From nobody Wed Feb 28 13:29:16 2024 X-Original-To: dev-commits-ports-all@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 4TlFZ51hPTz5BZwc; Wed, 28 Feb 2024 13:29:17 +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 4TlFZ510vxz4c49; Wed, 28 Feb 2024 13:29:17 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1709126957; 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=1EnxrGd/GUJ3M7f8QS2FTaGc+QsSOsPnc/vVlFxL784=; b=lGAQKeygoIWd3/53DI1bRqUbZGbdtIDB/07xusPpxn78DzFHoDBunEaDkY98ZTxgPv9UaR sNSP2eLe3dF6rMHzMueKBntP/FoDJd/DScMN0V5Zxz2YMTL3E9s/os6tgF2eG2Pez402bP bXXTT5Ext+s+Y0tfwjFL7DbitlX7GKo1GSfP3hYETHQaJtZFFvoS/MWbPa7oO2tUmy0Bkq 6Dfvy1D4rHbAjC3kAE91URq1R/nmVZWaKi89p3/OEWzG3wABJ8eY0LQUR/Pwg/1P+ifnct VOoGXmKzqErAbu1KVRFAsY9pDW2AMWuy/5avBSEwnT2N0zm0C/92X/E7zKqiZg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1709126957; a=rsa-sha256; cv=none; b=Z5yWd7N7N0D4NCU3FNkhY7oxesWniS2i6Eo9ZAMSxEBbgj42mo85qg4kp+9FmoK+NQQlmm TFTnqijUnQ/SevSxN/20ktk3lwFGhKt1kOReAnWjQHlDylcOMeQ+CXx6pnbPeGLaPXCQqS Nj0Yqdocctwfbaj3ZiAeRAaU2GVdoz//7skpaV9LhSvs61fRPNdAOp4aeCN233Du8hZX0s pW+9u1I/7FFoS4usJs/JQy9WdMFWlXEcdIlY3/mrJ+Hxlnm5ahctk6HIFW+OxvoRHjEE8L 42nu0+wENBo/XxT0NPlF3C+QUELZxrBFkYXoQ1vMwiqMZzc5ZXRD1FnGf7scUg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1709126957; 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=1EnxrGd/GUJ3M7f8QS2FTaGc+QsSOsPnc/vVlFxL784=; b=JHKNVKtF0jkWDHqmrQJ3BlGCQBq+FOWcPVrdh7cfAiLkm85mwAHiH7wv5FkEHqPlsTrqBJ PMKWFM/nTluicbqp2WvLQE5GKwpI5ErWHZlwMyvKMPSqNDM4g9QaElu9BqOqqQm24TrldR /hs3rOYr68QX0WSIvD8sB1YiNm/wSLQQalaGtk66tb/KzoT3WC6DSfFoIc9lXYQR9hQ7lw Yn7sAo4mIGCoNH3HXTuWJaNjASBah6u7KvtMJLv+BE3IpgnrMz3lFqaWCpiimoTj7lwvx2 k7obQSroiHisDRLESA9xWIGXS1ClKen8EzYz6N7Ar8++ljwMcLT9pVOq3hnF4w== 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 4TlFZ501vGzyW2; Wed, 28 Feb 2024 13:29:17 +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 41SDTGlZ080666; Wed, 28 Feb 2024 13:29:16 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 41SDTGML080663; Wed, 28 Feb 2024 13:29:16 GMT (envelope-from git) Date: Wed, 28 Feb 2024 13:29:16 GMT Message-Id: <202402281329.41SDTGML080663@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: ddb11fbe9778 - main - biology/py-macs3: Update to 3.0.1 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: ddb11fbe9778b0b8c66d0b7f77b0b16c2140634e Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=ddb11fbe9778b0b8c66d0b7f77b0b16c2140634e commit ddb11fbe9778b0b8c66d0b7f77b0b16c2140634e Author: Jason W. Bacon AuthorDate: 2024-02-28 13:26:03 +0000 Commit: Jason W. Bacon CommitDate: 2024-02-28 13:29:15 +0000 biology/py-macs3: Update to 3.0.1 Minor bug fix release Changes: https://github.com/macs3-project/MACS/releases --- biology/py-macs3/Makefile | 4 ++-- biology/py-macs3/distinfo | 6 +++--- biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c | 2 +- biology/py-macs3/files/patch-pyproject.toml | 9 +++++---- biology/py-macs3/files/patch-requirements.txt | 9 ++++++--- biology/py-macs3/files/patch-setup.py | 11 +---------- 6 files changed, 18 insertions(+), 23 deletions(-) diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile index d2cad2892df4..6ad3d9000471 100644 --- a/biology/py-macs3/Makefile +++ b/biology/py-macs3/Makefile @@ -1,6 +1,6 @@ PORTNAME= MACS3 DISTVERSIONPREFIX= v -DISTVERSION= 3.0.0 +DISTVERSION= 3.0.1 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -42,7 +42,7 @@ post-stage: # FIXME: Some tests fail due to a py-threadpoolctl issue # https://github.com/joblib/threadpoolctl/pull/148 -do-test: deinstall install +do-test: deinstall reinstall @${RM} -rf ${WRKSRC}/temp @cd ${WRKSRC}/test && ./cmdlinetest tag diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo index 757e9bbaf640..b06631987784 100644 --- a/biology/py-macs3/distinfo +++ b/biology/py-macs3/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1703890666 -SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d -SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439 +TIMESTAMP = 1708785426 +SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce +SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439 diff --git a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c index d66d83f33606..e385ca2fc010 100644 --- a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c +++ b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c @@ -1,4 +1,4 @@ ---- MACS3/fermi-lite/ksw.c.orig 2023-11-15 16:09:23 UTC +--- MACS3/fermi-lite/ksw.c.orig 2024-02-24 15:09:33 UTC +++ MACS3/fermi-lite/ksw.c @@ -28,7 +28,7 @@ diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml index cf54cae8892f..15f55a86a701 100644 --- a/biology/py-macs3/files/patch-pyproject.toml +++ b/biology/py-macs3/files/patch-pyproject.toml @@ -1,6 +1,7 @@ ---- pyproject.toml.orig 2024-01-06 15:00:01 UTC +--- pyproject.toml.orig 2024-02-23 05:43:44 UTC +++ pyproject.toml -@@ -1,2 +1,2 @@ +@@ -1,3 +1,3 @@ [build-system] --requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3'] -+requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3'] +-requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.4', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3'] ++requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3'] + diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt index 0c8106f79680..81c9a1f75f88 100644 --- a/biology/py-macs3/files/patch-requirements.txt +++ b/biology/py-macs3/files/patch-requirements.txt @@ -1,8 +1,11 @@ ---- requirements.txt.orig 2024-01-06 14:55:53 UTC +--- requirements.txt.orig 2024-02-23 05:43:44 UTC +++ requirements.txt -@@ -1,4 +1,4 @@ +@@ -1,6 +1,6 @@ -Cython~=3.0 +Cython>=0 - numpy>=1.19 + numpy>=1.24.2 +-scipy>=1.11.4 ++scipy>=1.11.1 + scikit-learn>=1.2.1 hmmlearn>=0.3 cykhash>=2.0,<3.0 diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py index 58dde13ba2c2..f309f3139736 100644 --- a/biology/py-macs3/files/patch-setup.py +++ b/biology/py-macs3/files/patch-setup.py @@ -1,14 +1,5 @@ ---- setup.py.orig 2023-11-15 16:09:23 UTC +--- setup.py.orig 2024-02-24 14:39:02 UTC +++ setup.py -@@ -40,7 +40,7 @@ classifiers =[\ - install_requires = [ "numpy>=1.19", - "hmmlearn>=0.3", - "cykhash>=2.0,<3.0", -- "Cython~=3.0" ] -+ "Cython>=0" ] - - tests_requires = [ 'pytest' ] - @@ -70,7 +70,7 @@ def main(): if not clang: