openbabel, new recipe (#13479)

requirement for upcomming Kalzium (KDE)
2026-04-08 21:00:05 +02:00 · 2025-12-24 19:01:58 +01:00
parent 3741e91163
commit df42b79213
3 changed files with 297 additions and 0 deletions
--- a/sci-chemistry/openbabel/openbabel-3.1.1.recipe
+++ b/sci-chemistry/openbabel/openbabel-3.1.1.recipe
@@ -0,0 +1,145 @@
+SUMMARY="A chemical toolbox designed to speak the many languages of chemical data"
+DESCRIPTION="Open Babel is a chemical toolbox designed to speak the many languages of chemical \
+data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store \
+data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
+
+* Ready-to-use programs, and complete programmer’s toolkit
+* Read, write and convert over 110 chemical file formats
+* Filter and search molecular files using SMARTS and other methods
+* Supports molecular modeling, cheminformatics, bioinformatics
+* Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry
+* Downloaded over 700,000 times and used by over 40 related projects
+* How to cite Open Babel: The Open Babel and Pybel papers"
+HOMEPAGE="http://openbabel.org/"
+COPYRIGHT="2023 The Open Babel Team"
+LICENSE="GNU GPL v2"
+REVISION="1"
+openbabelVersion=`echo $portVersion | sed 's/\./-/g'`
+SOURCE_URI="https://github.com/openbabel/openbabel/archive/refs/tags/openbabel-$openbabelVersion.tar.gz"
+CHECKSUM_SHA256="c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02"
+SOURCE_DIR="openbabel-openbabel-$openbabelVersion"
+PATCHES="openbabel-$portVersion.patchset
+	2297.patch"
+
+ARCHITECTURES="all !x86_gcc2"
+SECONDARY_ARCHITECTURES="x86"
+
+# On x86_gcc2 we don't want to install the commands in bin/<arch>/, but in bin/.
+commandSuffix=$secondaryArchSuffix
+commandBinDir=$binDir
+if [ "$targetArchitecture" = x86_gcc2 ]; then
+	commandSuffix=
+	commandBinDir=$prefix/bin
+fi
+
+openbabelLibVersion="7.0.0"
+openbabelLibVersionCompat="$openbabelLibVersion compat >= ${openbabelLibVersion%%.*}"
+inchiLibVersion="0.4.1"
+inchiLibVersionCompat="$inchiLibVersion compat >= ${inchiLibVersion%%.*}"
+
+PROVIDES="
+	openbabel$secondaryArchSuffix = $portVersion
+	lib:libinchi$secondaryArchSuffix = $inchiLibVersionCompat
+	lib:libopenbabel$secondaryArchSuffix = $openbabelLibVersionCompat
+	"
+REQUIRES="
+	haiku$secondaryArchSuffix
+	lib:libcairo$secondaryArchSuffix
+	lib:libcoordgen$secondaryArchSuffix
+	lib:libmaeparser$secondaryArchSuffix
+	lib:libxml2$secondaryArchSuffix
+	lib:libz$secondaryArchSuffix
+	"
+
+PROVIDES_devel="
+	openbabel${secondaryArchSuffix}_devel = $portVersion
+	devel:libinchi$secondaryArchSuffix = $inchiLibVersionCompat
+	devel:libopenbabel$secondaryArchSuffix = $openbabelLibVersionCompat
+	"
+REQUIRES_devel="
+	openbabel$secondaryArchSuffix == $portVersion base
+	"
+
+PROVIDES_tools="
+	openbabel${secondaryArchSuffix}_tools = $portVersion
+	cmd:obabel$commandSuffix = $portVersion
+	cmd:obconformer$commandSuffix = $portVersion
+	cmd:obdistgen$commandSuffix = $portVersion
+	cmd:obenergy$commandSuffix = $portVersion
+	cmd:obfit$commandSuffix = $portVersion
+	cmd:obfitall$commandSuffix = $portVersion
+	cmd:obgen$commandSuffix = $portVersion
+	cmd:obgrep$commandSuffix = $portVersion
+	cmd:obminimize$commandSuffix = $portVersion
+	cmd:obmm$commandSuffix = $portVersion
+	cmd:obprobe$commandSuffix = $portVersion
+	cmd:obprop$commandSuffix = $portVersion
+	cmd:obrms$commandSuffix = $portVersion
+	cmd:obrotamer$commandSuffix = $portVersion
+	cmd:obrotate$commandSuffix = $portVersion
+	cmd:obspectrophore$commandSuffix = $portVersion
+	cmd:obsym$commandSuffix = $portVersion
+	cmd:obtautomer$commandSuffix = $portVersion
+	cmd:obthermo$commandSuffix = $portVersion
+	cmd:roundtrip$commandSuffix = $portVersion
+	"
+REQUIRES_tools="
+	openbabel$secondaryArchSuffix == $portVersion base
+	$REQUIRES
+	"
+
+BUILD_REQUIRES="
+	haiku${secondaryArchSuffix}_devel
+	eigen3$secondaryArchSuffix
+	devel:libboost_iostreams$secondaryArchSuffix >= 1.88.0
+	devel:libboost_program_options$secondaryArchSuffix >= 1.88.0
+	devel:libcairo$secondaryArchSuffix
