PORTNAME=	scikit-bio
DISTVERSION=	0.7.4
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
WWW=		http://scikit-bio.org/

LICENSE=	BSD3CLAUSE
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
.if !exists(/usr/include/omp.h)
BROKEN=		requires OpenMP support that is missing on this architecture
.endif

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=	${PYTHON_PKGNAMEPREFIX}array-api-compat>=1.3:devel/py-array-api-compat@${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} \
		${PYTHON_PKGNAMEPREFIX}natsort>=4.0.3:devel/py-natsort@${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} \
		${PYTHON_PKGNAMEPREFIX}scipy>=1.9.0:science/py-scipy@${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} \
		MPLBACKEND=Agg \
		QT_QPA_PLATFORM=offscreen \
		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

.include <bsd.port.options.mk>

.if ${ARCH} == i386
CFLAGS+=	-msse2 # workaround for https://github.com/biocore/scikit-bio/issues/1727
CXXFLAGS+=	-msse2
.endif

post-install:
	@${STRIP_CMD} \
		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_TAG}.so \
		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_TAG}.so

do-test: # tests fail to run in a regular way, see https://github.com/biocore/scikit-bio/issues/1846
	@cd ${STAGEDIR}${PYTHON_SITELIBDIR} && \
		${SETENV} ${TEST_ENV} pytest .

# tests as of 0.7.4: 3740 passed, 22 skipped

.include <bsd.port.mk>