reinit the tree, so we can have metadata

4 files changed, 267 insertions, 0 deletions

diff --git a/sci-libs/cbflib/Manifest b/sci-libs/cbflib/Manifest
new file mode 100644
index 000000000000..9b096ee2591d
--- /dev/null
+++ b/sci-libs/cbflib/Manifest
@@ -0,0 +1,6 @@
+AUX cbflib-0.9.3.3-unbundle.patch 8308 SHA256 edb391b86b8157ce2cc84c23e167ae2ac1bea945543eed1ae03746c931e895be SHA512 21f39214e188cc8fb76326765aba7da4d15c1b70d41c193016733d5b3d14e499178e25c45c807e7c9cabaf3a7f4e3e97c5ed2a8b383472ec9f4e4cbea9b3522d WHIRLPOOL 8dc05512d5797a4e9e3c90363fe0c13d1a30c86e2b37b7f9134c4881b514d1b1505583592a71ef16002ef0b2751b77950dd68dd2ac00c1228220429fce5ec9dd
+DIST CBFlib-0.9.3.3.tar.gz 5787633 SHA256 d6c3cc2c6c0aed2a3aa7c74dc645ad223470dc76bb2181242534d4c322bb00dc SHA512 e041c26770e12e09110d7c4f39737406c6ade6cae6fa941cd31dd3b90432a034426272b8daa851a8a23baceb7189479d2d8bde882b7cfdb8ae666fadc5be57ff WHIRLPOOL 8e9e0004cdd2411c9d37b588afa274e1c2b955fe361fc3df597acc30526958d5722993f36f33672769ef55eca51b87917f57ec56528a7711a934d9f8de2b8019
+EBUILD cbflib-0.9.3.3.ebuild 1259 SHA256 215301b82cffeea07285e3e09dc01e8079801f28a9516474747dbb72f723045d SHA512 e7ce226580ddf3184aa3f511fe8a2cd1d3a41313dacba256c9eddd657691ef60996f2e1504f369972bc945270eaaf30b05c916c0972d69099debc9bf617f23d5 WHIRLPOOL 7f1adcfdf624cabfbc766cd80ab02397883dc02f171e239930667c5c03a5ce7bc0a483448ece51cec501167c8a538fb3cc66e22317bb8793149e4a00a179532e
+MISC ChangeLog 4045 SHA256 a87b35490f90b7d30152d13126669bf5e18231b44991593b0cad03f6cde2e30f SHA512 da21a767820e2a800b2c7f4258cede6cb7d16c3f185a18d7af904738d0360b3ad34d251cb2ab31218a150c818a1b19689dbe4c391422abbe851ebc7ec4ff75af WHIRLPOOL fc5e6d66330d27b83a8de2f7f8506ff7efabcf45f9e108dedc1a434a774200aca6a310c7f70df785163d00cf74386907e57dca8e908acb32fc03ba03dca9fa28
+MISC ChangeLog-2015 5903 SHA256 b9a4402bab656bbab69af9cedfd71353e62a74b7cf6434bfc9339ff67b06cfb5 SHA512 4f34ff58268e419bf92e68da5927c33b8860d5b0c24099e65c116ac2d35e13ca581308a7290dc48a68e562c401cab5c8cc545c7a39d136bc80f10271f7fae51e WHIRLPOOL ab4278a96557e1a2374c91231428736c115d51339a8a00b2c5e7b4fc8407e3443bb628c7d06b78aca4e98fcf61124c2dc3b86c5474b11014441b63e4c9014a54
+MISC metadata.xml 987 SHA256 14b84adad09029a8dedf88f306171d6f9353340875549dc39a8bc126a1730ee1 SHA512 1917afb5bc1a5dbcd9e5ec175ac355e79929fd5ece8be7ea8606bf1ef7329affffa56efa5281df7d2c2eea4e1e3ef224c8310ee8cbeb1c44a0b32b232dadf007 WHIRLPOOL 777d5adc3a47b0fbf3a6274041768a4550cb82d155428e7095b992379ccbd9e1a48fb7bad79d327ac7d8cdc98912b2be7f65a117ae17741f1a6984417d626fcc
diff --git a/sci-libs/cbflib/cbflib-0.9.3.3.ebuild b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild
new file mode 100644
index 000000000000..066ea3ca26ea
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+CMAKE_MAKEFILE_GENERATOR=emake
+
+inherit cmake-utils eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.3"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
+#	test? (
+#		mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+#		mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+#	)"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+S=${WORKDIR}/${MY_P1}
+
+RDEPEND="sci-libs/hdf5:="
+DEPEND="${RDEPEND}"
+
+RESTRICT="test"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-unbundle.patch
+)
+
+src_prepare(){
+	rm -rf Py* drel* dRel* ply* || die
+
