diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile index 46ade4627c53..3884f6998dfb 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -1,32 +1,33 @@ PORTNAME= bx-python DISTVERSION= 0.14.0 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Python module for reading, manipulating and writing genomic data sets WWW= https://github.com/bxlab/bx-python LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} USES= compiler python USE_PYTHON= autoplist cython pep517 post-patch: # force cythonization, compilation fails otherwise for some reason @${TOUCH} `${FIND} ${WRKSRC} -name "*.pyx" -o -name "*.pxd"` post-install: @${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/bx -name "*.so" | ${XARGS} ${STRIP_CMD} .include diff --git a/biology/py-ete3/Makefile b/biology/py-ete3/Makefile index 66cbe3d09a76..f6d9518113bb 100644 --- a/biology/py-ete3/Makefile +++ b/biology/py-ete3/Makefile @@ -1,29 +1,29 @@ PORTNAME= ete3 DISTVERSION= 3.1.3 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Framework for the analysis and visualization of trees WWW= http://etetoolkit.org/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python pyqt:5 shebangfix USE_PYTHON= distutils concurrent autoplist pytest # some tests fail, see https://github.com/etetoolkit/ete/issues/643 USE_PYQT= pyqt5 SHEBANG_GLOB= *.py NO_ARCH= yes .include diff --git a/cad/py-pygmsh/Makefile b/cad/py-pygmsh/Makefile index d5f82a0d5e6f..78743ff241c7 100644 --- a/cad/py-pygmsh/Makefile +++ b/cad/py-pygmsh/Makefile @@ -1,32 +1,32 @@ PORTNAME= pygmsh DISTVERSION= 7.1.17 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= cad python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python frontend for Gmsh (on top of Gmsh's own binding) WWW= https://github.com/meshpro/pygmsh LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}gmsh>0:cad/py-gmsh@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}meshio>=4.3.2:science/py-meshio@${PY_FLAVOR} \ ${PYNUMPY} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist pytest # 1 error and many warnings in tests, see https://github.com/meshpro/pygmsh/issues/564 NO_ARCH= yes pre-configure: @( \ ${ECHO} "from setuptools import setup" && \ ${ECHO} "setup()" \ ) > ${WRKSRC}/setup.py .include diff --git a/comms/nanovna-saver/Makefile b/comms/nanovna-saver/Makefile index 4e9eecc29f04..bdd7edced48b 100644 --- a/comms/nanovna-saver/Makefile +++ b/comms/nanovna-saver/Makefile @@ -1,31 +1,31 @@ PORTNAME= nanovna-saver DISTVERSIONPREFIX= v DISTVERSION= 0.5.3 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= comms hamradio MAINTAINER= hamradio@FreeBSD.org COMMENT= Multiplatform tool to save Touchstone files from the NanoVNA WWW= https://github.com/NanoVNA-Saver/nanovna-saver LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyserial>0:comms/py-pyserial@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python pyqt:5 USE_PYTHON= distutils autoplist noflavors USE_GITHUB= yes GH_ACCOUNT= NanoVNA-Saver NO_ARCH= yes post-extract: ${CP} ${FILESDIR}/Sysctl.py ${WRKSRC}/NanoVNASaver/Hardware/ .include diff --git a/devel/cpp2py/Makefile b/devel/cpp2py/Makefile index bc1ed3bd9ce2..5357f429506c 100644 --- a/devel/cpp2py/Makefile +++ b/devel/cpp2py/Makefile @@ -1,38 +1,38 @@ PORTNAME= cpp2py DISTVERSION= 2.0.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel PATCH_SITES= https://github.com/${GH_ACCOUNT}/${GH_PROJECT}/commit/ PATCHFILES= 44d5238ab4f05ed4064736ffd2f2b63438d3f64c.patch:-p1 # fix build on i386 MAINTAINER= yuri@FreeBSD.org COMMENT= Reflection tools based on clang WWW= https://github.com/TRIQS/cpp2py LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mako>0:textproc/py-mako@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= cmake compiler:c++14-lang gettext-runtime python shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= TRIQS SHEBANG_FILES= bin/c* CMAKE_ARGS= -DPYTHON_INTERPRETER:STRING=${PYTHON_CMD} PORTSCOUT= limit:^[0-9\.]*$$ post-install: # remove the unnecessary file: https://github.com/TRIQS/cpp2py/issues/41 @${RM} ${STAGEDIR}${PREFIX}/share/cpp2pyvars.sh .include diff --git a/devel/py-qutip/Makefile b/devel/py-qutip/Makefile index e011d08ec477..e546b5f68f86 100644 --- a/devel/py-qutip/Makefile +++ b/devel/py-qutip/Makefile @@ -1,40 +1,40 @@ PORTNAME= qutip DISTVERSION= 5.0.4 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum toolbox in python WWW= https://qutip.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.9:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0.32.0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} # the optional graphics/py-mayavi dependency is omitted because it is python-2.7 -only USES= python USE_PYTHON= autoplist cython cython_run pep517 post-install: @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/qutip/*/*${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/qutip/*/*/*${PYTHON_TAG}.so do-test: # 3 tests fail, see https://github.com/qutip/qutip/issues/2190 @${ECHO} "==> Running tests. Please note that tests require X11 display access." @cd ${WRKDIR} && ${SETENV} ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHON_SITELIBDIR} \ ${PYTHON_CMD} -c "import qutip.testing as qt; qt.run();" .include diff --git a/finance/py-Nasdaq-Data-Link/Makefile b/finance/py-Nasdaq-Data-Link/Makefile index 72a2a6c7148b..ff722908be11 100644 --- a/finance/py-Nasdaq-Data-Link/Makefile +++ b/finance/py-Nasdaq-Data-Link/Makefile @@ -1,38 +1,38 @@ PORTNAME= Nasdaq-Data-Link DISTVERSION= 1.0.4 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= finance PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Package for Nasdaq Data Link API access WWW= https://github.com/Nasdaq/data-link-python LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}python-dateutil>0:devel/py-python-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}inflection>=0.3.1:devel/py-inflection@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}more-itertools>0:devel/py-more-itertools@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.14:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.7.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}httpretty>0:www/py-httpretty@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}factory-boy>0:devel/py-factory-boy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>0:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nose>=0:devel/py-nose@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-flake8>0:devel/py-pytest-flake8@${PY_FLAVOR} USES= python USE_PYTHON= autoplist concurrent distutils pytest # tests are broken, see https://github.com/Nasdaq/data-link-python/issues/24 USE_GITHUB= yes GH_ACCOUNT= Nasdaq GH_PROJECT= data-link-python NO_ARCH= yes .include diff --git a/finance/py-exchange-calendars/Makefile b/finance/py-exchange-calendars/Makefile index 6c8b9b26343a..170e65504bc1 100644 --- a/finance/py-exchange-calendars/Makefile +++ b/finance/py-exchange-calendars/Makefile @@ -1,34 +1,35 @@ PORTNAME= exchange-calendars DISTVERSION= 4.9 +PORTREVISION= 1 CATEGORIES= finance python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Calendars for securities exchanges WWW= https://github.com/gerrymanoim/exchange_calendars LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}korean-lunar-calendar>0:korean/py-korean-lunar-calendar@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyluach>0:hebrew/py-pyluach@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}toolz>0:devel/py-toolz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tzdata>0:devel/py-tzdata@${PY_FLAVOR} BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= pep517 autoplist pytest NO_ARCH= yes # tests as of 4.9: 8330 passed, 1 xfailed in 4621.81s (1:17:01) .include diff --git a/finance/py-investpy/Makefile b/finance/py-investpy/Makefile index ce8e6c512958..b96871ee8e04 100644 --- a/finance/py-investpy/Makefile +++ b/finance/py-investpy/Makefile @@ -1,29 +1,29 @@ PORTNAME= investpy PORTVERSION= 1.0.8 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= finance python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Financial Data Extraction from Investing.com with Python WWW= https://investpy.readthedocs.io/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.25.1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2019.3:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.22.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}unidecode>=1.1.1:converters/py-unidecode@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist NO_ARCH= yes .include diff --git a/finance/py-pandas-ta/Makefile b/finance/py-pandas-ta/Makefile index 61240946956a..3f9bd35e0787 100644 --- a/finance/py-pandas-ta/Makefile +++ b/finance/py-pandas-ta/Makefile @@ -1,33 +1,33 @@ PORTNAME= pandas-ta DISTVERSION= 0.3.14 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= finance python #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Market Technical Analysis indicators in Python and Pandas WWW= https://twopirllc.github.io/pandas-ta/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}python-dateutil>0:devel/py-python-dateutil@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.2.0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2021.1:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.16.0:devel/py-six@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ta-lib>0:finance/py-ta-lib@${PY_FLAVOR} USES= python USE_PYTHON= distutils autoplist pytest # 1 test fails, see https://github.com/twopirllc/pandas-ta/issues/631 USE_GITHUB= yes GH_ACCOUNT= twopirllc NO_ARCH= yes .include diff --git a/math/py-ambit/Makefile b/math/py-ambit/Makefile index 542249671f22..01431d123ed3 100644 --- a/math/py-ambit/Makefile +++ b/math/py-ambit/Makefile @@ -1,45 +1,45 @@ PORTNAME= ambit DISTVERSIONPREFIX= v DISTVERSION= 0.7.