diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index aa0f3083bca2..ffbf674a0ed3 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,34 +1,34 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.3 +DISTVERSION= 0.7.5 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities WWW= https://gemmi.readthedocs.io/en/latest/ \ https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt USES= cmake:testing compiler:c++20-lang # tests don't run, see https://github.com/project-gemmi/gemmi/issues/231 USE_GITHUB= yes GH_ACCOUNT= project-gemmi CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DCMAKE_CXX_VISIBILITY_PRESET=default # for the Python extension science/py-gemmi to see all symbols CMAKE_TESTING_TARGET= check OPTIONS_DEFINE= FORTRAN FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= USE_FORTRAN FORTRAN_BROKEN= project option doesn't do anything, see https://github.com/project-gemmi/gemmi/issues/232 # tests as of 0.7.3 (run work/.build/cpptest): # [doctest] test cases: 14 | 14 passed | 0 failed | 0 skipped # [doctest] assertions: 129 | 129 passed | 0 failed | # [doctest] Status: SUCCESS! .include diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo index a7884ddf53a9..d1bd408fcecf 100644 --- a/science/gemmi/distinfo +++ b/science/gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753139349 -SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 -SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 +TIMESTAMP = 1772523212 +SHA256 (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3 +SIZE (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 2096501 diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist index 965571f541a2..5fe81587562f 100644 --- a/science/gemmi/pkg-plist +++ b/science/gemmi/pkg-plist @@ -1,264 +1,271 @@ bin/gemmi +include/gemmi/ace_cc.hpp +include/gemmi/ace_graph.hpp +include/gemmi/acedrg_tables.hpp include/gemmi/addends.hpp include/gemmi/align.hpp include/gemmi/assembly.hpp include/gemmi/asudata.hpp include/gemmi/asumask.hpp include/gemmi/atof.hpp include/gemmi/atox.hpp include/gemmi/bessel.hpp include/gemmi/binner.hpp include/gemmi/blob.hpp include/gemmi/bond_idx.hpp include/gemmi/c4322.hpp include/gemmi/calculate.hpp include/gemmi/ccp4.hpp include/gemmi/cellred.hpp include/gemmi/chemcomp.hpp include/gemmi/cif.hpp include/gemmi/cif2mtz.hpp include/gemmi/cifdoc.hpp include/gemmi/contact.hpp include/gemmi/crd.hpp include/gemmi/ddl.hpp include/gemmi/dencalc.hpp include/gemmi/dirwalk.hpp include/gemmi/dssp.hpp include/gemmi/ecalc.hpp include/gemmi/eig3.hpp include/gemmi/elem.hpp include/gemmi/enumstr.hpp include/gemmi/fail.hpp include/gemmi/fileutil.hpp +include/gemmi/flat.hpp include/gemmi/floodfill.hpp include/gemmi/formfact.hpp include/gemmi/fourier.hpp include/gemmi/fprime.hpp include/gemmi/fstream.hpp +include/gemmi/glob.hpp include/gemmi/grid.hpp include/gemmi/gz.hpp include/gemmi/input.hpp include/gemmi/intensit.hpp include/gemmi/interop.hpp include/gemmi/it92.hpp include/gemmi/iterator.hpp include/gemmi/json.hpp include/gemmi/levmar.hpp include/gemmi/linkhunt.hpp include/gemmi/logger.hpp include/gemmi/math.hpp include/gemmi/metadata.hpp include/gemmi/mmcif.hpp include/gemmi/mmcif_impl.hpp include/gemmi/mmdb.hpp include/gemmi/mmread.hpp include/gemmi/mmread_gz.hpp include/gemmi/model.hpp include/gemmi/modify.hpp include/gemmi/monlib.hpp include/gemmi/mtz.hpp include/gemmi/mtz2cif.hpp include/gemmi/neighbor.hpp include/gemmi/neutron92.hpp include/gemmi/numb.hpp include/gemmi/pdb.hpp include/gemmi/pdb_id.hpp include/gemmi/pirfasta.hpp include/gemmi/polyheur.hpp +include/gemmi/pymol_select.hpp include/gemmi/qcp.hpp include/gemmi/read_cif.hpp include/gemmi/recgrid.hpp include/gemmi/reciproc.hpp include/gemmi/refln.hpp include/gemmi/resinfo.hpp include/gemmi/riding_h.hpp include/gemmi/scaling.hpp include/gemmi/select.hpp include/gemmi/seqalign.hpp include/gemmi/seqid.hpp include/gemmi/seqtools.hpp include/gemmi/serialize.hpp include/gemmi/sfcalc.hpp include/gemmi/small.hpp include/gemmi/smcif.hpp include/gemmi/solmask.hpp include/gemmi/span.hpp include/gemmi/sprintf.hpp include/gemmi/stats.hpp include/gemmi/symmetry.hpp include/gemmi/third_party/fast_float.h +include/gemmi/third_party/half.hpp include/gemmi/third_party/pocketfft_hdronly.h include/gemmi/third_party/tao/LICENSE include/gemmi/third_party/tao/NOTES include/gemmi/third_party/tao/pegtl.hpp include/gemmi/third_party/tao/pegtl/analysis/analyze_cycles.hpp include/gemmi/third_party/tao/pegtl/analysis/counted.hpp include/gemmi/third_party/tao/pegtl/analysis/generic.hpp include/gemmi/third_party/tao/pegtl/analysis/grammar_info.hpp include/gemmi/third_party/tao/pegtl/analysis/insert_guard.hpp include/gemmi/third_party/tao/pegtl/analysis/rule_info.hpp include/gemmi/third_party/tao/pegtl/analysis/rule_type.hpp include/gemmi/third_party/tao/pegtl/analyze.hpp include/gemmi/third_party/tao/pegtl/apply_mode.hpp include/gemmi/third_party/tao/pegtl/argv_input.hpp include/gemmi/third_party/tao/pegtl/ascii.hpp include/gemmi/third_party/tao/pegtl/buffer_input.hpp include/gemmi/third_party/tao/pegtl/change_action.hpp include/gemmi/third_party/tao/pegtl/change_action_and_state.hpp include/gemmi/third_party/tao/pegtl/change_action_and_states.hpp include/gemmi/third_party/tao/pegtl/change_control.hpp include/gemmi/third_party/tao/pegtl/change_state.hpp include/gemmi/third_party/tao/pegtl/change_states.hpp include/gemmi/third_party/tao/pegtl/config.hpp include/gemmi/third_party/tao/pegtl/cstream_input.hpp include/gemmi/third_party/tao/pegtl/disable_action.hpp include/gemmi/third_party/tao/pegtl/discard_input.hpp include/gemmi/third_party/tao/pegtl/discard_input_on_failure.hpp include/gemmi/third_party/tao/pegtl/discard_input_on_success.hpp include/gemmi/third_party/tao/pegtl/enable_action.hpp include/gemmi/third_party/tao/pegtl/eol.hpp include/gemmi/third_party/tao/pegtl/eol_pair.hpp include/gemmi/third_party/tao/pegtl/file_input.hpp include/gemmi/third_party/tao/pegtl/input_error.hpp include/gemmi/third_party/tao/pegtl/internal/action.hpp include/gemmi/third_party/tao/pegtl/internal/action_input.hpp include/gemmi/third_party/tao/pegtl/internal/alnum.hpp include/gemmi/third_party/tao/pegtl/internal/alpha.hpp include/gemmi/third_party/tao/pegtl/internal/always_false.hpp include/gemmi/third_party/tao/pegtl/internal/any.hpp include/gemmi/third_party/tao/pegtl/internal/apply.hpp include/gemmi/third_party/tao/pegtl/internal/apply0.hpp include/gemmi/third_party/tao/pegtl/internal/apply0_single.hpp include/gemmi/third_party/tao/pegtl/internal/apply_single.hpp include/gemmi/third_party/tao/pegtl/internal/at.hpp include/gemmi/third_party/tao/pegtl/internal/bof.hpp include/gemmi/third_party/tao/pegtl/internal/bol.hpp include/gemmi/third_party/tao/pegtl/internal/bump.hpp include/gemmi/third_party/tao/pegtl/internal/bump_help.hpp include/gemmi/third_party/tao/pegtl/internal/bytes.hpp include/gemmi/third_party/tao/pegtl/internal/control.hpp include/gemmi/third_party/tao/pegtl/internal/cr_crlf_eol.hpp include/gemmi/third_party/tao/pegtl/internal/cr_eol.hpp include/gemmi/third_party/tao/pegtl/internal/crlf_eol.hpp include/gemmi/third_party/tao/pegtl/internal/cstream_reader.hpp include/gemmi/third_party/tao/pegtl/internal/cstring_reader.hpp include/gemmi/third_party/tao/pegtl/internal/demangle.hpp include/gemmi/third_party/tao/pegtl/internal/demangle_cxxabi.hpp include/gemmi/third_party/tao/pegtl/internal/demangle_nop.hpp include/gemmi/third_party/tao/pegtl/internal/demangle_sanitise.hpp include/gemmi/third_party/tao/pegtl/internal/disable.hpp include/gemmi/third_party/tao/pegtl/internal/discard.hpp include/gemmi/third_party/tao/pegtl/internal/dusel_mode.hpp include/gemmi/third_party/tao/pegtl/internal/duseltronik.hpp include/gemmi/third_party/tao/pegtl/internal/enable.hpp include/gemmi/third_party/tao/pegtl/internal/endian.hpp include/gemmi/third_party/tao/pegtl/internal/endian_gcc.hpp include/gemmi/third_party/tao/pegtl/internal/endian_win.hpp include/gemmi/third_party/tao/pegtl/internal/eof.hpp include/gemmi/third_party/tao/pegtl/internal/eol.hpp include/gemmi/third_party/tao/pegtl/internal/eolf.hpp include/gemmi/third_party/tao/pegtl/internal/file_mapper_posix.hpp include/gemmi/third_party/tao/pegtl/internal/file_opener.hpp include/gemmi/third_party/tao/pegtl/internal/file_reader.hpp include/gemmi/third_party/tao/pegtl/internal/has_apply.hpp include/gemmi/third_party/tao/pegtl/internal/has_apply0.hpp include/gemmi/third_party/tao/pegtl/internal/has_match.hpp include/gemmi/third_party/tao/pegtl/internal/identifier.hpp include/gemmi/third_party/tao/pegtl/internal/if_apply.hpp include/gemmi/third_party/tao/pegtl/internal/if_missing.hpp include/gemmi/third_party/tao/pegtl/internal/if_must.hpp include/gemmi/third_party/tao/pegtl/internal/if_must_else.hpp include/gemmi/third_party/tao/pegtl/internal/if_then_else.hpp include/gemmi/third_party/tao/pegtl/internal/input_pair.hpp include/gemmi/third_party/tao/pegtl/internal/integer_sequence.hpp include/gemmi/third_party/tao/pegtl/internal/istream_reader.hpp include/gemmi/third_party/tao/pegtl/internal/istring.hpp include/gemmi/third_party/tao/pegtl/internal/iterator.hpp include/gemmi/third_party/tao/pegtl/internal/lf_crlf_eol.hpp include/gemmi/third_party/tao/pegtl/internal/lf_eol.hpp include/gemmi/third_party/tao/pegtl/internal/list.hpp include/gemmi/third_party/tao/pegtl/internal/list_must.hpp include/gemmi/third_party/tao/pegtl/internal/list_tail.hpp include/gemmi/third_party/tao/pegtl/internal/list_tail_pad.hpp include/gemmi/third_party/tao/pegtl/internal/marker.hpp include/gemmi/third_party/tao/pegtl/internal/must.hpp include/gemmi/third_party/tao/pegtl/internal/not_at.hpp include/gemmi/third_party/tao/pegtl/internal/one.hpp include/gemmi/third_party/tao/pegtl/internal/opt.hpp include/gemmi/third_party/tao/pegtl/internal/pad.hpp include/gemmi/third_party/tao/pegtl/internal/pad_opt.hpp include/gemmi/third_party/tao/pegtl/internal/peek_char.hpp include/gemmi/third_party/tao/pegtl/internal/peek_mask_uint.hpp include/gemmi/third_party/tao/pegtl/internal/peek_mask_uint8.hpp include/gemmi/third_party/tao/pegtl/internal/peek_uint.hpp include/gemmi/third_party/tao/pegtl/internal/peek_uint8.hpp include/gemmi/third_party/tao/pegtl/internal/peek_utf16.hpp include/gemmi/third_party/tao/pegtl/internal/peek_utf32.hpp include/gemmi/third_party/tao/pegtl/internal/peek_utf8.hpp include/gemmi/third_party/tao/pegtl/internal/pegtl_string.hpp include/gemmi/third_party/tao/pegtl/internal/plus.hpp include/gemmi/third_party/tao/pegtl/internal/raise.hpp include/gemmi/third_party/tao/pegtl/internal/range.hpp include/gemmi/third_party/tao/pegtl/internal/ranges.hpp include/gemmi/third_party/tao/pegtl/internal/read_uint.hpp include/gemmi/third_party/tao/pegtl/internal/rematch.hpp include/gemmi/third_party/tao/pegtl/internal/rep.hpp include/gemmi/third_party/tao/pegtl/internal/rep_min.hpp include/gemmi/third_party/tao/pegtl/internal/rep_min_max.hpp include/gemmi/third_party/tao/pegtl/internal/rep_opt.hpp include/gemmi/third_party/tao/pegtl/internal/require.hpp include/gemmi/third_party/tao/pegtl/internal/result_on_found.hpp