git: 0f9f8aa4c37e - main - biology/py-scikit-bio: Update 0.5.8 → 0.5.9

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0f9f8aa4c37e2040645a26a544ca3fcc6b50d83d

commit 0f9f8aa4c37e2040645a26a544ca3fcc6b50d83d
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-08-03 05:09:53 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
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 = [