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library for tensor product calculations WWW= https://github.com/jturney/ambit LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/../COPYING PY_DEPENDS= ${PYNUMPY} BUILD_DEPENDS= pybind11>0:devel/pybind11 \ ${PY_DEPENDS} LIB_DEPENDS= libambit.so:math/ambit \ libhdf5.so:science/hdf5 \ libopenblas.so:math/openblas RUN_DEPENDS= ${PY_DEPENDS} USES= cmake compiler:c++17-lang python:build USE_PYTHON= flavors pytest USE_GITHUB= yes GH_ACCOUNT= jturney WRKSRC_SUBDIR= pyambit CMAKE_ARGS= -DPYMOD_INSTALL_LIBDIR:STRING=/python${_PYTHON_VERSION}/site-packages \ -DFREEBSD_PYTHON_VER=${PYTHON_VER} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC} post-install: # remove share/cmake/ambit/ambitTargets-Python-%%CMAKE_BUILD_TYPE%%.cmake, and tests @${RM} -r \ ${STAGEDIR}${PREFIX}/share \ ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/ambit/tests pre-test: @${RM} ${WRKSRC}/__init__.py # tests fail with __init__.py .include diff --git a/math/py-diffcp/Makefile b/math/py-diffcp/Makefile index 07711c68b370..dbad31a80f15 100644 --- a/math/py-diffcp/Makefile +++ b/math/py-diffcp/Makefile @@ -1,31 +1,32 @@ PORTNAME= diffcp DISTVERSION= 1.0.23 +PORTREVISION= 1 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Differentiation through cone programs WWW= https://github.com/cvxgrp/diffcp/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pybind11>0:devel/py-pybind11@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.13.2:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cvxpy>0:math/py-cvxpy@${PY_FLAVOR} USES= compiler:c++11-lang python USE_PYTHON= pep517 autoplist pytest TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/_diffcp${PYTHON_TAG}.so .include diff --git a/math/py-faiss/Makefile b/math/py-faiss/Makefile index c05a07a3f209..b6c7831efc31 100644 --- a/math/py-faiss/Makefile +++ b/math/py-faiss/Makefile @@ -1,50 +1,51 @@ PORTNAME= faiss DISTVERSIONPREFIX= v DISTVERSION= 1.14.1 +PORTREVISION= 1 CATEGORIES= math PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library for efficient similarity search & clustering of dense vectors WWW= https://github.com/facebookresearch/faiss LICENSE= MIT LICENSE_FILE= ${WRKSRC}/../../LICENSE BROKEN_i386= clang crashes, see bug#261580 PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} BUILD_DEPENDS= swig:devel/swig \ ${PY_DEPENDS} LIB_DEPENDS= libfaiss.so:math/faiss RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytorch>0:misc/py-pytorch@${PY_FLAVOR} USES= cmake compiler:c++11-lang localbase python USE_PYTHON= flavors pytest # tests fail to run, see https://github.com/facebookresearch/faiss/issues/3914 USE_GITHUB= yes GH_ACCOUNT= facebookresearch WRKSRC_SUBDIR= faiss/python CMAKE_ARGS= -DPython_EXECUTABLE:STRING=${PYTHON_CMD} TEST_WRKSRC= ${WRKSRC}/../../tests TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-patch: # remove GPU testcases @${RM} -r ${WRKSRC}/../../faiss/gpu do-install: # see https://github.com/facebookresearch/faiss/issues/2194 ${MKDIR} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} ${INSTALL_LIB} ${BUILD_WRKSRC}/_swigfaiss.so ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} .for f in __init__.py array_conversions.py class_wrappers.py extra_wrappers.py gpu_wrappers.py loader.py swigfaiss.py ${INSTALL_DATA} ${BUILD_WRKSRC}/${f} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME} .endfor cd ${BUILD_WRKSRC} && ${COPYTREE_SHARE} contrib ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME} # tests expect the modle common_io to be available, but this module is questionable, see https://github.com/facebookresearch/faiss/issues/4865 .include diff --git a/math/py-fsph/Makefile b/math/py-fsph/Makefile index ac16f7290684..655e3331daf0 100644 --- a/math/py-fsph/Makefile +++ b/math/py-fsph/Makefile @@ -1,37 +1,38 @@ PORTNAME= fsph DISTVERSIONPREFIX= v DISTVERSION= 0.3.0 +PORTREVISION= 1 CATEGORIES= math PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library to quickly compute series of complex spherical harmonics WWW= https://fsph.readthedocs.io/en/latest/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} # ${PYTHON_PKGNAMEPREFIX}tensorflow>0:science/py-tensorflow@${PY_FLAVOR} # tensorflow is an optional dependency that is currently broken: https://github.com/glotzerlab/fsph/issues/6 BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= compiler:c++14-lang localbase python USE_PYTHON= pep517 autoplist pytest USE_GITHUB= yes GH_ACCOUNT= glotzerlab TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests CONFLICTS_BUILD= ${PYTHON_PKGNAMEPREFIX}-tensorflow post-install: @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/fsph/_fsph${PYTHON_TAG}.so #${STAGEDIR}${PYTHON_SITELIBDIR}/fsph/_tf_ops${PYTHON_TAG}.so .include diff --git a/math/py-ipyopt/Makefile b/math/py-ipyopt/Makefile index 1e8cb5fe5692..3ec2e92f7872 100644 --- a/math/py-ipyopt/Makefile +++ b/math/py-ipyopt/Makefile @@ -1,35 +1,36 @@ PORTNAME= ipyopt DISTVERSION= 0.12.10 +PORTREVISION= 1 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python interface to Ipopt WWW= https://gitlab.com/g-braeunlich/ipyopt LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} LIB_DEPENDS= libipopt.so:math/ipopt RUN_DEPENDS= ${PY_DEPENDS} USES= compiler:c++17-lang pkgconfig python USE_PYTHON= distutils autoplist pytest CXXFLAGS+= $(pkg-config --cflags ipopt) TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/${PORTNAME}.cpython-*.so do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest # tests as of 0.12.10: 8 passed, 10 skipped in 18.39s .include diff --git a/math/py-libceed/Makefile b/math/py-libceed/Makefile index 56b478550db3..63524cceae78 100644 --- a/math/py-libceed/Makefile +++ b/math/py-libceed/Makefile @@ -1,45 +1,45 @@ PORTNAME= libceed DISTVERSIONPREFIX= v DISTVERSION= 0.12.0-763 -PORTREVISION= 1 +PORTREVISION= 2 DISTVERSIONSUFFIX= -ge3ae47f6 CATEGORIES= math # machine-learning PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= CEED Library: Code for Efficient Extensible Discretizations WWW= https://libceed.org/en/latest/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cffi>0:devel/py-cffi@${PY_FLAVOR} \ ${PYNUMPY} BUILD_DEPENDS= gmake:devel/gmake \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= fortran python USE_PYTHON= distutils autoplist pytest USE_GITHUB= yes GH_ACCOUNT= CEED GH_PROJECT= libCEED CFLAGS+= -fPIC # https://github.com/CEED/libCEED/issues/1706 BINARY_ALIAS= make=${GMAKE} # python3=${PYTHON_CMD} post-install: @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/_ceed_cffi.abi3.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/libceed/lib/libceed.so do-test: cd ${WRKSRC}/python/tests && \ ${SETENV} PYTHON=${PYTHON_CMD} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} ${GMAKE} test # rebuilds and reinstalls the C library, see https://github.com/CEED/libCEED/issues/1707 .include diff --git a/math/py-linearmodels/Makefile b/math/py-linearmodels/Makefile index 86d44be4ad5b..8cd1b23d3606 100644 --- a/math/py-linearmodels/Makefile +++ b/math/py-linearmodels/Makefile @@ -1,44 +1,44 @@ PORTNAME= linearmodels DISTVERSION= 6.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math python # statistics MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Linear Panel, Instrumental Variable, Asset Pricing and other models WWW= https://bashtage.github.io/linearmodels/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}formulaic>=1.0.0:math/py-formulaic@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mypy_extensions>=0.4:devel/py-mypy_extensions@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.4.0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}property-cached>=1.6.3:devel/py-property-cached@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyhdfe>=0.1:math/py-pyhdfe@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.8.