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Thu, 3 Aug 2023 07:02:10 GMT (envelope-from git) Date: Thu, 3 Aug 2023 07:02:10 GMT Message-Id: <202308030702.37372AX3094710@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 0f9f8aa4c37e - main - =?utf-8?Q?biology/py-scikit-bio:=20Update=200.5.8=20=E2=86=92=200.5.9?= 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: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0f9f8aa4c37e2040645a26a544ca3fcc6b50d83d Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=0f9f8aa4c37e2040645a26a544ca3fcc6b50d83d commit 0f9f8aa4c37e2040645a26a544ca3fcc6b50d83d Author: Yuri Victorovich AuthorDate: 2023-08-03 05:09:53 +0000 Commit: Yuri Victorovich CommitDate: 2023-08-03 07:02:05 +0000 biology/py-scikit-bio: Update 0.5.8 → 0.5.9 Reported by: portscout --- biology/py-scikit-bio/Makefile | 18 +++++++++--------- biology/py-scikit-bio/distinfo | 6 +++--- biology/py-scikit-bio/files/patch-pyproject.toml | 10 ++++++++++ 3 files changed, 22 insertions(+), 12 deletions(-) diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile index 99d32835ce6c..84fad483a3f0 100644 --- a/biology/py-scikit-bio/Makefile +++ b/biology/py-scikit-bio/Makefile @@ -1,6 +1,5 @@ PORTNAME= scikit-bio -DISTVERSION= 0.5.8 -PORTREVISION= 1 +DISTVERSION= 0.5.9 CATEGORIES= biology education python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,22 +13,23 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt BROKEN_aarch64= fails to build: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size, see https://github.com/biocore/scikit-bio/issues/1816 -BUILD_DEPENDS= ${PYNUMPY} +BUILD_DEPENDS= ${PYNUMPY} \ + ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}cachecontrol>=0.11.5:www/py-cachecontrol@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}decorator>=3.4.2:devel/py-decorator@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}h5py>=2.9.0:science/py-h5py@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}h5py>=3.6.0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hdmedians>=0.14.1:math/py-hdmedians@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipython>=3.2.0:devel/ipython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}lockfile>=0.10.2:devel/py-lockfile@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.4.3:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}natsort>=4.0.3:devel/py-natsort@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>=1.0.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.5.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.20.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.19.1:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.3.0:science/py-scipy@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= python -USE_PYTHON= distutils cython autoplist pytest # tests fail to run, see https://github.com/biocore/scikit-bio/issues/1846 +USE_PYTHON= pep517 cython autoplist pytest # tests fail to run, see https://github.com/biocore/scikit-bio/issues/1846 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} diff --git a/biology/py-scikit-bio/distinfo b/biology/py-scikit-bio/distinfo index 2f69722f7ffc..d65c97d3f9c3 100644 --- a/biology/py-scikit-bio/distinfo +++ b/biology/py-scikit-bio/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1679325956 -SHA256 (scikit-bio-0.5.8.tar.gz) = d55a83c3e5f2ca1132744e1409233fb61d9af0c5a95deb7b291e6e340712b86b -SIZE (scikit-bio-0.5.8.tar.gz) = 3534584 +TIMESTAMP = 1691038332 +SHA256 (scikit-bio-0.5.9.tar.gz) = 7ae044dc8bee231900248adc3a8659077e76140d56ac9f42bd01fb7981014910 +SIZE (scikit-bio-0.5.9.tar.gz) = 3542513 diff --git a/biology/py-scikit-bio/files/patch-pyproject.toml b/biology/py-scikit-bio/files/patch-pyproject.toml new file mode 100644 index 000000000000..67286b671d40 --- /dev/null +++ b/biology/py-scikit-bio/files/patch-pyproject.toml @@ -0,0 +1,10 @@ +--- pyproject.toml.orig 2023-08-03 04:59:44 UTC ++++ pyproject.toml +@@ -1,6 +1,6 @@ + [build-system] + # https://numpy.org/doc/stable/dev/depending_on_numpy.html#adding-a-dependency-on-numpy +-requires = ["Cython>=0.29.32", "oldest-supported-numpy", "setuptools", "wheel"] ++requires = ["Cython>=0.29.32", "numpy", "setuptools", "wheel"] + + [tool.pytest.ini_options] + filterwarnings = [