66 lines
2.8 KiB
Makefile
66 lines
2.8 KiB
Makefile
PORTNAME= scikit-bio
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DISTVERSION= 0.7.4
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CATEGORIES= biology education python
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MASTER_SITES= PYPI
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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DISTNAME= scikit_bio-${DISTVERSION}
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Data structures, algorithms, educational resources for bioinformatics
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WWW= http://scikit-bio.org/
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE.txt
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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
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.if !exists(/usr/include/omp.h)
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BROKEN= requires OpenMP support that is missing on this architecture
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.endif
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BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=2.0:math/py-numpy@${PY_FLAVOR} \
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${PY_SETUPTOOLS} \
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${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
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RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}array-api-compat>=1.3:devel/py-array-api-compat@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}biom-format>=2.1.16:biology/py-biom-format@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}decorator>=3.4.2:devel/py-decorator@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}h5py>=3.6.0:science/py-h5py@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}natsort>=4.0.3:devel/py-natsort@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}numpy>=2.0:math/py-numpy@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}pandas>=1.5.0:math/py-pandas@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}patsy>=0.5.0:math/py-patsy@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}requests>=2.20.0:www/py-requests@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}scipy>=1.9.0:science/py-scipy@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}statsmodels>=0.14.0:math/py-statsmodels@${PY_FLAVOR}
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TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}responses>0:devel/py-responses@${PY_FLAVOR}
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USES= python
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USE_PYTHON= pep517 cython autoplist pytest
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TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \
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MPLBACKEND=Agg \
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QT_QPA_PLATFORM=offscreen \
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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"
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CONFLICTS_INSTALL= ${PYTHON_PKGNAMEPREFIX}ddtrace # lib/python3.8/site-packages/benchmarks/__init__.py
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.include <bsd.port.options.mk>
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.if ${ARCH} == i386
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CFLAGS+= -msse2 # workaround for https://github.com/biocore/scikit-bio/issues/1727
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CXXFLAGS+= -msse2
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.endif
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post-install:
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@${STRIP_CMD} \
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${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_TAG}.so \
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${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_TAG}.so
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do-test: # tests fail to run in a regular way, see https://github.com/biocore/scikit-bio/issues/1846
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@cd ${STAGEDIR}${PYTHON_SITELIBDIR} && \
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${SETENV} ${TEST_ENV} pytest .
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# tests as of 0.7.4: 3740 passed, 22 skipped
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.include <bsd.port.mk>
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