+	devel:libcoordgen$secondaryArchSuffix
+	devel:libmaeparser$secondaryArchSuffix
+	devel:librapidjson$secondaryArchSuffix
+	devel:libxml2$secondaryArchSuffix
+	devel:libz$secondaryArchSuffix
+	"
+BUILD_PREREQUIRES="
+	cmd:cmake
+	cmd:gcc$secondaryArchSuffix
+	cmd:make
+	cmd:pkg_config$secondaryArchSuffix
+	"
+
+BUILD()
+{
+	cmake -B build -S . -DCMAKE_BUILD_TYPE=Release \
+		$cmakeDirArgs \
+		-DCMAKE_INSTALL_BINDIR=$commandBinDir \
+		-DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
+		-DCMAKE_SKIP_RPATH=YES \
+		-DBUILD_TESTING=OFF \
+		-Wno-dev
+
+	make -C build $jobArgs
+}
+
+INSTALL()
+{
+	make -C build install
+
+	prepareInstalledDevelLibs \
+		libinchi \
+		libopenbabel
+	fixPkgconfig
+
+	packageEntries devel \
+		$developDir \
+		$libDir/cmake
+
+	packageEntries tools \
+		$commandBinDir \
+		$manDir
+}
+
+TEST()
+{
+	export LIBRARY_PATH="$sourceDir/build/lib${LIBRARY_PATH:+:$LIBRARY_PATH}"
+	ctest --test-dir build --output-on-failure
+}
--- a/sci-chemistry/openbabel/patches/2297.patch
+++ b/sci-chemistry/openbabel/patches/2297.patch
@@ -0,0 +1,47 @@
+From b6887a8a82162278983a8489e365e61a0372b1b8 Mon Sep 17 00:00:00 2001
+From: Benny Siegert <bsiegert@gmail.com>
+Date: Wed, 4 Nov 2020 20:31:17 +0100
+Subject: [PATCH] Do not search for coordgen template files.
+
+The coordgen upstream does not install the template file. It is
+also not required at runtime, since its contents are compiled into
+the coordgen library itself.
+
+Fixes #2214
+---
+ cmake/modules/Findcoordgen.cmake | 13 +------------
+ 1 file changed, 1 insertion(+), 12 deletions(-)
+
+diff --git a/cmake/modules/Findcoordgen.cmake b/cmake/modules/Findcoordgen.cmake
+index ded0a4de7d..9bc5c9557f 100644
+--- a/cmake/modules/Findcoordgen.cmake
+++ b/cmake/modules/Findcoordgen.cmake
+@@ -6,7 +6,6 @@
+ #
+ # coordgen_INCLUDE_DIRS   - CoordGen's includes directory
+ # coordgen_LIBRARIES      - CoordGen's shared libraries
+-# coordgen_TEMPLATE_FILE  - CoordGen templates file
+ #
+ #
+ 
+@@ -28,19 +27,9 @@ find_library(coordgen_LIBRARIES
+ )
+ message(STATUS "coordgen libraries set as '${coordgen_LIBRARIES}'")
+ 
+-# Just in case, add parent directory above libraries to templates search hints
+-get_filename_component(libs_parent_dir ${coordgen_LIBRARIES} PATH)
+-find_file(coordgen_TEMPLATE_FILE
+-    NAMES templates.mae
+-    HINTS ${coordgen_DIR} ${libs_parent_dir}
+-    PATH_SUFFIXES "share" "share/coordgen"
+-    DOC "templates file for coordgen"
+-)
+-message(STATUS "coordgen templates file set as '${coordgen_TEMPLATE_FILE}'")
+-
+ find_package_handle_standard_args(coordgen FOUND_VAR coordgen_FOUND
+                                   REQUIRED_VARS coordgen_INCLUDE_DIRS
+-                                  coordgen_LIBRARIES coordgen_TEMPLATE_FILE)
+                                  coordgen_LIBRARIES)
+ 
+ 
+ 
--- a/sci-chemistry/openbabel/patches/openbabel-3.1.1.patchset
+++ b/sci-chemistry/openbabel/patches/openbabel-3.1.1.patchset
@@ -0,0 +1,105 @@
+From 5059937972d25bdbf83a79e96820fd8212035454 Mon Sep 17 00:00:00 2001
+From: Luc Schrijvers <begasus@gmail.com>
+Date: Wed, 24 Dec 2025 10:21:06 +0100
+Subject: Fixes for cmake (4), fPIC and deprecated warnings
+
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index c39db4a..d4dcf67 100644
+--- a/CMakeLists.txt
+++ b/CMakeLists.txt
+@@ -10,9 +10,6 @@ set (CMAKE_CXX_STANDARD 11)
+ 
+ if(COMMAND cmake_policy)
+   cmake_policy(SET CMP0003 NEW)
+-  if(POLICY CMP0042)
+-    cmake_policy(SET CMP0042 OLD)
+-  endif()
+ endif()
+ 
+ include (CheckCXXCompilerFlag)
+@@ -111,7 +108,7 @@ if(BUILD_SHARED)
+   set(BUILD_TYPE SHARED)
+   set(PLUGIN_TYPE MODULE)
+   add_definitions(-DUSING_DYNAMIC_LIBS)
+-  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+  set(CMAKE_POSITION_INDEPENDENT_CODE OFF)
+ else()
+   set(BUILD_TYPE STATIC)
+   set(PLUGIN_TYPE STATIC)
+@@ -137,6 +134,10 @@ else()
+   endif()
+ endif()
+ 
+if(HAIKU)
+  add_definitions(-Wno-deprecated-declarations)
+endif(HAIKU)
+
+ # Should we attempt to use the system inchi library?
