science/{,py-}gemmi: update 0.6.7 → 0.7.1

Reported by:	portscout

7 files changed, 63 insertions, 51 deletions

diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index 38ba4f45c227..bca3ebaed373 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.6.7
+DISTVERSION=	0.7.1
 CATEGORIES=	science # chemistry
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -25,4 +25,9 @@ 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 0.7.1 (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 <bsd.port.mk>
diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo
index 16fd0521e1d4..49c83ebc50e8 100644
--- a/science/gemmi/distinfo
+++ b/science/gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1725684236
-SHA256 (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = f3dd7c3aac0b01f0338ff5034c11be0e7b23639f018c8d6b1db7cc9d77a8dee9
-SIZE (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = 1833549
+TIMESTAMP = 1742884325
+SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393
+SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265
diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist
index 4f43aefef81f..c28c9d130ae7 100644
--- a/science/gemmi/pkg-plist
+++ b/science/gemmi/pkg-plist
@@ -15,7 +15,6 @@ include/gemmi/calculate.hpp
 include/gemmi/ccp4.hpp
 include/gemmi/cellred.hpp
 include/gemmi/chemcomp.hpp
-include/gemmi/chemcomp_xyz.hpp
 include/gemmi/cif.hpp
 include/gemmi/cif2mtz.hpp
 include/gemmi/cifdoc.hpp
@@ -45,6 +44,7 @@ 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
@@ -66,7 +66,6 @@ include/gemmi/pirfasta.hpp
 include/gemmi/polyheur.hpp
 include/gemmi/qcp.hpp
 include/gemmi/read_cif.hpp
-include/gemmi/read_map.hpp
 include/gemmi/recgrid.hpp
 include/gemmi/reciproc.hpp
 include/gemmi/refln.hpp
@@ -255,6 +254,7 @@ 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
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile
index 53bdd5038597..2aac5d8717f0 100644
--- a/science/py-gemmi/Makefile
+++ b/science/py-gemmi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.6.7
+DISTVERSION=	0.7.1
 CATEGORIES=	science python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -12,7 +12,7 @@ LICENSE=	MPL20
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pybind11>0:devel/py-pybind11@${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
diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo
index 57a82e02e696..9050772d8cc8 100644
--- a/science/py-gemmi/distinfo
+++ b/science/py-gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1725686168
-SHA256 (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = f3dd7c3aac0b01f0338ff5034c11be0e7b23639f018c8d6b1db7cc9d77a8dee9
-SIZE (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = 1833549
+TIMESTAMP = 1742885714
+SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393
+SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265
diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt
index 9446f2ca1c13..d75096e3228b 100644
--- a/science/py-gemmi/files/patch-CMakeLists.txt
+++ b/science/py-gemmi/files/patch-CMakeLists.txt
@@ -1,4 +1,4 @@
---- CMakeLists.txt.orig	2024-09-06 14:24:17 UTC
+--- CMakeLists.txt.orig	2025-03-24 16:35:30 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)
-@@ -200,71 +202,9 @@ endif()
+@@ -203,70 +205,6 @@ endif()
  #  target_link_libraries(fgemmi PRIVATE cgemmi)
  #endif()
  
@@ -27,16 +27,19 @@
 -target_include_directories(gemmi_headers INTERFACE
 -    "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
 -    "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
--target_compile_features(gemmi_headers INTERFACE cxx_std_11)
+-target_compile_features(gemmi_headers INTERFACE cxx_std_17)
 -set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers)
 -
 -add_library(gemmi_cpp
--            src/align.cpp src/assembly.cpp src/calculate.cpp src/crd.cpp
--            src/ddl.cpp src/eig3.cpp src/gz.cpp src/intensit.cpp src/json.cpp
--            src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp
--            src/pdb.cpp src/polyheur.cpp src/read_cif.cpp src/read_map.cpp
--            src/resinfo.cpp src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp
--            src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.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/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/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)
@@ -86,28 +89,16 @@
  ### programs from prog/ ###
  