include/gemmi/third_party/tao/pegtl/internal/rules.hpp include/gemmi/third_party/tao/pegtl/internal/seq.hpp include/gemmi/third_party/tao/pegtl/internal/skip_control.hpp include/gemmi/third_party/tao/pegtl/internal/sor.hpp include/gemmi/third_party/tao/pegtl/internal/star.hpp include/gemmi/third_party/tao/pegtl/internal/star_must.hpp include/gemmi/third_party/tao/pegtl/internal/state.hpp include/gemmi/third_party/tao/pegtl/internal/string.hpp include/gemmi/third_party/tao/pegtl/internal/trivial.hpp include/gemmi/third_party/tao/pegtl/internal/try_catch_type.hpp include/gemmi/third_party/tao/pegtl/internal/until.hpp include/gemmi/third_party/tao/pegtl/istream_input.hpp include/gemmi/third_party/tao/pegtl/match.hpp include/gemmi/third_party/tao/pegtl/memory_input.hpp include/gemmi/third_party/tao/pegtl/mmap_input.hpp include/gemmi/third_party/tao/pegtl/normal.hpp include/gemmi/third_party/tao/pegtl/nothing.hpp include/gemmi/third_party/tao/pegtl/parse.hpp include/gemmi/third_party/tao/pegtl/parse_error.hpp include/gemmi/third_party/tao/pegtl/position.hpp include/gemmi/third_party/tao/pegtl/read_input.hpp include/gemmi/third_party/tao/pegtl/require_apply.hpp include/gemmi/third_party/tao/pegtl/require_apply0.hpp include/gemmi/third_party/tao/pegtl/rewind_mode.hpp include/gemmi/third_party/tao/pegtl/rules.hpp include/gemmi/third_party/tao/pegtl/string_input.hpp include/gemmi/third_party/tao/pegtl/tracking_mode.hpp include/gemmi/third_party/tao/pegtl/uint16.hpp include/gemmi/third_party/tao/pegtl/uint32.hpp include/gemmi/third_party/tao/pegtl/uint64.hpp include/gemmi/third_party/tao/pegtl/uint8.hpp include/gemmi/third_party/tao/pegtl/utf16.hpp include/gemmi/third_party/tao/pegtl/utf32.hpp include/gemmi/third_party/tao/pegtl/utf8.hpp include/gemmi/third_party/tao/pegtl/version.hpp include/gemmi/third_party/tinydir.h include/gemmi/to_chemcomp.hpp include/gemmi/to_cif.hpp include/gemmi/to_json.hpp include/gemmi/to_mmcif.hpp include/gemmi/to_pdb.hpp include/gemmi/topo.hpp include/gemmi/twin.hpp include/gemmi/unitcell.hpp include/gemmi/utf.hpp include/gemmi/util.hpp include/gemmi/version.hpp include/gemmi/xds2mtz.hpp include/gemmi/xds_ascii.hpp lib/cmake/gemmi/gemmi-config-version.cmake lib/cmake/gemmi/gemmi-config.cmake lib/cmake/gemmi/gemmi-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/gemmi/gemmi-targets.cmake lib/libgemmi_cpp.so diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 9e7f9f8d7544..4efea34b369e 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,42 +1,42 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.3 +DISTVERSION= 0.7.5 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Macromolecular crystallography library and utilities WWW= https://gemmi.readthedocs.io/en/latest/ \ https://github.com/project-gemmi/gemmi LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nanobind>0:devel/py-nanobind@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ pybind11>=2.6:devel/pybind11 LIB_DEPENDS= libgemmi_cpp.so:science/gemmi TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} USES= cmake compiler:c++17-lang localbase:ldflags python USE_PYTHON= flavors USE_GITHUB= yes GH_ACCOUNT= project-gemmi CMAKE_ON= USE_PYTHON CMAKE_OFF= BUILD_GEMMI_PROGRAM STANDALONE_PYTHON_MODULE CMAKE_ARGS= -DPython_EXECUTABLE=${PYTHON_CMD} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${BUILD_WRKSRC}/tests PLIST_SUB= VER=${PORTVERSION} do-test: @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/ # tests as of 0.7.3: test 'test_syntax_error' fails with syntax error, see https://github.com/project-gemmi/gemmi/issues/384 .include diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index b40d35b8cada..8bf9d039c207 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753140186 -SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 -SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 +TIMESTAMP = 1772523199 +SHA256 (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3 +SIZE (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 2096501 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index 62637e7014cd..ff9e347bd9b2 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,204 +1,204 @@ ---- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC +--- CMakeLists.txt.orig 2026-03-02 03:06:09 UTC +++ CMakeLists.txt @@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1" gemmi_version_str ${gemmi_version_line}) -project(gemmi LANGUAGES C CXX VERSION ${gemmi_version_str}) +project(gemmi_python LANGUAGES C CXX VERSION ${gemmi_version_str}) message(STATUS "Gemmi version ${PROJECT_VERSION}") include(GNUInstallDirs) # for CMAKE_INSTALL_LIBDIR, etc @@ -18,6 +18,8 @@ endif() #set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}") endif() +find_package(gemmi REQUIRED) + option(BUILD_SHARED_LIBS "Build shared library" ON) option(BUILD_GEMMI_PROGRAM "Build gemmi command-line program" ON) option(INSTALL_DEV_FILES "Install C++ headers, cmake configs, static lib" ON) -@@ -203,70 +205,6 @@ endif() +@@ -203,70 +205,7 @@ endif() # target_link_libraries(fgemmi PRIVATE cgemmi) #endif() -add_library(gemmi_headers INTERFACE) -add_library(gemmi::headers ALIAS gemmi_headers) -target_include_directories(gemmi_headers INTERFACE - "$" - "$") -target_compile_features(gemmi_headers INTERFACE cxx_std_14) -set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers) -- + -add_library(gemmi_cpp -- src/align.cpp src/assembly.cpp src/calculate.cpp src/ccp4.cpp -- src/crd.cpp src/ddl.cpp src/eig3.cpp src/fprime.cpp src/gz.cpp +- src/ace_cc.cpp src/ace_graph.cpp src/acedrg_tables.cpp src/align.cpp src/assembly.cpp src/calculate.cpp src/ccp4.cpp +- src/crd.cpp src/ddl.cpp src/eig3.cpp src/flat.cpp src/fprime.cpp src/gz.cpp - src/intensit.cpp src/json.cpp src/mmcif.cpp src/mmread_gz.cpp - src/monlib.cpp src/mtz.cpp src/mtz2cif.cpp - src/pdb.cpp src/polyheur.cpp src/read_cif.cpp - src/resinfo.cpp src/riding_h.cpp - src/select.cpp src/sprintf.cpp src/dssp.cpp src/symmetry.cpp - src/to_json.cpp src/to_mmcif.cpp src/to_pdb.cpp src/topo.cpp - src/xds_ascii.cpp) -add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp) -set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON) -#set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden) -target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD) -target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") - -if (BUILD_SHARED_LIBS) - target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED) - if (ADD_SOVERSION) - set_target_properties(gemmi_cpp PROPERTIES VERSION ${PROJECT_VERSION} - SOVERSION "0") - endif() -endif() -target_link_libraries(gemmi_cpp PUBLIC gemmi_headers) - -if (FETCH_ZLIB_NG) - target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) - target_link_libraries(gemmi_cpp PRIVATE zlib) -elseif (ZLIB_NG_FOUND) - target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1) - target_link_libraries(gemmi_cpp PRIVATE ZLIB_NG::ZLIB_NG) -elseif (ZLIB_FOUND) - target_link_libraries(gemmi_cpp PRIVATE ZLIB::ZLIB) -else() - target_sources(gemmi_cpp PRIVATE - "third_party/zlib/adler32.c" - "third_party/zlib/crc32.c" - "third_party/zlib/gzlib.c" - "third_party/zlib/gzread.c" - "third_party/zlib/inflate.c" - "third_party/zlib/inftrees.c" - "third_party/zlib/inffast.c" - "third_party/zlib/zutil.c") - check_include_file(unistd.h has_unistd_h) - target_compile_definitions(gemmi_cpp PRIVATE NO_GZCOMPRESS=1 DYNAMIC_CRC_TABLE=1) - if (has_unistd_h) - target_compile_definitions(gemmi_cpp