science/{,py-}avogadrolibs: update 1.97.0 → 1.99.0

Reported by:	portscout

science/avogadrolibs/Makefile

@@ -1,6 +1,5 @@
 PORTNAME=	avogadrolibs
-DISTVERSION=	1.97.0
-PORTREVISION=	3
+DISTVERSION=	1.99.0
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -13,19 +12,20 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 TEST_DEPENDS=	googletest>0:devel/googletest \
 		molequeue>0:misc/molequeue
 
-USES=		cmake:testing compiler:c++17-lang eigen:3,build,run # eigen needs to be 'run' because it is written into cmake files
+USES=		cmake:testing compiler:c++17-lang eigen:3,build,run localbase # eigen needs to be 'run' because it is written into cmake files
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	OpenChemistry
 GH_TUPLE=	OpenChemistry:molecules:b1e16c5:molecules/../molecules \
-		OpenChemistry:crystals:73a5bbc:crystals/../crystals
+		OpenChemistry:crystals:73a5bbc:crystals/../crystals \
+		OpenChemistry:fragments:8dc711a:fragments/../fragments
 
 CMAKE_ON=		BUILD_SHARED_LIBS
 CMAKE_TESTING_ON=	ENABLE_TESTING
 
 OPTIONS_DEFINE=		HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB VTK
-OPTIONS_DEFAULT=	LIBARCHIVE LIBMSYM OPENGL QT5 SPGLIB # MMTF
+OPTIONS_DEFAULT=	HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB
 OPTIONS_SUB=		yes
 
 HDF5_CMAKE_BOOL=	USE_HDF5
@@ -44,8 +44,8 @@ LIBMSYM_IMPLIES=	QT5 # enables the 'symmetry' Qt plugin
 
 MMTF_DESC=		Enable optional features using mmtf
 MMTF_CMAKE_BOOL=	USE_MMTF
-MMTF_BUILD_DEPENDS=	mmtf-cpp>0:science/mmtf-cpp
-MMTF_BROKEN=		see https://github.com/OpenChemistry/avogadrolibs/issues/1185
+MMTF_BUILD_DEPENDS=	mmtf-cpp>0:science/mmtf-cpp \
+			${LOCALBASE}/include/boost/predef/other/endian.h:devel/boost-libs # needed by /usr/local/include/msgpack/sysdep.hpp:102 while boost is an optional dependency there
 
 OPENGL_CMAKE_BOOL=	USE_OPENGL
 OPENGL_USES=		gl
@@ -58,7 +58,7 @@ QT5_IMPLIES=		OPENGL
 
 SPGLIB_DESC=		Enable optional features using spglib
 SPGLIB_CMAKE_BOOL=	USE_SPGLIB
-SPGLIB_CMAKE_ON=	-DSPGLIB_INCLUDE_DIR=${LOCALBASE}/include/spglib
+SPGLIB_CMAKE_ON=	-DSPGLIB_INCLUDE_DIR=${LOCALBASE}/include
 SPGLIB_LIB_DEPENDS=	libsymspg.so:science/spglib
 SPGLIB_IMPLIES=		QT5 # USE_SPGLIB only installs header file without USE_QT, and also installs SpaceGroup.a with USE_QT, see https://github.com/OpenChemistry/avogadrolibs/issues/610
 

science/avogadrolibs/distinfo

@@ -1,7 +1,9 @@
-TIMESTAMP = 1665902523
-SHA256 (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 46641504a1808c5ff6fb7d66be48d866848203899025fd386cc6e3dd5d9ec342
-SIZE (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 11456702
+TIMESTAMP = 1707763072
+SHA256 (OpenChemistry-avogadrolibs-1.99.0_GH0.tar.gz) = 34808e3c602b0f60f3c160ff0220832aee777db86e962e3f958c6327fb434063
+SIZE (OpenChemistry-avogadrolibs-1.99.0_GH0.tar.gz) = 4858298
 SHA256 (OpenChemistry-molecules-b1e16c5_GH0.tar.gz) = 9aa48dd94022e022d2c9eb9802ba72a4bfd69c04a08a36d562bfffc7d24bf99b
 SIZE (OpenChemistry-molecules-b1e16c5_GH0.tar.gz) = 207309
 SHA256 (OpenChemistry-crystals-73a5bbc_GH0.tar.gz) = f48a06bb9e4bdc1f7dbed22fe31b187b5aa490f5796f6927001228e9ced41a5e
 SIZE (OpenChemistry-crystals-73a5bbc_GH0.tar.gz) = 157627
+SHA256 (OpenChemistry-fragments-8dc711a_GH0.tar.gz) = 9d8060a66716f9c78d0ed2bb3b9a2a4f57700ce880ce548dc062698505b7eae7
+SIZE (OpenChemistry-fragments-8dc711a_GH0.tar.gz) = 2553176

science/avogadrolibs/files/patch-CMakeLists.txt

@@ -1,8 +1,8 @@
 - git is only needed when 'molecules' and 'crystals' aren't supplied by the caller
 
---- CMakeLists.txt.orig	2021-06-04 09:02:43 UTC
+--- CMakeLists.txt.orig	2024-02-10 14:49:49 UTC
 +++ CMakeLists.txt
-@@ -31,8 +31,8 @@ set(AvogadroLibs_VERSION_MINOR   "94")
+@@ -26,8 +26,8 @@ set(AvogadroLibs_VERSION
  set(AvogadroLibs_VERSION_PATCH   "0")
  set(AvogadroLibs_VERSION
    "${AvogadroLibs_VERSION_MAJOR}.${AvogadroLibs_VERSION_MINOR}.${AvogadroLibs_VERSION_PATCH}")

science/avogadrolibs/files/patch-avogadro_qtplugins_templatetool_CMakeLists.txt

@@ -0,0 +1,13 @@
+- backport a fix
+
+--- avogadro/qtplugins/templatetool/CMakeLists.txt.orig	2024-02-12 18:50:42 UTC
++++ avogadro/qtplugins/templatetool/CMakeLists.txt
+@@ -24,7 +24,7 @@ avogadro_plugin(TemplateTool
+ )
+
+ # Install the fragments
+-set(_molecules "${AvogadroLibs_SOURCE_DIR}/../fragments")
++set(_fragments "${AvogadroLibs_SOURCE_DIR}/../fragments")
+
+ # Look in parallel directory for the molecule fragment repository
+ if(NOT EXISTS "${_fragments}")