  add_library(options OBJECT prog/options.cpp)
--target_link_libraries(options PUBLIC gemmi_headers)
- target_include_directories(options PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
- if (GEMMI_VERSION_INFO)
-   target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO})
-@@ -276,11 +216,11 @@ function(add_single_prog target)
-   cmake_parse_arguments(arg "NOLIB" "ADD_SRC" "" ${ARGN})
+@@ -282,7 +220,7 @@ 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}
                   $<TARGET_OBJECTS:options>)
--  if (arg_NOLIB)
--    target_link_libraries(gemmi-${target} PRIVATE gemmi_headers)
--  else()
--    target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp)
--  endif()
-+  #if (arg_NOLIB)
-+  #  target_link_libraries(gemmi-${target} PRIVATE gemmi_headers)
-+  #else()
-+  #  target_link_libraries(gemmi-${target} PRIVATE gemmi)
-+  #endif()
+-  target_link_libraries(gemmi-${target} PRIVATE gemmi_cpp)
++  target_link_libraries(gemmi-${target} PRIVATE gemmi)
    target_include_directories(gemmi-${target} PRIVATE
                               "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
  endfunction()
-@@ -334,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog)
+@@ -336,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog)
                 prog/xds2mtz.cpp
                 $<TARGET_OBJECTS:options>)
  add_executable(gemmi::prog ALIAS gemmi_prog)
@@ -116,26 +107,37 @@
  target_include_directories(gemmi_prog PRIVATE "${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)
-@@ -386,9 +326,9 @@ add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/
+@@ -376,7 +314,7 @@ 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(hello EXCLUDE_FROM_ALL examples/hello.cpp)
+@@ -384,11 +322,11 @@ add_executable(doc_example EXCLUDE_FROM_ALL
+ 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 src/resinfo.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_maybegz EXCLUDE_FROM_ALL docs/code/maybegz.cpp docs/code/mutate.cpp)
--target_link_libraries(doc_maybegz PRIVATE gemmi_cpp)
-+target_link_libraries(doc_maybegz PRIVATE gemmi)
  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")
-@@ -396,14 +336,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu
+@@ -396,14 +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 <experimental/filesystem> and -lstdc++fs
+ # auth_label requires C++17 for <filesystem>
  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)
@@ -146,18 +148,18 @@
  
  enable_testing()
  
-@@ -440,7 +380,7 @@ if (benchmark_FOUND)
+@@ -440,7 +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 "resinfo|pdb|writecif")
+     if (b MATCHES "elem|resinfo|pdb|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
-@@ -482,11 +422,11 @@ if (USE_PYTHON)
-           python/sf.cpp python/sym.cpp python/topo.cpp
+@@ -481,11 +419,11 @@ if (USE_PYTHON)
            python/unitcell.cpp python/write.cpp)
+ 
    if (STANDALONE_PYTHON_MODULE)
 -    target_sources(gemmi_py PRIVATE $<TARGET_OBJECTS:gemmi_cpp>)
 -    get_target_property(_gemmi_cpp_libs gemmi_cpp LINK_LIBRARIES)
@@ -168,9 +170,9 @@
 -    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)
-   if(CMAKE_CXX_FLAGS MATCHES "-Wshadow")
-@@ -541,19 +481,19 @@ endif()
+   set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi_ext)
+   if (CMAKE_CONFIGURATION_TYPES)
+@@ -568,19 +506,19 @@ endif()
    install(TARGETS gemmi_prog EXPORT GemmiTargets)
  endif()
  
diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist
index 7583c7ed2cdc..52ebda9cb374 100644
--- a/science/py-gemmi/pkg-plist
+++ b/science/py-gemmi/pkg-plist
@@ -1,4 +1,6 @@
-%%PYTHON_SITELIBDIR%%/gemmi%%PYTHON_EXT_SUFFIX%%.so
+%%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
@@ -17,6 +19,7 @@
 %%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/refln-stats.py
@@ -24,3 +27,5 @@
 %%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py
 %%PYTHON_SITELIBDIR%%/gemmi/examples/to_rdkit.py
 %%PYTHON_SITELIBDIR%%/gemmi/examples/weight.py
+%%PYTHON_SITELIBDIR%%/gemmi/gemmi_ext%%PYTHON_EXT_SUFFIX%%.so
+%%PYTHON_SITELIBDIR%%/gemmi/py.typed