PORTNAME=	cutadapt
DISTVERSION=	5.0
CATEGORIES=	biology python
MASTER_SITES=	PYPI
PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}

MAINTAINER=	jadawin@FreeBSD.org
COMMENT=	Trim adapters from high-throughput sequencing reads
WWW=		https://github.com/marcelm/cutadapt/

LICENSE=	MIT
LICENSE_FILE=	${WRKSRC}/LICENSE

BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}xopen>=1.6.0:archivers/py-xopen@${PY_FLAVOR} \
		${PYTHON_PKGNAMEPREFIX}dnaio>=1.2.0:biology/py-dnaio@${PY_FLAVOR}
TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
		${PYTHON_PKGNAMEPREFIX}pytest-timeout>0:devel/py-pytest-timeout@${PY_FLAVOR} \
		${PYTHON_PKGNAMEPREFIX}pytest-mock>0:devel/py-pytest-mock@${PY_FLAVOR}

USES=		python
USE_PYTHON=	autoplist concurrent cython distutils

post-install:
	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so

do-test:
	@cd ${WRKSRC} && ${PYTHON_CMD} -m pytest

.include <bsd.port.mk>
