[gentoo-commits] proj/sci:master commit in: sci-libs/rdkit/, sci-libs/rdkit/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/rdkit/, sci-libs/rdkit/files/

[Andrew Ammerlaan]

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>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>

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
 }