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

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.typed