git: f349e4d06924 - main - biology/libsbml: Update to 5.20.5
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Date: Mon, 19 May 2025 20:02:54 UTC
The branch main has been updated by sunpoet:
URL: https://cgit.FreeBSD.org/ports/commit/?id=f349e4d0692493ce175d9b7f8b16ad90a376e4a4
commit f349e4d0692493ce175d9b7f8b16ad90a376e4a4
Author: Po-Chuan Hsieh <sunpoet@FreeBSD.org>
AuthorDate: 2025-05-19 19:07:02 +0000
Commit: Po-Chuan Hsieh <sunpoet@FreeBSD.org>
CommitDate: 2025-05-19 19:57:56 +0000
biology/libsbml: Update to 5.20.5
Changes: https://github.com/sbmlteam/libsbml/releases
---
biology/libsbml/Makefile | 6 ++----
biology/libsbml/distinfo | 6 +++---
biology/libsbml/files/patch-CMakeLists.txt | 26 ++++++++++++--------------
biology/libsbml/pkg-plist | 26 ++++++++++++++++++++++++++
4 files changed, 43 insertions(+), 21 deletions(-)
diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
index 383b06145b85..fec0997b39be 100644
--- a/biology/libsbml/Makefile
+++ b/biology/libsbml/Makefile
@@ -1,7 +1,6 @@
PORTNAME= libsbml
-PORTVERSION= 5.20.4
+PORTVERSION= 5.20.5
DISTVERSIONPREFIX= v
-PORTREVISION= 1
CATEGORIES= biology devel
MAINTAINER= sunpoet@FreeBSD.org
@@ -74,7 +73,6 @@ post-patch:
@${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt
post-install-EXAMPLES-on:
- ${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR}
- ${RMDIR} ${STAGEDIR}${DATADIR}
+ ${MV} ${STAGEDIR}${DATADIR}examples ${STAGEDIR}${EXAMPLESDIR}
.include <bsd.port.mk>
diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo
index 7884ce4f4a5c..7908d7960b79 100644
--- a/biology/libsbml/distinfo
+++ b/biology/libsbml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1725559551
-SHA256 (sbmlteam-libsbml-v5.20.4_GH0.tar.gz) = 02c225d3513e1f5d6e3c0168456f568e67f006eddaab82f09b4bdf0d53d2050e
-SIZE (sbmlteam-libsbml-v5.20.4_GH0.tar.gz) = 28796139
+TIMESTAMP = 1747546406
+SHA256 (sbmlteam-libsbml-v5.20.5_GH0.tar.gz) = 21c88c753a4a031f157a033de3810488b86f003e684c6ca7aa3d6e26e7e0acfc
+SIZE (sbmlteam-libsbml-v5.20.5_GH0.tar.gz) = 28852940
diff --git a/biology/libsbml/files/patch-CMakeLists.txt b/biology/libsbml/files/patch-CMakeLists.txt
index 037277324c79..32366d12deb1 100644
--- a/biology/libsbml/files/patch-CMakeLists.txt
+++ b/biology/libsbml/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig 2023-04-03 10:48:28 UTC
+--- CMakeLists.txt.orig 2025-05-05 04:53:07 UTC
+++ CMakeLists.txt
-@@ -430,8 +430,6 @@ if(WITH_EXPAT)
+@@ -445,8 +445,6 @@ if(WITH_EXPAT)
set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR})
set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY})
@@ -9,7 +9,7 @@
endif(WITH_EXPAT)
-@@ -452,8 +450,6 @@ if(WITH_LIBXML)
+@@ -467,8 +465,6 @@ if(WITH_LIBXML)
set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
@@ -18,7 +18,7 @@
endif(WITH_LIBXML)
-@@ -473,8 +469,6 @@ if(WITH_XERCES)
+@@ -488,8 +484,6 @@ if(WITH_XERCES)
set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
@@ -27,7 +27,7 @@
endif(WITH_XERCES)
###############################################################################
-@@ -498,7 +492,6 @@ if(WITH_BZIP2)
+@@ -513,7 +507,6 @@ if(WITH_BZIP2)
set(USE_BZ2 ON)
add_definitions( -DUSE_BZ2 )
list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
@@ -35,16 +35,16 @@
endif(WITH_BZIP2)
-@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does
- INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}")
- endif()
-
+@@ -550,8 +543,6 @@ if(WITH_ZLIB)
+ set(USE_ZLIB ON)
+ add_definitions( -DUSE_ZLIB )
+ list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB)
- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake")
-
endif(WITH_ZLIB)
# install find scripts only for used dependencies
-@@ -981,22 +972,6 @@ if(WITH_DOXYGEN)
+@@ -923,20 +914,6 @@ endif()
add_subdirectory(docs)
endif()
@@ -62,8 +62,6 @@
- README.md
- VERSION.txt
-)
--
--install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
- ###############################################################################
- #
+ install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
+
diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist
index 7a382979c5e4..df36c508c663 100644
--- a/biology/libsbml/pkg-plist
+++ b/biology/libsbml/pkg-plist
@@ -107,6 +107,31 @@ include/sbml/extension/SBaseExtensionPoint.h
include/sbml/extension/SBasePlugin.h
include/sbml/extension/SBasePluginCreator.h
include/sbml/extension/SBasePluginCreatorBase.h
+include/sbml/html2md/html2md.h
+include/sbml/html2md/table.h
+include/sbml/maddy/blockparser.h
+include/sbml/maddy/breaklineparser.h
+include/sbml/maddy/checklistparser.h
+include/sbml/maddy/codeblockparser.h
+include/sbml/maddy/emphasizedparser.h
+include/sbml/maddy/headlineparser.h
+include/sbml/maddy/horizontallineparser.h
+include/sbml/maddy/htmlparser.h
+include/sbml/maddy/imageparser.h
+include/sbml/maddy/inlinecodeparser.h
+include/sbml/maddy/italicparser.h
+include/sbml/maddy/latexblockparser.h
+include/sbml/maddy/lineparser.h
+include/sbml/maddy/linkparser.h
+include/sbml/maddy/orderedlistparser.h
+include/sbml/maddy/paragraphparser.h
+include/sbml/maddy/parser.h
+include/sbml/maddy/parserconfig.h
+include/sbml/maddy/quoteparser.h
+include/sbml/maddy/strikethroughparser.h
+include/sbml/maddy/strongparser.h
+include/sbml/maddy/tableparser.h
+include/sbml/maddy/unorderedlistparser.h
include/sbml/math/ASTNode.h
include/sbml/math/ASTNodeType.h
include/sbml/math/DefinitionURLRegistry.h
@@ -236,6 +261,7 @@ share/cmake/Modules/FindLIBSBML.cmake
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferReactions.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp