Date: Sun, 6 Aug 2023 18:17:53 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e97c3457489f - main - biology/py-macs2: Update to 2.2.9.1 Message-ID: <202308061817.376IHrEj009098@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e97c3457489f2abb3cda2b6b023ba580b6382c07 commit e97c3457489f2abb3cda2b6b023ba580b6382c07 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-08-06 18:14:56 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> 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 <bsd.port.mk> 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()] -
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