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}statsmodels>=0.13.0:math/py-statsmodels@${PY_FLAVOR} BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}black>0:devel/py-black@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}coverage>0:devel/py-coverage@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}flake8>0:devel/py-flake8@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}isort>0:devel/py-isort@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-cov>0:devel/py-pytest-cov@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-xdist>0:devel/py-pytest-xdist@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}seaborn>0:math/py-seaborn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xarray>=0.13:devel/py-xarray@${PY_FLAVOR} USES= python shebangfix USE_PYTHON= autoplist cython distutils pytest # 14 tests fail, see https://github.com/bashtage/linearmodels/issues/550 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/linearmodels/panel/_utility${PYTHON_TAG}.so .include diff --git a/math/py-minorminer/Makefile b/math/py-minorminer/Makefile index 9b36301fa920..522d79c2fe34 100644 --- a/math/py-minorminer/Makefile +++ b/math/py-minorminer/Makefile @@ -1,42 +1,43 @@ PORTNAME= minorminer DISTVERSION= 0.2.19 +PORTREVISION= 1 CATEGORIES= math python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Heuristic tool for minor embedding of graphs WWW= https://docs.ocean.dwavesys.com/projects/minorminer/en/latest/ \ https://github.com/dwavesystems/minorminer LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}fasteners>=0.19:devel/py-fasteners@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.1:devel/py-homebase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=3.2.1:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.15:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}rectangle-packer>=2.0.1:math/py-rectangle-packer@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.13.1:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils cython autoplist pytest USE_GITHUB= yes GH_ACCOUNT= dwavesystems GH_TUPLE= boothby:glasgow-subgraph-solver:568c45f:glasgow_subgraph_solver/external/glasgow-subgraph-solver \ nemequ:portable-snippets:84abba9:portable_snippets/external/portable-snippets TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests post-install: @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/minorminer/_extern/rpack/_core${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/minorminer/_minorminer${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/minorminer/busclique${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/minorminer/subgraph${PYTHON_TAG}.so .include diff --git a/math/py-mnnpy/Makefile b/math/py-mnnpy/Makefile index 505523b429e4..38fecc82cedd 100644 --- a/math/py-mnnpy/Makefile +++ b/math/py-mnnpy/Makefile @@ -1,40 +1,40 @@ PORTNAME= mnnpy DISTVERSION= 0.1.9.5 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= MNN (Mutual Nearest Neighbors) correct in python WWW= https://github.com/chriscainx/mnnpy LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}anndata>0:devel/py-anndata@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numba>0:devel/py-numba@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils cython autoplist post-patch: .if defined(CPUTYPE) . if ${ARCH:Mpowerpc*} @${REINPLACE_CMD} -e "s|'-march=native'|'-mcpu=${CPUTYPE}'|" ${WRKSRC}/setup.py . else @${REINPLACE_CMD} -e "s|'-march=native'|'-march=${CPUTYPE}'|" ${WRKSRC}/setup.py . endif .else @${REINPLACE_CMD} -e "s|'-march=native', ||" ${WRKSRC}/setup.py .endif post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/mnnpy/_utils.cpython-${PYTHON_SUFFIX}.so .include diff --git a/math/py-or-tools/Makefile b/math/py-or-tools/Makefile index 10b21956a76c..f96fe82b9422 100644 --- a/math/py-or-tools/Makefile +++ b/math/py-or-tools/Makefile @@ -1,89 +1,89 @@ PORTNAME= or-tools DISTVERSIONPREFIX= v DISTVERSION= 9.6 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= math PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Google's Operations Research tools (Python binding) WWW= https://github.com/google/or-tools LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= SWIG wrapped code invalid in 32 bit architecture, regenerate code using -DSWIGWORDSIZE32 BROKEN_i386= SWIG wrapped code invalid in 32 bit architecture, regenerate code using -DSWIGWORDSIZE32 # see https://github.com/google/or-tools/issues/2130 PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}absl-py>0:devel/py-absl-py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}protobuf>0:devel/py-protobuf@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ ${PY_SETUPTOOLS} \ pybind11>0:devel/pybind11 \ protoc-gen-mypy:devel/py-mypy-protobuf@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}virtualenv>0:devel/py-virtualenv@${PY_FLAVOR} \ swig:devel/swig LIB_DEPENDS= libabsl_base.so:devel/abseil \ libCbc.so:math/cbc \ libCgl.so:math/cgl \ libcoinasl.so:math/asl \ libcoinmumps.so:math/coin-or-mumps \ libCoinUtils.so:math/coinutils \ libnauty.so:math/nauty \ libopenblas.so:math/openblas \ libOsi.so:math/osi \ libOsiClp.so:math/clp \ libgflags.so:devel/gflags \ libglog.so:devel/glog \ libprotobuf.so:devel/protobuf \ libre2.so:devel/re2 RUN_DEPENDS= ${PY_DEPENDS} USES= blaslapack cmake:insource compiler:c++17-lang eigen:3 pkgconfig python USE_PYTHON= flavors pytest # tests fail, see https://github.com/google/or-tools/issues/3464 USE_GITHUB= yes GH_ACCOUNT= google CMAKE_OFF= BUILD_DEPS BUILD_pybind11 INSTALL_BUILD_DEPS BUILD_TESTING BUILD_EXAMPLES CMAKE_ON= BUILD_PYTHON CMAKE_ARGS= -DSWIG_EXECUTABLE=${LOCALBASE}/bin/swig -DFREEBSD_PYTHON_VER=${PYTHON_VER} CONFIGURE_ENV= UNIX_CBC_DIR=${LOCALBASE} UNIX_CLP_DIR=${LOCALBASE} BUILD_ENV= UNIX_CBC_DIR=${LOCALBASE} UNIX_CLP_DIR=${LOCALBASE} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} OPTIONS_DEFINE= SCIP SCIP_DESC= Use the SCIP solver # SCIP package isn't built because of licensing restrictions SCIP_CMAKE_BOOL= USE_SCIP SCIP_LIB_DEPENDS= libscip.so:math/SCIP post-patch: @${REINPLACE_CMD} -e '/absl::container/s,^,#,' \ ${WRKSRC}/ortools/constraint_solver/CMakeLists.txt \ ${WRKSRC}/ortools/glop/CMakeLists.txt \ ${WRKSRC}/ortools/linear_solver/CMakeLists.txt \ ${WRKSRC}/ortools/sat/CMakeLists.txt @${REINPLACE_CMD} -e '17,19d ; /AbslStringify/,+10d' \ ${WRKSRC}/ortools/base/logging.h do-install: # by default cmake installs the whole or-tools project without the python part, so extract the wheel and install python files manually here ${MKDIR} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} cd ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} && \ unzip ${BUILD_WRKSRC}/python/dist/ortools-${DISTVERSION}*.whl && \ ${RM} -rf ortools-*.dist-info ${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -name "*.so" -o -name "*.so.*" | ${XARGS} ${STRIP_CMD} run-examples: # one of the examples fail: https://github.com/google/or-tools/issues/3463 .for e in arc_flow_cutting_stock_sat.py bus_driver_scheduling_sat.py cover_rectangle_sat.py cvrptw_plot.py qubo_sat.py # list is from examples/python/CMakeLists.txt @cd ${WRKSRC}/examples/python && \ ${ECHO} "==> Running ${PORTNAME} test ${e} ..." && \ ${SETENV} ${TEST_ENV} ${PYTHON_CMD} ${e} && \ ${ECHO} "... test ${e} succeeded" .endfor .include diff --git a/math/py-osqp/Makefile b/math/py-osqp/Makefile index 8310f86e9b4a..77ef754eb5b7 100644 --- a/math/py-osqp/Makefile +++ b/math/py-osqp/Makefile @@ -1,26 +1,26 @@ PORTNAME= osqp PORTVERSION= 0.6.2.post5 -PORTREVISION= 2 +PORTREVISION= 3 PORTEPOCH= 1 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python binding for Operator Splitting QP Solver WWW= https://osqp.org LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}qdldl>0:math/py-qdldl@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.13.2:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ cmake:devel/cmake-core RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist .include diff --git a/math/py-pyFFTW/Makefile b/math/py-pyFFTW/Makefile index 671fd436d99f..d29bb023a68f 100644 --- a/math/py-pyFFTW/Makefile +++ b/math/py-pyFFTW/Makefile @@ -1,34 +1,34 @@ PORTNAME= pyFFTW DISTVERSION= 0.15.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:tl}-${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Pythonic wrapper around FFTW, the FFT library WWW= https://hgomersall.github.io/pyFFTW/ \ https://github.com/pyFFTW/pyFFTW LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}dask>=1.0.0:devel/py-dask@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.2.0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float RUN_DEPENDS= ${PY_DEPENDS} USES= python localbase:ldflags USE_PYTHON= autoplist cython distutils pytest # tests fail with "attempted relative import with no known parent package", see https://github.com/pyFFTW/pyFFTW/issues/405 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/pyfftw/pyfftw${PYTHON_TAG}.so .include diff --git a/math/py-slepc4py/Makefile b/math/py-slepc4py/Makefile index 86831632ec1d..6b408fb0b223 100644 --- a/math/py-slepc4py/Makefile +++ b/math/py-slepc4py/Makefile @@ -1,33 +1,33 @@ PORTNAME= slepc4py DISTVERSION= 3.22.2 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= SLEPc for Python WWW= https://bitbucket.org/slepc/slepc4py LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.rst PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}petsc4py>0:math/py-petsc4py@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} LIB_DEPENDS= libmpich.so:net/mpich \ libpetsc.so:science/PETSc \ libslepc.so:math/slepc RUN_DEPENDS= ${PYNUMPY} USES= fortran python USE_PYTHON= autoplist cython distutils pytest MAKE_ENV= PETSC_DIR=${LOCALBASE} SLEPC_DIR=${LOCALBASE} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/slepc4py/lib/SLEPc${PYTHON_TAG}.so .include diff --git a/math/py-ssm/Makefile b/math/py-ssm/Makefile index 89f6dc59573b..979e2b7c4cd7 100644 --- a/math/py-ssm/Makefile +++ b/math/py-ssm/Makefile @@ -1,32 +1,32 @@ PORTNAME= ssm DISTVERSION= 0.0.