git: 0e793c131a97 - main - science/{,py-}avogadrolibs: Update 1.95.1 -> 1.97.0

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 16 Oct 2022 07:09:42 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0e793c131a9783b574c744fdcb1dfa8a0d590eec

commit 0e793c131a9783b574c744fdcb1dfa8a0d590eec
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-10-16 07:07:24 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-10-16 07:09:36 +0000

    science/{,py-}avogadrolibs: Update 1.95.1 -> 1.97.0
---
 science/avogadrolibs/Makefile    | 18 ++++++++-----
 science/avogadrolibs/distinfo    | 10 +++----
 science/avogadrolibs/pkg-plist   | 56 +++++++++++++++++++++++++++++++++-------
 science/py-avogadrolibs/Makefile |  2 +-
 science/py-avogadrolibs/distinfo |  6 ++---
 5 files changed, 66 insertions(+), 26 deletions(-)

diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile
index 6ca97f1f378c..d7d8859067ea 100644
--- a/science/avogadrolibs/Makefile
+++ b/science/avogadrolibs/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	avogadrolibs
-DISTVERSION=	1.95.1
-PORTREVISION=	3
+DISTVERSION=	1.97.0
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -10,7 +9,8 @@ WWW=		https://www.openchemistry.org/projects/avogadro2/
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-TEST_DEPENDS=	googletest>0:devel/googletest
+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
 USE_LDCONFIG=	yes
@@ -18,13 +18,13 @@ USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	OpenChemistry
 GH_TUPLE=	OpenChemistry:molecules:b1e16c5:molecules/../molecules \
-		OpenChemistry:crystals:c3e2468:crystals/../crystals
+		OpenChemistry:crystals:73a5bbc:crystals/../crystals
 
 CMAKE_ON=		BUILD_SHARED_LIBS
 CMAKE_TESTING_ON=	ENABLE_TESTING
 
 OPTIONS_DEFINE=		HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB VTK
-OPTIONS_DEFAULT=	LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB
+OPTIONS_DEFAULT=	LIBARCHIVE LIBMSYM OPENGL QT5 SPGLIB # MMTF
 OPTIONS_SUB=		yes
 
 HDF5_CMAKE_BOOL=	USE_HDF5
@@ -44,6 +44,7 @@ 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
 
 OPENGL_CMAKE_BOOL=	USE_OPENGL
 OPENGL_USES=		gl
@@ -61,10 +62,13 @@ 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
 
 VTK_DESC=		Enable libraries that use VTK
+VTK_USES=		xorg
+VTK_USE=		QT=opengl XORG=x11
 VTK_CMAKE_BOOL=		USE_VTK
-VTK_LIB_DEPENDS=	libvtksys-8.2.so:math/vtk8
+VTK_LIB_DEPENDS=	libvtksys-9.1.so:math/vtk9 \
+			libfreetype.so:print/freetype2
 VTK_IMPLIES=		QT5
-VTK_BROKEN=		Needs https://github.com/psavery/genXrdPattern, etc
+VTK_BROKEN=		Needs https://github.com/psavery/genXrdPattern, see https://github.com/OpenChemistry/avogadrolibs/issues/1186
 
