diff --git a/science/Makefile b/science/Makefile index 3019d3e97cd6..b1371a5909d0 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,384 +1,385 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-FAdist SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += apbs SUBDIR += ascent SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += buddy SUBDIR += cantera SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += code_saturne SUBDIR += colt SUBDIR += conduit SUBDIR += coordgenlibs SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += crf++ SUBDIR += csvtk SUBDIR += dakota SUBDIR += dalton SUBDIR += dcl SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dvc SUBDIR += dynare SUBDIR += eccodes SUBDIR += elk SUBDIR += elmerfem SUBDIR += epte SUBDIR += erd SUBDIR += ergo SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fastjet SUBDIR += fisicalab SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += helfem SUBDIR += hepmc3 SUBDIR += highfive SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kim-api SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmsym SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += octopus SUBDIR += openbabel SUBDIR += openems SUBDIR += openkim SUBDIR += openkim-models SUBDIR += openmx SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin SUBDIR += orthanc SUBDIR += orthanc-dicomweb SUBDIR += orthanc-mysql SUBDIR += orthanc-postgresql SUBDIR += orthanc-webviewer SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += packmol SUBDIR += pagmo2 SUBDIR += paje SUBDIR += pcmsolver SUBDIR += phonopy SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PubChemPy SUBDIR += py-PyFR + SUBDIR += py-PyNE SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-access SUBDIR += py-asdf SUBDIR += py-ase SUBDIR += py-avogadrolibs SUBDIR += py-cdo SUBDIR += py-chainer SUBDIR += py-chainer-chemistry SUBDIR += py-chempy SUBDIR += py-cirq-aqt SUBDIR += py-cirq-core SUBDIR += py-cirq-google SUBDIR += py-cirq-ionq SUBDIR += py-cirq-pasqal SUBDIR += py-coards SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-eccodes SUBDIR += py-esda SUBDIR += py-geolinks SUBDIR += py-geomet SUBDIR += py-geometer SUBDIR += py-geometric SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5json SUBDIR += py-h5py SUBDIR += py-hiphive SUBDIR += py-inequality SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-liac-arff SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nibabel SUBDIR += py-nilearn SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pyked SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-rmsd SUBDIR += py-ruffus SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-optimize SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-tobler SUBDIR += py-veusz SUBDIR += pybrain SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += scidavis SUBDIR += segyio SUBDIR += shelxle SUBDIR += siconos SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simbody SUBDIR += simgrid SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += tfel-edf SUBDIR += thermofun SUBDIR += tinker SUBDIR += udunits SUBDIR += v_sim SUBDIR += vipster SUBDIR += vmd SUBDIR += voro++ SUBDIR += votca SUBDIR += wannier90 SUBDIR += wwplot SUBDIR += wxmacmolplt SUBDIR += xcfun SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xtb SUBDIR += yoda .include diff --git a/science/py-PyNE/Makefile b/science/py-PyNE/Makefile new file mode 100644 index 000000000000..70882d74548d --- /dev/null +++ b/science/py-PyNE/Makefile @@ -0,0 +1,60 @@ +PORTNAME= PyNE +DISTVERSION= 0.7.5 +CATEGORIES= science +MASTER_SITES= http://raw.githubusercontent.com/pyne/data/master/:decay \ + http://raw.githubusercontent.com/pyne/data/master/:cram \ + http://raw.githubusercontent.com/pyne/data/master/:dlc \ + http://raw.githubusercontent.com/pyne/data/master/:clc +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTFILES= decay.tar.gz:decay \ + cram.tar.gz:cram \ + decay-linux-clang.tar.gz:dlc \ + cram-linux-clang.tar.gz:clc +DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} +EXTRACT_ONLY= ${DISTNAME}.tar.gz + +MAINTAINER= yuri@FreeBSD.org +COMMENT= PyNE: The Nuclear Engineering Toolkit + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/license.txt + +PY_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}tables>0:devel/py-tables@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} +BUILD_DEPENDS= cmake:devel/cmake \ + ${PY_DEPENDS} +LIB_DEPENDS= libhdf5.so:science/hdf5 \ + libsz.so:science/szip +RUN_DEPENDS= ${PY_DEPENDS} + +USES= compiler:c++17-lang fortran python:3.7+ +USE_PYTHON= distutils cython flavors + +USE_GITHUB= yes +GH_ACCOUNT= pyne +GH_PROJECT= pyne + +MAKE_ENV= DESTDIR=${STAGEDIR} +FFLAGS+= -fallow-argument-mismatch + +PYDISTUTILS_BUILDARGS= --slow # this chooses slow compilation of sources from {decay,cram}.tar.gz + # over incompatible pre-compiled assembly from {decay,cram}-linux-clang.tar.gz + +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 + cd ${INSTALL_WRKSRC} && \ + ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYDISTUTILS_SETUP} ${PYDISTUTILS_INSTALL_TARGET} + # strip + ${STRIP_CMD} \ + ${STAGEDIR}${LOCALBASE}/lib/lib*.