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science/{,py-}gemmi: update 0.7.3 → 0.7.5

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This commit is contained in:
Yuri Victorovich
2026-03-03 00:04:42 -08:00
parent 1dee824a42
commit 07caffc6c6
7 changed files with 28 additions and 20 deletions
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science/gemmi/Makefile
+1 -1
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@@ -1,6 +1,6 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
DISTVERSION= 0.7.3
DISTVERSION= 0.7.5
CATEGORIES= science # chemistry
MAINTAINER= yuri@FreeBSD.org
science/gemmi/distinfo
+3 -3
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@@ -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
science/gemmi/pkg-plist
+7
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@@ -1,4 +1,7 @@
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
@@ -30,11 +33,13 @@ 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
@@ -65,6 +70,7 @@ 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
@@ -87,6 +93,7 @@ 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
science/py-gemmi/Makefile
+1 -1
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@@ -1,6 +1,6 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
DISTVERSION= 0.7.3
DISTVERSION= 0.7.5
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
science/py-gemmi/distinfo
+3 -3
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@@ -1,3 +1,3 @@
TIMESTAMP = 1753140186
SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3
SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234
TIMESTAMP = 1772523199
SHA256 (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3
SIZE (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 2096501
science/py-gemmi/files/patch-CMakeLists.txt
+12 -12
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@@ -1,4 +1,4 @@
--- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC
--- CMakeLists.txt.orig 2026-03-02 03:06:09 UTC
+++ CMakeLists.txt
@@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de
string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1"
@@ -18,7 +18,7 @@
option(BUILD_SHARED_LIBS "Build shared library" ON)
option(BUILD_GEMMI_PROGRAM "Build gemmi command-line program" ON)
option(INSTALL_DEV_FILES "Install C++ headers, cmake configs, static lib" ON)
@@ -203,70 +205,6 @@ endif()
@@ -203,70 +205,7 @@ endif()
# target_link_libraries(fgemmi PRIVATE cgemmi)
#endif()
@@ -29,10 +29,10 @@
- "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
-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
@@ -89,7 +89,7 @@
### 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}
$<TARGET_OBJECTS:options>)
@@ -98,7 +98,7 @@
target_include_directories(gemmi-${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
$<TARGET_OBJECTS:options>)
add_executable(gemmi::prog ALIAS gemmi_prog)
@@ -107,7 +107,7 @@
target_include_directories(gemmi_prog PRIVATE "${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)
@@ -128,7 +128,7 @@
# 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)
@@ -146,7 +146,7 @@
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")
@@ -155,7 +155,7 @@
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)
@@ -170,7 +170,7 @@
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()
science/py-gemmi/pkg-plist
+1
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@@ -27,5 +27,6 @@
%%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