+	append-fflags -fno-range-check
+
+	tc-export CC CXX AR RANLIB FC F77
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUNPACKED_DIRECTORY="${S}"
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	dosym ${PN} /usr/include/cbf
+}
diff --git a/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch
new file mode 100644
index 000000000000..ef24c4b94b22
--- /dev/null
+++ b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch
@@ -0,0 +1,181 @@
+ CMakeLists.txt | 118 +++------------------------------------------------------
+ 1 file changed, 6 insertions(+), 112 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 75054d6..15bab99 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -279,7 +279,7 @@ project (CBFlib C CXX Fortran)
+ enable_testing()
+ set (CBF_CMAKE_DEBUG "ON")
+ 
+-set(CMAKE_C_FLAGS "-Wall -fno-strict-aliasing")
++set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -fno-strict-aliasing")
+ 
+ #
+ #  User setable parameters
+@@ -530,42 +530,6 @@ find_package(ZLIB)
+ 
+ 
+ 
+-#Load external packages in build directory at cmake time
+-add_subdirectory(${CBF__EXTERNAL_PACKAGES}  "${CBF__EXT_PKG}")
+-
+-find_file(CBF_EXT_PKG_BLD_RUNNING cbf_ext_pkg_build_running "${CBF__EXT_PKG}")
+-if (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND")
+-  file(WRITE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running" "cbf_ext_pkg_build_running")
+-  CBF_DEBUG_MESSAGE("CMAKE_COMMAND:        ${CMAKE_COMMAND}")
+-  CBF_DEBUG_MESSAGE("CBFlib_SOURCE_DIR:    ${CBFlib_SOURCE_DIR} ")
+-  execute_process(
+-    COMMAND ${CMAKE_COMMAND} ${CBFlib_SOURCE_DIR}
+-    RESULT_VARIABLE CBF_BUILD_RESULT)
+-  CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
+-  execute_process(
+-    COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target HDF5
+-    RESULT_VARIABLE CBF_BUILD_RESULT)
+-  CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
+-  execute_process(
+-    COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target TIFF
+-    RESULT_VARIABLE CBF_BUILD_RESULT)
+-  CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}")
+-  file(REMOVE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running")
+-endif (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND")
+-
+-
+-file(GLOB CBF_HDF5_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*hdf5*")
+-CBF_DEBUG_MESSAGE( "CBF_HDF5_LIBRARY_PATH:  ${CBF_HDF5_LIBRARY_PATH}")
+-file(GLOB CBF_TIFF_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*tif*")
+-CBF_DEBUG_MESSAGE( "CBF_TIFF_LIBRARY_PATH: ${CBF_TIFF_LIBRARY_PATH}")
+-
+-if ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||")
+-  MESSAGE(STATUS "Must build external packages in ${CBF__EXT_PKG}")
+-  MESSAGE(STATUS "Then rerun cmake")
+-  MESSAGE(WARNING "Finishing run to make Makefiles")
+-endif ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||")
+-
+-
+ #
+ # Data Directories
+ #
+@@ -579,35 +543,6 @@ set(CBF_DATAURLBASE	"http://downloads.sf.net/cbflib")
+ set(CBF_DATAURLI  "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Input.tar.gz")
+ set(CBF_DATAURLO  "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output.tar.gz")
+ set(CBF_DATAURLS  "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output_Sigs_Only.tar.gz")
+-#
+-# Load and unpack the Data Files
+-#
+-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRI} ${CBF_DATAURLI})
