svn commit: r568296 - in head: . biology biology/py-fastTSNE math math/py-openTSNE math/py-openTSNE/files
Yuri Victorovich
yuri at FreeBSD.org
Sat Mar 13 23:37:14 UTC 2021
Author: yuri
Date: Sat Mar 13 23:37:12 2021
New Revision: 568296
URL: https://svnweb.freebsd.org/changeset/ports/568296
Log:
Move: biology/py-fastTSNE -> math/py-openTSNE
Project was renamed and reimplemented.
Added:
head/math/py-openTSNE/
- copied from r568295, head/biology/py-fastTSNE/
head/math/py-openTSNE/files/patch-openTSNE_dependencies_annoy_annoymodule.cc (contents, props changed)
Deleted:
head/biology/py-fastTSNE/
head/math/py-openTSNE/files/patch-setup.py
Modified:
head/MOVED
head/biology/Makefile
head/math/Makefile
head/math/py-openTSNE/Makefile
head/math/py-openTSNE/distinfo
head/math/py-openTSNE/pkg-descr
Modified: head/MOVED
==============================================================================
--- head/MOVED Sat Mar 13 23:01:40 2021 (r568295)
+++ head/MOVED Sat Mar 13 23:37:12 2021 (r568296)
@@ -16193,3 +16193,4 @@ devel/llvm60|devel/llvm80|2021-03-06|Has expired: Uses
audio/fplib||2021-03-07|Dead service since 2015
sysutils/prelink||2021-03-11|Has expired: Have no users in the ports tree
x11-fonts/vtfontcvt-ng||2021-03-12|no longer useful on any supported releases; use vtfontcvt(8) instead
+biology/py-fastTSNE|math/py-openTSNE|2021-03-13|project renamed/reimplemented under a different name
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Sat Mar 13 23:01:40 2021 (r568295)
+++ head/biology/Makefile Sat Mar 13 23:37:12 2021 (r568296)
@@ -131,7 +131,6 @@
SUBDIR += py-cutadapt
SUBDIR += py-dnaio
SUBDIR += py-ete3
- SUBDIR += py-fastTSNE
SUBDIR += py-gffutils
SUBDIR += py-gtfparse
SUBDIR += py-hits
Modified: head/math/Makefile
==============================================================================
--- head/math/Makefile Sat Mar 13 23:01:40 2021 (r568295)
+++ head/math/Makefile Sat Mar 13 23:37:12 2021 (r568296)
@@ -817,6 +817,7 @@
SUBDIR += py-numpoly
SUBDIR += py-numpy
SUBDIR += py-numpy-stl
+ SUBDIR += py-openTSNE
SUBDIR += py-opt-einsum
SUBDIR += py-optuna
SUBDIR += py-or-tools
Modified: head/math/py-openTSNE/Makefile
==============================================================================
--- head/biology/py-fastTSNE/Makefile Sat Mar 13 23:01:40 2021 (r568295)
+++ head/math/py-openTSNE/Makefile Sat Mar 13 23:37:12 2021 (r568296)
@@ -1,9 +1,8 @@
# $FreeBSD$
-PORTNAME= fastTSNE
-DISTVERSION= 0.2.13
-PORTREVISION= 4
-CATEGORIES= biology python
+PORTNAME= openTSNE
+DISTVERSION= 0.5.1
+CATEGORIES= math python # statistics
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -15,13 +14,13 @@ LICENSE= BSD3CLAUSE
BUILD_DEPENDS= ${PYNUMPY}
LIB_DEPENDS= libfftw3.so:math/fftw3
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+
+USES= localbase:ldflags python:3.6+
USE_PYTHON= distutils autoplist
-PORTSCOUT= skipv:0.2.14 # no such version, not sure where does portscout see it
+post-install:
+ @${FIND} ${STAGEDIR}${PREFIX} -name "*.so" | ${XARGS} ${STRIP_CMD}
.include <bsd.port.mk>
Modified: head/math/py-openTSNE/distinfo
==============================================================================
--- head/biology/py-fastTSNE/distinfo Sat Mar 13 23:01:40 2021 (r568295)
+++ head/math/py-openTSNE/distinfo Sat Mar 13 23:37:12 2021 (r568296)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1544862153
-SHA256 (fastTSNE-0.2.13.tar.gz) = c602acf5e61f80bdda1bdfe91838ec89d7fdbdbb072e54c0d8da31c35fc964a0
-SIZE (fastTSNE-0.2.13.tar.gz) = 687321
+TIMESTAMP = 1615668058
+SHA256 (openTSNE-0.5.1.tar.gz) = 755a54ca10c1300e78181e24144fc24481cb8ab4379d27d4c8782a0a1ee37db9
+SIZE (openTSNE-0.5.1.tar.gz) = 878691
Added: head/math/py-openTSNE/files/patch-openTSNE_dependencies_annoy_annoymodule.cc
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/math/py-openTSNE/files/patch-openTSNE_dependencies_annoy_annoymodule.cc Sat Mar 13 23:37:12 2021 (r568296)
@@ -0,0 +1,13 @@
+- see https://github.com/pavlin-policar/openTSNE/issues/165
+
+--- openTSNE/dependencies/annoy/annoymodule.cc.orig 2021-03-13 20:45:35 UTC
++++ openTSNE/dependencies/annoy/annoymodule.cc
+@@ -177,7 +177,7 @@ py_an_init(py_annoy *self, PyObject *args, PyObject *k
+ int f;
+ static char const * kwlist[] = {"f", "metric", NULL};
+ if (!PyArg_ParseTupleAndKeywords(args, kwargs, "i|s", (char**)kwlist, &f, &metric))
+- return (int) NULL;
++ return 0;
+ return 0;
+ }
+
Modified: head/math/py-openTSNE/pkg-descr
==============================================================================
--- head/biology/py-fastTSNE/pkg-descr Sat Mar 13 23:01:40 2021 (r568295)
+++ head/math/py-openTSNE/pkg-descr Sat Mar 13 23:37:12 2021 (r568296)
@@ -1,6 +1,9 @@
-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.
+openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor
+Embedding (t-SNE), a popular dimensionality-reduction algorithm for visualizing
+high-dimensional data sets. openTSNE incorporates the latest improvements to the
+t-SNE algorithm, including the ability to add new data points to existing
+embeddings, massive speed improvements, enabling t-SNE to scale to millions of
+data points and various tricks to improve global alignment of the resulting
+visualizations.
-WWW: https://github.com/pavlin-policar/fastTSNE
+WWW: https://github.com/pavlin-policar/openTSNE
More information about the svn-ports-head
mailing list