git: 7adb8c360bf5 - main - biology/py-pyrodigal: update 3.5.2 → 3.6.3

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=7adb8c360bf587e65ba496fd9b7fc249ec795b10

commit 7adb8c360bf587e65ba496fd9b7fc249ec795b10
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-11-12 08:25:53 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-11-12 08:32:35 +0000

    biology/py-pyrodigal: update 3.5.2 → 3.6.3
---
 biology/py-pyrodigal/Makefile | 16 +++++++++-------
 biology/py-pyrodigal/distinfo |  6 +++---
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile
index dce43d4c39ef..490813e388a2 100644
--- a/biology/py-pyrodigal/Makefile
+++ b/biology/py-pyrodigal/Makefile
@@ -1,31 +1,33 @@
 PORTNAME=	pyrodigal
-DISTVERSION=	3.5.2
+DISTVERSION=	3.6.3
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Python binding for Prodigal, an ORF finder for genomes and metagenomes
-WWW=		https://github.com/althonos/pyrodigal/
+WWW=		https://pyrodigal.readthedocs.io/en/stable/ \
+		https://github.com/althonos/pyrodigal/
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}cython3>0:lang/cython3@${PY_FLAVOR}
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}cython3>0:lang/cython3@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}archspec>0:devel/py-archspec@${PY_FLAVOR}
 
-USES=		python
-USE_PYTHON=	distutils concurrent autoplist pytest # cython: cython3 isn't yet supported by python.mk
+USES=		cmake:indirect python
+USE_PYTHON=	pep517 concurrent autoplist pytest # cython: cython3 isn't yet supported by python.mk
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
-post-build:
+xpost-build:
 	@cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build_ext --inplace
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyrodigal/lib${PYTHON_EXT_SUFFIX}.so
 
-do-test:
+do-test: # as of 3.6.3 this doesn't work: https://github.com/althonos/pyrodigal/issues/63
 	@cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -vv
 
 .include <bsd.port.mk>
diff --git a/biology/py-pyrodigal/distinfo b/biology/py-pyrodigal/distinfo
index 26a6af630d7d..19c6cf076683 100644
--- a/biology/py-pyrodigal/distinfo
+++ b/biology/py-pyrodigal/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1725511908
-SHA256 (pyrodigal-3.5.2.tar.gz) = 2a40eb6113e720ada51c326958b295944cdc33ecee9f25d5bad4e9a8e6e6f7f5
-SIZE (pyrodigal-3.5.2.tar.gz) = 1857311
+TIMESTAMP = 1731398873
+SHA256 (pyrodigal-3.6.3.tar.gz) = 3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78
+SIZE (pyrodigal-3.6.3.tar.gz) = 3589356