From nobody Mon Jun 23 18:49:33 2025 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4bQxvd2P9gz5yfP8; Mon, 23 Jun 2025 18:49:33 +0000 (UTC) (envelope-from git@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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4bQxvd1LYrz3s6r; Mon, 23 Jun 2025 18:49:33 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1750704573; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=jwDea563KEr02wshLJrCUkSji7X9icWTI3UxsWjNn48=; b=W6gTbBRCLXPQtG8/27nTp+3f/ZsoE4HTeqSSxTRiNd5CahLBzzzt20DjnQxJqcsXl/ZTp8 38Xtdbw3ek5HH+TrLgfx987koFzBZGWeHkH4wzKhY6ZFTZKUbXRlU/YMvEBlekRD5Uthsx ewFovuOtS9f0dHMgQlb6cLrGa6L/VZr0FPhBvkQa79G/96J1nRHq4QUjopDesI1G2VUP5e 5U7TNBz9Mb4RDNtdHyNlazLPdFOKsTz+1/KE6pvwvQ/G3ewvCuOrI4Pgm3VCOQ5LdPWswh CvGJ8rnfUK1QuzhHrQLzfJN9FLi5CZ5/uszbNy6v2i752qQDx96hezv5eKn8jQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1750704573; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=jwDea563KEr02wshLJrCUkSji7X9icWTI3UxsWjNn48=; b=sGg4dCmcjXDN+2ZghnmnjOESEvE23JoSkpp2b1THxaOY+2JKOXmxj1KyZCCLh2YwvPZ5yV DbNJ2ovrNwfAtep7zksfQJWHMOiJTG88iWg2Ph8IXIwl/7IDHc3q5W5zLyr0Ss49nrKt6L m2Ou2xpLg/5WOfdKePLqEw48Cy2PPPbuFKmA6xwlLWR3RIaGEKQ4kZ4r8OKTqN7agIX3TC QTKuYlp8wKA558jUr8tYDbHoqpeey34q2VMSPXhmH5S9hYPBGPvBEvKwPhuZkfoqdiO0yW qQFM1vIuP292isQU1Z/0mTSIypm9v9LijGy8VAkl8+Bkl/DXMD65WremLfwkxw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1750704573; a=rsa-sha256; cv=none; b=sevw3mXGjeTb57FPwjupeZRP5eqVAYrEK+Ik6PdXdw4u5XW7ukOIJXDRcENSeiRMyQ0tB4 wNmzdY4dKkoc04LsPmD0SH1gSny8vqUV4SIkFBAvUG007R8mMPW6sxumFhOQWuY3UzYE9k +D1aORGhekWCkMquXRW+jywgJ6PQ/4PtMR5/4C51IFfqiEbOXsbUumnk8jxS6L96YDY3LI AZud18rhGSygkLmjprI0UTLCKOOYkQUtpnJBoFX9RgmeV2vc0aIW+HoCaDEWBIxDxu9UDD flcxG6UgVgpLeNsf4F9sBLeHO1RIoahKJHfys88SAgwOVFa0MOsurp1G+LNKPg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4bQxvd0w8hz9F; Mon, 23 Jun 2025 18:49:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 55NInXD0011872; Mon, 23 Jun 2025 18:49:33 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 55NInXS7011870; Mon, 23 Jun 2025 18:49:33 GMT (envelope-from git) Date: Mon, 23 Jun 2025 18:49:33 GMT Message-Id: <202506231849.55NInXS7011870@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Rene Ladan Subject: git: 8821501c8ec8 - main - biology/py-orange3-single-cell: Remove expired port List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: rene X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 8821501c8ec873758bd70f04b64d756edddf6202 Auto-Submitted: auto-generated The branch main has been updated by rene: URL: https://cgit.FreeBSD.org/ports/commit/?id=8821501c8ec873758bd70f04b64d756edddf6202 commit 8821501c8ec873758bd70f04b64d756edddf6202 Author: Rene Ladan AuthorDate: 2025-06-23 18:49:24 +0000 Commit: Rene Ladan CommitDate: 2025-06-23 18:49:24 +0000 biology/py-orange3-single-cell: Remove expired port 2025-06-21 biology/py-orange3-single-cell: Depends on expired math/py-fastdtw and expiring misc/orange3 --- MOVED | 1 + biology/Makefile | 1 - biology/py-orange3-single-cell/Makefile | 46 ---------------------- biology/py-orange3-single-cell/distinfo | 3 -- .../py-orange3-single-cell/files/patch-doc_conf.py | 10 ----- biology/py-orange3-single-cell/pkg-descr | 2 - 6 files changed, 1 insertion(+), 62 deletions(-) diff --git a/MOVED b/MOVED index 2be325716984..d793a29c8da3 100644 --- a/MOVED +++ b/MOVED @@ -4525,3 +4525,4 @@ devel/py-pytest4-cov||2025-06-23|Has expired: Depends on expiring devel/py-pytes devel/py-spyder-unittest||2025-06-23|Has expired: Depends on expiring devel/spyder