+-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRO} ${CBF_DATAURLO})
+-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRS} ${CBF_DATAURLS})
+-#
+-# Verify the checksums
+-#
+-file(GLOB CBF_DATADIRI_FILES "${CBF_DATADIRI}/*")
+-file(GLOB CBF_DATADIRO_FILES "${CBF_DATADIRO}/*")
+-foreach(loop_file ${CBF_DATADIRI_FILES} )
+-  if (NOT "${loop_file}" MATCHES "[*.]md5")
+-    file(MD5 "${loop_file}" loop_file_md5)
+-    file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1)
+-    if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+-      message(WARNINH "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|")
+-    endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+-  endif (NOT "${loop_file}" MATCHES "[*.]md5")
+-endforeach(loop_file)
+-foreach(loop_file ${CBF_DATADIRO_FILES} )
+-  if (NOT "${loop_file}" MATCHES "[*.]md5")
+-    file(MD5 "${loop_file}" loop_file_md5)
+-    file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1)
+-    if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+-      message(WARNING "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|")
+-    endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}"))
+-  endif (NOT "${loop_file}" MATCHES "[*.]md5")
+-endforeach(loop_file)
+ 
+ 
+ #
+@@ -775,7 +710,7 @@ add_library(cbf_shared SHARED  ${CBF_C_SOURCES})
+ set_target_properties(cbf_shared PROPERTIES OUTPUT_NAME "cbf")
+ set_target_properties(cbf_shared PROPERTIES LINKER_LANGUAGE C)
+ set_target_properties(cbf_shared PROPERTIES SOVERSION "${CBF_APIVERSION}")
+-target_link_libraries(cbf_shared ${CBF_HDF5_LIBRARY_PATH})
++target_link_libraries(cbf_shared hdf5)
+ 
+ #
+ # Build the static and shared IMG libraries
+@@ -791,7 +726,7 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CBFlib_BINARY_DIR}/solib")
+ add_library(img_shared SHARED  ${CBF__EXAMPLES}/img.c)
+ set_target_properties(img_shared PROPERTIES OUTPUT_NAME "img")
+ set_target_properties(img_shared PROPERTIES LINKER_LANGUAGE C)
+-target_link_libraries(img_shared ${CBF_HDF5_LIBRARY_PATH})
++target_link_libraries(img_shared hdf5 m )
+ 
+ 
+ #
+@@ -829,26 +764,6 @@ target_link_libraries(fcb_shared ${CBF_HDF5_LIBRARY_PATH})
+ #
+ #  C and C++ examples
+ #
+-CBF_ADD_C_EXAMPLE(convert_image "${CBF__EXAMPLES}" "" "img_static")
+-CBF_ADD_C_EXAMPLE(convert_minicbf "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(makecbf "${CBF__EXAMPLES}" "" "img_static")
+-CBF_ADD_C_EXAMPLE(adscimg2cbf "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/adscimg2cbf_sub.c" "")
+-CBF_ADD_C_EXAMPLE(cbf2adscimg "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/cbf2adscimg_sub.c" "")
+-CBF_ADD_C_EXAMPLE(cbf_tail "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(changtestcompression "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(img2cif "${CBF__EXAMPLES}" "" "img_static")
+-CBF_ADD_C_EXAMPLE(cif2cbf "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(cbf2nexus "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(minicbf2nexus "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(cbf_template_t "${CBF__DECTRIS_EXAMPLES}" "" "")
+-CBF_ADD_CXX_EXAMPLE(testcell "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_CXX_EXAMPLE(sauter_test "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(sequence_match "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(tiff2cbf "${CBF__EXAMPLES}" "${CBF__EXT_PKG}/${CBF_TIFF}/libtiff/tif_sprint.c" "${CBF_TIFF_LIBRARY_PATH}")
