From owner-dev-commits-ports-all@freebsd.org Sun Sep 19 06:48:08 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 9E2C46ADFAA; Sun, 19 Sep 2021 06:48:08 +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 4HBytw42qXz3qG7; Sun, 19 Sep 2021 06:48:08 +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 6C43218B2A; Sun, 19 Sep 2021 06:48:08 +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 18J6m8HA009095; Sun, 19 Sep 2021 06:48:08 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 18J6m8ea009094; Sun, 19 Sep 2021 06:48:08 GMT (envelope-from git) Date: Sun, 19 Sep 2021 06:48:08 GMT Message-Id: <202109190648.18J6m8ea009094@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: 74c998634a39 - main - biology/py-libnuml: New port: Numerical Markup Language for Python 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: 74c998634a3910153179e59ed3fa5f43df3d7332 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 06:48:08 -0000 The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=74c998634a3910153179e59ed3fa5f43df3d7332 commit 74c998634a3910153179e59ed3fa5f43df3d7332 Author: Yuri Victorovich AuthorDate: 2021-09-19 06:46:04 +0000 Commit: Yuri Victorovich CommitDate: 2021-09-19 06:47:03 +0000 biology/py-libnuml: New port: Numerical Markup Language for Python --- biology/Makefile | 1 + biology/py-libnuml/Makefile | 31 +++++++++++++++++++++++++++ biology/py-libnuml/distinfo | 3 +++ biology/py-libnuml/files/patch-CMakeLists.txt | 22 +++++++++++++++++++ biology/py-libnuml/pkg-descr | 8 +++++++ biology/py-libnuml/pkg-plist | 3 +++ 6 files changed, 68 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index e24861f2a317..ec370d664a52 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -150,6 +150,7 @@ SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc + SUBDIR += py-libnuml SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell diff --git a/biology/py-libnuml/Makefile b/biology/py-libnuml/Makefile new file mode 100644 index 000000000000..dcd1b9df3d08 --- /dev/null +++ b/biology/py-libnuml/Makefile @@ -0,0 +1,31 @@ +PORTNAME= libnuml +DISTVERSIONPREFIX= v +DISTVERSION= 1.1.4 +CATEGORIES= biology devel +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Numerical Markup Language for Python + +LICENSE= LGPL21 + +BUILD_DEPENDS= swig:devel/swig +LIB_DEPENDS= libnuml.so:biology/libnuml + +USES= cmake localbase:ldflags python +USE_PYTHON= flavors + +USE_GITHUB= yes +GH_ACCOUNT= NuML +GH_PROJECT= NuML + +WKSRC_SUBDIR= ${PORTNAME}/src/bindings/python + +CMAKE_ARGS= -DCMAKE_INSTALL_LIBDIR=lib + +LDFLAGS+= -lnuml # otherwise it builds a broken shared object, see https://github.com/NuML/NuML/issues/21 + +post-extract: + @${RLN} ${WRKSRC}/../../../VERSION.txt ${WRKSRC}/VERSION.txt + +.include diff --git a/biology/py-libnuml/distinfo b/biology/py-libnuml/distinfo new file mode 100644 index 000000000000..6d10a1bca0ea --- /dev/null +++ b/biology/py-libnuml/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1632027367 +SHA256 (NuML-NuML-v1.1.4_GH0.tar.gz) = 18e8f6d9b0c261f34123bc2e1bd601730993d63fb53f7434b5901b1059aa9109 +SIZE (NuML-NuML-v1.1.4_GH0.tar.gz) = 3419841 diff --git a/biology/py-libnuml/files/patch-CMakeLists.txt b/biology/py-libnuml/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..12167a58575d --- /dev/null +++ b/biology/py-libnuml/files/patch-CMakeLists.txt @@ -0,0 +1,22 @@ +--- CMakeLists.txt.orig 2021-04-29 08:24:05 UTC ++++ CMakeLists.txt +@@ -62,6 +62,7 @@ ADD_CUSTOM_COMMAND( + OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libnuml_wrap.cpp + COMMAND "${SWIG_EXECUTABLE}" + ARGS -I${CMAKE_CURRENT_SOURCE_DIR}/../swig/ ++ -I${CMAKE_INSTALL_PREFIX}/include + -I${CMAKE_SOURCE_DIR}/ + -I${CMAKE_BINARY_DIR}/ + -I${CMAKE_BINARY_DIR}/src +@@ -142,9 +143,9 @@ 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 ${LIBNUML_LIBRARY}-static) ++ target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY}) + else() +- target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY}-static ${PYTHON_LIBRARIES}) ++ target_link_libraries(binding_python_lib ${LIBNUML_LIBRARY} ${PYTHON_LIBRARIES}) + endif() + + diff --git a/biology/py-libnuml/pkg-descr b/biology/py-libnuml/pkg-descr new file mode 100644 index 000000000000..a8a267cc7f76 --- /dev/null +++ b/biology/py-libnuml/pkg-descr @@ -0,0 +1,8 @@ +This is a Python binding for libnuml, the Numerical Markup Language library. + +The Numerical Markup Language (NuML) aims to standardize the exchange and +archiving of numerical results. NuML originates from the numerical aspects of +the Systems Biology Results Markup Language (SBRML) with the aim of re-using it +in multiple other standardization efforts. + +WWW: https://github.com/NuML/NuML diff --git a/biology/py-libnuml/pkg-plist b/biology/py-libnuml/pkg-plist new file mode 100644 index 000000000000..8156ea3a6416 --- /dev/null +++ b/biology/py-libnuml/pkg-plist @@ -0,0 +1,3 @@ +%%PYTHON_SITELIBDIR%%/libnuml.pth +%%PYTHON_SITELIBDIR%%/libnuml/_libnuml.so +%%PYTHON_SITELIBDIR%%/libnuml/libnuml.py