science/{,py-}spglib: update 2.0.2 → 2.1.0

Reported by:	portscout

11 files changed, 93 insertions, 35 deletions

diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile
index 80d49b2cea1b..c4a14c195afb 100644
--- a/science/avogadrolibs/Makefile
+++ b/science/avogadrolibs/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	avogadrolibs
 DISTVERSION=	1.97.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/octopus/Makefile b/science/octopus/Makefile
index 2db6784a4d57..1440b846b8b8 100644
--- a/science/octopus/Makefile
+++ b/science/octopus/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	octopus
 DISTVERSION=	11.4
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	science # chemistry
 MASTER_SITES=	https://octopus-code.org/download/${DISTVERSION}/
 
diff --git a/science/py-spglib/Makefile b/science/py-spglib/Makefile
index 00be8b2ed1ba..3a1a7b4d8bc3 100644
--- a/science/py-spglib/Makefile
+++ b/science/py-spglib/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	spglib
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.0.2
-PORTREVISION=	1
+DISTVERSION=	2.1.0
 CATEGORIES=	science python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -12,15 +11,19 @@ WWW=		https://atztogo.github.io/spglib/
 LICENSE=	BSD3CLAUSE
 
 BUILD_DEPENDS=	${PYNUMPY}
+LIB_DEPENDS=	libsymspg.so:science/spglib
 RUN_DEPENDS=	${PYNUMPY}
 
-USES=		python
-USE_PYTHON=	distutils autoplist pytest # tests fail to run, see https://github.com/spglib/spglib/issues/192
+USES=		cmake python
+USE_PYTHON=	flavors pytest # tests fail to run, see https://github.com/spglib/spglib/issues/192
 USE_GITHUB=	yes
 
+CMAKE_ARGS=	-DPython3_EXECUTABLE=${PYTHON_CMD}
+
 WRKSRC_SUBDIR=	python
 
-post-install:
-	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/spglib/_spglib*.so
+post-patch:
+	#@cd ${WRKSRC} && ${RLN} ../test .
+	@cd ${WRKSRC} && ${CP} -r ../test .
 
