svn commit: r487491 - in head/biology: . py-fastTSNE py-fastTSNE/files
Yuri Victorovich
yuri at FreeBSD.org
Sat Dec 15 08:58:07 UTC 2018
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 at 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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