sci-libs/rdkit: version bump 2024.03.4

Signed-off-by: Michael Schubert <mschu.dev@gmail.com>
Closes: #1288
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

sci-libs/rdkit/Manifest

@@ -1 +1 @@
-DIST rdkit-2021.09.4.tar.gz 78474802 BLAKE2B 8c78c787a0e414b5e035998d9575322edca955acecb6d2df173610398f91cffd0b9053e7fc2c9284a2117afd720f313b7a63ed7e9ab67c708f25a5735b838f59 SHA512 c761fd5c3340ec38141165996b8666c3dcd4ed46ab91ca0d5a43ae3daedfc423ae36ec5882f085e1bd0c4c13dfe1f09497d05ec95e4847048c0acff8bcd0b1db
+DIST rdkit-2024.03.4.tar.gz 80452802 BLAKE2B 2f121ccb1f590848d2415a63a0a891e9c107334d2e11b31829415b73f64a2f6aeeb99eaafc0fa3ebd99c72bd9bb5ac1eef5c00f6eabf397561de1e7202c91719 SHA512 4c9737e29e21aab6271e427160fc24179410d98119d728b95da94be0dcd1f75f5cab45f8ea52e4dda8abed5c6af386f1f0d671d55e7053d108ca7a51e5584cf1

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;"

sci-libs/rdkit/metadata.xml

@@ -5,10 +5,6 @@
 		<email>mschu.dev@gmail.com</email>
 		<name>Michael Schubert</name>
 	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
 	<upstream>
 		<remote-id type="github">rdkit/rdkit</remote-id>
 	</upstream>

sci-libs/rdkit/rdkit-2021.09.4.ebuild → 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
 }