "${RAPIDJSON_DOCUMENT_H}") +-else() +- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") +-endif() +- +-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) ++include_directories(/usr/include/rapidjson) + + + rdkit_library(MolInterchange +diff --git a/Code/MinimalLib/CMakeLists.txt b/Code/MinimalLib/CMakeLists.txt +index 84808a971..987b155f8 100644 +--- a/Code/MinimalLib/CMakeLists.txt ++++ b/Code/MinimalLib/CMakeLists.txt +@@ -1,5 +1,4 @@ + include_directories(${RDKit_ExternalDir}) +-include_directories(${RDKit_ExternalDir}/rapidjson-1.1.0/include) + + if(RDK_BUILD_MINIMAL_LIB) + set(MINIMAL_LIB_LIBRARIES "MolInterchange_static;Abbreviations_static;" diff --git a/sci-libs/rdkit/metadata.xml b/sci-libs/rdkit/metadata.xml index be6cc7780..3f69d40d1 100644 --- a/sci-libs/rdkit/metadata.xml +++ b/sci-libs/rdkit/metadata.xml @@ -5,10 +5,6 @@ <email>[email protected]</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Chemistry Project</name> - </maintainer> <upstream> <remote-id type="github">rdkit/rdkit</remote-id> </upstream> diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2024.03.4.ebuild similarity index 82% rename from sci-libs/rdkit/rdkit-2021.09.4.ebuild rename to sci-libs/rdkit/rdkit-2024.03.4.ebuild index a1621ea79..a827cd8c6 100644 --- a/sci-libs/rdkit/rdkit-2021.09.4.ebuild +++ b/sci-libs/rdkit/rdkit-2024.03.4.ebuild @@ -1,14 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..12} ) +CMAKE_IN_SOURCE_BUILD=1 inherit cmake python-single-r1 DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python" -HOMEPAGE="http://www.rdkit.org/"; +HOMEPAGE="https://www.rdkit.org/"; SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz" S="${WORKDIR}/rdkit-Release_${PV//./_}" @@ -33,12 +34,11 @@ RDEPEND="dev-libs/boost DEPEND="${RDEPEND}" PATCHES=( - "${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch" + "${FILESDIR}/${PN}-2024.03.4-find-rapidjson.patch" ) src_configure() { local mycmakeargs=( - -DCATCH_DIR="${EPREFIX}/usr/include/catch2" -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr" -DRDK_INSTALL_INTREE=0 -DRDK_BUILD_CPP_TESTS="$(usex test)" @@ -54,5 +54,5 @@ src_configure() { } src_test() { - RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test + RDBASE="${S}" cmake_src_test }