comms/py-pynitrokey||2025-06-23|Has expired: Depends on expiring comms/py-spsdk devel/bit||2025-06-23|Has expired: Upstream ceased development +biology/py-orange3-single-cell||2025-06-23|Has expired: Depends on expired math/py-fastdtw and expiring misc/orange3 diff --git a/biology/Makefile b/biology/Makefile index 590109724958..45fce4f6412c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -190,7 +190,6 @@ SUBDIR += py-newick SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics - SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig diff --git a/biology/py-orange3-single-cell/Makefile b/biology/py-orange3-single-cell/Makefile deleted file mode 100644 index 54d72a4516fd..000000000000 --- a/biology/py-orange3-single-cell/Makefile +++ /dev/null @@ -1,46 +0,0 @@ -PORTNAME= orange3-single-cell -DISTVERSION= 0.8.2 -PORTREVISION= 6 -CATEGORIES= biology python -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Orange add-on for gene expression of single cell data -WWW= https://singlecell.biolab.si/ - -LICENSE= AGPLv3+ - -DEPRECATED= Depends on expired math/py-fastdtw and expiring misc/orange3 -EXPIRATION_DATE=2025-06-21 - -RUN_DEPENDS= orange3>0:misc/orange3 \ - ${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}astropy>0:astro/py-astropy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}fastdtw>0:math/py-fastdtw@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}joblib>=0.11:devel/py-joblib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}loompy>=2.0.10:biology/py-loompy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>=0.23:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYNUMPY} - -# Supports 3.4+ but loompy 3.6+ only. -USES= python -USE_GITHUB= yes -GH_ACCOUNT= biolab -USE_PYTHON= distutils autoplist - -NO_ARCH= yes - -OPTIONS_DEFINE= DOCS - -DOCS_BUILD_DEPENDS= gmake:devel/gmake \ - ${PYTHON_PKGNAMEPREFIX}sphinx>=0,1:textproc/py-sphinx@${PY_FLAVOR} - -pre-build-DOCS-on: - @cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${GMAKE} html htmlhelp SPHINXBUILD=${LOCALBASE}/bin/sphinx-build-${PYTHON_VER} - -pre-build-DOCS-off: - @${REINPLACE_CMD} "s|^ include_documentation| #include_documentation|" ${WRKSRC}/setup.py - -.include diff --git a/biology/py-orange3-single-cell/distinfo b/biology/py-orange3-single-cell/distinfo deleted file mode 100644 index ed5f301ce6e1..000000000000 --- a/biology/py-orange3-single-cell/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1539761270 -SHA256 (biolab-orange3-single-cell-0.8.2_GH0.tar.gz) = eebda4303c208951fcbe8f383e0f310b20abedba425b0c68bbe65ae2806cc1bb -SIZE (biolab-orange3-single-cell-0.8.2_GH0.tar.gz) = 5521782 diff --git a/biology/py-orange3-single-cell/files/patch-doc_conf.py b/biology/py-orange3-single-cell/files/patch-doc_conf.py deleted file mode 100644 index a3ecb4c652db..000000000000 --- a/biology/py-orange3-single-cell/files/patch-doc_conf.py +++ /dev/null @@ -1,10 +0,0 @@ -# add_stylesheet() deprecated on Sphinx 4.0 -# https://www.sphinx-doc.org/en/master/extdev/deprecated.html ---- doc/conf.py.orig 2018-10-15 08:43:14 UTC -+++ doc/conf.py -@@ -288,4 +288,4 @@ texinfo_documents = [ - #texinfo_no_detailmenu = False - - def setup(app): -- app.add_stylesheet('style.css') -+ app.add_css_file('style.css') diff --git a/biology/py-orange3-single-cell/pkg-descr b/biology/py-orange3-single-cell/pkg-descr deleted file mode 100644 index 05cf4bfc5f8a..000000000000 --- a/biology/py-orange3-single-cell/pkg-descr +++ /dev/null @@ -1,2 +0,0 @@ -The Single Cell add-on for Orange3 adds functionality for analysis of single -cell data.