git: 122e253d6b17 - main - science/{,py-}gemmi: update 0.6.6 → 0.6.7
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Date: Sat, 07 Sep 2024 06:25:08 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=122e253d6b179d61591fd168edf111c12fe5539b
commit 122e253d6b179d61591fd168edf111c12fe5539b
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-09-07 05:26:00 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-09-07 06:24:52 +0000
science/{,py-}gemmi: update 0.6.6 → 0.6.7
Reported by: portscout
---
science/gemmi/Makefile | 2 +-
science/gemmi/distinfo | 6 +-
science/gemmi/pkg-plist | 1 -
science/py-gemmi/Makefile | 4 +-
science/py-gemmi/distinfo | 6 +-
science/py-gemmi/files/patch-CMakeLists.txt | 90 +++++++----------------------
6 files changed, 30 insertions(+), 79 deletions(-)
diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index a52e1099ff3a..38ba4f45c227 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -1,6 +1,6 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
-DISTVERSION= 0.6.6
+DISTVERSION= 0.6.7
CATEGORIES= science # chemistry
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo
index c318b2645757..16fd0521e1d4 100644
--- a/science/gemmi/distinfo
+++ b/science/gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1716957697
-SHA256 (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 722369495f7374bb938d14da2c3a9f8444b753e2d9536cf097c161a53dbbae19
-SIZE (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 1819188
+TIMESTAMP = 1725684236
+SHA256 (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = f3dd7c3aac0b01f0338ff5034c11be0e7b23639f018c8d6b1db7cc9d77a8dee9
+SIZE (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = 1833549
diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist
index c910ac13e611..4f43aefef81f 100644
--- a/science/gemmi/pkg-plist
+++ b/science/gemmi/pkg-plist
@@ -70,7 +70,6 @@ include/gemmi/read_map.hpp
include/gemmi/recgrid.hpp
include/gemmi/reciproc.hpp
include/gemmi/refln.hpp
-include/gemmi/remarks.hpp
include/gemmi/resinfo.hpp
include/gemmi/riding_h.hpp
include/gemmi/scaling.hpp
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile
index 89b60d4aa7b1..53bdd5038597 100644
--- a/science/py-gemmi/Makefile
+++ b/science/py-gemmi/Makefile
@@ -1,6 +1,6 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
-DISTVERSION= 0.6.6
+DISTVERSION= 0.6.7
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \
LIB_DEPENDS= libgemmi_cpp.so:science/gemmi
TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR}
-USES= cmake compiler:c++20-lang localbase:ldflags python
+USES= cmake compiler:c++17-lang localbase:ldflags python
USE_PYTHON= flavors
USE_GITHUB= yes
diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo
index 0b7ff31c6841..57a82e02e696 100644
--- a/science/py-gemmi/distinfo
+++ b/science/py-gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1716960965
-SHA256 (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 722369495f7374bb938d14da2c3a9f8444b753e2d9536cf097c161a53dbbae19
-SIZE (project-gemmi-gemmi-v0.6.6_GH0.tar.gz) = 1819188
+TIMESTAMP = 1725686168
+SHA256 (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = f3dd7c3aac0b01f0338ff5034c11be0e7b23639f018c8d6b1db7cc9d77a8dee9
+SIZE (project-gemmi-gemmi-v0.6.7_GH0.tar.gz) = 1833549
diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt
index 15c6e8d7f824..9446f2ca1c13 100644
--- a/science/py-gemmi/files/patch-CMakeLists.txt
+++ b/science/py-gemmi/files/patch-CMakeLists.txt
@@ -1,4 +1,4 @@
---- CMakeLists.txt.orig 2024-02-17 11:35:57 UTC
+--- CMakeLists.txt.orig 2024-09-06 14:24:17 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)
-@@ -192,67 +194,67 @@ endif()
+@@ -200,71 +202,9 @@ endif()
# target_link_libraries(fgemmi PRIVATE cgemmi)
#endif()
@@ -29,47 +29,29 @@
- "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
-target_compile_features(gemmi_headers INTERFACE cxx_std_11)
-set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers)
-+#add_library(gemmi_headers INTERFACE)
-+#add_library(gemmi::headers ALIAS gemmi_headers)
-+#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)
-+#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/polyheur.cpp src/read_cif.cpp src/resinfo.cpp
-- src/riding_h.cpp src/sprintf.cpp src/to_mmcif.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)
-add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp)
-set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON)
-+#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/polyheur.cpp src/read_cif.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)
