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| author | Yuri Victorovich <yuri@FreeBSD.org> | 2018-12-15 08:58:05 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2018-12-15 08:58:05 +0000 |
| commit | a8badfa6b1a9a72595012f296b2706241e1f7fdb (patch) | |
| tree | f9471c32871b212eaad2d6c05e9b85dff1f3870a /biology/py-fastTSNE | |
| parent | 0f5694db950190056be7b7d190a4604379eeb95e (diff) | |
| download | ports-a8badfa6b1a9a72595012f296b2706241e1f7fdb.tar.gz ports-a8badfa6b1a9a72595012f296b2706241e1f7fdb.zip | |
Notes
Diffstat (limited to 'biology/py-fastTSNE')
| -rw-r--r-- | biology/py-fastTSNE/Makefile | 25 | ||||
| -rw-r--r-- | biology/py-fastTSNE/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-fastTSNE/files/patch-setup.py | 12 | ||||
| -rw-r--r-- | biology/py-fastTSNE/pkg-descr | 6 |
4 files changed, 46 insertions, 0 deletions
diff --git a/biology/py-fastTSNE/Makefile b/biology/py-fastTSNE/Makefile new file mode 100644 index 000000000000..6314aca0a910 --- /dev/null +++ b/biology/py-fastTSNE/Makefile @@ -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> diff --git a/biology/py-fastTSNE/distinfo b/biology/py-fastTSNE/distinfo new file mode 100644 index 000000000000..1d05309d308e --- /dev/null +++ b/biology/py-fastTSNE/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1544862153 +SHA256 (fastTSNE-0.2.13.tar.gz) = c602acf5e61f80bdda1bdfe91838ec89d7fdbdbb072e54c0d8da31c35fc964a0 +SIZE (fastTSNE-0.2.13.tar.gz) = 687321 diff --git a/biology/py-fastTSNE/files/patch-setup.py b/biology/py-fastTSNE/files/patch-setup.py new file mode 100644 index 000000000000..d2bb2d1d4607 --- /dev/null +++ b/biology/py-fastTSNE/files/patch-setup.py @@ -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( diff --git a/biology/py-fastTSNE/pkg-descr b/biology/py-fastTSNE/pkg-descr new file mode 100644 index 000000000000..5d168f46e2d6 --- /dev/null +++ b/biology/py-fastTSNE/pkg-descr @@ -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 |