 post-install:
 	@${RM} -r ${STAGEDIR}${PREFIX}/share/doc
diff --git a/science/avogadrolibs/distinfo b/science/avogadrolibs/distinfo
index d81d8a9fd98a..01ea7c4d5ffa 100644
--- a/science/avogadrolibs/distinfo
+++ b/science/avogadrolibs/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1644049029
-SHA256 (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 52817eebfc0cf700e5f6c0c4455b460618ec0dd7cb4ede5d8fabc5a2d73a7816
-SIZE (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 11015910
+TIMESTAMP = 1665902523
+SHA256 (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 46641504a1808c5ff6fb7d66be48d866848203899025fd386cc6e3dd5d9ec342
+SIZE (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 11456702
 SHA256 (OpenChemistry-molecules-b1e16c5_GH0.tar.gz) = 9aa48dd94022e022d2c9eb9802ba72a4bfd69c04a08a36d562bfffc7d24bf99b
 SIZE (OpenChemistry-molecules-b1e16c5_GH0.tar.gz) = 207309
-SHA256 (OpenChemistry-crystals-c3e2468_GH0.tar.gz) = db4ff16c3b5e6741914ae8b5e6e7b33b1f0e8b59d28916dab4e6fa9dd65fc633
-SIZE (OpenChemistry-crystals-c3e2468_GH0.tar.gz) = 151836
+SHA256 (OpenChemistry-crystals-73a5bbc_GH0.tar.gz) = f48a06bb9e4bdc1f7dbed22fe31b187b5aa490f5796f6927001228e9ced41a5e
+SIZE (OpenChemistry-crystals-73a5bbc_GH0.tar.gz) = 157627
diff --git a/science/avogadrolibs/pkg-plist b/science/avogadrolibs/pkg-plist
index a34e864be5aa..f10e1f0d253d 100644
--- a/science/avogadrolibs/pkg-plist
+++ b/science/avogadrolibs/pkg-plist
@@ -1,16 +1,21 @@
+%%VTK%%bin/genXrdPattern
+include/avogadro/calc/avogadrocalcexport.h
+include/avogadro/calc/chargemanager.h
+include/avogadro/calc/chargemodel.h
+include/avogadro/calc/defaultmodel.h
 include/avogadro/core/angleiterator.h
 include/avogadro/core/angletools.h
 include/avogadro/core/array.h
 include/avogadro/core/atom.h
 include/avogadro/core/atomtyper-inline.h
 include/avogadro/core/atomtyper.h
+include/avogadro/core/atomutilities.h
 include/avogadro/core/avogadrocore.h
 include/avogadro/core/avogadrocoreexport.h
 %%SPGLIB%%include/avogadro/core/avospglib.h
 include/avogadro/core/basisset.h
 include/avogadro/core/bond.h
 include/avogadro/core/color3f.h
-include/avogadro/core/connectedgroup.h
 include/avogadro/core/coordinateblockgenerator.h
 include/avogadro/core/coordinateset.h
 include/avogadro/core/crystaltools.h
@@ -27,6 +32,7 @@ include/avogadro/core/mesh.h
 include/avogadro/core/molecule.h
 include/avogadro/core/mutex.h
 include/avogadro/core/nameatomtyper.h
+include/avogadro/core/neighborperceiver.h
 include/avogadro/core/residue.h
 include/avogadro/core/ringperceiver.h
 include/avogadro/core/secondarystructure.h
@@ -56,6 +62,7 @@ include/avogadro/io/mdlformat.h
 %%MMTF%%include/avogadro/io/mmtfformat.h
 include/avogadro/io/pdbformat.h
 include/avogadro/io/trrformat.h
+include/avogadro/io/turbomoleformat.h
 include/avogadro/io/vaspformat.h
 include/avogadro/io/xyzformat.h