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Bayesian learning and inference for state space models WWW= https://github.com/lindermanlab/ssm LICENSE= MIT PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}autograd>0:math/py-autograd@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>0:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numba>0:devel/py-numba@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}seaborn>0:math/py-seaborn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils cython concurrent autoplist post-install: ${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME}/*.so .include diff --git a/misc/adios2/Makefile b/misc/adios2/Makefile index f87af0134b60..91fc09b8ad87 100644 --- a/misc/adios2/Makefile +++ b/misc/adios2/Makefile @@ -1,64 +1,64 @@ PORTNAME= adios2 DISTVERSIONPREFIX= v DISTVERSION= 2.10.2 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= misc science MAINTAINER= yuri@FreeBSD.org COMMENT= Next generation of ADIOS developed in the Exascale Computing Program WWW= https://github.com/ornladios/ADIOS2 LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails: non-constant-expression cannot be narrowed from type 'uint64_t' (aka 'unsigned long long') to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing] BROKEN_i386= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 BROKEN_powerpc= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}mpi4py-mpich>=3.0.3:net/py-mpi4py-mpich@${PY_FLAVOR} BUILD_DEPENDS= bash:shells/bash \ pybind11>0:devel/pybind11 \ ${PYTHON_PKGNAMEPREFIX}pybind11>=2.4:devel/py-pybind11@${PY_FLAVOR} \ ${PY_DEPENDS} LIB_DEPENDS= libblosc2.so:archivers/c-blosc2 \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libhdf5.so:science/hdf5 \ liblz4.so:archivers/liblz4 \ libmpi.so:net/mpich \ libpng16.so:graphics/png \ libsodium.so:security/libsodium \ libzmq.so:net/libzmq4 \ libzfp.so:devel/zfp \ libzstd.so:archivers/zstd RUN_DEPENDS= bash:shells/bash \ ${PY_DEPENDS} USES= bison cmake:testing compiler:c++11-lang fortran localbase:ldflags pkgconfig \ perl5 python shebangfix sqlite USE_LDCONFIG= yes SHEBANG_FILES= cmake/install/post/adios2-config.pre.sh.in cmake/install/post/generate-adios2-config.sh.in \ source/utils/adios_reorganize/adios2_reorganize_wrapper source/utils/adios2_deactivate_bp SHEBANG_GLOB= *.sh *.py USE_GITHUB= yes GH_ACCOUNT= ornladios GH_PROJECT= ADIOS2 CMAKE_ARGS= -DFREEBSD_PYTHON_VERSION=${PYTHON_VER} CMAKE_OFF= BUILD_TESTING ADIOS2_BUILD_EXAMPLES LDFLAGS+= -lepoll-shim OPTIONS_DEFINE= DOCS DOCSDIR= ${PREFIX}/share/doc/ADIOS2 PORTDOCS= * # several tests fail, see https://github.com/ornladios/ADIOS2/issues/3286 post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/adios2/bindings/adios2_bindings${PYTHON_TAG}.so .include diff --git a/misc/py-apache-beam/Makefile b/misc/py-apache-beam/Makefile index 189b0f759f34..cd51c929faec 100644 --- a/misc/py-apache-beam/Makefile +++ b/misc/py-apache-beam/Makefile @@ -1,61 +1,61 @@ PORTNAME= apache-beam DISTVERSION= 2.43.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= misc MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Apache Beam SDK for Python WWW= https://beam.apache.org/ LICENSE= APACHE20 PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cloudpickle>=2.2.0:devel/py-cloudpickle@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}crcmod>=1.7:devel/py-crcmod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}python-dateutil>=2.8.0:devel/py-python-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dill>=0.3.1.1:devel/py-dill@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}fastavro>=0.23.6:textproc/py-fastavro@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}fasteners>=0.3:devel/py-fasteners@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}grpcio>=1.33.1>0:devel/py-grpcio@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hdfs>=2.1.0:www/py-hdfs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}httplib2>=0.8:www/py-httplib2@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}orjson<4.0:devel/py-orjson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}objsize>=0.5.2:devel/py-objsize@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}proto-plus>=1.7.1:devel/py-proto-plus@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}protobuf>=3.12.2:devel/py-protobuf@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydot>=1.2.0:graphics/py-pydot@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pymongo>=3.8.0:databases/py-pymongo@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2018.3:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}regex>=2020.6.8:textproc/py-regex@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.24.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=3.7.0:devel/py-typing-extensions@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}zstandard>=0.18.0:archivers/py-zstandard@${PY_FLAVOR} BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}freezegun>=0.3.12:devel/py-freezegun@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>=0.3.12:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>=1.0.1:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}parameterized>=0.7.1:devel/py-parameterized@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psycopg2>=2.8.5:databases/py-psycopg2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}PyHamcrest>=1.9:textproc/py-pyhamcrest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-timeout>=1.3.3:devel/py-pytest-timeout@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-xdist>=1.29.0:devel/py-pytest-xdist@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests-mock>=1.7:www/py-requests-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tenacity>=5.0.2:devel/py-tenacity@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.20.0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=1.3:databases/py-sqlalchemy14@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=3.12:devel/py-pyyaml@${PY_FLAVOR} # testcontainers[mysql]>=3.0.3 is also required USES= python zip USE_PYTHON= autoplist concurrent cryptography_test cython0 distutils pytest # 5 tests fail, depending on pyarrow, MySqlContainer, threadpoolctl post-install: # strip binaries @${FIND} ${STAGEDIR}${PREFIX} -name "*${PYTHON_TAG}.so" | ${XARGS} ${STRIP_CMD} .include diff --git a/misc/py-detecta/Makefile b/misc/py-detecta/Makefile index 2e912ee407a2..c5878fc06bc4 100644 --- a/misc/py-detecta/Makefile +++ b/misc/py-detecta/Makefile @@ -1,24 +1,24 @@ PORTNAME= detecta DISTVERSION= 0.0.5 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= misc python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library to detect events in data WWW= https://github.com/demotu/detecta LICENSE= APACHE20 PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist NO_ARCH= yes .include diff --git a/misc/py-lightgbm/Makefile b/misc/py-lightgbm/Makefile index 9739a7f7ed7e..2b1027475cc1 100644 --- a/misc/py-lightgbm/Makefile +++ b/misc/py-lightgbm/Makefile @@ -1,37 +1,38 @@ PORTNAME= lightgbm DISTVERSION= 4.6.0 +PORTREVISION= 1 CATEGORIES= misc # machine-learning MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Gradient boosting framework that uses tree based learning algorithms WWW= https://lightgbm.readthedocs.io/en/latest/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE NOT_FOR_ARCHS= armv6 armv7 i386 # Exception: Cannot install LightGBM in 32-bit Python, please use 64-bit Python instead PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.22.0:science/py-scikit-learn@${PY_FLAVOR} BUILD_DEPENDS= cmake:devel/cmake-core \ gmake:devel/gmake \ ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}pyproject-metadata>0:devel/py-pyproject-metadata@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} USES= eigen:3 python USE_PYTHON= pep517 autoplist CXXFLAGS+= -I${LOCALBASE}/include/eigen3 BINARY_ALIAS= make=${GMAKE} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/lightgbm/lib/lib_lightgbm.so .include diff --git a/misc/py-shap2/Makefile b/misc/py-shap2/Makefile index 0578c71451c2..3639dc0e21b3 100644 --- a/misc/py-shap2/Makefile +++ b/misc/py-shap2/Makefile @@ -1,31 +1,31 @@ PORTNAME= shap2 DISTVERSION= 0.42.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= misc # machine-learning MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Unified approach to explain the output of any machine learning model WWW= https://github.com/slundberg/shap LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}numba>0:devel/py-numba@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xgboost>0:misc/py-xgboost@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/shap2/_cext${PYTHON_TAG}.so .include diff --git a/misc/py-torchao/Makefile b/misc/py-torchao/Makefile index afe8d2314df5..77461d18f247 100644 --- a/misc/py-torchao/Makefile +++ b/misc/py-torchao/Makefile @@ -1,32 +1,33 @@ PORTNAME= torchao DISTVERSIONPREFIX= v DISTVERSION= 0.13.0 +PORTREVISION= 1 CATEGORIES= misc # machine-learning PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= PyTorch: Package for applying ao techniques to GPU models WWW= https://docs.pytorch.org/ao/stable/index.html \ https://github.com/pytorch/ao LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pytorch>0:misc/py-pytorch@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist pytest USE_GITHUB= yes GH_ACCOUNT= pytorch GH_PROJECT= ao GH_TUPLE= NVIDIA:cutlass:e51efbf:cutlass/third_party/cutlass NO_ARCH= yes # tests fail with: caught unexpected SystemExit! .include diff --git a/misc/py-torchmetrics/Makefile b/misc/py-torchmetrics/Makefile index 4dc09c972a44..b2f5fea4fd8c 100644 --- a/misc/py-torchmetrics/Makefile +++ b/misc/py-torchmetrics/Makefile @@ -1,37 +1,37 @@ PORTNAME= torchmetrics DISTVERSIONPREFIX= v DISTVERSION= 1.8.