science/plumed: Update 2.7.2 -> 2.8b

3 files changed, 43 insertions, 32 deletions

diff --git a/science/plumed/Makefile b/science/plumed/Makefile
index f5a4192bf5e9..7d6f4c961c4a 100644
--- a/science/plumed/Makefile
+++ b/science/plumed/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	plumed
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.7.2
+DISTVERSION=	2.8b
 CATEGORIES=	science graphics
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -11,20 +11,23 @@ LICENSE_FILE=	${WRKSRC}/COPYING.LESSER
 
 BROKEN_i386=	undefined reference to `__atomic_load'
 
-BUILD_DEPENDS=	bash:shells/bash \
-		xxd:editors/vim
+BUILD_DEPENDS=	bash:shells/bash
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		autoreconf compiler:c++11-lang gmake pkgconfig shebangfix
+USE_LDCONFIG=	yes
+
 SHEBANG_GLOB=	*.sh
-SHEBANG_FILES=	src/maketools/makecmd
-GNU_CONFIGURE=	yes
+SHEBANG_FILES=	src/maketools/makecmd src/maketools/xxd
+
 USE_GITHUB=	yes
 GH_PROJECT=	plumed2
-USE_LDCONFIG=	yes
 
+GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--enable-shared --disable-python
 
+TEST_TARGET=	test # https://github.com/plumed/plumed2/issues/781
+
 post-patch:
 	@${REINPLACE_CMD} -e 's|#! /bin/bash|#! ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/lib/Makefile
 
diff --git a/science/plumed/distinfo b/science/plumed/distinfo
index 14c498df04f7..01fa05ef64b1 100644
--- a/science/plumed/distinfo
+++ b/science/plumed/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1627490858
-SHA256 (plumed-plumed2-v2.7.2_GH0.tar.gz) = c9a31e68d6440828cf186ca43c9e11a5e5c7ad1c96b2b66ed5a5a141fc954373
-SIZE (plumed-plumed2-v2.7.2_GH0.tar.gz) = 106485846
+TIMESTAMP = 1641277208
+SHA256 (plumed-plumed2-v2.8b_GH0.tar.gz) = 1fccc6040951d64dfb34b10f0ed6ad8755c08e47921f2176e8121e54038ce29f
+SIZE (plumed-plumed2-v2.8b_GH0.tar.gz) = 107891161
diff --git a/science/plumed/pkg-plist b/science/plumed/pkg-plist
index 99b93e4e1d95..ce031e5ccc6b 100644
--- a/science/plumed/pkg-plist
+++ b/science/plumed/pkg-plist
@@ -195,6 +195,8 @@ include/plumed/tools/SwitchingFunction.h
 include/plumed/tools/Tensor.h
 include/plumed/tools/Tools.h
 include/plumed/tools/Torsion.h
+include/plumed/tools/Tree.h
+include/plumed/tools/TypesafePtr.h
 include/plumed/tools/Units.h
 include/plumed/tools/Vector.h
 include/plumed/tools/h36.h
@@ -215,10 +217,15 @@ include/plumed/vesselbase/ValueVessel.h
 include/plumed/vesselbase/Vessel.h
 include/plumed/vesselbase/VesselRegister.h
 include/plumed/wrapper/Plumed.h
+include/plumed/xdrfile/xdrfile.h
+include/plumed/xdrfile/xdrfile_trr.h
+include/plumed/xdrfile/xdrfile_xtc.h
 lib/libplumed.a
 lib/libplumed.so
 lib/libplumedKernel.so
 lib/libplumedWrapper.a
+lib/plumed/fortran/plumed.f90
+lib/plumed/fortran/plumed_f08.f90
 lib/plumed/modulefile
 lib/plumed/patches/gromacs-2019.6.config
 lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt
@@ -262,29 +269,29 @@ lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.h
 lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
 lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/runner.cpp
 lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/runner.cpp.preplumed
-lib/plumed/patches/gromacs-2021.config
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/CMakeLists.txt
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/CMakeLists.txt.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdlib/expanded.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdlib/expanded.cpp.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdlib/expanded.h
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdlib/expanded.h.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdlib/sim_util.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdlib/sim_util.cpp.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/legacymdrunoptions.h
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/md.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/md.cpp.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/minimize.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/minimize.cpp.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/replicaexchange.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/replicaexchange.h
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/runner.cpp
-lib/plumed/patches/gromacs-2021.diff/src/gromacs/mdrun/runner.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.config
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/CMakeLists.txt
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/CMakeLists.txt.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.h
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.h.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/sim_util.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/sim_util.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.h
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/md.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/md.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/minimize.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/minimize.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.h
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/runner.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/runner.cpp.preplumed
 lib/plumed/patches/gromacs-4.5.7.config
 lib/plumed/patches/gromacs-4.5.7.diff
 lib/plumed/patches/namd-2.12.config
@@ -406,6 +413,7 @@ lib/plumed/vim/help/FRET.txt
 lib/plumed/vim/help/FUNCPATHGENERAL.txt
 lib/plumed/vim/help/FUNCPATHMSD.txt
 lib/plumed/vim/help/FUNCSUMHILLS.txt
+lib/plumed/vim/help/GHBFIX.txt
 lib/plumed/vim/help/GHOST.txt
 lib/plumed/vim/help/GPROPERTYMAP.txt
 lib/plumed/vim/help/GRID_TO_XYZ.txt