 %%QT5%%include/avogadro/molequeue/avogadromolequeueexport.h
@@ -126,6 +133,7 @@ include/avogadro/quantumio/nwchemlog.h
 %%OPENGL%%include/avogadro/rendering/cartoongeometry.h
 %%OPENGL%%include/avogadro/rendering/curvegeometry.h
 %%OPENGL%%include/avogadro/rendering/cylindergeometry.h
+%%OPENGL%%include/avogadro/rendering/dashedlinegeometry.h
 %%OPENGL%%include/avogadro/rendering/drawable.h
 %%OPENGL%%include/avogadro/rendering/geometrynode.h
 %%OPENGL%%include/avogadro/rendering/geometryvisitor.h
@@ -151,14 +159,21 @@ include/avogadro/quantumio/nwchemlog.h
 %%OPENGL%%include/avogadro/rendering/visitor.h
 %%OPENGL%%include/avogadro/rendering/volumegeometry.h
 %%OPENGL%%include/avogadro/rendering/vrmlvisitor.h
+%%VTK%%include/avogadro/vtk/avogadrovtkexport.h
+%%VTK%%include/avogadro/vtk/vtkAvogadroActor.h
+%%VTK%%include/avogadro/vtk/vtkglwidget.h
+%%VTK%%include/avogadro/vtk/vtkplot.h
 %%QT5%%lib/avogadro2/libgwavi.a
-%%QT5%%lib/avogadro2/scripts/commands/scale.py
+%%QT5%%lib/avogadro2/scripts/charges/antechamber.py
+%%QT5%%lib/avogadro2/scripts/charges/xtb.py
 %%QT5%%lib/avogadro2/scripts/formatScripts/zyx.py
 %%QT5%%lib/avogadro2/staticplugins/ApplyColors.a
 %%QT5%%lib/avogadro2/staticplugins/BallStick.a
 %%QT5%%lib/avogadro2/staticplugins/BondCentric.a
 %%QT5%%lib/avogadro2/staticplugins/Bonding.a
 %%QT5%%lib/avogadro2/staticplugins/Cartoons.a
+%%QT5%%lib/avogadro2/staticplugins/CloseContacts.a
+%%VTK%%lib/avogadro2/staticplugins/ColorOpacityMap.a
 %%QT5%%lib/avogadro2/staticplugins/CoordinateEditor.a
 %%QT5%%lib/avogadro2/staticplugins/CopyPaste.a
 %%QT5%%lib/avogadro2/staticplugins/Cp2kInput.a
@@ -167,12 +182,14 @@ include/avogadro/quantumio/nwchemlog.h
 %%QT5%%lib/avogadro2/staticplugins/CustomElements.a
 %%QT5%%lib/avogadro2/staticplugins/Editor.a
 %%QT5%%lib/avogadro2/staticplugins/FetchPDB.a
+%%QT5%%lib/avogadro2/staticplugins/Focus.a
 %%QT5%%lib/avogadro2/staticplugins/Force.a
 %%QT5%%lib/avogadro2/staticplugins/GamessInput.a
 %%QT5%%lib/avogadro2/staticplugins/Hydrogens.a
 %%QT5%%lib/avogadro2/staticplugins/ImportPQR.a
 %%QT5%%lib/avogadro2/staticplugins/InsertFragment.a
 %%QT5%%lib/avogadro2/staticplugins/Label.a
+%%QT5%%lib/avogadro2/staticplugins/LabelEditor.a
 %%QT5%%lib/avogadro2/staticplugins/LammpsInput.a
 %%QT5%%lib/avogadro2/staticplugins/Licorice.a
 %%QT5%%lib/avogadro2/staticplugins/LineFormatInput.a
@@ -183,16 +200,22 @@ include/avogadro/quantumio/nwchemlog.h
 %%QT5%%lib/avogadro2/staticplugins/MongoChem.a
 %%QT5%%lib/avogadro2/staticplugins/Navigator.a
 %%QT5%%lib/avogadro2/staticplugins/NetworkDatabases.a
+%%QT5%%lib/avogadro2/staticplugins/NonCovalent.a
+%%QT5%%lib/avogadro2/staticplugins/NucleicInput.a
 %%QT5%%lib/avogadro2/staticplugins/OpenBabel.a
 %%QT5%%lib/avogadro2/staticplugins/OpenMMInput.a
 %%QT5%%lib/avogadro2/staticplugins/OverlayAxes.a
 %%QT5%%lib/avogadro2/staticplugins/POVRay.a
 %%QT5%%lib/avogadro2/staticplugins/PlayerTool.a
