Date: Sun, 19 Apr 2026 07:10:38 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 6978db2dccd9 - main - science/gromacs: update 2025.4=?utf-8?Q? =E2=86=92 202?=6.1 Message-ID: <69e47fee.42be9.220a2d16@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=6978db2dccd902340ac8733dd88b958d1dd09215 commit 6978db2dccd902340ac8733dd88b958d1dd09215 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-04-19 04:46:06 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-04-19 07:10:33 +0000 science/gromacs: update 2025.4 → 2026.1 --- science/gromacs/Makefile | 6 +- science/gromacs/distinfo | 6 +- science/gromacs/pkg-plist | 228 +++++++++++++++++++++++++++------------------- science/votca/Makefile | 1 + 4 files changed, 140 insertions(+), 101 deletions(-) diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index 558eab81f1ba..310a92e93c3f 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,6 +1,5 @@ PORTNAME= gromacs -DISTVERSION= 2025.4 -PORTREVISION= 1 +DISTVERSION= 2026.1 CATEGORIES= science MASTER_SITES= https://ftp.gromacs.org/pub/gromacs/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} # only for googletest @@ -126,7 +125,6 @@ post-patch: @${REINPLACE_CMD} -e '/CMAKE_REQUIRED_LIBRARIES/d' \ ${WRKSRC}/cmake/gmxTestdlopen.cmake -# tests as of 2025.3: 100% tests passed, 0 tests failed out of 92 -# 2025.4: tests fail to compile: https://gitlab.com/gromacs/gromacs/-/issues?show=eyJpaWQiOiI1NTAxIiwiZnVsbF9wYXRoIjoiZ3JvbWFjcy9ncm9tYWNzIiwiaWQiOjE3NzU1MDUzMn0%3D +# tests as of 2026.1: 100% tests passed, 0 tests failed out of 104 .include <bsd.port.mk> diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo index 4cf0d1f50a41..d2944f6d15f0 100644 --- a/science/gromacs/distinfo +++ b/science/gromacs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1763922155 -SHA256 (gromacs-2025.4.tar.gz) = ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3 -SIZE (gromacs-2025.4.tar.gz) = 44406127 +TIMESTAMP = 1776566754 +SHA256 (gromacs-2026.1.tar.gz) = d95a313f56db7e05ee3a21e50f582fdee5176c2f60b900bab2461fd95c5e81be +SIZE (gromacs-2026.1.tar.gz) = 45914061 diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist index ef617f0ab641..6ba4b46dbb29 100644 --- a/science/gromacs/pkg-plist +++ b/science/gromacs/pkg-plist @@ -24,92 +24,92 @@ include/gmxapi/session/resources.h include/gmxapi/status.h include/gmxapi/system.h include/gmxapi/version.h -%%LEGACY%%include/gromacs/analysisdata/abstractdata.h -%%LEGACY%%include/gromacs/analysisdata/analysisdata.h -%%LEGACY%%include/gromacs/analysisdata/arraydata.h -%%LEGACY%%include/gromacs/analysisdata/dataframe.h -%%LEGACY%%include/gromacs/analysisdata/datamodule.h -%%LEGACY%%include/gromacs/analysisdata/modules/average.h -%%LEGACY%%include/gromacs/analysisdata/modules/displacement.h -%%LEGACY%%include/gromacs/analysisdata/modules/histogram.h -%%LEGACY%%include/gromacs/analysisdata/modules/lifetime.h -%%LEGACY%%include/gromacs/analysisdata/modules/plot.h -%%LEGACY%%include/gromacs/external/boost/stl_interfaces/fwd.hpp -%%LEGACY%%include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -%%LEGACY%%include/gromacs/fileio/confio.h -%%LEGACY%%include/gromacs/fileio/filetypes.h -%%LEGACY%%include/gromacs/fileio/oenv.h -%%LEGACY%%include/gromacs/fileio/pdbio.h -%%LEGACY%%include/gromacs/fileio/tpxio.h -%%LEGACY%%include/gromacs/fileio/trxio.h -%%LEGACY%%include/gromacs/libgromacs_export.h -%%LEGACY%%include/gromacs/math/do_fit.h -%%LEGACY%%include/gromacs/math/functions.h -%%LEGACY%%include/gromacs/math/units.h -%%LEGACY%%include/gromacs/math/utilities.h -%%LEGACY%%include/gromacs/math/vec.h -%%LEGACY%%include/gromacs/math/vectypes.h +include/gromacs/analysisdata/abstractdata.h +include/gromacs/analysisdata/analysisdata.h +include/gromacs/analysisdata/arraydata.h +include/gromacs/analysisdata/dataframe.h +include/gromacs/analysisdata/datamodule.h +include/gromacs/analysisdata/modules/average.h +include/gromacs/analysisdata/modules/displacement.h +include/gromacs/analysisdata/modules/histogram.h +include/gromacs/analysisdata/modules/lifetime.h +include/gromacs/analysisdata/modules/plot.h +include/gromacs/external/boost/stl_interfaces/fwd.hpp +include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp +include/gromacs/fileio/confio.h +include/gromacs/fileio/filetypes.h +include/gromacs/fileio/oenv.h +include/gromacs/fileio/pdbio.h +include/gromacs/fileio/tpxio.h +include/gromacs/fileio/trxio.h +include/gromacs/libgromacs_export.h +include/gromacs/math/do_fit.h +include/gromacs/math/functions.h +include/gromacs/math/units.h +include/gromacs/math/utilities.h include/gromacs/mdrun/simulationinputhandle.h -%%LEGACY%%include/gromacs/mdtypes/inputrec.h -%%LEGACY%%include/gromacs/mdtypes/md_enums.h -%%LEGACY%%include/gromacs/options/abstractoption.h -%%LEGACY%%include/gromacs/options/basicoptions.h -%%LEGACY%%include/gromacs/options/filenameoption.h -%%LEGACY%%include/gromacs/options/filenameoptionmanager.h -%%LEGACY%%include/gromacs/options/ioptionsbehavior.h -%%LEGACY%%include/gromacs/options/ioptionscontainer.h -%%LEGACY%%include/gromacs/options/ioptionscontainerwithsections.h -%%LEGACY%%include/gromacs/options/ivaluestore.h -%%LEGACY%%include/gromacs/options/optionfiletype.h -%%LEGACY%%include/gromacs/options/optionflags.h -%%LEGACY%%include/gromacs/options/options.h -%%LEGACY%%include/gromacs/options/timeunitmanager.h -%%LEGACY%%include/gromacs/pbcutil/pbc.h -%%LEGACY%%include/gromacs/restraint/restraintpotential.h -%%LEGACY%%include/gromacs/selection/indexutil.h -%%LEGACY%%include/gromacs/selection/nbsearch.h -%%LEGACY%%include/gromacs/selection/position.h -%%LEGACY%%include/gromacs/selection/selection.h -%%LEGACY%%include/gromacs/selection/selectioncollection.h -%%LEGACY%%include/gromacs/selection/selectionenums.h -%%LEGACY%%include/gromacs/selection/selectionoption.h -%%LEGACY%%include/gromacs/selection/selectionoptionbehavior.h -%%LEGACY%%include/gromacs/selection/selectionoptionmanager.h -%%LEGACY%%include/gromacs/topology/atomprop.h -%%LEGACY%%include/gromacs/topology/atoms.h -%%LEGACY%%include/gromacs/topology/block.h -%%LEGACY%%include/gromacs/topology/forcefieldparameters.h -%%LEGACY%%include/gromacs/topology/idef.h -%%LEGACY%%include/gromacs/topology/ifunc.h -%%LEGACY%%include/gromacs/topology/index.h -%%LEGACY%%include/gromacs/topology/symtab.h -%%LEGACY%%include/gromacs/topology/topology.h -%%LEGACY%%include/gromacs/topology/topology_enums.h -%%LEGACY%%include/gromacs/trajectory/trajectoryframe.h -%%LEGACY%%include/gromacs/trajectoryanalysis/analysismodule.h -%%LEGACY%%include/gromacs/trajectoryanalysis/analysissettings.h -%%LEGACY%%include/gromacs/trajectoryanalysis/cmdlinerunner.h -%%LEGACY%%include/gromacs/trajectoryanalysis/topologyinformation.h -%%LEGACY%%include/gromacs/utility/arrayref.h -%%LEGACY%%include/gromacs/utility/basedefinitions.h -%%LEGACY%%include/gromacs/utility/baseversion.h -%%LEGACY%%include/gromacs/utility/classhelpers.h -%%LEGACY%%include/gromacs/utility/current_function.h -%%LEGACY%%include/gromacs/utility/enumerationhelpers.h -%%LEGACY%%include/gromacs/utility/exceptions.h -%%LEGACY%%include/gromacs/utility/fileptr.h -%%LEGACY%%include/gromacs/utility/flags.h -%%LEGACY%%include/gromacs/utility/futil.h -%%LEGACY%%include/gromacs/utility/gmxassert.h -%%LEGACY%%include/gromacs/utility/listoflists.h -%%LEGACY%%include/gromacs/utility/pleasecite.h -%%LEGACY%%include/gromacs/utility/programcontext.h -%%LEGACY%%include/gromacs/utility/range.h -%%LEGACY%%include/gromacs/utility/real.h -%%LEGACY%%include/gromacs/utility/smalloc.h -%%LEGACY%%include/gromacs/utility/stringutil.h -%%LEGACY%%include/gromacs/utility/unique_cptr.h -%%LEGACY%%include/gromacs/version.h +include/gromacs/mdtypes/inputrec.h +include/gromacs/mdtypes/md_enums.h +include/gromacs/options/abstractoption.h +include/gromacs/options/basicoptions.h +include/gromacs/options/filenameoption.h +include/gromacs/options/filenameoptionmanager.h +include/gromacs/options/ioptionsbehavior.h +include/gromacs/options/ioptionscontainer.h +include/gromacs/options/ioptionscontainerwithsections.h +include/gromacs/options/ivaluestore.h +include/gromacs/options/optionfiletype.h +include/gromacs/options/optionflags.h +include/gromacs/options/options.h +include/gromacs/options/timeunitmanager.h +include/gromacs/pbcutil/pbc.h +include/gromacs/restraint/restraintpotential.h +include/gromacs/selection/indexutil.h +include/gromacs/selection/nbsearch.h +include/gromacs/selection/position.h +include/gromacs/selection/selection.h +include/gromacs/selection/selectioncollection.h +include/gromacs/selection/selectionenums.h +include/gromacs/selection/selectionoption.h +include/gromacs/selection/selectionoptionbehavior.h +include/gromacs/selection/selectionoptionmanager.h +include/gromacs/topology/atomprop.h +include/gromacs/topology/atoms.h +include/gromacs/topology/block.h +include/gromacs/topology/forcefieldparameters.h +include/gromacs/topology/idef.h +include/gromacs/topology/ifunc.h +include/gromacs/topology/index.h +include/gromacs/topology/symtab.h +include/gromacs/topology/topology.h +include/gromacs/topology/topology_enums.h +include/gromacs/trajectory/trajectoryframe.h +include/gromacs/trajectoryanalysis/analysismodule.h +include/gromacs/trajectoryanalysis/analysissettings.h +include/gromacs/trajectoryanalysis/cmdlinerunner.h +include/gromacs/trajectoryanalysis/topologyinformation.h +include/gromacs/utility/arrayref.h +include/gromacs/utility/basedefinitions.h +include/gromacs/utility/baseversion.h +include/gromacs/utility/classhelpers.h +include/gromacs/utility/current_function.h +include/gromacs/utility/enumerationhelpers.h +include/gromacs/utility/exceptions.h +include/gromacs/utility/fileptr.h +include/gromacs/utility/flags.h +include/gromacs/utility/futil.h +include/gromacs/utility/gmxassert.h +include/gromacs/utility/listoflists.h +include/gromacs/utility/pleasecite.h +include/gromacs/utility/programcontext.h +include/gromacs/utility/range.h +include/gromacs/utility/real.h +include/gromacs/utility/smalloc.h +include/gromacs/utility/stringutil.h +include/gromacs/utility/unique_cptr.h +include/gromacs/utility/vec.h +include/gromacs/utility/vectypes.h +include/gromacs/version.h include/nblib/basicdefinitions.h include/nblib/box.h include/nblib/exception.h @@ -136,8 +136,8 @@ lib/libgmxapi%%SUFFIX_D%%.so lib/libgmxapi%%SUFFIX_D%%.so.0 lib/libgmxapi%%SUFFIX_D%%.so.0.4.0 lib/libgromacs%%SUFFIX_D%%.so -lib/libgromacs%%SUFFIX_D%%.so.10 -lib/libgromacs%%SUFFIX_D%%.so.10.0.0 +lib/libgromacs%%SUFFIX_D%%.so.11 +lib/libgromacs%%SUFFIX_D%%.so.11.0.0 lib/libnblib_gmx.so lib/libnblib_gmx.so.0 lib/libnblib_gmx.so.0.1.0 @@ -205,6 +205,53 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/top/amber03.ff/tip5p.itp %%DATADIR%%/top/amber03.ff/urea.itp %%DATADIR%%/top/amber03.ff/watermodels.dat +%%DATADIR%%/top/amber14sb.ff/aminoacids.c.tdb +%%DATADIR%%/top/amber14sb.ff/aminoacids.hdb +%%DATADIR%%/top/amber14sb.ff/aminoacids.n.tdb +%%DATADIR%%/top/amber14sb.ff/aminoacids.r2b +%%DATADIR%%/top/amber14sb.ff/aminoacids.rtp +%%DATADIR%%/top/amber14sb.ff/atomtypes.atp +%%DATADIR%%/top/amber14sb.ff/ffbonded.itp +%%DATADIR%%/top/amber14sb.ff/ffnonbonded.itp +%%DATADIR%%/top/amber14sb.ff/forcefield.doc +%%DATADIR%%/top/amber14sb.ff/forcefield.itp +%%DATADIR%%/top/amber14sb.ff/ions_opc.itp +%%DATADIR%%/top/amber14sb.ff/ions_opc3.itp +%%DATADIR%%/top/amber14sb.ff/ions_spc.itp +%%DATADIR%%/top/amber14sb.ff/ions_spce.itp +%%DATADIR%%/top/amber14sb.ff/ions_tip3p.itp +%%DATADIR%%/top/amber14sb.ff/ions_tip4pew.itp +%%DATADIR%%/top/amber14sb.ff/opc.itp +%%DATADIR%%/top/amber14sb.ff/opc3.itp +%%DATADIR%%/top/amber14sb.ff/spc.itp +%%DATADIR%%/top/amber14sb.ff/spce.itp +%%DATADIR%%/top/amber14sb.ff/tip3p.itp +%%DATADIR%%/top/amber14sb.ff/tip4pew.itp +%%DATADIR%%/top/amber14sb.ff/watermodels.dat +%%DATADIR%%/top/amber19sb.ff/aminoacids.c.tdb +%%DATADIR%%/top/amber19sb.ff/aminoacids.hdb +%%DATADIR%%/top/amber19sb.ff/aminoacids.n.tdb +%%DATADIR%%/top/amber19sb.ff/aminoacids.r2b +%%DATADIR%%/top/amber19sb.ff/aminoacids.rtp +%%DATADIR%%/top/amber19sb.ff/atomtypes.atp +%%DATADIR%%/top/amber19sb.ff/cmap.itp +%%DATADIR%%/top/amber19sb.ff/ffbonded.itp +%%DATADIR%%/top/amber19sb.ff/ffnonbonded.itp +%%DATADIR%%/top/amber19sb.ff/forcefield.doc +%%DATADIR%%/top/amber19sb.ff/forcefield.itp +%%DATADIR%%/top/amber19sb.ff/ions_opc.itp +%%DATADIR%%/top/amber19sb.ff/ions_opc3.itp +%%DATADIR%%/top/amber19sb.ff/ions_spc.itp +%%DATADIR%%/top/amber19sb.ff/ions_spce.itp +%%DATADIR%%/top/amber19sb.ff/ions_tip3p.itp +%%DATADIR%%/top/amber19sb.ff/ions_tip4pew.itp +%%DATADIR%%/top/amber19sb.ff/opc.itp +%%DATADIR%%/top/amber19sb.ff/opc3.itp +%%DATADIR%%/top/amber19sb.ff/spc.itp +%%DATADIR%%/top/amber19sb.ff/spce.itp +%%DATADIR%%/top/amber19sb.ff/tip3p.itp +%%DATADIR%%/top/amber19sb.ff/tip4pew.itp +%%DATADIR%%/top/amber19sb.ff/watermodels.dat %%DATADIR%%/top/amber94.ff/aminoacids.arn %%DATADIR%%/top/amber94.ff/aminoacids.c.tdb %%DATADIR%%/top/amber94.ff/aminoacids.hdb @@ -421,12 +468,10 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/top/charmm27.ff/tips3p.itp %%DATADIR%%/top/charmm27.ff/watermodels.dat %%DATADIR%%/top/co-shift.dat -%%DATADIR%%/top/defselection.dat %%DATADIR%%/top/dgsolv.dat %%DATADIR%%/top/edissoc.dat %%DATADIR%%/top/electroneg.dat %%DATADIR%%/top/elements.dat -%%DATADIR%%/top/export.dlg %%DATADIR%%/top/ffG43a1.itp %%DATADIR%%/top/ffG43a2.itp %%DATADIR%%/top/ffG45a3.itp @@ -581,9 +626,6 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/top/phbres.dat %%DATADIR%%/top/ps.m2p %%DATADIR%%/top/random.dat -%%DATADIR%%/top/refi_aa.dat -%%DATADIR%%/top/residues.dtd -%%DATADIR%%/top/residues.xml %%DATADIR%%/top/residuetypes.dat %%DATADIR%%/top/scatteringfactors.dat %%DATADIR%%/top/sfactor.dat @@ -592,7 +634,6 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/top/spce.itp %%DATADIR%%/top/specbond.dat %%DATADIR%%/top/ss.map -%%DATADIR%%/top/surface.dat %%DATADIR%%/top/sw.itp %%DATADIR%%/top/table6-10.xvg %%DATADIR%%/top/table6-11.xvg @@ -603,7 +644,6 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/top/tip4p.gro %%DATADIR%%/top/tip4p.itp %%DATADIR%%/top/tip5p.gro -%%DATADIR%%/top/vdw-msms.dat %%DATADIR%%/top/vdwradii.dat %%DATADIR%%/top/xlateat.dat share/man/man1/gmx-anaeig.1.gz diff --git a/science/votca/Makefile b/science/votca/Makefile index b4417e9fffc7..34386f43f3c4 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,6 +1,7 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2026 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.orghome | help
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