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/*.so \ + ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/xs/models.so + +.include diff --git a/science/py-PyNE/distinfo b/science/py-PyNE/distinfo new file mode 100644 index 000000000000..fc8c2dadf0b6 --- /dev/null +++ b/science/py-PyNE/distinfo @@ -0,0 +1,11 @@ +TIMESTAMP = 1633733586 +SHA256 (PyNE-0.7.5/decay.tar.gz) = aa1aa69cb84685731eb234c046c56f9167a0bcc9686ccd5437f62186ac9bd441 +SIZE (PyNE-0.7.5/decay.tar.gz) = 8012492 +SHA256 (PyNE-0.7.5/cram.tar.gz) = 5ea1443226234787e0b8ef7f1d4c9cb0a6846b9da00bc843557051ad74e4a2f5 +SIZE (PyNE-0.7.5/cram.tar.gz) = 2110526 +SHA256 (PyNE-0.7.5/decay-linux-clang.tar.gz) = 6fa05231e7fbfe5994e9a6705131bdcac2fc5845e362d3607e96c46ed418a0db +SIZE (PyNE-0.7.5/decay-linux-clang.tar.gz) = 18904467 +SHA256 (PyNE-0.7.5/cram-linux-clang.tar.gz) = 0a7a04b5268db91fea7bec75dbefe3ec23036f9e250aacc6fb353d17d8e84538 +SIZE (PyNE-0.7.5/cram-linux-clang.tar.gz) = 20477898 +SHA256 (PyNE-0.7.5/pyne-pyne-0.7.5_GH0.tar.gz) = 80143d5e232b89ffd89121363c0e1e615acc28c26f5d7682521eb9baf98311c4 +SIZE (PyNE-0.7.5/pyne-pyne-0.7.5_GH0.tar.gz) = 9262728 diff --git a/science/py-PyNE/files/patch-cmake_SetupSubPyInstall.cmake.in b/science/py-PyNE/files/patch-cmake_SetupSubPyInstall.cmake.in new file mode 100644 index 000000000000..e70e7905f014 --- /dev/null +++ b/science/py-PyNE/files/patch-cmake_SetupSubPyInstall.cmake.in @@ -0,0 +1,12 @@ +- make 'install' DESTDIR-aware + +--- cmake/SetupSubPyInstall.cmake.in.orig 2021-10-09 05:02:12 UTC ++++ cmake/SetupSubPyInstall.cmake.in +@@ -9,6 +9,7 @@ message(" CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFI + message(" CMAKE_CURRENT_BINARY_DIR: ${CMAKE_CURRENT_BINARY_DIR}") + execute_process(COMMAND ${PYTHON_EXECUTABLE} setup_sub.py install + "--prefix=${CMAKE_INSTALL_PREFIX}" ++ "--root=$ENV{DESTDIR}" + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + RESULT_VARIABLE res_var) + if(NOT "${res_var}" STREQUAL "0") diff --git a/science/py-PyNE/pkg-descr b/science/py-PyNE/pkg-descr new file mode 100644 index 000000000000..0a0ecb6320fa --- /dev/null +++ b/science/py-PyNE/pkg-descr @@ -0,0 +1,6 @@ +PyNE is a suite of tools to aid in computational nuclear science & engineering. +PyNE seeks to provide native implementations of common nuclear algorithms, as +well as Python bindings and I/O support for other industry standard nuclear +codes. + +WWW: https://pyne.io/ diff --git a/science/py-PyNE/pkg-plist b/science/py-PyNE/pkg-plist new file mode 100644 index 000000000000..0e0196d6cbb8 --- /dev/null +++ b/science/py-PyNE/pkg-plist @@ -0,0 +1,252 @@ +bin/aceviewer +bin/activation_responses.py +bin/expand_tags.py +bin/gtcadis.py +bin/meshtal_to_mesh +bin/nuc_data_make +bin/ptrac_to_hdf5 +bin/r2s.py +bin/ssw_combine.py +bin/tape9 +include/pyne/_atomic_data.h +include/pyne/_decay.h +include/pyne/atomic_data.h +include/pyne/cram.h +include/pyne/cram.hpp +include/pyne/dagmc_bridge.h +include/pyne/data.h +include/pyne/decay.h +include/pyne/enrichment.h +include/pyne/enrichment_cascade.h +include/pyne/enrichment_symbolic.h +include/pyne/extra_types.h +include/pyne/h5wrap.h +include/pyne/json-forwards.h +include/pyne/json.h +include/pyne/jsoncustomwriter.h +include/pyne/material.h +include/pyne/material_library.h +include/pyne/measure.h +include/pyne/nucname.h +include/pyne/particle.h +include/pyne/pyne.h +include/pyne/rxname.h +include/pyne/source.h +include/pyne/source_sampling.h +include/pyne/tally.h +include/pyne/transmuters.h +include/pyne/utils.h +lib/libpyne.so +%%PYTHON_SITELIBDIR%%/pyne-0.7.1-py%%PYTHON_VER%%.egg-info +%%PYTHON_SITELIBDIR%%/pyne/__init__.pxd +%%PYTHON_SITELIBDIR%%/pyne/__init__.py +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/_argparse%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/alara%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/api%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/binaryreader%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/cccc%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/decay_tape9%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/endl%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf_processing%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fispact%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fluka%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/gammaspec%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mcnp%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mesh%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/pyne/__pycache__/njoy%%PYTHON_EXT_SUFFIX%%.pyc 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