+-CBF_ADD_C_EXAMPLE(testulp "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(testhdf5 "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(testtree "${CBF__EXAMPLES}" "" "")
+-CBF_ADD_C_EXAMPLE(testalloc "${CBF__EXAMPLES}" "" "")
+ 
+ 
+ 
+@@ -876,26 +791,9 @@ target_link_libraries(test_xds_binary     fcb_static)
+ #
+ # install
+ #
+-install (TARGETS makecbf DESTINATION bin)
+-install (TARGETS img2cif DESTINATION bin)
+-install (TARGETS cif2cbf DESTINATION bin)
+-install (TARGETS adscimg2cbf DESTINATION bin)
+-install (TARGETS cbf2adscimg DESTINATION bin)
+-install (TARGETS changtestcompression DESTINATION bin)
+-install (TARGETS convert_image DESTINATION bin)
+-install (TARGETS convert_minicbf DESTINATION bin)
+-install (TARGETS minicbf2nexus DESTINATION bin)
+-install (TARGETS cbf_template_t DESTINATION bin)
+-install (TARGETS testcell DESTINATION bin)
+-install (TARGETS sauter_test DESTINATION bin)
+-install (TARGETS sequence_match DESTINATION bin)
+-install (TARGETS tiff2cbf DESTINATION bin)
+-install (TARGETS cbf_static DESTINATION lib)
+-install (TARGETS cbf_shared DESTINATION lib)
+-install (TARGETS fcb_static DESTINATION lib)
+-install (TARGETS fcb_shared DESTINATION lib)
+-install (TARGETS img_static DESTINATION lib)
+-install (TARGETS img_shared DESTINATION lib)
++install (TARGETS cbf_shared DESTINATION lib${LIB_SUFFIX})
++install (TARGETS fcb_shared DESTINATION lib${LIB_SUFFIX})
++install (TARGETS img_shared DESTINATION lib${LIB_SUFFIX})
+ install (DIRECTORY ${CBF__INCLUDE}/ DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h")
+ install (DIRECTORY ${CBF__BIN_INCLUDE}/* DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h")
+ 
+@@ -914,10 +812,6 @@ endif ()
+ #
+ # tests  -- to be extended
+ #
+-add_test(NAME cbftest_makecbf
+-  COMMAND ${CMAKE_COMMAND}
+-    -DCMD1=$<TARGET_FILE:makecbf> -DARG11=${CBF_DATADIRI}/example.mar2300 -DARG12=makecbf.cbf
+-    -P ${CMAKE_CURRENT_SOURCE_DIR}/runcommands.cmake)
+ add_test(cbftest_testalloc ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testalloc)
+ add_test(cbftest_testhdf5 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testhdf5)
+ add_test(cbftest_testtree ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testtree)
diff --git a/sci-libs/cbflib/metadata.xml b/sci-libs/cbflib/metadata.xml
new file mode 100644
index 000000000000..e0080f59068f
--- /dev/null
+++ b/sci-libs/cbflib/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription>
+CBFLIB is a library of ANSI-C functions providing a simple mechanism
+for accessing Crystallographic Binary Files (CBF files) and Image-supporting
+CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for
+mmCIF files. Starting with this release, CBFLIB performs validation checks
+on reading of a CBF. If a dictionary is provided, values will be validated
+against dictionary ranges and enumerations. Tags missing under parent-child
+relationships or category key requirements will be reported. CBFlib provides
+functions to create, read, modify and write CBF binary data files and imgCIF
+ASCII data files.
+</longdescription>
+	<upstream>
+		<remote-id type="sourceforge">cbflib</remote-id>
+	</upstream>
+</pkgmetadata>