biology/py-scikit-bio: update 0.6.3 → 0.7.3

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"}