git: 6721fd024d6b - main - science/{,py-}gemmi: update 0.6.7 → 0.7.1
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Date: Tue, 25 Mar 2025 08:26:45 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=6721fd024d6b0b788925faf41d093472d9b6dc9b
commit 6721fd024d6b0b788925faf41d093472d9b6dc9b
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-03-25 08:26:03 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-03-25 08:26:20 +0000
science/{,py-}gemmi: update 0.6.7 → 0.7.1
Reported by: portscout
---
science/gemmi/Makefile | 7 ++-
science/gemmi/distinfo | 6 +--
science/gemmi/pkg-plist | 4 +-
science/py-gemmi/Makefile | 4 +-
science/py-gemmi/distinfo | 6 +--
science/py-gemmi/files/patch-CMakeLists.txt | 80 +++++++++++++++--------------
science/py-gemmi/pkg-plist | 7 ++-
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