Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 473651) +++ head/science/Makefile (revision 473652) @@ -1,245 +1,246 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi 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 += aircraft-datcom SUBDIR += antioch SUBDIR += atompaw SUBDIR += avogadro SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += clhep SUBDIR += colt SUBDIR += crf++ SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lamprop SUBDIR += libaec SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libint SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += mpqc-mpich SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += openbabel SUBDIR += openkim 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-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities + SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qcl SUBDIR += qtresistors 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 += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simlib SUBDIR += simsmith SUBDIR += spglib SUBDIR += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += tfel SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/py-rmf/Makefile =================================================================== --- head/science/py-rmf/Makefile (nonexistent) +++ head/science/py-rmf/Makefile (revision 473652) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= rmf +DISTVERSION= g20180614 +CATEGORIES= science graphics +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Library to support reading and writing of Rich Molecular Format files + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/COPYING + +BUILD_DEPENDS= swig3.0:devel/swig30 +LIB_DEPENDS= libRMF.so:science/rmf + +USES= cmake:outsource python shebangfix +USE_GITHUB= yes +GH_ACCOUNT= salilab +GH_TAGNAME= f917cf2 +SHEBANG_GLOB= *.py +USE_PYTHON= flavors + +CMAKE_ARGS= -DCMAKE_INSTALL_PYTHONDIR:STRING=${PYTHON_SITELIBDIR} +BINARY_ALIAS= python=${PYTHON_CMD} +LDFLAGS+= -lRMF + +.include Property changes on: head/science/py-rmf/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/py-rmf/distinfo =================================================================== --- head/science/py-rmf/distinfo (nonexistent) +++ head/science/py-rmf/distinfo (revision 473652) @@ -0,0 +1,3 @@ +TIMESTAMP = 1530396872 +SHA256 (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 9c877539b8c7a6af38b3d7155522a90b16b3e28596ec27ac941c7f812f1a1c6f +SIZE (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 15087905 Property changes on: head/science/py-rmf/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/py-rmf/files/patch-CMakeLists.txt =================================================================== --- head/science/py-rmf/files/patch-CMakeLists.txt (nonexistent) +++ head/science/py-rmf/files/patch-CMakeLists.txt (revision 473652) @@ -0,0 +1,62 @@ +--- CMakeLists.txt.orig 2018-06-15 00:56:51 UTC ++++ CMakeLists.txt +@@ -4,15 +4,15 @@ project(RMF) + # needs to be in main CMakeLists.txt + enable_testing() + +-execute_process(COMMAND python setup_git.py +- RESULT_VARIABLE setup +- OUTPUT_VARIABLE toutput +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} +- OUTPUT_STRIP_TRAILING_WHITESPACE) +-if(NOT ${setup} EQUAL 0) +- message(FATAL_ERROR " Failed to run setup_git.py: ${setup}; ${error}") +-endif() ++#execute_process(COMMAND python setup_git.py ++# RESULT_VARIABLE setup ++# OUTPUT_VARIABLE toutput ++# ERROR_VARIABLE error ++# WORKING_DIRECTORY ${PROJECT_SOURCE_DIR} ++# OUTPUT_STRIP_TRAILING_WHITESPACE) ++#if(NOT ${setup} EQUAL 0) ++# message(FATAL_ERROR " Failed to run setup_git.py: ${setup}; ${error}") ++#endif() + + set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_modules) + +@@ -116,14 +116,14 @@ configure_file ( + "${PROJECT_BINARY_DIR}/include/RMF/config.h" + ) + +-add_subdirectory(data) ++#add_subdirectory(data) + add_subdirectory(include) + +-add_subdirectory(src) +-add_subdirectory(bin) ++#add_subdirectory(src) ++#add_subdirectory(bin) + +-add_subdirectory(plugins/vmd/) +-add_subdirectory(plugins/pymol/) ++#add_subdirectory(plugins/vmd/) ++#add_subdirectory(plugins/pymol/) + + # swig support is a little broken + +@@ -142,10 +142,10 @@ endif() + + add_subdirectory(swig) + +-add_subdirectory(test) +-add_subdirectory(examples) +-add_subdirectory(benchmark) +-add_subdirectory(doc) ++#add_subdirectory(test) ++#add_subdirectory(examples) ++#add_subdirectory(benchmark) ++#add_subdirectory(doc) + + add_custom_target(RMF DEPENDS ${RMF_BINS} ${RMF_SWIG} ${RMF_TESTS} ${RMF_VMD} RMF-decorators) + set_property(TARGET "RMF" PROPERTY FOLDER "RMF") Property changes on: head/science/py-rmf/files/patch-CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/py-rmf/files/patch-include_CMakeLists.txt =================================================================== --- head/science/py-rmf/files/patch-include_CMakeLists.txt (nonexistent) +++ head/science/py-rmf/files/patch-include_CMakeLists.txt (revision 473652) @@ -0,0 +1,10 @@ +--- include/CMakeLists.txt.orig 2018-06-30 22:26:02 UTC ++++ include/CMakeLists.txt +@@ -16,5 +16,5 @@ add_custom_target(RMF-decorators ALL DEP + "${PROJECT_SOURCE_DIR}/tools/build/make_decorators.py") + set_property(TARGET "RMF-decorators" PROPERTY FOLDER "RMF") + +-INSTALL(DIRECTORY ${PROJECT_SOURCE_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +-INSTALL(DIRECTORY ${PROJECT_BINARY_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) ++#INSTALL(DIRECTORY ${PROJECT_SOURCE_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) ++#INSTALL(DIRECTORY ${PROJECT_BINARY_DIR}/include/RMF DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) Property changes on: head/science/py-rmf/files/patch-include_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/py-rmf/files/patch-swig_CMakeLists.txt =================================================================== --- head/science/py-rmf/files/patch-swig_CMakeLists.txt (nonexistent) +++ head/science/py-rmf/files/patch-swig_CMakeLists.txt (revision 473652) @@ -0,0 +1,37 @@ +--- swig/CMakeLists.txt.orig 2018-06-15 00:56:51 UTC ++++ swig/CMakeLists.txt +@@ -59,7 +59,7 @@ set_target_properties("${SWIG_MODULE_RMF + IF(WIN32) + SWIG_LINK_LIBRARIES(RMF ${PYTHON_LIBRARIES} RMF-lib) + ELSE(WIN32) +- SWIG_LINK_LIBRARIES(RMF RMF-lib) ++ #SWIG_LINK_LIBRARIES(RMF RMF-lib) + ENDIF(WIN32) + + INSTALL(TARGETS ${SWIG_MODULE_RMF_REAL_NAME} DESTINATION ${CMAKE_INSTALL_PYTHONDIR}) +@@ -95,7 +95,7 @@ set_target_properties("${SWIG_MODULE_RMF + set(RMF_SWIG _RMF CACHE INTERNAL "" FORCE) + + +-INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} DESTINATION "${CMAKE_INSTALL_SWIGDIR}") ++#INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} DESTINATION "${CMAKE_INSTALL_SWIGDIR}") + + + # Don't link in libpython (that prevents the extension from being used in +@@ -104,7 +104,7 @@ INSTALL(FILES "RMF.i" ${SWIG_INCLUDES} D + IF(WIN32) + SWIG_LINK_LIBRARIES(RMF_HDF5 ${PYTHON_LIBRARIES} RMF-lib) + ELSE(WIN32) +- SWIG_LINK_LIBRARIES(RMF_HDF5 RMF-lib) ++ #SWIG_LINK_LIBRARIES(RMF_HDF5 RMF-lib) + ENDIF(WIN32) + # Apple linkers complain by default if there are undefined symbols + IF(APPLE) +@@ -116,6 +116,6 @@ INSTALL(TARGETS ${SWIG_MODULE_RMF_HDF5_R + INSTALL(FILES "${CMAKE_BINARY_DIR}/lib/RMF_HDF5.py" DESTINATION ${CMAKE_INSTALL_PYTHONDIR}) + + set(RMF_SWIG _RMF _RMF_HDF5 CACHE INTERNAL "" FORCE) +-INSTALL(FILES "RMF_HDF5.i" DESTINATION "${CMAKE_INSTALL_SWIGDIR}") ++#INSTALL(FILES "RMF_HDF5.i" DESTINATION "${CMAKE_INSTALL_SWIGDIR}") + + endif() Property changes on: head/science/py-rmf/files/patch-swig_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/py-rmf/pkg-descr =================================================================== --- head/science/py-rmf/pkg-descr (nonexistent) +++ head/science/py-rmf/pkg-descr (revision 473652) @@ -0,0 +1,6 @@ +The Python binding for Rich Molecular Format (RMF) file format library +storing hierarchical molecular data (such as atomic or coarse grained +representations of proteins), along with markup, including geometry and score +data. + +WWW: https://integrativemodeling.org/rmf/ Property changes on: head/science/py-rmf/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/py-rmf/pkg-plist =================================================================== --- head/science/py-rmf/pkg-plist (nonexistent) +++ head/science/py-rmf/pkg-plist (revision 473652) @@ -0,0 +1,4 @@ +%%PYTHON_SITELIBDIR%%/RMF.py +%%PYTHON_SITELIBDIR%%/RMF_HDF5.py +%%PYTHON_SITELIBDIR%%/_RMF.so +%%PYTHON_SITELIBDIR%%/_RMF_HDF5.so Property changes on: head/science/py-rmf/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property