From owner-dev-commits-ports-all@freebsd.org Tue Aug 17 21:30:17 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 A59E266C103; Tue, 17 Aug 2021 21:30:17 +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 4Gq4213j7lz4Smf; Tue, 17 Aug 2021 21:30:17 +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 490A224FAC; Tue, 17 Aug 2021 21:30:17 +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 17HLUHDM097097; Tue, 17 Aug 2021 21:30:17 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17HLUH5Y097092; Tue, 17 Aug 2021 21:30:17 GMT (envelope-from git) Date: Tue, 17 Aug 2021 21:30:17 GMT Message-Id: <202108172130.17HLUH5Y097092@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: 1c0e78eb4b28 - main - biology/py-PySCeS: New port: Python Simulator for Cellular Systems 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: 1c0e78eb4b2833ec20fb0addbb001e1e99235982 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: Tue, 17 Aug 2021 21:30:17 -0000 The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=1c0e78eb4b2833ec20fb0addbb001e1e99235982 commit 1c0e78eb4b2833ec20fb0addbb001e1e99235982 Author: Yuri Victorovich AuthorDate: 2021-08-17 21:29:13 +0000 Commit: Yuri Victorovich CommitDate: 2021-08-17 21:30:08 +0000 biology/py-PySCeS: New port: Python Simulator for Cellular Systems --- biology/Makefile | 1 + biology/py-PySCeS/Makefile | 38 ++++++++++++++++++++++++++++++++++++++ biology/py-PySCeS/distinfo | 3 +++ biology/py-PySCeS/pkg-descr | 3 +++ 4 files changed, 45 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index d02ab1ac20eb..081fb65708b1 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -130,6 +130,7 @@ SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI + SUBDIR += py-PySCeS SUBDIR += py-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython diff --git a/biology/py-PySCeS/Makefile b/biology/py-PySCeS/Makefile new file mode 100644 index 000000000000..a399b65938fc --- /dev/null +++ b/biology/py-PySCeS/Makefile @@ -0,0 +1,38 @@ +PORTNAME= PySCeS +DISTVERSION= 0.9.8post1 +DISTVERSIONSUFFIX= -31-g28dd259 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Python Simulator for Cellular Systems + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +PY_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} +BUILD_DEPENDS= ${PY_DEPENDS} +RUN_DEPENDS= ${PY_DEPENDS} + +USES= fortran python +USE_PYTHON= distutils autoplist + +USE_GITHUB= yes +GH_PROJECT= ${PORTNAME:tl} + +LDFLAGS+= -lpython${PYTHON_VER} -shared # see https://github.com/PySCeS/pysces/issues/29 + +post-install: + @${STRIP_CMD} \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/pitcon/pitcon.cpython-38.so \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/nleq2/nleq2.cpython-38.so + +do-test: install # from section 2.1 Loading PySCeS in http://pysces.sourceforge.net/pdf/userguide.pdf + @${PYTHON_CMD} -c "import pysces; pysces.test();" + +.include diff --git a/biology/py-PySCeS/distinfo b/biology/py-PySCeS/distinfo new file mode 100644 index 000000000000..5eb6ca09af67 --- /dev/null +++ b/biology/py-PySCeS/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1629133609 +SHA256 (PySCeS-pysces-0.9.8post1-31-g28dd259_GH0.tar.gz) = e8634ae766331b57dcc697a4a59c8c2844e744a63e47727a15b4a7f5e32c537d +SIZE (PySCeS-pysces-0.9.8post1-31-g28dd259_GH0.tar.gz) = 2670650 diff --git a/biology/py-PySCeS/pkg-descr b/biology/py-PySCeS/pkg-descr new file mode 100644 index 000000000000..72ca017a7c61 --- /dev/null +++ b/biology/py-PySCeS/pkg-descr @@ -0,0 +1,3 @@ +PySCeS provides a variety of tools for the analysis of cellular systems. + +WWW: http://pysces.sourceforge.net/