From owner-svn-ports-head@freebsd.org Sat Mar 13 23:37:14 2021 Return-Path: Delivered-To: svn-ports-head@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id A4D2D5AF49C; Sat, 13 Mar 2021 23:37:14 +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) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4DyfGy4Fy9z3qXh; Sat, 13 Mar 2021 23:37:14 +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 80B8D13999; Sat, 13 Mar 2021 23:37:14 +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 12DNbEAC088071; Sat, 13 Mar 2021 23:37:14 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 12DNbCBd088063; Sat, 13 Mar 2021 23:37:12 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202103132337.12DNbCBd088063@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sat, 13 Mar 2021 23:37:12 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r568296 - in head: . biology biology/py-fastTSNE math math/py-openTSNE math/py-openTSNE/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head: . biology biology/py-fastTSNE math math/py-openTSNE math/py-openTSNE/files X-SVN-Commit-Revision: 568296 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 13 Mar 2021 23:37:14 -0000 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 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