Date: Tue, 03 Mar 2026 08:05:28 +0000
From: Yuri Victorovich <yuri@FreeBSD.org>
To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org
Subject: git: 07caffc6c652 - main - science/{,py-}gemmi: update 0.=?utf-8?Q?7.3 =E2=86=92?= 0.7.5
Message-ID: <69a69648.23d6b.6b726949@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=07caffc6c652df95c2560a879bdc6d06f260d81d commit 07caffc6c652df95c2560a879bdc6d06f260d81d Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-03-03 08:04:42 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-03-03 08:05:23 +0000 science/{,py-}gemmi: update 0.7.3 → 0.7.5 --- science/gemmi/Makefile | 2 +- science/gemmi/distinfo | 6 +++--- science/gemmi/pkg-plist | 7 +++++++ science/py-gemmi/Makefile | 2 +- science/py-gemmi/distinfo | 6 +++--- science/py-gemmi/files/patch-CMakeLists.txt | 24 ++++++++++++------------ science/py-gemmi/pkg-plist | 1 + 7 files changed, 28 insertions(+), 20 deletions(-) diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index aa0f3083bca2..ffbf674a0ed3 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.3 +DISTVERSION= 0.7.5 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org 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 @@ -1,4 +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 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 @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.7.3 +DISTVERSION= 0.7.5 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index b40d35b8cada..8bf9d039c207 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753140186 -SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3 -SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234 +TIMESTAMP = 1772523199 +SHA256 (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3 +SIZE (project-gemmi-gemmi-v0.7.5_GH0.tar.gz) = 2096501 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index 62637e7014cd..ff9e347bd9b2 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,4 +1,4 @@ ---- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC +--- CMakeLists.txt.orig 2026-03-02 03:06:09 UTC +++ CMakeLists.txt @@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1" @@ -18,7 +18,7 @@ option(BUILD_SHARED_LIBS "Build shared library" ON) option(BUILD_GEMMI_PROGRAM "Build gemmi command-line program" ON) option(INSTALL_DEV_FILES "Install C++ headers, cmake configs, static lib" ON) -@@ -203,70 +205,6 @@ endif() +@@ -203,70 +205,7 @@ endif() # target_link_libraries(fgemmi PRIVATE cgemmi) #endif() @@ -29,10 +29,10 @@ - "$<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() 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 @@ -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.typedhome | help
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