PRIVATE Z_HAVE_UNISTD_H=1) - endif() - target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party/zlib") - if (CMAKE_CXX_COMPILER_ID MATCHES "MSVC") - # /wd4267 - conversion from 'size_t' to 'unsigned int', possible loss of data - target_compile_options(gemmi_cpp PRIVATE /wd4267) - endif() -endif() - - ### programs from prog/ ### add_library(options OBJECT prog/options.cpp) -@@ -282,7 +220,7 @@ function(add_single_prog target) +@@ -282,7 +221,7 @@ function(add_single_prog target) cmake_parse_arguments(arg "" "ADD_SRC" "" ${ARGN}) add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC} $) - target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp) + target_link_libraries(gemmi-${target} PRIVATE gemmi) target_include_directories(gemmi-${target} PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") endfunction() -@@ -337,7 +275,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) +@@ -337,7 +276,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog) prog/wcn.cpp prog/xds2mtz.cpp $) add_executable(gemmi::prog ALIAS gemmi_prog) -target_link_libraries(gemmi_prog PRIVATE gemmi_cpp) +target_link_libraries(gemmi_prog PRIVATE gemmi::gemmi_cpp) target_include_directories(gemmi_prog PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) set_target_properties(gemmi_prog PROPERTIES OUTPUT_NAME gemmi EXPORT_NAME prog) -@@ -377,17 +315,17 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP +@@ -377,17 +316,17 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP add_executable(cpptest EXCLUDE_FROM_ALL tests/main.cpp tests/cif.cpp tests/windowsh.cpp) target_compile_definitions(cpptest PRIVATE USE_STD_SNPRINTF=1) -target_link_libraries(cpptest PRIVATE gemmi_cpp) +target_link_libraries(cpptest PRIVATE gemmi) target_include_directories(cpptest PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party") add_executable(doc_example EXCLUDE_FROM_ALL docs/code/sym.cpp docs/code/elem.cpp docs/code/resinfo.cpp docs/code/cell.cpp docs/code/mutate.cpp) -target_link_libraries(doc_example PRIVATE gemmi_cpp) +target_link_libraries(doc_example PRIVATE gemmi) add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) target_link_libraries(doc_example2 PRIVATE gemmi_headers) add_executable(doc_newmtz EXCLUDE_FROM_ALL docs/code/newmtz.cpp) -target_link_libraries(doc_newmtz PRIVATE gemmi_cpp) +target_link_libraries(doc_newmtz PRIVATE gemmi) # always compile these tests with assertions enabled if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") -@@ -395,14 +333,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu +@@ -395,14 +334,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu endif() add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) -target_link_libraries(test_disulf PRIVATE gemmi_cpp) +target_link_libraries(test_disulf PRIVATE gemmi) # auth_label requires C++17 for add_executable(auth_label EXCLUDE_FROM_ALL examples/auth_label.cpp) -target_link_libraries(auth_label PRIVATE gemmi_cpp) +target_link_libraries(auth_label PRIVATE gemmi) add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp) -target_link_libraries(check_conn PRIVATE gemmi_cpp) +target_link_libraries(check_conn PRIVATE gemmi) enable_testing() -@@ -439,7 +377,7 @@ if (benchmark_FOUND) +@@ -439,7 +378,7 @@ if (benchmark_FOUND) foreach(b stoi elem mod niggli pdb resinfo round sym writecif) add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp) if (b MATCHES "elem|resinfo|pdb|sym|writecif") - target_link_libraries(${b}-bm PRIVATE gemmi_cpp) + target_link_libraries(${b}-bm PRIVATE gemmi) endif() target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -480,11 +418,11 @@ if (USE_PYTHON) +@@ -484,11 +423,11 @@ if (USE_PYTHON) python/unitcell.cpp