 .include <bsd.port.mk>
diff --git a/science/py-spglib/distinfo b/science/py-spglib/distinfo
index 4b1eec8259f9..3f4784db3f19 100644
--- a/science/py-spglib/distinfo
+++ b/science/py-spglib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1674925944
-SHA256 (spglib-spglib-v2.0.2_GH0.tar.gz) = 10e44a35099a0a5d0fc6ee0cdb39d472c23cb98b1f5167c0e2b08f6069f3db1e
-SIZE (spglib-spglib-v2.0.2_GH0.tar.gz) = 2880537
+TIMESTAMP = 1694412381
+SHA256 (spglib-spglib-v2.1.0_GH0.tar.gz) = 31bca273a1bc54e1cff4058eebe7c0a35d5f9b489579e84667d8e005c73dcc13
+SIZE (spglib-spglib-v2.1.0_GH0.tar.gz) = 2901649
diff --git a/science/py-spglib/files/patch-CMakeLists.txt b/science/py-spglib/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..ffabaf7a1e8c
--- /dev/null
+++ b/science/py-spglib/files/patch-CMakeLists.txt
@@ -0,0 +1,39 @@
+--- CMakeLists.txt.orig	2023-09-10 07:23:28 UTC
++++ CMakeLists.txt
+@@ -1,8 +1,13 @@
++cmake_minimum_required(VERSION 3.15)
++
++find_package(Spglib REQUIRED)
++find_package(Python3 COMPONENTS REQUIRED Interpreter Development.Module NumPy)
++
+ Python3_add_library(Spglib_python MODULE WITH_SOABI _spglib.c)
+ set_target_properties(Spglib_python PROPERTIES
+ 		OUTPUT_NAME _spglib)
+ target_link_libraries(Spglib_python PRIVATE
+-		Spglib_symspg Python3::NumPy)
++		Spglib::symspg Python3::NumPy)
+ if (NOT Python_INSTALL_DIR)
+ 	if (SKBUILD)
+ 		# If built with scikit-build-core, let it handle the installation
+@@ -12,7 +17,7 @@ if (NOT Python_INSTALL_DIR)
+ 		set(Python_INSTALL_DIR ${Python3_SITEARCH}/spglib)
+ 	endif ()
+ endif ()
+-if (SPGLIB_INSTALL)
++if (TRUE)
+ 	if (WIN32)
+ 		# Windows needs RUNTIME as well to install the .dll file to
+ 		install(TARGETS Spglib_symspg
+@@ -22,9 +27,9 @@ if (SPGLIB_INSTALL)
+ 	else ()
+ 		# TODO: Cmake forces to install PUBLIC_HEADER when defined
+ 		# https://gitlab.kitware.com/cmake/cmake/-/issues/24326
+-		install(TARGETS Spglib_symspg
+-				LIBRARY DESTINATION ${Python_INSTALL_DIR} COMPONENT Spglib_Runtime
+-				PUBLIC_HEADER DESTINATION ${Python_INSTALL_DIR} COMPONENT Spglib_Runtime)
++		#install(TARGETS Spglib_symspg
++		#		LIBRARY DESTINATION ${Python_INSTALL_DIR} COMPONENT Spglib_Runtime
++		#		PUBLIC_HEADER DESTINATION ${Python_INSTALL_DIR} COMPONENT Spglib_Runtime)
+ 	endif ()
+ 	install(TARGETS Spglib_python
+ 			LIBRARY DESTINATION ${Python_INSTALL_DIR} COMPONENT Spglib_Runtime)
diff --git a/science/py-spglib/pkg-plist b/science/py-spglib/pkg-plist
new file mode 100644
index 000000000000..55a2e8a2dc92
--- /dev/null
+++ b/science/py-spglib/pkg-plist
@@ -0,0 +1,3 @@
+%%PYTHON_SITELIBDIR%%/spglib/__init__.py
+%%PYTHON_SITELIBDIR%%/spglib/_spglib%%PYTHON_EXT_SUFFIX%%.so
+%%PYTHON_SITELIBDIR%%/spglib/spglib.py
diff --git a/science/sirius/Makefile b/science/sirius/Makefile
index 87a6b3de5ccf..2dead0619269 100644
--- a/science/sirius/Makefile
+++ b/science/sirius/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	sirius
 DISTVERSIONPREFIX=	v
 DISTVERSION=	7.4.3
+PORTREVISION=	1
 CATEGORIES=	science
 PKGNAMESUFFIX=	-quantum-chemistry # other software also has the name "sirius"
 
diff --git a/science/spglib/Makefile b/science/spglib/Makefile
index 0f3dcdf481fb..2196e898c783 100644
--- a/science/spglib/Makefile
+++ b/science/spglib/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	spglib
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.0.2
-PORTREVISION=	1
+DISTVERSION=	2.1.0
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -11,12 +10,15 @@ WWW=		https://spglib.github.io/spglib/
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-USES=		cmake
+USES=		cmake:testing
 USE_GITHUB=	yes
 USE_LDCONFIG=	yes
 
+CMAKE_OFF=	SPGLIB_WITH_TESTS
+CMAKE_TESTING_ON=	SPGLIB_WITH_TESTS
+
 .if !exists(/usr/include/omp.h)
-CMAKE_OFF+=	USE_OMP
+CMAKE_OFF+=	SPGLIB_USE_OMP
 .else
 FORTRAN_LDFLAGS=	-lomp # workaround for: undefined reference to `__kmpc_fork_call'
 .endif
@@ -26,13 +28,6 @@ OPTIONS_DEFAULT=	FORTRAN
 OPTIONS_SUB=		yes
 
 FORTRAN_USES=		fortran
-FORTRAN_CMAKE_BOOL=	WITH_Fortran
-
-do-test: # from test/README.md
-	cd ${WRKSRC}/test && \
-		${CMAKE_BIN} -S . -B build -DUSE_SANITIZER="Address" -DCMAKE_BUILD_TYPE="Debug" && \
-		${CMAKE_BIN} --build build -j ${_MAKE_JOBS} && \
-		cd build && \
-		ctest
+FORTRAN_CMAKE_BOOL=	SPGLIB_WITH_Fortran
 
