diff --git a/science/Makefile b/science/Makefile index c67e3684888c..e9d5ac65faf8 100644 --- a/science/Makefile +++ b/science/Makefile @@ -1,493 +1,494 @@ COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += ChipmunkPhysics SUBDIR += InsightToolkit SUBDIR += InsightToolkit501 SUBDIR += InsightToolkit521 SUBDIR += PETSc 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-ks 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 += arbor SUBDIR += ascent SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += axom SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw SUBDIR += bodr SUBDIR += buddy SUBDIR += cantera SUBDIR += cardioid SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdk SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemicalfun SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chimes-calculator SUBDIR += chrono SUBDIR += cif-tools 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 += dd_package SUBDIR += devisor SUBDIR += dftbplus SUBDIR += dftd4 SUBDIR += dimod SUBDIR += dirac SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += drawxtl SUBDIR += dssp SUBDIR += dvc SUBDIR += dwave-preprocessing 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 += feff10 SUBDIR += fisicalab SUBDIR += fleur SUBDIR += frontistr SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gbtolib SUBDIR += gchemutils SUBDIR += gdma SUBDIR += gemmi 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 += hdf5-110 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 += kplib SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcifpp SUBDIR += libcint SUBDIR += libctl SUBDIR += libecpint SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libgetar SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libint2-psi4 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmbd SUBDIR += libmsym SUBDIR += libnegf SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libtensorflow1 SUBDIR += libvdwxc SUBDIR += libxc SUBDIR += liggghts SUBDIR += linux-zotero SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mctc-lib SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mercantile SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf-cpp SUBDIR += mol2ps SUBDIR += molgif SUBDIR += molscript SUBDIR += molsketch SUBDIR += mopac SUBDIR += mpb SUBDIR += mpqc SUBDIR += mrchem SUBDIR += mrcpp SUBDIR += msms SUBDIR += mstore SUBDIR += multicharge SUBDIR += multiwfn SUBDIR += namd SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nlcglib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += ocean SUBDIR += octopus SUBDIR += openbabel SUBDIR += openems SUBDIR += openkim-models SUBDIR += openmc SUBDIR += openmolcas 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-Calc 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 += paraview SUBDIR += pastix SUBDIR += pcmsolver SUBDIR += phonopy SUBDIR += plumed SUBDIR += pnetcdf SUBDIR += precice SUBDIR += psi4 SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-OpenFermion-Dirac SUBDIR += py-OpenFermion-PySCF SUBDIR += py-OpenMC SUBDIR += py-PubChemPy SUBDIR += py-PyFR SUBDIR += py-PyNE SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-access + SUBDIR += py-arbor SUBDIR += py-asap3 SUBDIR += py-asdf SUBDIR += py-asdf-standard SUBDIR += py-asdf-transform-schemas SUBDIR += py-ase SUBDIR += py-atomium 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-cirq-rigetti SUBDIR += py-coards SUBDIR += py-dimod SUBDIR += py-dipy SUBDIR += py-dlib SUBDIR += py-dwave-cloud-client SUBDIR += py-dwave-greedy SUBDIR += py-dwave-hybrid SUBDIR += py-dwave-inspector SUBDIR += py-dwave-neal SUBDIR += py-dwave-networkx SUBDIR += py-dwave-ocean-sdk SUBDIR += py-dwave-preprocessing SUBDIR += py-dwave-samplers SUBDIR += py-dwave-system SUBDIR += py-dwave-tabu SUBDIR += py-dwavebinarycsp SUBDIR += py-earthpy SUBDIR += py-eccodes SUBDIR += py-esda SUBDIR += py-fresnel SUBDIR += py-gemmi 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-hoomd-blue SUBDIR += py-inequality SUBDIR += py-jupyter_jsmol SUBDIR += py-kim-query SUBDIR += py-kimpy SUBDIR += py-kinematics SUBDIR += py-kliff SUBDIR += py-kpLib SUBDIR += py-liac-arff SUBDIR += py-libgetar SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-meshio SUBDIR += py-mmcif SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate SUBDIR += py-mrchem SUBDIR += py-netCDF4 SUBDIR += py-netcdf-flattener SUBDIR += py-nibabel SUBDIR += py-nilearn SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openbabel SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-penaltymodel SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-py3Dmol SUBDIR += py-pyaixi SUBDIR += py-pyberny SUBDIR += py-pycsw SUBDIR += py-pydicom SUBDIR += py-pygeodesy SUBDIR += py-pygeometa SUBDIR += py-pygmo2 SUBDIR += py-pyked SUBDIR += py-pymatgen SUBDIR += py-pymbd SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pyprecice SUBDIR += py-pyqubo SUBDIR += py-pysal SUBDIR += py-pyscf SUBDIR += py-pyteomics SUBDIR += py-qcelemental SUBDIR += py-qcengine SUBDIR += py-qiskit SUBDIR += py-qiskit-aer SUBDIR += py-qiskit-experiments SUBDIR += py-qiskit-finance SUBDIR += py-qiskit-ibm-experiment SUBDIR += py-qiskit-ibm-provider SUBDIR += py-qiskit-ibmq-provider SUBDIR += py-qiskit-nature SUBDIR += py-qiskit-optimization SUBDIR += py-qiskit-terra 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-sdf SUBDIR += py-segregation SUBDIR += py-segyio SUBDIR += py-sklearn-pandas SUBDIR += py-skrebate SUBDIR += py-spaghetti SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-thewalrus SUBDIR += py-tobler SUBDIR += py-trainstation SUBDIR += py-tweedledum SUBDIR += py-veusz SUBDIR += pybrain SUBDIR += pynn SUBDIR += q SUBDIR += qbox SUBDIR += qcl SUBDIR += qiskit-aer SUBDIR += qmcpack SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += quantum-jet 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 += sciplot SUBDIR += segyio SUBDIR += serac 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 += simple-dftd3 SUBDIR += simsmith SUBDIR += sirius SUBDIR += smoldyn SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += tblite SUBDIR += teem SUBDIR += tfel SUBDIR += tfel-edf SUBDIR += thermofun SUBDIR += tinker SUBDIR += trilinos SUBDIR += ttk SUBDIR += tweedledum SUBDIR += udunits SUBDIR += ukrmol+ 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 SUBDIR += zotero SUBDIR += zx .include diff --git a/science/py-arbor/Makefile b/science/py-arbor/Makefile new file mode 100644 index 000000000000..567c01f16f9c --- /dev/null +++ b/science/py-arbor/Makefile @@ -0,0 +1,35 @@ +PORTNAME= arbor +DISTVERSIONPREFIX= v +DISTVERSION= 0.8 +CATEGORIES= science +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Multi-compartment neural network simulation library +WWW= https://arbor-sim.org/ + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/../LICENSE + +BUILD_DEPENDS= pybind11>0:devel/pybind11 +LIB_DEPENDS= libarbor.so:science/arbor + +USES= cmake compiler:c++17-lang localbase:ldflags python + +USE_GITHUB= yes +GH_ACCOUNT= arbor-sim + +WRKSRC_SUBDIR= python + +CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} \ + -DARB_PYTHON_LIB_PATH=${PYTHONPREFIX_SITELIBDIR} + +CXXFLAGS+= -fPIC + +post-patch: + @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION + +post-install: + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/arbor/_arbor${PYTHON_EXT_SUFFIX}.so + +.include diff --git a/science/py-arbor/distinfo b/science/py-arbor/distinfo new file mode 100644 index 000000000000..6a64e8f1e731 --- /dev/null +++ b/science/py-arbor/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1669535366 +SHA256 (arbor-sim-arbor-v0.8_GH0.tar.gz) = ee6b2486b1142cf4412dddd1caece0926d1712b8d1868283e3bfe73e4ec2cb71 +SIZE (arbor-sim-arbor-v0.8_GH0.tar.gz) = 7794543 diff --git a/science/py-arbor/files/patch-CMakeLists.txt b/science/py-arbor/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..9441da10091c --- /dev/null +++ b/science/py-arbor/files/patch-CMakeLists.txt @@ -0,0 +1,28 @@ +--- CMakeLists.txt.orig 2022-11-15 15:19:19 UTC ++++ CMakeLists.txt +@@ -1,3 +1,7 @@ ++cmake_minimum_required(VERSION 3.19) ++ ++find_package(Python3 ${arb_py_version} COMPONENTS Interpreter Development REQUIRED) ++ + include(GNUInstallDirs) + + set(PYBIND11_CPP_STANDARD -std=c++17) +@@ -79,14 +83,14 @@ if (ARB_WITH_MPI) + endif() + + # For unit tests on C++ side of Python wrappers +-add_subdirectory(test) ++#add_subdirectory(test) + + # Create the Python module in the build directory. + # The module contains the dynamic library, __init__.py and VERSION information. + set(python_mod_path "${CMAKE_CURRENT_BINARY_DIR}/arbor") + set_target_properties(pyarb PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${python_mod_path}") +-file(COPY "${PROJECT_SOURCE_DIR}/python/__init__.py" DESTINATION "${python_mod_path}") +-file(COPY "${PROJECT_SOURCE_DIR}/VERSION" DESTINATION "${python_mod_path}") ++file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/__init__.py" DESTINATION "${python_mod_path}") ++file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/VERSION" DESTINATION "${python_mod_path}") + + # Set the installation path + diff --git a/science/py-arbor/pkg-descr b/science/py-arbor/pkg-descr new file mode 100644 index 000000000000..6350b89f2e28 --- /dev/null +++ b/science/py-arbor/pkg-descr @@ -0,0 +1,3 @@ +Arbor is a multi-compartment neuron simulation library; compatible with +next-generation accelerators; best-practices applied to research software; +focussed on community-driven development. diff --git a/science/py-arbor/pkg-plist b/science/py-arbor/pkg-plist new file mode 100644 index 000000000000..c4ff5834b200 --- /dev/null +++ b/science/py-arbor/pkg-plist @@ -0,0 +1,3 @@ +%%PYTHON_SITELIBDIR%%/arbor/VERSION +%%PYTHON_SITELIBDIR%%/arbor/__init__.py +%%PYTHON_SITELIBDIR%%/arbor/_arbor%%PYTHON_EXT_SUFFIX%%.so