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= misc python # machine-learning #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= PyTorch native metrics WWW= https://lightning.ai/docs/torchmetrics/stable/ \ https://github.com/Lightning-AI/torchmetrics LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lightning-utilities>=0.8.0:misc/py-lightning-utilities@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nltk>=3.6:textproc/py-nltk@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}packaging>17.1:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytorch>0:misc/py-pytorch@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}regex>=2021.9.24:textproc/py-regex@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.0.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}torchvision>0:misc/py-torchvision@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>=4.41.0:misc/py-tqdm@${PY_FLAVOR} # some optional dependencies for some sections are missing BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist USE_GITHUB= yes GH_ACCOUNT= Lightning-AI NO_ARCH= yes .include diff --git a/misc/py-torchvision/Makefile b/misc/py-torchvision/Makefile index af2ffb62594c..b63b7f4d902c 100644 --- a/misc/py-torchvision/Makefile +++ b/misc/py-torchvision/Makefile @@ -1,43 +1,44 @@ PORTNAME= torchvision DISTVERSIONPREFIX= v DISTVERSION= 0.25.0 +PORTREVISION= 1 CATEGORIES= misc # machine-learning PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= PyTorch: Datasets, transforms and models specific to computer vision WWW= https://pytorch.org/vision/stable/index.html \ https://github.com/pytorch/vision LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libpng16.so:graphics/png \ libwebp.so:graphics/webp PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytorch>0:misc/py-pytorch@${PY_FLAVOR} PY_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pillow>=5.3.0:graphics/py-pillow@${PY_FLAVOR} # image backend BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}fsspec>0:filesystems/py-fsspec@${PY_FLAVOR} \ pybind11>0:devel/pybind11 \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} BUILD_DEPENDS+= ninja:devel/ninja # build uses the C compiler for C++ files w/out ninja, and fails RUN_DEPENDS= ${PY_DEPENDS} USES= compiler:c++17-lang jpeg python USE_PYTHON= pep517 autoplist pytest # tests run in a very high memory ; in 0.17.1 tests fail to run, see https://github.com/pytorch/vision/issues/8278 USE_GITHUB= yes GH_ACCOUNT= pytorch GH_PROJECT= vision MAKE_ENV= TORCHVISION_INCLUDE=${LOCALBASE}/include # workaround for build failure suggested here: https://github.com/pytorch/vision/issues/8397#issuecomment-2168351425 post-install: # strip binaries @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/torchvision/_C.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/torchvision/image.so .include diff --git a/science/py-OpenMC/Makefile b/science/py-OpenMC/Makefile index 32fa25a62689..a13e6abab86a 100644 --- a/science/py-OpenMC/Makefile +++ b/science/py-OpenMC/Makefile @@ -1,51 +1,51 @@ PORTNAME= OpenMC DISTVERSIONPREFIX= v DISTVERSION= 0.15.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Monte Carlo neutron and photon transport simulation code (Python) WWW= https://openmc.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}uncertainties>0:math/py-uncertainties@${PY_FLAVOR} BUILD_DEPENDS= openmc>0:science/openmc \ ${PY_DEPENDS} RUN_DEPENDS= openmc>0:science/openmc \ ${PY_DEPENDS} USES= python USE_PYTHON= distutils cython concurrent autoplist pytest # tests fail and abort in the middle, see https://github.com/openmc-dev/openmc/issues/2186 USE_GITHUB= yes GH_ACCOUNT= ${PORTNAME:tl}-dev GH_PROJECT= ${PORTNAME:tl} PLIST_FILES= ${PYTHON_SITELIBDIR}/openmc/lib/libopenmc.so TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: # strip @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openmc/data/*.so # link the library @${LN} -s ${LOCALBASE}/lib/libopenmc.so ${STAGEDIR}${PYTHON_SITELIBDIR}/openmc/lib/libopenmc.so pre-test: # link the library @if ! [ -e ${WRKSRC}/openmc/lib/libopenmc.so ]; then ${LN} -s ${LOCALBASE}/lib/libopenmc.so ${WRKSRC}/openmc/lib/libopenmc.so; fi # Some tests fail with the message: RuntimeError: No cross_sections.xml file was specified in materials.xml or in the OPENMC_CROSS_SECTIONS environment variable, see https://github.com/openmc-dev/openmc/issues/3053 .include diff --git a/science/py-PyNE/Makefile b/science/py-PyNE/Makefile index ea9dd4c53a1e..391126e6c6e9 100644 --- a/science/py-PyNE/Makefile +++ b/science/py-PyNE/Makefile @@ -1,88 +1,88 @@ PORTNAME= PyNE DISTVERSION= 0.7.8 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science # physics MASTER_SITES= https://raw.githubusercontent.com/pyne/data/master/:decay \ https://raw.githubusercontent.com/pyne/data/master/:cram \ https://raw.githubusercontent.com/pyne/data/master/:dlc \ https://raw.githubusercontent.com/pyne/data/master/:clc \ https://raw.githubusercontent.com/pyne/data/master/:nuc_data PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTFILES= decay.tar.gz:decay \ cram.tar.gz:cram \ decay-linux-clang.tar.gz:dlc \ cram-linux-clang.tar.gz:clc \ prebuilt_nuc_data.h5:nuc_data DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} EXTRACT_ONLY= ${DISTNAME}.tar.gz MAINTAINER= yuri@FreeBSD.org COMMENT= PyNE: The Nuclear Engineering Toolkit WWW= https://pyne.io/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt BROKEN_armv7= clang runs out of memory PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}future>0:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}progress>0:devel/py-progress@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tables>0:devel/py-tables@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tables>0:devel/py-tables@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=0:devel/py-pyyaml@${PY_FLAVOR} # the dependency list is only in ubuntu.sh, see https://github.com/pyne/pyne/issues/1518 PY_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}OpenMC>0:science/py-OpenMC@${PY_FLAVOR} BUILD_DEPENDS= cmake:devel/cmake-core \ ${PY_DEPENDS} LIB_DEPENDS= libhdf5.so:science/hdf5 \ libMOAB.so:math/moab RUN_DEPENDS= ${PY_DEPENDS} USES= compiler:c++17-lang fortran python USE_PYTHON= distutils cython flavors USE_GITHUB= yes GH_ACCOUNT= pyne GH_PROJECT= pyne MAKE_ENV= DESTDIR=${STAGEDIR} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} FFLAGS+= -fallow-argument-mismatch # all arguments are described here: http://pyne.io/install/source.html#source PY_EXTRA_ARGS= --slow # this chooses slow compilation of sources from {decay,cram}.tar.gz # over incompatible pre-compiled assembly from {decay,cram}-linux-clang.tar.gz PY_EXTRA_ARGS+= ${_MAKE_JOBS} PY_EXTRA_ARGS+= --hdf5 ${LOCALBASE} PY_EXTRA_ARGS+= --moab ${LOCALBASE} PYDISTUTILS_CONFIGUREARGS= ${PY_EXTRA_ARGS} PYDISTUTILS_BUILDARGS= ${PY_EXTRA_ARGS} BINARY_ALIAS= python=${PYTHON_CMD} post-extract: .for f in decay.tar.gz cram.tar.gz decay-linux-clang.tar.gz cram-linux-clang.tar.gz @${CP} ${DISTDIR}/${DIST_SUBDIR}/${f} ${WRKSRC}/src .endfor do-install: # install project cd ${INSTALL_WRKSRC} && \ ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYDISTUTILS_SETUP} ${PYDISTUTILS_INSTALL_TARGET} # also install nuc_data.h5 because it is referred to in the code and is required by Jupyter notebooks ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/prebuilt_nuc_data.h5 ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/nuc_data.h5 # remove stray files ${RM} ${STAGEDIR}${PREFIX}/bin/ubuntu.sh # strip ${STRIP_CMD} \ ${STAGEDIR}${LOCALBASE}/lib/lib*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/xs/models.so # CAVEAT: due to the failure to find MOAB-5.5.1 the file pyne/source_sampling.so isn't built, and is removed from plist # - see https://github.com/pyne/pyne/issues/1537 .include diff --git a/science/py-arch/Makefile b/science/py-arch/Makefile index 1208ad8f6fec..86a39761607e 100644 --- a/science/py-arch/Makefile +++ b/science/py-arch/Makefile @@ -1,36 +1,37 @@ PORTNAME= arch DISTVERSION= 6.3.0 +PORTREVISION= 1 CATEGORIES= science finance python # economics MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Autoregressive Conditional Heteroskedasticity (ARCH) models WWW= https://github.com/bashtage/arch LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.1:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}property-cached>=1.6.4:devel/py-property-cached@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.5:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}statsmodels>=0.12:math/py-statsmodels@${PY_FLAVOR} BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= pep517 cython autoplist pytest # tests fail to run, see https://github.com/bashtage/arch/issues/668 TEST_WRKSRC= ${WRKSRC}/arch/tests TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} \ ${STAGEDIR}${PYTHON_SITELIBDIR}/arch/bootstrap/_samplers${PYTHON_TAG}.