diff --git a/biology/libsedml/Makefile b/biology/libsedml/Makefile index 6f13d1379a99..9709fa517d13 100644 --- a/biology/libsedml/Makefile +++ b/biology/libsedml/Makefile @@ -1,30 +1,30 @@ PORTNAME= libsedml DISTVERSIONPREFIX= v -DISTVERSION= 2.0.26 +DISTVERSION= 2.0.27 CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org COMMENT= C++ SED-ML library LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= libsbml>0:biology/libsbml \ libnuml>0:biology/libnuml # statically linked, even into a shared library, see https://github.com/fbergmann/libSEDML/issues/155 RUN_DEPENDS= libsbml>0:biology/libsbml \ libnuml>0:biology/libnuml # when static lib libnuml.a is fixed these should be run-time dependency USES= cmake gnome USE_GNOME= libxml2 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= fbergmann GH_PROJECT= libSEDML post-install: @${RM} -r ${STAGEDIR}${DATADIR} # the project builds static libs with -fPIC, see https://github.com/fbergmann/libSEDML/issues/155 .include diff --git a/biology/libsedml/distinfo b/biology/libsedml/distinfo index 305ade0a4d35..ebba10b5a108 100644 --- a/biology/libsedml/distinfo +++ b/biology/libsedml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1632069547 -SHA256 (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 74334f2d2e0f4aae2f58f4013c432220ba12a6a6be4cf9478adbbefab7441b41 -SIZE (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 956845 +TIMESTAMP = 1645031414 +SHA256 (fbergmann-libSEDML-v2.0.27_GH0.tar.gz) = c18a1f893104e12b20e95f6a15630e9cd29ef34af915950229b771da5bd8dd01 +SIZE (fbergmann-libSEDML-v2.0.27_GH0.tar.gz) = 959802 diff --git a/biology/libsedml/pkg-plist b/biology/libsedml/pkg-plist index e88aa1bac57f..24581d796c46 100644 --- a/biology/libsedml/pkg-plist +++ b/biology/libsedml/pkg-plist @@ -1,111 +1,111 @@ include/sedml/SedAbstractCurve.h include/sedml/SedAbstractTask.h include/sedml/SedAddXML.h include/sedml/SedAdjustableParameter.h include/sedml/SedAlgorithm.h include/sedml/SedAlgorithmParameter.h include/sedml/SedAnalysis.h include/sedml/SedAppliedDimension.h include/sedml/SedAxis.h include/sedml/SedBase.h include/sedml/SedBounds.h include/sedml/SedChange.h include/sedml/SedChangeAttribute.h include/sedml/SedChangeXML.h include/sedml/SedComputeChange.h include/sedml/SedConstructorException.h include/sedml/SedCurve.h include/sedml/SedDataDescription.h include/sedml/SedDataGenerator.h include/sedml/SedDataRange.h include/sedml/SedDataSet.h include/sedml/SedDataSource.h include/sedml/SedDocument.h include/sedml/SedElementFilter.h include/sedml/SedError.h include/sedml/SedErrorLog.h include/sedml/SedErrorTable.h include/sedml/SedExperimentReference.h include/sedml/SedFigure.h include/sedml/SedFill.h include/sedml/SedFitExperiment.h include/sedml/SedFitMapping.h include/sedml/SedFunctionalRange.h include/sedml/SedLeastSquareObjectiveFunction.h include/sedml/SedLine.h include/sedml/SedListOf.h include/sedml/SedListOfAdjustableParameters.h include/sedml/SedListOfAlgorithmParameters.h include/sedml/SedListOfAppliedDimensions.h include/sedml/SedListOfChanges.h include/sedml/SedListOfCurves.h include/sedml/SedListOfDataDescriptions.h include/sedml/SedListOfDataGenerators.h include/sedml/SedListOfDataSets.h include/sedml/SedListOfDataSources.h include/sedml/SedListOfExperimentReferences.h include/sedml/SedListOfFitExperiments.h include/sedml/SedListOfFitMappings.h include/sedml/SedListOfModels.h include/sedml/SedListOfOutputs.h include/sedml/SedListOfParameters.h include/sedml/SedListOfRanges.h include/sedml/SedListOfSetValues.h include/sedml/SedListOfSimulations.h include/sedml/SedListOfSlices.h include/sedml/SedListOfStyles.h include/sedml/SedListOfSubPlots.h include/sedml/SedListOfSubTasks.h include/sedml/SedListOfSurfaces.h include/sedml/SedListOfTasks.h include/sedml/SedListOfVariables.h include/sedml/SedMarker.h include/sedml/SedModel.h include/sedml/SedNamespaces.h include/sedml/SedObjective.h include/sedml/SedOneStep.h include/sedml/SedOutput.h include/sedml/SedParameter.h include/sedml/SedParameterEstimationReport.h include/sedml/SedParameterEstimationResultPlot.h include/sedml/SedParameterEstimationTask.h include/sedml/SedPlot.h include/sedml/SedPlot2D.h include/sedml/SedPlot3D.h include/sedml/SedRange.h include/sedml/SedReader.h include/sedml/SedRemoveXML.h include/sedml/SedRepeatedTask.h