 .include <bsd.port.mk>
diff --git a/science/spglib/distinfo b/science/spglib/distinfo
index ae6151d27fc1..0fba2daad36c 100644
--- a/science/spglib/distinfo
+++ b/science/spglib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1674925518
-SHA256 (spglib-spglib-v2.0.2_GH0.tar.gz) = 10e44a35099a0a5d0fc6ee0cdb39d472c23cb98b1f5167c0e2b08f6069f3db1e
-SIZE (spglib-spglib-v2.0.2_GH0.tar.gz) = 2880537
+TIMESTAMP = 1694406506
+SHA256 (spglib-spglib-v2.1.0_GH0.tar.gz) = 31bca273a1bc54e1cff4058eebe7c0a35d5f9b489579e84667d8e005c73dcc13
+SIZE (spglib-spglib-v2.1.0_GH0.tar.gz) = 2901649
diff --git a/science/spglib/files/patch-fortran_CMakeLists.txt b/science/spglib/files/patch-fortran_CMakeLists.txt
new file mode 100644
index 000000000000..5cbec0d72be8
--- /dev/null
+++ b/science/spglib/files/patch-fortran_CMakeLists.txt
@@ -0,0 +1,13 @@
+- remove compiler ID from include path
+
+--- fortran/CMakeLists.txt.orig	2023-09-11 04:42:53 UTC
++++ fortran/CMakeLists.txt
+@@ -22,7 +22,7 @@ if (SPGLIB_INSTALL)
+ 	# Adapting the standard from fortran-stdlib
+ 	# https://gitlab.kitware.com/cmake/cmake/-/issues/19608
+ 	# https://discourse.cmake.org/t/api-design-c-modules-source-listings-and-interface-properties/5389/14
+-	cmake_path(APPEND CMAKE_INSTALL_INCLUDEDIR ${PROJECT_NAME} "${CMAKE_Fortran_COMPILER_ID}-${CMAKE_Fortran_COMPILER_VERSION}"
++	cmake_path(APPEND CMAKE_INSTALL_INCLUDEDIR
+ 			OUTPUT_VARIABLE _DEFAULT_CMAKE_INSTALL_MODULEDIR)
+ 	set(CMAKE_INSTALL_MODULEDIR ${_DEFAULT_CMAKE_INSTALL_MODULEDIR}
+ 			CACHE STRING
diff --git a/science/spglib/pkg-plist b/science/spglib/pkg-plist
index 241ebc0b5c93..065a9b090382 100644
--- a/science/spglib/pkg-plist
+++ b/science/spglib/pkg-plist
@@ -1,14 +1,18 @@
-%%FORTRAN%%bin/spglib_example_fortran.X
 include/spglib.h
-include/spglib_f08.f90
-%%FORTRAN%%lib/libspglib_f08.a
+%%FORTRAN%%include/spglib_f08.F90
+%%FORTRAN%%include/spglib_f08.mod
+lib/cmake/Spglib/PackageCompsHelper.cmake
+lib/cmake/Spglib/SpglibConfig.cmake
+lib/cmake/Spglib/SpglibConfigVersion.cmake
+%%FORTRAN%%lib/cmake/Spglib/SpglibTargets_fortran-%%CMAKE_BUILD_TYPE%%.cmake
+%%FORTRAN%%lib/cmake/Spglib/SpglibTargets_fortran.cmake
+lib/cmake/Spglib/SpglibTargets_shared-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/Spglib/SpglibTargets_shared.cmake
 %%FORTRAN%%lib/libspglib_f08.so
-%%FORTRAN%%lib/libspglib_f08.so.1
-%%FORTRAN%%lib/libspglib_f08.so.2.0.2
-lib/libsymspg.a
+%%FORTRAN%%lib/libspglib_f08.so.2
+%%FORTRAN%%lib/libspglib_f08.so.2.1.0
 lib/libsymspg.so
-lib/libsymspg.so.1
-lib/libsymspg.so.2.0.2
-%%FORTRAN%%lib/spglib_f08.mod
+lib/libsymspg.so.2
+lib/libsymspg.so.2.1.0
 libdata/pkgconfig/spglib.pc
 %%FORTRAN%%libdata/pkgconfig/spglib_f08.pc