science/{,py-}gemmi: update 0.6.2 → 0.6.3

Reported by:	portscout

6 files changed, 25 insertions, 21 deletions

diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index db62f5f0ecbd..b257a807cf24 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.6.2
+DISTVERSION=	0.6.3
 CATEGORIES=	science # chemistry
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo
index 64807762f6b8..2aa772096904 100644
--- a/science/gemmi/distinfo
+++ b/science/gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1685300431
-SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929
-SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298
+TIMESTAMP = 1694327240
+SHA256 (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091
+SIZE (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = 1756098
diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist
index 27bea19e9241..1e66eed2eccb 100644
--- a/science/gemmi/pkg-plist
+++ b/science/gemmi/pkg-plist
@@ -21,8 +21,10 @@ include/gemmi/cif2mtz.hpp
 include/gemmi/cifdoc.hpp
 include/gemmi/contact.hpp
 include/gemmi/crd.hpp
+include/gemmi/ddl.hpp
 include/gemmi/dencalc.hpp
 include/gemmi/dirwalk.hpp
+include/gemmi/ecalc.hpp
 include/gemmi/eig3.hpp
 include/gemmi/elem.hpp
 include/gemmi/enumstr.hpp
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile
index 9e09144588fb..caea06f40f2e 100644
--- a/science/py-gemmi/Makefile
+++ b/science/py-gemmi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.6.2
+DISTVERSION=	0.6.3
 CATEGORIES=	science python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo
index f3c4d131e6b0..de2cc003fbcb 100644
--- a/science/py-gemmi/distinfo
+++ b/science/py-gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1685301047
-SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929
-SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298
+TIMESTAMP = 1694328516
+SHA256 (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091
+SIZE (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = 1756098
diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt
index 943a0ad5a5cc..802f60ebf944 100644
--- a/science/py-gemmi/files/patch-CMakeLists.txt
+++ b/science/py-gemmi/files/patch-CMakeLists.txt
@@ -1,18 +1,20 @@
---- CMakeLists.txt.orig	2023-05-25 12:37:36 UTC
+--- CMakeLists.txt.orig	2023-09-07 09:12:22 UTC
 +++ CMakeLists.txt
-@@ -187,20 +187,21 @@ if (GEMMI_VERSION_INFO)
+@@ -187,21 +187,22 @@ if (GEMMI_VERSION_INFO)
    target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO})
  endif()
  
 -add_library(gemmi_cpp
--            src/assembly.cpp src/calculate.cpp src/crd.cpp src/eig3.cpp
+-            src/assembly.cpp src/calculate.cpp src/crd.cpp
+-            src/ddl.cpp src/eig3.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)
 -set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON)
 +#add_library(gemmi_cpp
-+#            src/assembly.cpp src/calculate.cpp src/crd.cpp src/eig3.cpp
++#            src/assembly.cpp src/calculate.cpp src/crd.cpp
++#            src/ddl.cpp src/eig3.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
@@ -34,7 +36,7 @@
  
  # Gemmi subcommands compiled as individual binaries.
  # Not built by default and used mostly for testing.
-@@ -209,7 +210,7 @@ function(add_single_prog target)
+@@ -210,7 +211,7 @@ function(add_single_prog target)
    add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC}
                   $<TARGET_OBJECTS:options>)
    if (NOT arg_NOLIB)
@@ -43,7 +45,7 @@
    endif()
    if (arg_GZ)
      support_gz(gemmi-${target})
-@@ -261,7 +262,7 @@ add_executable(gemmi_prog
+@@ -264,7 +265,7 @@ add_executable(gemmi_prog
                 prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp
                 prog/xds2mtz.cpp
                 $<TARGET_OBJECTS:options>)
@@ -52,7 +54,7 @@
  support_gz(gemmi_prog)
  target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1)
  set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi)
-@@ -301,10 +302,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL
+@@ -304,10 +305,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL
                 docs/code/cell.cpp src/resinfo.cpp)
  add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp)
  add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/maybegz.cpp docs/code/mutate.cpp)
@@ -65,7 +67,7 @@
  support_gz(doc_newmtz)
  
  # always compile these tests with assertions enabled
-@@ -313,7 +314,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
+@@ -316,7 +317,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
  endif()
  
  add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp)
@@ -74,7 +76,7 @@
  support_gz(test_disulf)
  
  # auth_label requires <experimental/filesystem> and -lstdc++fs
-@@ -324,7 +325,7 @@ endif()
+@@ -327,7 +328,7 @@ endif()
  support_gz(auth_label)
  
  add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp)
@@ -83,7 +85,7 @@
  
  enable_testing()
  
-@@ -361,7 +362,7 @@ if (benchmark_FOUND)
+@@ -364,7 +365,7 @@ if (benchmark_FOUND)
    foreach(b stoi elem mod niggli pdb resinfo round sym)
      add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp)
      if (b MATCHES "resinfo|pdb")
@@ -92,7 +94,7 @@
      endif()
      target_link_libraries(${b}-bm PRIVATE benchmark::benchmark)
      set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY
-@@ -389,8 +390,8 @@ if (USE_PYTHON)
+@@ -392,8 +393,8 @@ if (USE_PYTHON)
            python/mtz.cpp python/read.cpp python/recgrid.cpp
            python/scaling.cpp python/search.cpp
            python/sf.cpp python/sym.cpp python/topo.cpp
@@ -103,7 +105,7 @@
    set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi)
    if(CMAKE_CXX_FLAGS MATCHES "-Wshadow")
      target_compile_options(gemmi_py PRIVATE "-Wno-shadow")
-@@ -413,21 +414,21 @@ write_basic_package_version_file(gemmi-config-version.
+@@ -416,21 +417,21 @@ write_basic_package_version_file(gemmi-config-version.
                                   COMPATIBILITY AnyNewerVersion)
  
  # In CMake 3.23 we'll be able to use FILE_SET to install the headers
@@ -135,7 +137,7 @@
  
  if (USE_PYTHON)
    if (DEFINED PYTHON_INSTALL_DIR)
-@@ -441,8 +442,8 @@ if (USE_PYTHON)
+@@ -444,8 +445,8 @@ if (USE_PYTHON)
    # and don't respect CMAKE_INSTALL_PREFIX.
    # https://discourse.cmake.org/t/findpython3-how-to-specify-local-installation-directory-for-python-module/3580/5
    install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}")