New port: science/py-rmf: Library to support reading and writing of Rich Molecular Format files

8 files changed, 151 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 5ca73af1e20c..348b02f86a5f 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -196,6 +196,7 @@
     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
diff --git a/science/py-rmf/Makefile b/science/py-rmf/Makefile
new file mode 100644
index 000000000000..17288a958d41
--- /dev/null
+++ b/science/py-rmf/Makefile
@@ -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 <bsd.port.mk>
diff --git a/science/py-rmf/distinfo b/science/py-rmf/distinfo
new file mode 100644
index 000000000000..735bd3bf311a
--- /dev/null
+++ b/science/py-rmf/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1530396872
+SHA256 (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 9c877539b8c7a6af38b3d7155522a90b16b3e28596ec27ac941c7f812f1a1c6f
+SIZE (salilab-rmf-g20180614-f917cf2_GH0.tar.gz) = 15087905
diff --git a/science/py-rmf/files/patch-CMakeLists.txt b/science/py-rmf/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..77ab9ec45a9d
--- /dev/null
+++ b/science/py-rmf/files/patch-CMakeLists.txt
@@ -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} ${RMF_VMD} RMF-decorators)
+ set_property(TARGET "RMF" PROPERTY FOLDER "RMF")
diff --git a/science/py-rmf/files/patch-include_CMakeLists.txt b/science/py-rmf/files/patch-include_CMakeLists.txt
new file mode 100644
index 000000000000..8570c72f3abf
--- /dev/null
+++ b/science/py-rmf/files/patch-include_CMakeLists.txt
@@ -0,0 +1,10 @@
+--- include/CMakeLists.txt.orig	2018-06-30 22:26:02 UTC
++++ include/CMakeLists.txt
+@@ -16,5 +16,5 @@ add_custom_target(RMF-decorators ALL DEP
+   "${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 ${CMAKE_INSTALL_INCLUDEDIR})
diff --git a/science/py-rmf/files/patch-swig_CMakeLists.txt b/science/py-rmf/files/patch-swig_CMakeLists.txt
new file mode 100644
index 000000000000..2deb3fa057a3
--- /dev/null
+++ b/science/py-rmf/files/patch-swig_CMakeLists.txt
@@ -0,0 +1,37 @@
+--- swig/CMakeLists.txt.orig	2018-06-15 00:56:51 UTC
++++ swig/CMakeLists.txt
+@@ -59,7 +59,7 @@ set_target_properties("${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()
diff --git a/science/py-rmf/pkg-descr b/science/py-rmf/pkg-descr
new file mode 100644
index 000000000000..e95cceab4e79
--- /dev/null
+++ b/science/py-rmf/pkg-descr
@@ -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/
diff --git a/science/py-rmf/pkg-plist b/science/py-rmf/pkg-plist
new file mode 100644
index 000000000000..2a1ea0ea236d
--- /dev/null
+++ b/science/py-rmf/pkg-plist
@@ -0,0 +1,4 @@
+%%PYTHON_SITELIBDIR%%/RMF.py
+%%PYTHON_SITELIBDIR%%/RMF_HDF5.py
+%%PYTHON_SITELIBDIR%%/_RMF.so
+%%PYTHON_SITELIBDIR%%/_RMF_HDF5.so