include/sedml/SedReport.h include/sedml/SedSetValue.h include/sedml/SedShadedArea.h include/sedml/SedSimulation.h include/sedml/SedSlice.h include/sedml/SedSteadyState.h include/sedml/SedStyle.h include/sedml/SedSubPlot.h include/sedml/SedSubTask.h include/sedml/SedSurface.h include/sedml/SedTask.h include/sedml/SedTypeCodes.h include/sedml/SedTypes.h include/sedml/SedUniformRange.h include/sedml/SedUniformTimeCourse.h include/sedml/SedVariable.h include/sedml/SedVectorRange.h include/sedml/SedVisitor.h include/sedml/SedWaterfallPlot.h include/sedml/SedWriter.h include/sedml/common/SedOperationReturnValues.h include/sedml/common/SedmlEnumerations.h include/sedml/common/common.h include/sedml/common/extern.h include/sedml/common/libsedml-config-common.h include/sedml/common/libsedml-config.h include/sedml/common/libsedml-namespace.h include/sedml/common/libsedml-version.h include/sedml/common/sedmlfwd.h lib/libsedml-static.a lib/libsedml.so lib/libsedml.so.2 -lib/libsedml.so.2.0.26 +lib/libsedml.so.2.0.27 diff --git a/biology/py-libsedml/Makefile b/biology/py-libsedml/Makefile index d1432f390993..67b310fe2cfa 100644 --- a/biology/py-libsedml/Makefile +++ b/biology/py-libsedml/Makefile @@ -1,34 +1,34 @@ PORTNAME= libsedml DISTVERSIONPREFIX= v -DISTVERSION= 2.0.26 +DISTVERSION= 2.0.27 CATEGORIES= biology devel PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= SED-ML library for Python LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/../../../LICENSE.txt BUILD_DEPENDS= swig:devel/swig LIB_DEPENDS= libsedml.so:biology/libsedml \ libsbml.so:biology/libsbml \ libnuml.so:biology/libnuml USES= cmake localbase:ldflags python USE_PYTHON= flavors USE_GITHUB= yes GH_ACCOUNT= fbergmann GH_PROJECT= libSEDML CMAKE_ARGS= -DCMAKE_INSTALL_LIBDIR=lib LDFLAGS+= -lsedml -lsbml -lnuml # otherwise it builds a broken shared object, see https://github.com/NuML/NuML/issues/21 WRKSRC_SUBDIR= src/bindings/python do-test: install @${PYTHON_CMD} ${FILESDIR}/quick-test.py .include diff --git a/biology/py-libsedml/distinfo b/biology/py-libsedml/distinfo index 305ade0a4d35..9bab66378064 100644 --- a/biology/py-libsedml/distinfo +++ b/biology/py-libsedml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1632069547 -SHA256 (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 74334f2d2e0f4aae2f58f4013c432220ba12a6a6be4cf9478adbbefab7441b41 -SIZE (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 956845 +TIMESTAMP = 1645031777 +SHA256 (fbergmann-libSEDML-v2.0.27_GH0.tar.gz) = c18a1f893104e12b20e95f6a15630e9cd29ef34af915950229b771da5bd8dd01 +SIZE (fbergmann-libSEDML-v2.0.27_GH0.tar.gz) = 959802 diff --git a/biology/py-libsedml/files/patch-CMakeLists.txt b/biology/py-libsedml/files/patch-CMakeLists.txt index ec9da0ad9c7a..bf9fb52e3943 100644 --- a/biology/py-libsedml/files/patch-CMakeLists.txt +++ b/biology/py-libsedml/files/patch-CMakeLists.txt @@ -1,31 +1,22 @@ ---- CMakeLists.txt.orig 2021-09-07 06:43:55 UTC +--- CMakeLists.txt.orig 2022-02-15 14:40:48 UTC +++ CMakeLists.txt @@ -49,6 +49,7 @@ ADD_CUSTOM_COMMAND( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libsedml_wrap.cpp COMMAND "${SWIG_EXECUTABLE}" ARGS -I${CMAKE_CURRENT_SOURCE_DIR}/../swig/ + -I${CMAKE_INSTALL_PREFIX}/include -I${CMAKE_CURRENT_SOURCE_DIR}/../../ -I${CMAKE_CURRENT_BINARY_DIR}/../../ -I${CMAKE_CURRENT_SOURCE_DIR}/../../sedml @@ -125,9 +126,9 @@ if (PYTHON_USE_DYNAMIC_LOOKUP) if (APPLE) set_target_properties (binding_python_lib PROPERTIES LINK_FLAGS "-undefined dynamic_lookup") endif() - target_link_libraries(binding_python_lib ${LIBSEDML_LIBRARY}-static) + target_link_libraries(binding_python_lib ${LIBSEDML_LIBRARY}) else() - target_link_libraries(binding_python_lib ${LIBSEDML_LIBRARY}-static ${PYTHON_LIBRARIES}) + target_link_libraries(binding_python_lib ${LIBSEDML_LIBRARY} ${PYTHON_LIBRARIES}) endif() # -@@ -135,7 +136,7 @@ endif() - # - set(PYTHON_PACKAGE_INSTALL_DIR) - if (UNIX OR CYGWIN) -- execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c "import sys;import platform; sys.stdout.write(platform.python_version()[:3])" -+ execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c "import sys;import platform; sys.stdout.write(platform.python_version().rsplit('.', 1)[0])" - OUTPUT_VARIABLE PYTHON_VERSION) - set(PYTHON_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION}/site-packages) - else()