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science/{,py-}gemmi: Update 0.6.0 → 0.6.2

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Reported by:	portscout
This commit is contained in:
Yuri Victorovich 2023-05-28 14:26:27 -07:00
parent 7830e9f8ae
commit 294400f8d0
7 changed files with 54 additions and 91 deletions
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4
science/gemmi/Makefile
View file

@ -1,6 +1,6 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
DISTVERSION= 0.6.0
DISTVERSION= 0.6.2
CATEGORIES= science # chemistry
MAINTAINER= yuri@FreeBSD.org
@ -10,7 +10,7 @@ WWW= https://gemmi.readthedocs.io/en/latest/
LICENSE= MPL20
LICENSE_FILE= ${WRKSRC}/LICENSE.txt
USES= cmake:testing compiler:c++17-lang # tests don't run, see https://github.com/project-gemmi/gemmi/issues/231
USES= cmake:testing compiler:c++20-lang # tests don't run, see https://github.com/project-gemmi/gemmi/issues/231
USE_GITHUB= yes
GH_ACCOUNT= project-gemmi

6
science/gemmi/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1678123316
SHA256 (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 5f033dded4bf1f3d8fa88636d798aea70bfb2a2f0e209fd517b36d773f83588d
SIZE (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 1737083
TIMESTAMP = 1685300431
SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929
SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298

6
science/gemmi/pkg-plist
View file

@ -9,6 +9,7 @@ include/gemmi/atox.hpp
include/gemmi/bessel.hpp
include/gemmi/binner.hpp
include/gemmi/blob.hpp
include/gemmi/bond_idx.hpp
include/gemmi/c4322.hpp
include/gemmi/calculate.hpp
include/gemmi/ccp4.hpp
@ -58,6 +59,7 @@ include/gemmi/neighbor.hpp
include/gemmi/neutron92.hpp
include/gemmi/numb.hpp
include/gemmi/pdb.hpp
include/gemmi/pdb_id.hpp
include/gemmi/pirfasta.hpp
include/gemmi/polyheur.hpp
include/gemmi/qcp.hpp
@ -65,10 +67,7 @@ include/gemmi/read_cif.hpp
include/gemmi/read_map.hpp
include/gemmi/recgrid.hpp
include/gemmi/reciproc.hpp
include/gemmi/refine/geom.hpp
include/gemmi/refine/ll.hpp
include/gemmi/refln.hpp
include/gemmi/reindex.hpp
include/gemmi/remarks.hpp
include/gemmi/resinfo.hpp
include/gemmi/riding_h.hpp
@ -87,7 +86,6 @@ include/gemmi/symmetry.hpp
include/gemmi/third_party/fast_float.h
include/gemmi/third_party/pocketfft_hdronly.h
include/gemmi/third_party/sajson.h
include/gemmi/third_party/stb_sprintf.h
include/gemmi/third_party/tao/LICENSE
include/gemmi/third_party/tao/NOTES
include/gemmi/third_party/tao/pegtl.hpp

5
science/py-gemmi/Makefile
View file

@ -1,6 +1,6 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
DISTVERSION= 0.6.0
DISTVERSION= 0.6.2
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@ -24,11 +24,14 @@ USE_GITHUB= yes
GH_ACCOUNT= project-gemmi
CMAKE_ON= USE_PYTHON
CMAKE_OFF= BUILD_GEMMI_PROGRAM
CMAKE_ARGS= -DPython_EXECUTABLE=${PYTHON_CMD}
TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
TEST_WRKSRC= ${BUILD_WRKSRC}/tests
PLIST_SUB= VER=${PORTVERSION}
do-test:
@cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/

6
science/py-gemmi/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1678255262
SHA256 (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 5f033dded4bf1f3d8fa88636d798aea70bfb2a2f0e209fd517b36d773f83588d
SIZE (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 1737083
TIMESTAMP = 1685301047
SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929
SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298

108
science/py-gemmi/files/patch-CMakeLists.txt
View file

@ -1,42 +1,40 @@
- workaround for https://github.com/project-gemmi/gemmi/issues/257
--- CMakeLists.txt.orig 2023-03-06 11:12:31 UTC
--- CMakeLists.txt.orig 2023-05-25 12:37:36 UTC
+++ CMakeLists.txt
@@ -182,21 +182,23 @@ if (GEMMI_VERSION_INFO)
@@ -187,20 +187,21 @@ if (GEMMI_VERSION_INFO)
target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO})
endif()
-add_library(gemmi_cpp
- src/crd.cpp src/mmcif.cpp src/mtz.cpp src/mtz2cif.cpp
- src/polyheur.cpp
- src/read_cif.cpp src/mmread_gz.cpp src/resinfo.cpp
- src/assembly.cpp src/calculate.cpp src/crd.cpp src/eig3.cpp
- src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp
- src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp
- src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp
- src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp)
-set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON)
+#add_library(gemmi_cpp
+# src/crd.cpp src/mmcif.cpp src/mtz.cpp src/mtz2cif.cpp
+# src/polyheur.cpp
+# src/read_cif.cpp src/mmread_gz.cpp src/resinfo.cpp
+# src/assembly.cpp src/calculate.cpp src/crd.cpp src/eig3.cpp
+# src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp
+# src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp
+# src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp
+# src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp)
+#set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON)
#set_property(TARGET gemmi_cpp PROPERTY CXX_VISIBILITY_PRESET hidden)
-target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
+#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
if (BUILD_SHARED_LIBS)
-if (BUILD_SHARED_LIBS)
- target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
+ #target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
endif()
-endif()
-support_gz(gemmi_cpp)
+#target_compile_definitions(gemmi_cpp PRIVATE GEMMI_BUILD)
+#if (BUILD_SHARED_LIBS)
+# target_compile_definitions(gemmi_cpp PUBLIC GEMMI_SHARED)
+#endif()
+#support_gz(gemmi_cpp)
+find_package(gemmi REQUIRED)
+
# Gemmi subcommands compiled as individual binaries.
# Not built by default and used mostly for testing.
function(add_single_prog target)
@@ -204,7 +206,7 @@ function(add_single_prog target)
@@ -209,7 +210,7 @@ function(add_single_prog target)
add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC}
$<TARGET_OBJECTS:options>)
if (NOT arg_NOLIB)
@ -45,55 +43,16 @@
endif()
if (arg_GZ)
support_gz(gemmi-${target})
@@ -243,29 +245,29 @@ add_single_prog(wcn)
add_single_prog(xds2mtz GZ)
# gemmi program with a number of subcommands
-add_executable(gemmi_prog
- prog/align.cpp prog/blobs.cpp
- prog/cif2mtz.cpp prog/cif2json.cpp prog/contact.cpp
- prog/contents.cpp prog/convert.cpp prog/fprime.cpp
- prog/grep.cpp prog/h.cpp prog/json2cif.cpp
- prog/main.cpp prog/map.cpp prog/map2sf.cpp
- prog/mapcoef.cpp prog/mask.cpp
- prog/merge.cpp prog/mondiff.cpp prog/mtz.cpp prog/mtz2cif.cpp
- prog/prep.cpp prog/reindex.cpp prog/residues.cpp prog/rmsz.cpp
- prog/sf2map.cpp prog/sfcalc.cpp prog/sg.cpp prog/tags.cpp
- prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp
- prog/xds2mtz.cpp
- $<TARGET_OBJECTS:options>)
@@ -261,7 +262,7 @@ add_executable(gemmi_prog
prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp
prog/xds2mtz.cpp
$<TARGET_OBJECTS:options>)
-target_link_libraries(gemmi_prog PRIVATE gemmi_cpp)
-support_gz(gemmi_prog)
-target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1)
-set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi)
+#add_executable(gemmi_prog
+# prog/align.cpp prog/blobs.cpp
+# prog/cif2mtz.cpp prog/cif2json.cpp prog/contact.cpp
+# prog/contents.cpp prog/convert.cpp prog/fprime.cpp
+# prog/grep.cpp prog/h.cpp prog/json2cif.cpp
+# prog/main.cpp prog/map.cpp prog/map2sf.cpp
+# prog/mapcoef.cpp prog/mask.cpp
+# prog/merge.cpp prog/mondiff.cpp prog/mtz.cpp prog/mtz2cif.cpp
+# prog/prep.cpp prog/reindex.cpp prog/residues.cpp prog/rmsz.cpp
+# prog/sf2map.cpp prog/sfcalc.cpp prog/sg.cpp prog/tags.cpp
+# prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp
+# prog/xds2mtz.cpp
+# $<TARGET_OBJECTS:options>)
+#target_link_libraries(gemmi_prog PRIVATE gemmi_cpp)
+#support_gz(gemmi_prog)
