From owner-svn-ports-all@freebsd.org Sat Dec 15 08:58:07 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id D040D133CAD7; Sat, 15 Dec 2018 08:58:06 +0000 (UTC) (envelope-from yuri@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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 6F28D8CC73; Sat, 15 Dec 2018 08:58:06 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 5BFCDD2D9; Sat, 15 Dec 2018 08:58:06 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id wBF8w6Wa074309; Sat, 15 Dec 2018 08:58:06 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id wBF8w5E8074305; Sat, 15 Dec 2018 08:58:05 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201812150858.wBF8w5E8074305@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sat, 15 Dec 2018 08:58:05 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r487491 - in head/biology: . py-fastTSNE py-fastTSNE/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . py-fastTSNE py-fastTSNE/files X-SVN-Commit-Revision: 487491 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 6F28D8CC73 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.83 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-0.99)[-0.990,0]; NEURAL_HAM_SHORT(-0.96)[-0.958,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-0.88)[-0.881,0] X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 15 Dec 2018 08:58:07 -0000 Author: yuri Date: Sat Dec 15 08:58:05 2018 New Revision: 487491 URL: https://svnweb.freebsd.org/changeset/ports/487491 Log: New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE Added: head/biology/py-fastTSNE/ head/biology/py-fastTSNE/Makefile (contents, props changed) head/biology/py-fastTSNE/distinfo (contents, props changed) head/biology/py-fastTSNE/files/ head/biology/py-fastTSNE/files/patch-setup.py (contents, props changed) head/biology/py-fastTSNE/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Dec 15 08:16:06 2018 (r487490) +++ head/biology/Makefile Sat Dec 15 08:58:05 2018 (r487491) @@ -106,6 +106,7 @@ SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt + SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy Added: head/biology/py-fastTSNE/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-fastTSNE/Makefile Sat Dec 15 08:58:05 2018 (r487491) @@ -0,0 +1,25 @@ +# $FreeBSD$ + +PORTNAME= fastTSNE +DISTVERSION= 0.2.13 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Fast, parallel implementations of t-SNE + +LICENSE= BSD3CLAUSE + +BUILD_DEPENDS= ${PYNUMPY} +LIB_DEPENDS= libfftw3.so:math/fftw3 \ + libomp.so:devel/openmp +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}numba>=0.38.1:devel/py-numba@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.20.0:science/py-scikit-learn@${PY_FLAVOR} + +USES= localbase:ldflags python:3.5+ +USE_PYTHON= distutils autoplist + +.include Added: head/biology/py-fastTSNE/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-fastTSNE/distinfo Sat Dec 15 08:58:05 2018 (r487491) @@ -0,0 +1,3 @@ +TIMESTAMP = 1544862153 +SHA256 (fastTSNE-0.2.13.tar.gz) = c602acf5e61f80bdda1bdfe91838ec89d7fdbdbb072e54c0d8da31c35fc964a0 +SIZE (fastTSNE-0.2.13.tar.gz) = 687321 Added: head/biology/py-fastTSNE/files/patch-setup.py ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-fastTSNE/files/patch-setup.py Sat Dec 15 08:58:05 2018 (r487491) @@ -0,0 +1,12 @@ +--- setup.py.orig 2018-12-15 08:37:12 UTC ++++ setup.py +@@ -87,7 +87,8 @@ extensions = [ + ] + + # Check if we have access to FFTW3 and if so, use that implementation +-if has_c_library('fftw3'): ++# has_c_library fails to use CFLAGS: https://github.com/pavlin-policar/fastTSNE/issues/43 ++if True or has_c_library('fftw3'): + lm_opt = '/lm' if IS_WINDOWS else '-lm' + fftw3_opt = '/lfftw3' if IS_WINDOWS else '-lfftw3' + extensions.append( Added: head/biology/py-fastTSNE/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-fastTSNE/pkg-descr Sat Dec 15 08:58:05 2018 (r487491) @@ -0,0 +1,6 @@ +Fast, parallel implementations of t-SNE allows, for example, in one case +to visualize 160,796 single cell transcriptomes from the mouse nervous system +computed in under 2 minutes using FFT accelerated interpolation and approximate +nearest neighbors. + +WWW: https://github.com/pavlin-policar/fastTSNE