Date: Fri, 21 Oct 2022 07:05:10 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 47f90fecad58 - main - biology/libcombine: New port: C++ library for working with the COMBINE archive format Message-ID: <202210210705.29L75APO085038@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=47f90fecad58186514d8c977f75c2db2c5252e35 commit 47f90fecad58186514d8c977f75c2db2c5252e35 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-10-21 07:04:23 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-10-21 07:05:07 +0000 biology/libcombine: New port: C++ library for working with the COMBINE archive format --- biology/Makefile | 1 + biology/libcombine/Makefile | 30 +++++++++++++++ biology/libcombine/distinfo | 7 ++++ .../files/patch-CMakeModules_FindLIBSBML.cmake | 23 ++++++++++++ .../files/patch-dev_generated_CMakeLists.txt | 11 ++++++ biology/libcombine/pkg-descr | 4 ++ biology/libcombine/pkg-plist | 43 ++++++++++++++++++++++ 7 files changed, 119 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 1c570b26ebb9..25ed50f54925 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -80,6 +80,7 @@ SUBDIR += kmcp SUBDIR += lamarc SUBDIR += libbigwig + SUBDIR += libcombine SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim diff --git a/biology/libcombine/Makefile b/biology/libcombine/Makefile new file mode 100644 index 000000000000..888059b5caad --- /dev/null +++ b/biology/libcombine/Makefile @@ -0,0 +1,30 @@ +PORTNAME= libcombine +DISTVERSIONPREFIX= v +DISTVERSION= 0.2.19 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C++ library for working with the COMBINE archive format +WWW= https://sbml.org/software/libsbml/ + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +LIB_DEPENDS= libsbml.so:biology/libsbml + +USES= cmake:testing gnome localbase:ldflags +USE_GNOME= libxml2 +USE_LDCONFIG= yes + +USE_GITHUB= yes +GH_ACCOUNT= sbmlteam +GH_PROJECT= libCombine +GH_TUPLE= fbergmann:zipper:6f54c03:zipper/src/zipper \ + sebastiandev:minizip:e3a8cb7:zipper_minizip/src/zipper/minizip + +CMAKE_OFF= BUILD_TEST +CMAKE_TESTING_ON= BUILD_TEST # tests fail to build, see https://github.com/sbmlteam/libCombine/issues/58 + +LDFLAGS+= -lsbml # FindSBML.cmake fails to set this link flag + +.include <bsd.port.mk> diff --git a/biology/libcombine/distinfo b/biology/libcombine/distinfo new file mode 100644 index 000000000000..935e8183950b --- /dev/null +++ b/biology/libcombine/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1666331339 +SHA256 (sbmlteam-libCombine-v0.2.19_GH0.tar.gz) = a9ac562cca70cd8862b3f3cd65c98e8e455896732a8e1d3ee1ff32bf8ec02ac5 +SIZE (sbmlteam-libCombine-v0.2.19_GH0.tar.gz) = 1524012 +SHA256 (fbergmann-zipper-6f54c03_GH0.tar.gz) = 61aba13ecc2cb23617cf6496bc67739820a7b8c203b3dbb0ce9fddd0a68598d6 +SIZE (fbergmann-zipper-6f54c03_GH0.tar.gz) = 124726 +SHA256 (sebastiandev-minizip-e3a8cb7_GH0.tar.gz) = 14492faf0694bf075312626ffba0fe6fcfccb450001db5b01fece2134d69a75d +SIZE (sebastiandev-minizip-e3a8cb7_GH0.tar.gz) = 85593 diff --git a/biology/libcombine/files/patch-CMakeModules_FindLIBSBML.cmake b/biology/libcombine/files/patch-CMakeModules_FindLIBSBML.cmake new file mode 100644 index 000000000000..c7d6e386f2c3 --- /dev/null +++ b/biology/libcombine/files/patch-CMakeModules_FindLIBSBML.cmake @@ -0,0 +1,23 @@ +--- CMakeModules/FindLIBSBML.cmake.orig 2022-10-21 06:11:59 UTC ++++ CMakeModules/FindLIBSBML.cmake +@@ -124,9 +124,7 @@ endif (NOT LIBSBML_INCLUDE_DIR) + + + find_library(LIBSBML_LIBRARY +- NAMES sbml-static +- sbml +- libsbml-static ++ NAMES sbml + libsbml + PATHS $ENV{LIBSBML_DIR}/lib + $ENV{LIBSBML_DIR} +@@ -144,8 +142,7 @@ find_library(LIBSBML_LIBRARY + + if (NOT LIBSBML_LIBRARY) + find_library(LIBSBML_LIBRARY +- NAMES sbml-static +- sbml) ++ NAMES sbml) + endif (NOT LIBSBML_LIBRARY) + + if (NOT LIBSBML_LIBRARY) diff --git a/biology/libcombine/files/patch-dev_generated_CMakeLists.txt b/biology/libcombine/files/patch-dev_generated_CMakeLists.txt new file mode 100644 index 000000000000..5907bbf5a841 --- /dev/null +++ b/biology/libcombine/files/patch-dev_generated_CMakeLists.txt @@ -0,0 +1,11 @@ +--- dev/generated/CMakeLists.txt.orig 2022-10-21 06:12:43 UTC ++++ dev/generated/CMakeLists.txt +@@ -221,7 +221,7 @@ endif(WITH_SWIG) + # Locate libsbml + # + find_library(LIBSBML_LIBRARY +- NAMES libsbml-static.lib sbml-static libsbml.lib sbml ++ NAMES libsbml.lib sbml + PATHS ${LIBCOMBINE_DEPENDENCY_DIR}/lib + /usr/local/lib + /usr/lib diff --git a/biology/libcombine/pkg-descr b/biology/libcombine/pkg-descr new file mode 100644 index 000000000000..6cee46bab321 --- /dev/null +++ b/biology/libcombine/pkg-descr @@ -0,0 +1,4 @@ +LibCombine implements a C++ API library providing support for the Combine +Archive. The library is written after the likeness of libSBML (and in fact some +classes have been generated using DEVISER). Thus even thought he core is +written in C++, the classes can be accessed via SWIG from .NET, Java and Python. diff --git a/biology/libcombine/pkg-plist b/biology/libcombine/pkg-plist new file mode 100644 index 000000000000..d453477f9f49 --- /dev/null +++ b/biology/libcombine/pkg-plist @@ -0,0 +1,43 @@ +include/combine/combinearchive.h +include/combine/knownformats.h +include/combine/omexdescription.h +include/combine/util.h +include/combine/vcard.h +include/omex/CaBase.h +include/omex/CaConstructorException.h +include/omex/CaContent.h +include/omex/CaCrossRef.h +include/omex/CaError.h +include/omex/CaErrorLog.h +include/omex/CaErrorTable.h +include/omex/CaListOf.h +include/omex/CaListOfContents.h +include/omex/CaListOfCrossRefs.h +include/omex/CaNamespaces.h +include/omex/CaOmexManifest.h +include/omex/CaReader.h +include/omex/CaTypeCodes.h +include/omex/CaTypes.h +include/omex/CaVisitor.h +include/omex/CaWriter.h +include/omex/common/CaOperationReturnValues.h +include/omex/common/combinefwd.h +include/omex/common/common.h +include/omex/common/extern.h +include/omex/common/libcombine-config-common.h +include/omex/common/libcombine-config.h +include/omex/common/libcombine-namespace.h +include/omex/common/libcombine-version.h +lib/cmake/Combine-config-version.cmake +lib/cmake/Combine-config.cmake +lib/cmake/Combine-static-config-version.cmake +lib/cmake/Combine-static-config.cmake +lib/cmake/Combine-static-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Combine-static-targets.cmake +lib/cmake/Combine-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Combine-targets.cmake +lib/libCombine-static.a +lib/libCombine.so +lib/libCombine.so.0 +lib/libCombine.so.0.2.19 +share/cmake/Modules/FindLIBCOMBINE.cmake
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