python/write.cpp) if (STANDALONE_PYTHON_MODULE) - target_sources(gemmi_py PRIVATE $) - get_target_property(_gemmi_cpp_libs gemmi_cpp LINK_LIBRARIES) + target_sources(gemmi_py PRIVATE gemmi::gemmi_cpp) + get_target_property(_gemmi_cpp_libs gemmi::gemmi_cpp LINK_LIBRARIES) set_property(TARGET gemmi_py APPEND PROPERTY LINK_LIBRARIES ${_gemmi_cpp_libs}) else() - target_link_libraries(gemmi_py PRIVATE gemmi_cpp) + target_link_libraries(gemmi_py PRIVATE gemmi::gemmi_cpp) endif() set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi_ext) if (CMAKE_CONFIGURATION_TYPES) -@@ -567,19 +505,19 @@ endif() +@@ -577,19 +516,19 @@ endif() install(TARGETS gemmi_prog EXPORT GemmiTargets) endif() -if (INSTALL_DEV_FILES) +#if (INSTALL_DEV_FILES) # In CMake 3.23 we'll be able to use FILE_SET to install the headers - install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}") - install(TARGETS gemmi_headers gemmi_cpp EXPORT GemmiTargets) - install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi:: - DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") - install(FILES - "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake" - "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake" - DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") -elseif (BUILD_SHARED_LIBS AND BUILD_GEMMI_PROGRAM) - install(TARGETS gemmi_cpp) -endif() + #install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}") + #install(TARGETS gemmi_headers gemmi_cpp EXPORT GemmiTargets) + #install(EXPORT GemmiTargets FILE gemmi-targets.cmake NAMESPACE gemmi:: + # DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") + #install(FILES + # "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config.cmake" + # "${CMAKE_CURRENT_BINARY_DIR}/gemmi-config-version.cmake" + # DESTINATION "${GEMMI_INSTALL_CMAKEDIR}") +#elseif (BUILD_SHARED_LIBS AND BUILD_GEMMI_PROGRAM) +# install(TARGETS gemmi_cpp) +#endif() if (USE_PYTHON) if (DEFINED PYTHON_INSTALL_DIR) diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist index 9201705db9d6..44fa19c96c89 100644 --- a/science/py-gemmi/pkg-plist +++ b/science/py-gemmi/pkg-plist @@ -1,31 +1,32 @@ %%PYTHON_SITELIBDIR%%/gemmi/__init__.py %%PYTHON_SITELIBDIR%%/gemmi/__init__.pyi %%PYTHON_SITELIBDIR%%/gemmi/cif.pyi %%PYTHON_SITELIBDIR%%/gemmi/examples/aafreq.py %%PYTHON_SITELIBDIR%%/gemmi/examples/ccd_gi.py %%PYTHON_SITELIBDIR%%/gemmi/examples/ccd_subgraph.py %%PYTHON_SITELIBDIR%%/gemmi/examples/cif_i_sigi.py %%PYTHON_SITELIBDIR%%/gemmi/examples/col_order.py %%PYTHON_SITELIBDIR%%/gemmi/examples/from_json.py %%PYTHON_SITELIBDIR%%/gemmi/examples/long_geom.py %%PYTHON_SITELIBDIR%%/gemmi/examples/map2mtz.py %%PYTHON_SITELIBDIR%%/gemmi/examples/maskcheck.py %%PYTHON_SITELIBDIR%%/gemmi/examples/maskdiff.py %%PYTHON_SITELIBDIR%%/gemmi/examples/matthews.py %%PYTHON_SITELIBDIR%%/gemmi/examples/merge_mtz_mmcif.py %%PYTHON_SITELIBDIR%%/gemmi/examples/monomers.py %%PYTHON_SITELIBDIR%%/gemmi/examples/mtrix_iso.py %%PYTHON_SITELIBDIR%%/gemmi/examples/mtz_i_sigi.py %%PYTHON_SITELIBDIR%%/gemmi/examples/multiproc.py %%PYTHON_SITELIBDIR%%/gemmi/examples/patterson_slice.py %%PYTHON_SITELIBDIR%%/gemmi/examples/qq-plot.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_gather.py %%PYTHON_SITELIBDIR%%/gemmi/examples/rama_plot.py %%PYTHON_SITELIBDIR%%/gemmi/examples/read_cif.py %%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py %%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py %%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py %%PYTHON_SITELIBDIR%%/gemmi/examples/to_rdkit.py %%PYTHON_SITELIBDIR%%/gemmi/examples/weight.py +%%PYTHON_SITELIBDIR%%/gemmi/fetch.py %%PYTHON_SITELIBDIR%%/gemmi/gemmi_ext%%PYTHON_TAG%%.so %%PYTHON_SITELIBDIR%%/gemmi/py.typed