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/arch/univariate/recursions${PYTHON_TAG}.so .include diff --git a/science/py-atomium/Makefile b/science/py-atomium/Makefile index a2dc0462781d..68b26c51660c 100644 --- a/science/py-atomium/Makefile +++ b/science/py-atomium/Makefile @@ -1,34 +1,34 @@ PORTNAME= atomium DISTVERSIONPREFIX= v DISTVERSION= 1.0.11 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Molecular modeller and file parser WWW= https://atomium.bio/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}coveralls>0:devel/py-coveralls@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}msgpack>=0.6.1:devel/py-msgpack@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}paramiko>0:security/py-paramiko@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rmsd>0:science/py-rmsd@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sphinx>0:textproc/py-sphinx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sphinx_rtd_theme>0:textproc/py-sphinx_rtd_theme@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}valerius>=0.2:biology/py-valerius@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist pytest USE_GITHUB= yes GH_ACCOUNT= samirelanduk .include diff --git a/science/py-boutdata/Makefile b/science/py-boutdata/Makefile index 4ca3557cad33..482c573f8f1c 100644 --- a/science/py-boutdata/Makefile +++ b/science/py-boutdata/Makefile @@ -1,37 +1,38 @@ PORTNAME= boutdata DISTVERSION= 0.4.0 +PORTREVISION= 1 CATEGORIES= science education MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python package for collecting BOUT++ data WWW= https://github.com/boutproject/boutdata LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8.0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}natsort>=8.1.0:devel/py-natsort@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}netCDF4>0:science/py-netCDF4@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.12.0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>=1.5.1:math/py-sympy@${PY_FLAVOR} BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools_scm_git_archive>0:devel/py-setuptools_scm_git_archive@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0.37.1:devel/py-wheel@${PY_FLAVOR} \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= pep517 autoplist pytest NO_ARCH= yes post-patch: @${REINPLACE_CMD} \ -e 's/license = "LGPL-3.0-or-later"/license = {text = "LGPL-3.0-or-later"}/' \ -e "/^license-files/d" \ ${WRKSRC}/pyproject.toml .include diff --git a/science/py-boututils/Makefile b/science/py-boututils/Makefile index 06975aeb6658..d9582f172304 100644 --- a/science/py-boututils/Makefile +++ b/science/py-boututils/Makefile @@ -1,30 +1,31 @@ PORTNAME= boututils DISTVERSION= 0.2.1 +PORTREVISION= 1 CATEGORIES= science education MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python package containing BOUT++ utils WWW= https://github.com/boutproject/boututils LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.2.1:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}netCDF4>=1.5.3:science/py-netCDF4@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.4.1:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools_scm_git_archive>0:devel/py-setuptools_scm_git_archive@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0.37.1:devel/py-wheel@${PY_FLAVOR} \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}mayavi>0:graphics/py-mayavi@${PY_FLAVOR} # optional USES= python USE_PYTHON= pep517 autoplist pytest NO_ARCH= yes .include diff --git a/science/py-chempy/Makefile b/science/py-chempy/Makefile index 1d2d39cd5256..ee41f452c44f 100644 --- a/science/py-chempy/Makefile +++ b/science/py-chempy/Makefile @@ -1,54 +1,54 @@ PORTNAME= chempy DISTVERSION= 0.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Package useful for solving problems in chemistry WWW= https://github.com/bjodah/chempy LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dot2tex>=2.11.3:print/dot2tex@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.3:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}PuLP>=1.6.8:math/py-PuLP@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyneqsys>=0.5.7:math/py-pyneqsys@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyodesys>=0.14.1:math/py-pyodesys@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyparsing>=2.0.3:devel/py-pyparsing@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}quantities>=0.12.1:science/py-quantities@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.0.1:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sym>=0.3.7:math/py-sym@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>=1.1.1:math/py-sympy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tabulate>0:devel/py-tabulate@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}black>0:devel/py-black@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-cov>0:devel/py-pytest-cov@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-flakes>0:devel/py-pytest-flakes@${PY_FLAVOR} \ gsl>0:math/gsl USES= localbase:ldflags python # localbase and math/gsl are only for tests USE_PYTHON= distutils autoplist pytest # 5 tests fail, see https://github.com/bjodah/chempy/issues/222 NO_ARCH= yes CONFLICTS_INSTALL= ${PYTHON_PKGNAMEPREFIX}pymol # https://github.com/schrodinger/pymol-open-source/issues/100 OPTIONS_DEFINE= EXTRAS OPTIONS_DEFAULT= EXTRAS EXTRAS_DESC= Install optional dependencies for additional functionality # this seems to be a copy of what extras pyodesys requires, see https://github.com/bjodah/chempy/issues/241 EXTRAS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}appdirs>0:devel/py-appdirs@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}bokeh>=0.13.0:www/py-bokeh@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ipywidgets>0:devel/py-ipywidgets@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pycodeexport>=0.1.3:devel/py-pycodeexport@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pycompilation>=0.4.12:devel/py-pycompilation@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygslodeiv2>=0.9.4:math/py-pygslodeiv2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyodeint>=0.10.4:math/py-pyodeint@${PY_FLAVOR} # TODO pycvodes>=0.14.0, pykinsol>=0.1.6 .include diff --git a/science/py-dwave-cloud-client/Makefile b/science/py-dwave-cloud-client/Makefile index a557d3839ee7..4c324c16383a 100644 --- a/science/py-dwave-cloud-client/Makefile +++ b/science/py-dwave-cloud-client/Makefile @@ -1,48 +1,49 @@ PORTNAME= dwave-cloud-client DISTVERSION= 0.14.4 +PORTREVISION= 1 CATEGORIES= science python www # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: REST interface to communicate with D-Wave Solver API servers WWW= https://github.com/dwavesystems/dwave-cloud-client LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}authlib>=1.2:security/py-authlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}click>=7.0:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}python-dateutil>=2.7:devel/py-python-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}diskcache>=5.2.1:devel/py-diskcache@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.9:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0:devel/py-homebase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}http-sf>=1.0.4:www/py-http-sf@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}importlib-metadata>=5.0.0:devel/py-importlib-metadata@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}orjson>=3.10:devel/py-orjson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=19:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plucky>=0.4.3:devel/py-plucky@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pydantic2>=2:devel/py-pydantic2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.25:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.5.0:devel/py-typing-extensions@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}urllib3>=1.26:net/py-urllib3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}werkzeug>=2.2:www/py-werkzeug@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}coverage>0:devel/py-coverage@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.9:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>0:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests-mock>0:www/py-requests-mock@${PY_FLAVOR} USES= python USE_PYTHON= distutils cython autoplist unittest # 2 tests fail, see https://github.com/dwavesystems/dwave-cloud-client/issues/637 USE_GITHUB= yes GH_ACCOUNT= dwavesystems NO_ARCH= yes TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} .include diff --git a/science/py-dwave-hybrid/Makefile b/science/py-dwave-hybrid/Makefile index ad30cac906cf..8a9a7b18140d 100644 --- a/science/py-dwave-hybrid/Makefile +++ b/science/py-dwave-hybrid/Makefile @@ -1,37 +1,38 @@ PORTNAME= dwave-hybrid DISTVERSION= 0.6.15 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Hybrid asynchronous decomposition sampler prototype framework WWW= https://docs.ocean.dwavesys.com/projects/hybrid/en/stable/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>5:devel/py-click@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.2:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.10.6:science/py-dwave-cloud-client@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.8:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.5.4:science/py-dwave-preprocessing@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.0.0:science/py-dwave-samplers@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-system>=1.16.0:science/py-dwave-system@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}minorminer>=0.1.7:math/py-minorminer@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plucky>=0.4.3:devel/py-plucky@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils autoplist unittest # several tests fail, see https://github.com/dwavesystems/dwave-hybrid/issues/276 USE_GITHUB= yes GH_ACCOUNT= dwavesystems TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} NO_ARCH= yes .include diff --git a/science/py-dwave-networkx/Makefile b/science/py-dwave-networkx/Makefile index ea480887bd30..7d2e5ad15f75 100644 --- a/science/py-dwave-networkx/Makefile +++ b/science/py-dwave-networkx/Makefile @@ -1,32 +1,33 @@ PORTNAME= dwave-networkx DISTVERSION= 0.8.18 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Extension of the NetworkX Python package for graphs WWW= https://github.com/dwavesystems/dwave-networkx LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.0:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} USES= python USE_PYTHON= distutils cython autoplist unittest USE_GITHUB= yes GH_ACCOUNT= dwavesystems NO_ARCH= yes TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} .include diff --git a/science/py-dwave-samplers/Makefile b/science/py-dwave-samplers/Makefile index 7e42bca2c136..784e83b2aa29 100644 --- a/science/py-dwave-samplers/Makefile +++ b/science/py-dwave-samplers/Makefile @@ -1,50 +1,51 @@ PORTNAME= dwave-samplers DISTVERSION= 1.7.