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PORTNAME= scikit-bio
DISTVERSION= 0.5.8
PORTREVISION= 1
CATEGORIES= biology education python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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
BUILD_DEPENDS= ${PYNUMPY}
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} \
${PYTHON_PKGNAMEPREFIX}hdmedians>=0.14.1:math/py-hdmedians@${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} \
${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.19.1:science/py-scikit-learn@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>=1.3.0:science/py-scipy@${PY_FLAVOR}
USES= python:3.7+
USE_PYTHON= distutils cython autoplist pytest # tests fail to run, see https://github.com/biocore/scikit-bio/issues/1846
TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
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_EXT_SUFFIX}.so \
${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_EXT_SUFFIX}.so
.include <bsd.port.mk>
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