Date: Tue, 04 Aug 2026 20:10:51 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: da360a1751e5 - main - biology/py-scikit-bio: update 0.6.3=?utf-8?Q? =E2=86=92 0.7?=.3 Message-ID: <6a72474b.3d5d9.42834c8b@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=da360a1751e58e7bc1e01253cef0be17e17ac30f commit da360a1751e58e7bc1e01253cef0be17e17ac30f Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-08-04 18:55:02 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-08-04 20:10:25 +0000 biology/py-scikit-bio: update 0.6.3 → 0.7.3 --- biology/py-scikit-bio/Makefile | 23 ++++++++++++----------- biology/py-scikit-bio/distinfo | 6 +++--- biology/py-scikit-bio/files/patch-pyproject.toml | 12 ++++++++++++ 3 files changed, 27 insertions(+), 14 deletions(-) diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile index 5b0f4ec7aff8..41205a58b6f1 100644 --- a/biology/py-scikit-bio/Makefile +++ b/biology/py-scikit-bio/Makefile @@ -1,9 +1,9 @@ PORTNAME= scikit-bio -DISTVERSION= 0.6.3 -PORTREVISION= 3 +DISTVERSION= 0.7.3 CATEGORIES= biology education python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= scikit_bio-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Data structures, algorithms, educational resources for bioinformatics @@ -17,27 +17,28 @@ BROKEN_aarch64= fails to build: invalid conversion between vector type '__m64' ( BROKEN= requires OpenMP support that is missing on this architecture .endif -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=2.0:math/py-numpy@${PY_FLAVOR} \ ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}array-api-compat>=1.3:devel/py-array-api-compat@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}biom-format>=2.1.16:biology/py-biom-format@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}decorator>=3.4.2:devel/py-decorator@${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} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.4.3:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}natsort>=4.0.3:devel/py-natsort@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=2.0:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.5.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}patsy>=0.5.0:math/py-patsy@${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} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.9.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}statsmodels>=0.14.0:math/py-statsmodels@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}responses>0:devel/py-responses@${PY_FLAVOR} USES= python USE_PYTHON= pep517 cython autoplist pytest -TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \ + PYTEST_ADDOPTS="-p no:black -p no:ruff -p no:mypy -p no:mypy-plugins -p no:flake8 -p no:cov -p no:benchmark -p no:inline-snapshot -p no:xdist -p no:randomly" CONFLICTS_INSTALL= ${PYTHON_PKGNAMEPREFIX}ddtrace # lib/python3.8/site-packages/benchmarks/__init__.py @@ -57,6 +58,6 @@ do-test: # tests fail to run in a regular way, see https://github.com/biocore/sc @cd ${STAGEDIR}${PYTHON_SITELIBDIR} && \ ${SETENV} ${TEST_ENV} pytest . -# tests as of 0.6.3: 2792 passed, 30 skipped, 56 warnings in 250.28s (0:04:10) +# tests as of 0.7.3: 3463 passed, 15 skipped in 70.28s (0:01:10) .include <bsd.port.mk> diff --git a/biology/py-scikit-bio/distinfo b/biology/py-scikit-bio/distinfo index 370eba0445bd..83bdba0f69c1 100644 --- a/biology/py-scikit-bio/distinfo +++ b/biology/py-scikit-bio/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1736808587 -SHA256 (scikit-bio-0.6.3.tar.gz) = f06cc87a1823902906821819e66f7cd704563a9f8cdf6720296a42dcbc2fe1c2 -SIZE (scikit-bio-0.6.3.tar.gz) = 5356619 +TIMESTAMP = 1785732406 +SHA256 (scikit_bio-0.7.3.tar.gz) = 2492ebf2f6432d24c1030a0cd96d7708c2b57bc31b097a5ec838881792401ec5 +SIZE (scikit_bio-0.7.3.tar.gz) = 5815177 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..9be446f0960c --- /dev/null +++ b/biology/py-scikit-bio/files/patch-pyproject.toml @@ -0,0 +1,12 @@ +-- Fix the PEP 621 license fields so that scikit-bio builds with the version of +-- setuptools available in FreeBSD Ports. +--- pyproject.toml.orig 2026-08-03 09:55:00 UTC ++++ pyproject.toml 2026-08-03 09:55:00 UTC +@@ -8,8 +8,7 @@ + readme = "README.rst" + requires-python = ">=3.10" +-license = "BSD-3-Clause" +-license-files = ["LICENSE.txt"] ++license = {text = "BSD-3-Clause"} + authors = [ + {name = "scikit-bio development team", email = "qiyunzhu@gmail.com"}home | help
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