Date: Sat, 15 Dec 2018 08:58:05 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> 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 Message-ID: <201812150858.wBF8w5E8074305@repo.freebsd.org>
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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 <bsd.port.mk> 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
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