+%%VTK%%lib/avogadro2/staticplugins/PlotPdf.a
+%%VTK%%lib/avogadro2/staticplugins/PlotRmsd.a
+%%VTK%%lib/avogadro2/staticplugins/PlotXrd.a
 %%LIBARCHIVE%%lib/avogadro2/staticplugins/PluginDownloader.a
 %%QT5%%lib/avogadro2/staticplugins/PropertyTables.a
 %%QT5%%lib/avogadro2/staticplugins/QuantumInput.a
 %%QT5%%lib/avogadro2/staticplugins/ResetView.a
 %%QT5%%lib/avogadro2/staticplugins/SVG.a
+%%QT5%%lib/avogadro2/staticplugins/ScriptCharges.a
 %%QT5%%lib/avogadro2/staticplugins/ScriptFileFormats.a
 %%QT5%%lib/avogadro2/staticplugins/Select.a
 %%QT5%%lib/avogadro2/staticplugins/Selection.a
@@ -216,30 +239,36 @@ lib/cmake/avogadrolibs/FindEigen3.cmake
 lib/cmake/avogadrolibs/FindGLEW.cmake
 lib/cmake/avogadrolibs/FindLibArchive.cmake
 lib/cmake/avogadrolibs/Findlibmsym.cmake
+lib/libAvogadroCalc.so
+lib/libAvogadroCalc.so.1
+lib/libAvogadroCalc.so.1.97.0
 lib/libAvogadroCore.so
 lib/libAvogadroCore.so.1
-lib/libAvogadroCore.so.1.95.1
+lib/libAvogadroCore.so.1.97.0
 lib/libAvogadroIO.so
 lib/libAvogadroIO.so.1
-lib/libAvogadroIO.so.1.95.1
+lib/libAvogadroIO.so.1.97.0
 %%QT5%%lib/libAvogadroMoleQueue.so
 %%QT5%%lib/libAvogadroMoleQueue.so.1
-%%QT5%%lib/libAvogadroMoleQueue.so.1.95.1
+%%QT5%%lib/libAvogadroMoleQueue.so.1.97.0
 %%QT5%%lib/libAvogadroQtGui.so
 %%QT5%%lib/libAvogadroQtGui.so.1
-%%QT5%%lib/libAvogadroQtGui.so.1.95.1
+%%QT5%%lib/libAvogadroQtGui.so.1.97.0
 %%QT5%%lib/libAvogadroQtOpenGL.so
 %%QT5%%lib/libAvogadroQtOpenGL.so.1
-%%QT5%%lib/libAvogadroQtOpenGL.so.1.95.1
+%%QT5%%lib/libAvogadroQtOpenGL.so.1.97.0
 %%QT5%%lib/libAvogadroQtPlugins.so
 %%QT5%%lib/libAvogadroQtPlugins.so.1
-%%QT5%%lib/libAvogadroQtPlugins.so.1.95.1
+%%QT5%%lib/libAvogadroQtPlugins.so.1.97.0
 lib/libAvogadroQuantumIO.so
 lib/libAvogadroQuantumIO.so.1
-lib/libAvogadroQuantumIO.so.1.95.1
+lib/libAvogadroQuantumIO.so.1.97.0
 %%OPENGL%%lib/libAvogadroRendering.so
 %%OPENGL%%lib/libAvogadroRendering.so.1
-%%OPENGL%%lib/libAvogadroRendering.so.1.95.1
+%%OPENGL%%lib/libAvogadroRendering.so.1.97.0
+%%VTK%%lib/libAvogadroVtk.so
+%%VTK%%lib/libAvogadroVtk.so.1
+%%VTK%%lib/libAvogadroVtk.so.1.97.0
 %%QT5%%share/avogadro2/crystals/README.md
 %%QT5%%share/avogadro2/crystals/antimonides/AlSb.cif
 %%QT5%%share/avogadro2/crystals/antimonides/GaSb.cif
@@ -260,9 +289,11 @@ lib/libAvogadroQuantumIO.so.1.95.1
 %%QT5%%share/avogadro2/crystals/carbides/WC.cif
 %%QT5%%share/avogadro2/crystals/carbonates/CaCO3-Calcite.cif
 %%QT5%%share/avogadro2/crystals/carbonates/CaMgC2O6-Dolomite.cif
+%%QT5%%share/avogadro2/crystals/carbonates/FeCO3-Siderte.cif
 %%QT5%%share/avogadro2/crystals/carbonates/Li2CO3-Zabuyelite.cif
 %%QT5%%share/avogadro2/crystals/carbonates/MgCO3-Magnesite.cif
 %%QT5%%share/avogadro2/crystals/carbonates/Na2CO3-Natrite.cif
+%%QT5%%share/avogadro2/crystals/carbonates/NaHCO3-Nahcolite.cif
 %%QT5%%share/avogadro2/crystals/clays/Al2Si2O9H4-Dickite.cif