-+#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)
+-#set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden)
-target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
-target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
-+#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
-+#target_include_directories(gemmi_cpp PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
-
+-
-if (BUILD_SHARED_LIBS)
- target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
+- if (ADD_SOVERSION)
+- set_target_properties(gemmi_cpp PROPERTIES VERSION ${PROJECT_VERSION}
+- SOVERSION "0")
+- endif()
-endif()
-target_link_libraries(gemmi_cpp PUBLIC gemmi_headers)
-+#if (BUILD_SHARED_LIBS)
-+# target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
-+#endif()
-+#target_link_libraries(gemmi_cpp PUBLIC gemmi_headers)
-
+-
-if (FETCH_ZLIB_NG)
- target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1)
- target_link_libraries(gemmi_cpp PRIVATE zlib)
@@ -99,46 +81,16 @@
- target_compile_options(gemmi_cpp PRIVATE /wd4267)
- endif()
-endif()
-+#if (FETCH_ZLIB_NG)
-+# target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1)
-+# target_link_libraries(gemmi_cpp PRIVATE zlib)
-+#elseif (ZLIB_NG_FOUND)
-+# target_compile_definitions(gemmi_cpp PRIVATE USE_ZLIB_NG=1)
-+# target_link_libraries(gemmi_cpp PRIVATE ZLIB_NG::ZLIB_NG)
-+#elseif (ZLIB_FOUND)
-+# target_link_libraries(gemmi_cpp PRIVATE ZLIB::ZLIB)
-+#else()
-+# target_sources(gemmi_cpp PRIVATE
-+# "third_party/zlib/adler32.c"
-+# "third_party/zlib/crc32.c"
-+# "third_party/zlib/gzlib.c"
-+# "third_party/zlib/gzread.c"
-+# "third_party/zlib/inflate.c"
-+# "third_party/zlib/inftrees.c"
-+# "third_party/zlib/inffast.c"
-+# "third_party/zlib/zutil.c")
-+# check_include_file(unistd.h has_unistd_h)
-+# target_compile_definitions(gemmi PRIVATE NO_GZCOMPRESS=1 DYNAMIC_CRC_TABLE=1)
-+# if (has_unistd_h)
-+# target_compile_definitions(gemmi PRIVATE Z_HAVE_UNISTD_H=1)
-+# endif()
-+# target_include_directories(gemmi PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party/zlib")
-+# if (CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-+# # /wd4267 - conversion from 'size_t' to 'unsigned int', possible loss of data
-+# target_compile_options(gemmi PRIVATE /wd4267)
-+# endif()
-+#endif()
-
-
+-
+-
### programs from prog/ ###
add_library(options OBJECT prog/options.cpp)
-target_link_libraries(options PUBLIC gemmi_headers)
-+#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})
-@@ -264,11 +266,11 @@ function(add_single_prog target)
+@@ -276,11 +216,11 @@ function(add_single_prog target)
cmake_parse_arguments(arg "NOLIB" "ADD_SRC" "" ${ARGN})
add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC}
$<TARGET_OBJECTS:options>)
@@ -155,7 +107,7 @@
target_include_directories(gemmi-${target} PRIVATE
"${CMAKE_CURRENT_SOURCE_DIR}/third_party")
endfunction()
-@@ -322,7 +324,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog)
+@@ -334,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog)
prog/xds2mtz.cpp
$<TARGET_OBJECTS:options>)
add_executable(gemmi::prog ALIAS gemmi_prog)
@@ -164,7 +116,7 @@
target_include_directories(gemmi_prog PRIVATE "${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)
-@@ -374,9 +376,9 @@ add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/
+@@ -386,9 +326,9 @@ add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/
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)
@@ -176,7 +128,7 @@
# always compile these tests with assertions enabled
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
-@@ -384,14 +386,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu
+@@ -396,14 +336,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu
endif()
add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp)
@@ -194,7 +146,7 @@
enable_testing()
-@@ -428,7 +430,7 @@ if (benchmark_FOUND)
+@@ -440,7 +380,7 @@ 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")
@@ -203,7 +155,7 @@
endif()
target_link_libraries(${b}-bm PRIVATE gemmi_headers benchmark::benchmark)
set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY
-@@ -466,11 +468,11 @@ if (USE_PYTHON)
+@@ -482,11 +422,11 @@ if (USE_PYTHON)
python/sf.cpp python/sym.cpp python/topo.cpp
python/unitcell.cpp python/write.cpp)
if (STANDALONE_PYTHON_MODULE)
@@ -218,7 +170,7 @@
endif()
set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi)
if(CMAKE_CXX_FLAGS MATCHES "-Wshadow")
-@@ -518,19 +520,19 @@ endif()
+@@ -541,19 +481,19 @@ endif()
install(TARGETS gemmi_prog EXPORT GemmiTargets)
endif()