git: 1d10f02d6c4d - main - science/{,py-}gemmi: update 0.7.1 → 0.7.3
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Date: Tue, 22 Jul 2025 07:11:09 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=1d10f02d6c4d703c46a0d1fd543669c936e40450
commit 1d10f02d6c4d703c46a0d1fd543669c936e40450
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-07-22 04:31:22 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-07-22 07:10:56 +0000
science/{,py-}gemmi: update 0.7.1 → 0.7.3
---
science/gemmi/Makefile | 7 ++++---
science/gemmi/distinfo | 6 +++---
science/gemmi/pkg-plist | 1 +
science/py-gemmi/Makefile | 7 +++++--
science/py-gemmi/distinfo | 6 +++---
science/py-gemmi/files/patch-CMakeLists.txt | 26 ++++++++++++--------------
science/py-gemmi/pkg-plist | 2 +-
7 files changed, 29 insertions(+), 26 deletions(-)
diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index bca3ebaed373..aa0f3083bca2 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -1,11 +1,12 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
-DISTVERSION= 0.7.1
+DISTVERSION= 0.7.3
CATEGORIES= science # chemistry
MAINTAINER= yuri@FreeBSD.org
COMMENT= Macromolecular crystallography library and utilities
-WWW= https://gemmi.readthedocs.io/en/latest/
+WWW= https://gemmi.readthedocs.io/en/latest/ \
+ https://github.com/project-gemmi/gemmi
LICENSE= MPL20
LICENSE_FILE= ${WRKSRC}/LICENSE.txt
@@ -25,7 +26,7 @@ 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):
+# tests as of 0.7.3 (run work/.build/cpptest):
# [doctest] test cases: 14 | 14 passed | 0 failed | 0 skipped
# [doctest] assertions: 129 | 129 passed | 0 failed |
# [doctest] Status: SUCCESS!
diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo
index 49c83ebc50e8..a7884ddf53a9 100644
--- a/science/gemmi/distinfo
+++ b/science/gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1742884325
-SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393
-SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265
+TIMESTAMP = 1753139349
+SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3
+SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234
diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist
index c28c9d130ae7..965571f541a2 100644
--- a/science/gemmi/pkg-plist
+++ b/science/gemmi/pkg-plist
@@ -23,6 +23,7 @@ include/gemmi/crd.hpp
include/gemmi/ddl.hpp
include/gemmi/dencalc.hpp
include/gemmi/dirwalk.hpp
+include/gemmi/dssp.hpp
include/gemmi/ecalc.hpp
include/gemmi/eig3.hpp
include/gemmi/elem.hpp
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile
index 2aac5d8717f0..9e7f9f8d7544 100644
--- a/science/py-gemmi/Makefile
+++ b/science/py-gemmi/Makefile
@@ -1,12 +1,13 @@
PORTNAME= gemmi
DISTVERSIONPREFIX= v
-DISTVERSION= 0.7.1
+DISTVERSION= 0.7.3
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Macromolecular crystallography library and utilities
-WWW= https://gemmi.readthedocs.io/en/latest/
+WWW= https://gemmi.readthedocs.io/en/latest/ \
+ https://github.com/project-gemmi/gemmi
LICENSE= MPL20
LICENSE_FILE= ${WRKSRC}/LICENSE.txt
@@ -36,4 +37,6 @@ PLIST_SUB= VER=${PORTVERSION}
do-test:
@cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/
+# tests as of 0.7.3: test 'test_syntax_error' fails with syntax error, see https://github.com/project-gemmi/gemmi/issues/384
+
.include <bsd.port.mk>
diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo
index 9050772d8cc8..b40d35b8cada 100644
--- a/science/py-gemmi/distinfo
+++ b/science/py-gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1742885714
-SHA256 (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393
-SIZE (project-gemmi-gemmi-v0.7.1_GH0.tar.gz) = 1910265
+TIMESTAMP = 1753140186
+SHA256 (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = ed5e1d0665f27d623d877fa36f6c99a5de21310cc8715337ff9f6b545bd2e9d3
+SIZE (project-gemmi-gemmi-v0.7.3_GH0.tar.gz) = 1924234
diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt
index d75096e3228b..62637e7014cd 100644
--- a/science/py-gemmi/files/patch-CMakeLists.txt
+++ b/science/py-gemmi/files/patch-CMakeLists.txt
@@ -1,4 +1,4 @@
---- CMakeLists.txt.orig 2025-03-24 16:35:30 UTC
+--- CMakeLists.txt.orig 2025-07-05 13:51:16 UTC
+++ CMakeLists.txt