+#target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1)
+#set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi)
if (WIN32 AND USE_WMAIN)
# _UNICODE=1 is now set globally
#target_compile_definitions(gemmi_prog PRIVATE _UNICODE=1)
if(MINGW)
# target_link_options were added in cmake 3.13
- set_property(TARGET gemmi_prog PROPERTY LINK_FLAGS "-municode")
+ #set_property(TARGET gemmi_prog PROPERTY LINK_FLAGS "-municode")
endif()
endif()
@@ -284,10 +286,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL
support_gz(gemmi_prog)
target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1)
set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi)
@@ -301,10 +302,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL
docs/code/cell.cpp src/resinfo.cpp)
add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp)
add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/maybegz.cpp docs/code/mutate.cpp)
@ -106,7 +65,7 @@
support_gz(doc_newmtz)
# always compile these tests with assertions enabled
@@ -296,7 +298,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
@@ -313,7 +314,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
endif()
add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp)
@ -115,7 +74,7 @@
support_gz(test_disulf)
# auth_label requires <experimental/filesystem> and -lstdc++fs
@@ -307,7 +309,7 @@ endif()
@@ -324,7 +325,7 @@ endif()
support_gz(auth_label)
add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp)
@ -124,7 +83,7 @@
enable_testing()
@@ -344,7 +346,7 @@ if (benchmark_FOUND)
@@ -361,7 +362,7 @@ if (benchmark_FOUND)
foreach(b stoi elem mod niggli pdb resinfo round sym)
add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp)
if (b MATCHES "resinfo|pdb")
@ -133,10 +92,10 @@
endif()
target_link_libraries(${b}-bm PRIVATE benchmark::benchmark)
set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY
@@ -372,8 +374,8 @@ if (USE_PYTHON)
@@ -389,8 +390,8 @@ 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 python/refine.cpp
python/sf.cpp python/sym.cpp python/topo.cpp
- python/unitcell.cpp python/write.cpp
- $<TARGET_OBJECTS:gemmi_cpp>)
+ python/unitcell.cpp python/write.cpp)
@ -144,17 +103,20 @@
set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi)
if(CMAKE_CXX_FLAGS MATCHES "-Wshadow")
target_compile_options(gemmi_py PRIVATE "-Wno-shadow")
@@ -396,18 +398,18 @@ write_basic_package_version_file(gemmi-config-version.
@@ -413,21 +414,21 @@ write_basic_package_version_file(gemmi-config-version.
COMPATIBILITY AnyNewerVersion)
# In CMake 3.23 we'll be able to use FILE_SET to install the headers
-install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
+#install(DIRECTORY include/gemmi DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
-install(TARGETS gemmi_prog gemmi_cpp
if (BUILD_GEMMI_PROGRAM)
install(TARGETS gemmi_prog EXPORT GemmiTargets)
endif()
-install(TARGETS gemmi_cpp
- EXPORT GemmiTargets
- INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
+#install(TARGETS gemmi_prog gemmi_cpp
+#install(TARGETS gemmi_cpp
+# EXPORT GemmiTargets
+# INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
@ -173,7 +135,7 @@
if (USE_PYTHON)
if (DEFINED PYTHON_INSTALL_DIR)
@@ -421,8 +423,8 @@ if (USE_PYTHON)
@@ -441,8 +442,8 @@ if (USE_PYTHON)
# and don't respect CMAKE_INSTALL_PREFIX.
# https://discourse.cmake.org/t/findpython3-how-to-specify-local-installation-directory-for-python-module/3580/5
install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}")

10
science/py-gemmi/pkg-plist
View file

@ -1,6 +1,6 @@
%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/PKG-INFO
%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/SOURCES.txt
%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/dependency_links.txt
%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/not-zip-safe
%%PYTHON_SITELIBDIR%%/gemmi-0.6.0-py%%PYTHON_VER%%.egg-info/top_level.txt
%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/PKG-INFO
%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/SOURCES.txt
%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/dependency_links.txt
%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/not-zip-safe
%%PYTHON_SITELIBDIR%%/gemmi-%%VER%%-py%%PYTHON_VER%%.egg-info/top_level.txt
%%PYTHON_SITELIBDIR%%/gemmi%%PYTHON_EXT_SUFFIX%%.so