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Classical algorithms for solving binary quadratic models WWW= https://github.com/dwavesystems/dwave-samplers LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}reno>0:textproc/py-reno@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}parameterized>0:devel/py-parameterized@${PY_FLAVOR} USES= python USE_PYTHON= autoplist cython distutils unittest # 2 tests fail, see https://github.com/dwavesystems/dwave-samplers/issues/66 USE_GITHUB= yes GH_ACCOUNT= dwavesystems TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests post-install: # fix file paths, workaround for https://github.com/dwavesystems/dwave-samplers/issues/31 @cd ${STAGEDIR}${PYTHON_SITELIBDIR} && ( \ for f in `${FIND} samplers -name "*.so"`; do \ ${MV} $$f dwave/$$f; \ done; \ ${RM} -r samplers; \ ) # strip binaries @${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/samplers -name "*${PYTHON_TAG}.so" | ${XARGS} ${STRIP_CMD} # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-system/issues/462 @${RM} -r \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__pycache__ post-test: @${SETENV} ${TEST_ENV} ${PYTHON_CMD} ${FILESDIR}/example.py # tests as of 1.6.0: Ran 522 tests in 102.085s .include diff --git a/science/py-dwave-system/Makefile b/science/py-dwave-system/Makefile index 72450e946059..c7e43db6650f 100644 --- a/science/py-dwave-system/Makefile +++ b/science/py-dwave-system/Makefile @@ -1,43 +1,44 @@ PORTNAME= dwave-system DISTVERSION= 1.34.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: API for incorporating the D-Wave system as a sampler WWW= https://github.com/dwavesystems/dwave-system LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.20:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-cloud-client>=0.12.0:science/py-dwave-cloud-client@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-networkx>=0.8.10:science/py-dwave-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-optimization>=0.6.6:science/py-dwave-optimization@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-preprocessing>=0.5.0:science/py-dwave-preprocessing@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-samplers>=1.0.0:science/py-dwave-samplers@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.0:devel/py-homebase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}minorminer>=0.2.19:math/py-minorminer@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils unittest autoplist # 1 test fails because the closed source dwave.drivers optional dependency is missing USE_GITHUB= yes GH_ACCOUNT= dwavesystems TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests NO_ARCH= yes post-install: # remove conflicting __init__.py, see https://github.com/dwavesystems/dwave-system/issues/462 @${RM} -r \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__init__.py \ ${STAGEDIR}${PYTHON_SITELIBDIR}/dwave/__pycache__ .include diff --git a/science/py-libgetar/Makefile b/science/py-libgetar/Makefile index 3d9881305244..6d7418ff1407 100644 --- a/science/py-libgetar/Makefile +++ b/science/py-libgetar/Makefile @@ -1,34 +1,34 @@ PORTNAME= libgetar DISTVERSIONPREFIX= v DISTVERSION= 1.1.7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library to read and write GEneric Trajectory ARchives WWW= https://github.com/glotzerlab/libgetar LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}breathe>0:devel/py-breathe@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils cython autoplist USE_GITHUB= yes GH_ACCOUNT= glotzerlab TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/gtar/_gtar${PYTHON_TAG}.so do-test: @cd ${WRKSRC}/test && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover .include diff --git a/science/py-oddt/Makefile b/science/py-oddt/Makefile index a867f158da80..60bed3a22c41 100644 --- a/science/py-oddt/Makefile +++ b/science/py-oddt/Makefile @@ -1,29 +1,29 @@ PORTNAME= oddt DISTVERSION= 0.7 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Open Drug Discovery Toolkit WWW= https://github.com/oddt/oddt LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}joblib>=0.9.4:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.19.2:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.18:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.17:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_GITHUB= yes USE_PYTHON= distutils concurrent autoplist NO_ARCH= yes .include diff --git a/science/py-penaltymodel/Makefile b/science/py-penaltymodel/Makefile index a99d122fbb4e..961548aa95b6 100644 --- a/science/py-penaltymodel/Makefile +++ b/science/py-penaltymodel/Makefile @@ -1,32 +1,33 @@ PORTNAME= penaltymodel DISTVERSION= 1.3.0 +PORTREVISION= 1 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Utilities and interfaces for using penalty models WWW= https://docs.ocean.dwavesys.com/projects/penaltymodel/en/latest/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dimod>=0.12.13:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}homebase>=1.0.1:devel/py-homebase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=3.0:math/py-networkx@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils cython autoplist unittest USE_GITHUB= yes GH_ACCOUNT= dwavesystems TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests NO_ARCH= yes .include diff --git a/science/py-phono3py/Makefile b/science/py-phono3py/Makefile index 3c75193f4a8e..d018c606fab4 100644 --- a/science/py-phono3py/Makefile +++ b/science/py-phono3py/Makefile @@ -1,41 +1,42 @@ PORTNAME= phono3py DISTVERSION= 3.28.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Software to calculate phonon-phonon interaction and related properties WWW= https://phonopy.github.io/phono3py/ \ https://github.com/phonopy/phono3py LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>=3.0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.2:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}phonopy>=2.32:science/py-phonopy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}spglib>=2.3:science/py-spglib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyyaml>=5.3:devel/py-pyyaml@${PY_FLAVOR} BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scikit-build-core>0:devel/py-scikit-build-core@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nanobind>0:devel/py-nanobind@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ cmake:devel/cmake-core \ ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} CFLAGS+= -fPIC USES= blaslapack:openblas fortran localbase python USE_PYTHON= pep517 cython autoplist pytest TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/test # tests as of 3.9.0: 11 failed, 179 passed, 8 skipped, 6 warnings, 4 errors in 2175.15s (0:36:15), see https://github.com/phonopy/phono3py/issues/307 # tests as of 3.25.0: 21 failed, 193 passed, 11 skipped, 30 warnings, 45 errors in 152.92s (0:02:32), see https://github.com/phonopy/phono3py/issues/307 # - tests fail to find submodules that are installed and import fine when run standalone .include diff --git a/science/py-pyprecice/Makefile b/science/py-pyprecice/Makefile index 018748767e20..80bae08c4b44 100644 --- a/science/py-pyprecice/Makefile +++ b/science/py-pyprecice/Makefile @@ -1,35 +1,35 @@ PORTNAME= pyprecice DISTVERSIONPREFIX= v DISTVERSION= 3.1.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Coupling library for partitioned multi-physics simulations WWW= https://precice.org/ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}mpi4py>0:net/py-mpi4py@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}pkgconfig>0:devel/py-pkgconfig@${PY_FLAVOR} LIB_DEPENDS= libprecice.so:science/precice RUN_DEPENDS= ${PY_DEPENDS} USES= localbase pkgconfig python USE_PYTHON= distutils cython autoplist pytest USE_GITHUB= yes GH_ACCOUNT= precice GH_PROJECT= python-bindings post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cyprecice.cpython-${PYTHON_SUFFIX}.so do-test: @cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} ${PYSETUP} test .include diff --git a/science/py-pyqubo/Makefile b/science/py-pyqubo/Makefile index f7b37bace0fa..19288a73796a 100644 --- a/science/py-pyqubo/Makefile +++ b/science/py-pyqubo/Makefile @@ -1,45 +1,45 @@ PORTNAME= pyqubo DISTVERSION= 1.4.