From nobody Sun Aug 06 18:17:53 2023 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 4RJnkB2WCnz4mChl; Sun, 6 Aug 2023 18:17:54 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4RJnkB1Dw3z4MB5; Sun, 6 Aug 2023 18:17:54 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691345874; 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=CXyzyZ36Zbm1Vdh+8eQBXmtxqNM5OyIJ4fskWmZeGVs=; b=mde4kuBl+eJ7U4GzjSw/Cft1w/K/sM49ZTjF2LvEGyFf0CoWcGWyLUVUUu2Ymr7LGWrhED GYtSybNzw0KIMU24oSxd+EKHP4CufGyGewQ4j141VbN265utyrjOr9kD94irFbN8tkj8zS oBXg0fHrUxExnvnnI0iswk9Yp1/F1U3rwT0VbffZocEb6C26FikpeC0WKVcTrg7nhOfSXR yIWZoIMEbAzm7j4jZ9C52QB3czNyPgcNKTjrR/MH/u44RYMZK3RCB5I/DZmx1yiZ6uv0NY k44rBZ2e+9rC+DiHcYDHzCcfOi09hG3zqZTZhh+kiZBeB3cR368GEYJlry9eMg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691345874; 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=CXyzyZ36Zbm1Vdh+8eQBXmtxqNM5OyIJ4fskWmZeGVs=; b=tL+QYLlJxgCfIL0KPF6ndq1giYso829oKerUP3alisERqDtKJUdtsg8jVIRwBxySJI5t3I mkr7/RO/deYN9FJD2UQGjI3jz8qhvnzFjRnScsC8n7zqyYFLXMqrbGL+0eTSqIbNKuresd ah6EhEujM32vFndFy1yUPDIB4jrA5v0UpmvMk7S1yL3yV1xysJQeI2wriuPfbXN2yGsVsO 2AY73Y5Ixf99DhW+8bQWtV/2KdwDanpyIBlBGFNhl7DLkPm/v0ZmXb0b6MBN9jD2l+aRNh Gv4vyTlULRe359F2ePOaN+5uu07R6n7IgjW9u3mAWXJPmknuu+GW5r0rAtSaow== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1691345874; a=rsa-sha256; cv=none; b=SwurIw39/ICWzc3xdMRY4bylYciTROrxETPFHir6h89TP4scOg3NZ034NYktIZt+T8gaSF jPupvLUzAY0JDMqHQ7AuBcCIytqahQgUEXvkdtscht6+w2MpWtwI09uBWjvSLyBM805HtC k0YD9jYNOSTrmVFLKtkpRGxG9Xcu+t2nd8T2XXnj9ca0EorDc66Urwxuyi8Bd/zgn62nPA OnIl90FylToewlD3ZqJcyRWkIcMAqZRfiLriDeCzxMa4h45M7EmduRdO4gULYBsedDSiUE s8oEl8XR/eL8ajtYKZ96DRYmaU0gX+BJVjk4ZkWriegrvDCCMa7O+Bqk37d6mQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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 4RJnkB0BGdz4r4; Sun, 6 Aug 2023 18:17:54 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 376IHrqg009099; Sun, 6 Aug 2023 18:17:53 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 376IHrEj009098; Sun, 6 Aug 2023 18:17:53 GMT (envelope-from git) Date: Sun, 6 Aug 2023 18:17:53 GMT Message-Id: <202308061817.376IHrEj009098@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: e97c3457489f - main - biology/py-macs2: Update to 2.2.9.1 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: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e97c3457489f2abb3cda2b6b023ba580b6382c07 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e97c3457489f2abb3cda2b6b023ba580b6382c07 commit e97c3457489f2abb3cda2b6b023ba580b6382c07 Author: Jason W. Bacon AuthorDate: 2023-08-06 18:14:56 +0000 Commit: Jason W. Bacon CommitDate: 2023-08-06 18:17:52 +0000 biology/py-macs2: Update to 2.2.9.1 Mainly updates to dependencies Changes: https://github.com/macs3-project/MACS/releases Added test target Reported by: portscout --- biology/py-macs2/Makefile | 15 +++++++++++---- biology/py-macs2/distinfo | 6 +++--- biology/py-macs2/files/patch-setup.py | 25 ------------------------- 3 files changed, 14 insertions(+), 32 deletions(-) diff --git a/biology/py-macs2/Makefile b/biology/py-macs2/Makefile index e8e1313b1da8..5a9d78cfe622 100644 --- a/biology/py-macs2/Makefile +++ b/biology/py-macs2/Makefile @@ -1,6 +1,6 @@ PORTNAME= macs2 DISTVERSIONPREFIX= v -DISTVERSION= 2.2.8 +DISTVERSION= 2.2.9.1 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,18 +12,25 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} -RUN_DEPENDS= ${PYNUMPY} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ + bash:shells/bash -USES= python +USES= python shebangfix +USE_GITHUB= yes USE_PYTHON= autoplist concurrent cython distutils -USE_GITHUB= yes GH_ACCOUNT= taoliu GH_PROJECT= MACS +SHEBANG_FILES= test/cmdlinetest_update test/cmdlinetest test/prockreport post-stage: ${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*/*.so +do-test: install + @cd ${WRKSRC}/test && ./cmdlinetest tag + .include diff --git a/biology/py-macs2/distinfo b/biology/py-macs2/distinfo index 1999b76a294d..e6da44033e73 100644 --- a/biology/py-macs2/distinfo +++ b/biology/py-macs2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1684361836 -SHA256 (taoliu-MACS-v2.2.8_GH0.tar.gz) = cab63d7e8b862dbd6bb8ed32325e4fee728d85306e47931167fef753ef0ee743 -SIZE (taoliu-MACS-v2.2.8_GH0.tar.gz) = 133108890 +TIMESTAMP = 1691269587 +SHA256 (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 8e461dde82288280fe708cd4f5fec986fbf2da67b344f4dea5693af849549163 +SIZE (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 133109075 diff --git a/biology/py-macs2/files/patch-setup.py b/biology/py-macs2/files/patch-setup.py deleted file mode 100644 index 3434e1146357..000000000000 --- a/biology/py-macs2/files/patch-setup.py +++ /dev/null @@ -1,25 +0,0 @@ ---- setup.py.orig 2020-04-12 14:46:03 UTC -+++ setup.py -@@ -26,22 +26,6 @@ def main(): - - cwd = os.path.abspath(os.path.dirname(__file__)) - -- # install required numpy -- p = subprocess.call([sys.executable, "-m", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd) -- if p != 0: -- # Could be due to a too old pip version and build isolation, check that -- try: -- # Note, pip may not be installed or not have been used -- import pip -- if LooseVersion(pip.__version__) < LooseVersion('18.0.0'): -- raise RuntimeError("Installing requirements failed. Possibly due " -- "to `pip` being too old, found version {}, " -- "needed is >= 18.0.0.".format(pip.__version__)) -- else: -- raise RuntimeError("Installing requirements failed!") -- except ImportError: -- raise RuntimeError("Installing requirement failed! `pip` has to be installed!") -- - from numpy import get_include as numpy_get_include - numpy_include_dir = [numpy_get_include()] -