git: 294400f8d06a - main - science/{,py-}gemmi: Update 0.6.0 → 0.6.2
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sun, 28 May 2023 23:41:11 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=294400f8d06a8ec06875462ce0a2cc792382efe3
commit 294400f8d06a8ec06875462ce0a2cc792382efe3
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-05-28 21:26:27 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-05-28 23:41:04 +0000
science/{,py-}gemmi: Update 0.6.0 → 0.6.2
Reported by: portscout
---
science/gemmi/Makefile | 4 +-
science/gemmi/distinfo | 6 +-
science/gemmi/pkg-plist | 6 +-
science/py-gemmi/Makefile | 5 +-
science/py-gemmi/distinfo | 6 +-
science/py-gemmi/files/patch-CMakeLists.txt | 108 +++++++++-------------------
science/py-gemmi/pkg-plist | 10 +--
7 files changed, 54 insertions(+), 91 deletions(-)
diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index d7c8acf02019..db62f5f0ecbd 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -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
diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo
index 51fc30631c42..64807762f6b8 100644
--- a/science/gemmi/distinfo
+++ b/science/gemmi/distinfo
@@ -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
diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist
index 5cf31def8fae..27bea19e9241 100644
--- a/science/gemmi/pkg-plist
+++ b/science/gemmi/pkg-plist
@@ -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
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile
index 167af8a9ef98..9e09144588fb 100644
--- a/science/py-gemmi/Makefile
+++ b/science/py-gemmi/Makefile
@@ -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} ${PYTHON_CMD} -m unittest discover -v tests/
diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo
index 78fe3395fb96..f3c4d131e6b0 100644
--- a/science/py-gemmi/distinfo
+++ b/science/py-gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1678255262
-SHA256 (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 5f033dded4bf1f3d8fa88636d798aea70bfb2a2f0e209fd517b36d773f83588d
-SIZE (project-gemmi-gemmi-v0.6.0_GH0.tar.gz) = 1737083
+TIMESTAMP = 1685301047
+SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929
+SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298
diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt
index aa925ae1bb93..943a0ad5a5cc 100644
--- a/science/py-gemmi/files/patch-CMakeLists.txt
+++ b/science/py-gemmi/files/patch-CMakeLists.txt
@@ -1,42 +1,40 @@
-- workaround for https://github.com/project-gemmi/gemmi/issues/257
-
---- CMakeLists.txt.orig 2023-03-06 11:12:31 UTC
+--- CMakeLists.txt.orig 2023-05-25 12:37:36 UTC
+++ CMakeLists.txt
-@@ -182,21 +182,23 @@ if (GEMMI_VERSION_INFO)
+@@ -187,20 +187,21 @@ if (GEMMI_VERSION_INFO)
target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${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}")
diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist
index 2ee4a839a8fb..78af5dd8e045 100644
--- a/science/py-gemmi/pkg-plist
+++ b/science/py-gemmi/pkg-plist
@@ -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