From owner-dev-commits-ports-all@freebsd.org Sun Sep 19 18:16:41 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 9CDF566F28F; Sun, 19 Sep 2021 18:16:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4HCG9P3bwdz4STb; Sun, 19 Sep 2021 18:16:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4D9FB21D8F; Sun, 19 Sep 2021 18:16:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 18JIGfwO027669; Sun, 19 Sep 2021 18:16:41 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 18JIGfYX027668; Sun, 19 Sep 2021 18:16:41 GMT (envelope-from git) Date: Sun, 19 Sep 2021 18:16:41 GMT Message-Id: <202109191816.18JIGfYX027668@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: dd804e98719a - main - biology/libsedml: New port: C++ SED-ML library MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: dd804e98719a5c2376d15b79e6b745f45ab1de40 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 19 Sep 2021 18:16:41 -0000 The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=dd804e98719a5c2376d15b79e6b745f45ab1de40 commit dd804e98719a5c2376d15b79e6b745f45ab1de40 Author: Yuri Victorovich AuthorDate: 2021-09-19 18:13:21 +0000 Commit: Yuri Victorovich CommitDate: 2021-09-19 18:15:35 +0000 biology/libsedml: New port: C++ SED-ML library --- biology/Makefile | 1 + biology/libsedml/Makefile | 30 ++++++++++++ biology/libsedml/distinfo | 3 ++ biology/libsedml/pkg-descr | 4 ++ biology/libsedml/pkg-plist | 111 +++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 149 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index ec370d664a52..f57fe3e300fd 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -78,6 +78,7 @@ SUBDIR += libgtextutils SUBDIR += libnuml SUBDIR += libsbml + SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 diff --git a/biology/libsedml/Makefile b/biology/libsedml/Makefile new file mode 100644 index 000000000000..6f13d1379a99 --- /dev/null +++ b/biology/libsedml/Makefile @@ -0,0 +1,30 @@ +PORTNAME= libsedml +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.26 +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 new file mode 100644 index 000000000000..305ade0a4d35 --- /dev/null +++ b/biology/libsedml/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1632069547 +SHA256 (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 74334f2d2e0f4aae2f58f4013c432220ba12a6a6be4cf9478adbbefab7441b41 +SIZE (fbergmann-libSEDML-v2.0.26_GH0.tar.gz) = 956845 diff --git a/biology/libsedml/pkg-descr b/biology/libsedml/pkg-descr new file mode 100644 index 000000000000..5a7f83016d46 --- /dev/null +++ b/biology/libsedml/pkg-descr @@ -0,0 +1,4 @@ +The libSEDML project makes use of libSBML XML layer as well as code generation +as starting point to produce a library for reading and writing of SED-ML models. + +WWW: https://github.com/fbergmann/libSEDML diff --git a/biology/libsedml/pkg-plist b/biology/libsedml/pkg-plist new file mode 100644 index 000000000000..e88aa1bac57f --- /dev/null +++ b/biology/libsedml/pkg-plist @@ -0,0 +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