@@ -6,7 +6,7 @@ string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-de
string(REGEX REPLACE ".+\"([0-9]+\.[0-9]+\.[0-9]+)(-dev)?\"" "\\1"
@@ -27,7 +27,7 @@
-target_include_directories(gemmi_headers INTERFACE
- "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
- "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
--target_compile_features(gemmi_headers INTERFACE cxx_std_17)
+-target_compile_features(gemmi_headers INTERFACE cxx_std_14)
-set_target_properties(gemmi_headers PROPERTIES EXPORT_NAME headers)
-
-add_library(gemmi_cpp
@@ -37,7 +37,7 @@
- src/monlib.cpp src/mtz.cpp src/mtz2cif.cpp
- src/pdb.cpp src/polyheur.cpp src/read_cif.cpp
- src/resinfo.cpp src/riding_h.cpp
-- src/select.cpp src/sprintf.cpp src/symmetry.cpp
+- src/select.cpp src/sprintf.cpp src/dssp.cpp src/symmetry.cpp
- src/to_json.cpp src/to_mmcif.cpp src/to_pdb.cpp src/topo.cpp
- src/xds_ascii.cpp)
-add_library(gemmi::gemmi_cpp ALIAS gemmi_cpp)
@@ -98,8 +98,8 @@
target_include_directories(gemmi-${target} PRIVATE
"${CMAKE_CURRENT_SOURCE_DIR}/third_party")
endfunction()
-@@ -336,7 +274,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog)
- prog/xds2mtz.cpp
+@@ -337,7 +275,7 @@ add_executable(gemmi::prog ALIAS gemmi_prog)
+ prog/wcn.cpp prog/xds2mtz.cpp
$<TARGET_OBJECTS:options>)
add_executable(gemmi::prog ALIAS gemmi_prog)
-target_link_libraries(gemmi_prog PRIVATE gemmi_cpp)
@@ -107,7 +107,7 @@
target_include_directories(gemmi_prog PRIVATE "${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)
-@@ -376,7 +314,7 @@ target_compile_definitions(cpptest PRIVATE USE_STD_SNP
+@@ -377,17 +315,17 @@ 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)
@@ -115,11 +115,9 @@
+target_link_libraries(cpptest PRIVATE gemmi)
target_include_directories(cpptest PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/third_party")
- add_executable(hello EXCLUDE_FROM_ALL examples/hello.cpp)
-@@ -384,11 +322,11 @@ add_executable(doc_example EXCLUDE_FROM_ALL
add_executable(doc_example EXCLUDE_FROM_ALL
docs/code/sym.cpp docs/code/elem.cpp docs/code/resinfo.cpp
- docs/code/cell.cpp docs/code/mutate.cpp src/resinfo.cpp)
+ docs/code/cell.cpp docs/code/mutate.cpp)
-target_link_libraries(doc_example PRIVATE gemmi_cpp)
+target_link_libraries(doc_example PRIVATE gemmi)
add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp)
@@ -130,7 +128,7 @@
# always compile these tests with assertions enabled
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel")
-@@ -396,14 +334,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu
+@@ -395,14 +333,14 @@ add_executable(test_disulf EXCLUDE_FROM_ALL tests/disu
endif()
add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp)
@@ -148,16 +146,16 @@
enable_testing()
-@@ -440,7 +378,7 @@ if (benchmark_FOUND)
+@@ -439,7 +377,7 @@ if (benchmark_FOUND)
foreach(b stoi elem mod niggli pdb resinfo round sym writecif)
add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp)
- if (b MATCHES "elem|resinfo|pdb|writecif")
+ if (b MATCHES "elem|resinfo|pdb|sym|writecif")
- target_link_libraries(${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
-@@ -481,11 +419,11 @@ if (USE_PYTHON)
+@@ -480,11 +418,11 @@ if (USE_PYTHON)
python/unitcell.cpp python/write.cpp)
if (STANDALONE_PYTHON_MODULE)
@@ -172,7 +170,7 @@
endif()
set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi_ext)
if (CMAKE_CONFIGURATION_TYPES)
-@@ -568,19 +506,19 @@ endif()
+@@ -567,19 +505,19 @@ endif()
install(TARGETS gemmi_prog EXPORT GemmiTargets)
endif()
diff --git a/science/py-gemmi/pkg-plist b/science/py-gemmi/pkg-plist
index 7cf8db927729..9201705db9d6 100644
--- a/science/py-gemmi/pkg-plist
+++ b/science/py-gemmi/pkg-plist
@@ -7,7 +7,6 @@
%%PYTHON_SITELIBDIR%%/gemmi/examples/cif_i_sigi.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/col_order.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/from_json.py
-%%PYTHON_SITELIBDIR%%/gemmi/examples/hello.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/long_geom.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/map2mtz.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/maskcheck.py
@@ -22,6 +21,7 @@
%%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/read_cif.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py