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science python # quantum-computing PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DWave: Python DSL for constructing QUBOs from mathematical expressions WWW= https://pyqubo.readthedocs.io/en/latest/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}deprecated>=1.2.10:devel/py-deprecated@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dimod>=0.9.14:science/py-dimod@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dwave-neal>=0.5.7:science/py-dwave-neal@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}six>=1.15.0:devel/py-six@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}nbsphinx>=0.8.3:textproc/py-nbsphinx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-build>=0.11.1:devel/py-scikit-build@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0.36.2:devel/py-wheel@${PY_FLAVOR} \ boost-libs>0:devel/boost-libs \ cimod>0:math/cimod \ cmake:devel/cmake-core \ ninja:devel/ninja \ pybind11>0:devel/pybind11 \ robin-hood-hashing>0:devel/robin-hood-hashing RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}codecov>=2.1.9:devel/py-codecov@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}coverage>=4.5.1:devel/py-coverage@${PY_FLAVOR} USES= eigen:3 python USE_PYTHON= distutils cython autoplist unittest USE_GITHUB= yes GH_ACCOUNT= recruit-communications CXXFLAGS+= -I${LOCALBASE}/include/cimod \ -I${LOCALBASE}/include/eigen3 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests .include diff --git a/science/py-pyscf/Makefile b/science/py-pyscf/Makefile index a77bc4e8ad2a..1877db577d91 100644 --- a/science/py-pyscf/Makefile +++ b/science/py-pyscf/Makefile @@ -1,50 +1,50 @@ PORTNAME= pyscf DISTVERSIONPREFIX= v DISTVERSION= 2.8.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python module for quantum chemistry WWW= https://pyscf.org/ \ https://github.com/pyscf/pyscf LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>=2.7:science/py-h5py@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ cmake:devel/cmake-core \ gmake:devel/gmake LIB_DEPENDS= libcint.so:science/libcint \ libxc.so:science/libxc \ libxcfun.so:science/xcfun RUN_DEPENDS= ${PY_DEPENDS} USES= fortran blaslapack:openblas compiler:c++11-lang python USE_PYTHON= distutils autoplist pytest USE_GITHUB= yes POST_PLIST= fix-plist TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/pyscf TEST_ARGS= -c ${WRKSRC}/setup.cfg post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/pyscf/lib/lib*.so fix-plist: @${REINPLACE_CMD} -e 's|.*pyscf_lib_placeholder.so$$||' ${TMPPLIST} post-test: @${ECHO} "==> simple test ..." @${SETENV} ${TEST_ENV} ${PYTHON_CMD} ${FILESDIR}/test.py # tests fail to run: https://github.com/pyscf/pyscf/issues/2601 .include diff --git a/science/py-scikit-fuzzy/Makefile b/science/py-scikit-fuzzy/Makefile index 658380d01336..ddc1db228e46 100644 --- a/science/py-scikit-fuzzy/Makefile +++ b/science/py-scikit-fuzzy/Makefile @@ -1,30 +1,30 @@ PORTNAME= scikit-fuzzy DISTVERSION= 0.5.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Fuzzy logic toolkit for SciPy WWW= https://github.com/scikit-fuzzy/scikit-fuzzy/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}networkx>=1.9:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.9:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= pep517 autoplist NO_ARCH= yes .include diff --git a/science/py-thewalrus/Makefile b/science/py-thewalrus/Makefile index 5a5994be440a..b1d8fa760e11 100644 --- a/science/py-thewalrus/Makefile +++ b/science/py-thewalrus/Makefile @@ -1,40 +1,40 @@ PORTNAME= thewalrus DISTVERSIONPREFIX= v DISTVERSION= 0.21.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python #MASTER_SITES= PYPI # doesn't contain tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Open source library for hafnian calculation WWW= https://the-walrus.readthedocs.io/en/latest/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dask>0:devel/py-dask@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numba>0:devel/py-numba@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>0:math/py-sympy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} TEST_DEPENDS= gmake:devel/gmake \ ${PYTHON_PKGNAMEPREFIX}flaky>=3.7.0:devel/py-flaky@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytest-randomly>0:devel/py-pytest-randomly@${PY_FLAVOR} USES= python USE_PYTHON= distutils autoplist pytest USE_GITHUB= yes GH_ACCOUNT= XanaduAI NO_ARCH= yes BINARY_ALIAS= python3=${PYTHON_CMD} do-test: # testsuite fails to run: https://github.com/XanaduAI/thewalrus/issues/344 @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${GMAKE} test .include diff --git a/science/salome-kernel/Makefile b/science/salome-kernel/Makefile index f2a8ad47c3ef..f92ab9840d67 100644 --- a/science/salome-kernel/Makefile +++ b/science/salome-kernel/Makefile @@ -1,49 +1,49 @@ PORTNAME= salome-kernel DISTVERSIONPREFIX= V DISTVERSION= 9_11_0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Salome Project: Multi-physics simulations: Kernel WWW= https://www.salome-platform.org/ \ https://github.com/SalomePlatform/kernel/ LICENSE= LGPL21+ LICENSE_FILE= ${WRKSRC}/COPYING PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}omniorb>0:devel/py-omniorb \ ${PYTHON_PKGNAMEPREFIX}psutil>0:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} \ salome-configuration>0:science/salome-configuration \ swig:devel/swig LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libomniORB4.so:devel/omniORB RUN_DEPENDS= ${PY_DEPENDS} \ bash:shells/bash USES= cmake compiler:c++11-lang gnome python shebangfix USE_GITHUB= yes GH_ACCOUNT= SalomePlatform GH_PROJECT= kernel USE_GNOME= libxml2 USE_LDCONFIG= yes SHEBANG_FILES= bin/appliskel/.bashrc bin/appliskel/.salome_run \ bin/appliskel/salome bin/appliskel/salome_mesa SHEBANG_GLOB= *.py *.sh CMAKE_ARGS= -DCONFIGURATION_ROOT_DIR=${LOCALBASE}/share/salome/configuration \ -DOMNIORBPY_ROOT_DIR=${LOCALBASE} \ -DPython_EXECUTABLE=${PYTHON_CMD} CMAKE_OFF= SALOME_BUILD_DOC SALOME_BUILD_TESTS CFLAGS+= -DSIZEOF_INT=4 -DSIZEOF_LONG=4 LDFLAGS+= -lexecinfo DATADIR= ${PREFIX}/share/salome .include diff --git a/science/ttk/Makefile b/science/ttk/Makefile index 279a40893b09..42f9e12a5572 100644 --- a/science/ttk/Makefile +++ b/science/ttk/Makefile @@ -1,49 +1,49 @@ PORTNAME= ttk DISTVERSION= 1.3.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Topology ToolKit: Topological data analysis and visualization WWW= https://topology-tool-kit.github.io \ https://github.com/topology-tool-kit/ttk LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scikit-build>0:devel/py-scikit-build@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} BUILD_DEPENDS= ${LOCALBASE}/include/boost/functional/hash.hpp:devel/boost-libs \ cli11>0:devel/cli11 \ exprtk>0:math/exprtk \ spectra>0:math/spectra \ utf8cpp>0:devel/utf8cpp \ websocketpp>0:devel/websocketpp \ ${PY_DEPENDS} BUILD_DEPENDS+= nlohmann-json>0:devel/nlohmann-json # is required by lib/cmake/paraview-5.11/vtk/VTK-vtk-module-find-packages.cmake:1167 BUILD_DEPENDS+= fast_float>0:math/fast_float # attempt to fix build failures triggered by find_package(fastfloat) from paraview's vtk cmake scripts LIB_DEPENDS= libcgraph.so:graphics/graphviz \ libembree3.so:graphics/embree3 \ libfreetype.so:print/freetype2 \ libjsoncpp.so:devel/jsoncpp \ libqhull_r.so:math/qhull \ libvtkRenderingCore-pv${PARAVIEW_VER}.so:science/paraview \ libzfp.so:devel/zfp RUN_DEPENDS= ${PY_DEPENDS} USES= cmake eigen:3 compiler:c++11-lang gl python sqlite xorg USE_GL= glew USE_XORG= x11 USE_GITHUB= yes GH_ACCOUNT= topology-tool-kit CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} CMAKE_OFF= TTK_ENABLE_WEBSOCKETPP # fix build with boost-1.87+ until this is fixed post-stage: ${RM} ${STAGEDIR}${PREFIX}/include/Python.h .include <../../science/paraview/Makefile.version> .include diff --git a/science/wwplot/Makefile b/science/wwplot/Makefile index 616d7305b5ff..36aa16a04c5f 100644 --- a/science/wwplot/Makefile +++ b/science/wwplot/Makefile @@ -1,33 +1,34 @@ PORTNAME= wwplot DISTVERSIONPREFIX= v DISTVERSION= 1.0.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Plotting tool for experimental physics classes WWW= https://github.com/wwmm/wwplot LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} \ qt6-base>0:devel/qt6-base PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pyside6>0:devel/pyside6@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= desktop-file-utils gettext meson python shebangfix USE_GITHUB= yes GH_ACCOUNT= wwmm SHEBANG_FILES= wwplot.in NO_ARCH= yes post-patch: @${REINPLACE_CMD} "s|find_installation('python3',|find_installation('python${PYTHON_VER}',|" ${WRKSRC}/meson.build .include diff --git a/textproc/py-pdf2docx/Makefile b/textproc/py-pdf2docx/Makefile index 560d00239999..e6cdc0661e60 100644 --- a/textproc/py-pdf2docx/Makefile +++ b/textproc/py-pdf2docx/Makefile @@ -1,30 +1,30 @@ PORTNAME= pdf2docx DISTVERSION= 0.5.8 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= textproc python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library and applicaton to convert pdf to docx WWW= https://github.com/dothinking/pdf2docx LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}fire>=0.3.0:devel/py-fire@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}PyMuPDF>=1.19.0:print/py-PyMuPDF@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}fonttools>=4.24.0:print/py-fonttools@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}python-docx>=0.8.10:textproc/py-python-docx@${PY_FLAVOR} \ opencv>0:graphics/opencv BUILD_DEPENDS= ${PY_DEPENDS} \ ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} RUN_DEPENDS= ${PY_DEPENDS} USES= python USE_PYTHON= distutils concurrent autoplist pytest # 2 tests fail, see https://github.com/ArtifexSoftware/pdf2docx/issues/276 NO_ARCH= yes .include