+ option(WITH_INCHI   "Build inchi support" ON)
+ option(OPENBABEL_USE_SYSTEM_INCHI
+-- 
+2.52.0
+
+
+From d39e1a02ac56e306c4f1a9940368b2c26336e99c Mon Sep 17 00:00:00 2001
+From: Luc Schrijvers <begasus@gmail.com>
+Date: Wed, 24 Dec 2025 14:21:42 +0100
+Subject: Fix some installation targets
+
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index d4dcf67..6b84000 100644
+--- a/CMakeLists.txt
+++ b/CMakeLists.txt
+@@ -68,7 +68,7 @@ else() # Windows - bin dir = lib dir to load libraries
+   endif()
+ endif()
+ if(NOT DEFINED OB_INCLUDE_DIRS)
+-  set(OB_INCLUDE_DIRS "include/openbabel${BABEL_MAJ_VER}")
+  set(OB_INCLUDE_DIRS "${CMAKE_INSTALL_INCLUDEDIR}/openbabel${BABEL_MAJ_VER}")
+ endif()
+ set(OB_EXPORTS_FILE "${openbabel_BINARY_DIR}/OpenBabel3_EXPORTS.cmake")
+ # Ensure a fresh file is made each time CMake is run
+diff --git a/data/CMakeLists.txt b/data/CMakeLists.txt
+index 4982989..02a7c62 100644
+--- a/data/CMakeLists.txt
+++ b/data/CMakeLists.txt
+@@ -58,7 +58,7 @@ set(to_install
+ )
+ 
+ if(NOT MSVC)
+-  install(FILES ${to_install} DESTINATION share/openbabel/${BABEL_VERSION})
+  install(FILES ${to_install} DESTINATION ${CMAKE_INSTALL_DATADIR}/openbabel/${BABEL_VERSION})
+ else(NOT MSVC)
+   install(FILES ${to_install} DESTINATION bin/data)
+ endif(NOT MSVC)
+diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
+index 7a09e84..25c140e 100644
+--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
+@@ -2,7 +2,7 @@ include(GNUInstallDirs)
+ 
+ file(GLOB man_1 *.1)
+ install(FILES ${man_1} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+-install(FILES splash.png DESTINATION share/openbabel/${BABEL_VERSION})
+install(FILES splash.png DESTINATION ${CMAKE_INSTALL_DATADIR}/openbabel/${BABEL_VERSION})
+ 
+ OPTION(BUILD_DOCS "Build Open Babel documentation" OFF)
+ IF(BUILD_DOCS)
+diff --git a/include/CMakeLists.txt b/include/CMakeLists.txt
+index eceb7aa..3201282 100644
+--- a/include/CMakeLists.txt
+++ b/include/CMakeLists.txt
+@@ -6,7 +6,7 @@ file(GLOB depict_headers      openbabel/depict/*.h)
+ file(GLOB lbfgs_headers       LBFGS/*.h)
+ 
+ if(NOT OPENBABEL_USE_SYSTEM_INCHI)
+-install(FILES inchi_api.h          DESTINATION include/inchi)
+install(FILES inchi_api.h          DESTINATION ${OB_INCLUDE_DIRS}/inchi)
+ endif(NOT OPENBABEL_USE_SYSTEM_INCHI)
+ install(FILES chemdrawcdx.h        DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+ install(FILES ${openbabel_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+-- 
+2.52.0
+