 %%QT5%%share/avogadro2/crystals/clays/Al2Si2O9H4-Kaolinite.cif
 %%QT5%%share/avogadro2/crystals/clays/Al2Si2O9H4-Nacrite.cif
@@ -385,6 +416,7 @@ lib/libAvogadroQuantumIO.so.1.95.1
 %%QT5%%share/avogadro2/crystals/halides/AgCl-Chlorargyrite.cif
 %%QT5%%share/avogadro2/crystals/halides/AlCl3.cif
 %%QT5%%share/avogadro2/crystals/halides/AlNa3F6-Cryolite.cif
+%%QT5%%share/avogadro2/crystals/halides/CaCl2-Hydrophilite.cif
 %%QT5%%share/avogadro2/crystals/halides/CaF2-Fluorite.cif
 %%QT5%%share/avogadro2/crystals/halides/CdCl2.cif
 %%QT5%%share/avogadro2/crystals/halides/CdI2.cif
@@ -395,6 +427,7 @@ lib/libAvogadroQuantumIO.so.1.95.1
 %%QT5%%share/avogadro2/crystals/halides/HgCl-Calomel.cif
 %%QT5%%share/avogadro2/crystals/halides/KBr.cif
 %%QT5%%share/avogadro2/crystals/halides/KCl-Sylvite.cif
+%%QT5%%share/avogadro2/crystals/halides/LiCl.cif
 %%QT5%%share/avogadro2/crystals/halides/NaCl-Halite.cif
 %%QT5%%share/avogadro2/crystals/halides/PbFCl-Matlockite.cif
 %%QT5%%share/avogadro2/crystals/hydrides/KH.cif
@@ -427,6 +460,7 @@ lib/libAvogadroQuantumIO.so.1.95.1
 %%QT5%%share/avogadro2/crystals/nitrides/GaN.cif
 %%QT5%%share/avogadro2/crystals/nitrides/InN.cif
 %%QT5%%share/avogadro2/crystals/nitrides/Si3N4-beta.cif
+%%QT5%%share/avogadro2/crystals/nitrides/TiN-Osbornite.cif
 %%QT5%%share/avogadro2/crystals/other/(NH4)MgPO4-6(H2O)-Struvite.cif
 %%QT5%%share/avogadro2/crystals/other/C10H10Fe-Ferrocene.cif
 %%QT5%%share/avogadro2/crystals/other/Ca2C4O10H2.57-Oxalate-Whewellite.cif
@@ -527,7 +561,9 @@ lib/libAvogadroQuantumIO.so.1.95.1
 %%QT5%%share/avogadro2/crystals/sulfates/CaSO4-Anhydrite.cif
 %%QT5%%share/avogadro2/crystals/sulfates/CoSO4.cif
 %%QT5%%share/avogadro2/crystals/sulfates/CuSO4.cif
+%%QT5%%share/avogadro2/crystals/sulfates/H4SO5.cif
 %%QT5%%share/avogadro2/crystals/sulfates/MgSO4.cif
+%%QT5%%share/avogadro2/crystals/sulfates/Na2SO4.cif
 %%QT5%%share/avogadro2/crystals/sulfates/PbSO4-Anglesite.cif
 %%QT5%%share/avogadro2/crystals/sulfates/SrSO4-Celestine.cif
 %%QT5%%share/avogadro2/crystals/sulfides/Bi2S3-Bismuthinite.cif
diff --git a/science/py-avogadrolibs/Makefile b/science/py-avogadrolibs/Makefile
index 2c8b2f8e1750..3e6de7923e53 100644
--- a/science/py-avogadrolibs/Makefile
+++ b/science/py-avogadrolibs/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	avogadrolibs
-DISTVERSION=	1.95.1
+DISTVERSION=	1.97.0
 CATEGORIES=	science
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
diff --git a/science/py-avogadrolibs/distinfo b/science/py-avogadrolibs/distinfo
index 07415b0eabc4..c339169fe1e1 100644
--- a/science/py-avogadrolibs/distinfo
+++ b/science/py-avogadrolibs/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1644050284
-SHA256 (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 52817eebfc0cf700e5f6c0c4455b460618ec0dd7cb4ede5d8fabc5a2d73a7816
-SIZE (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 11015910
+TIMESTAMP = 1665903668
+SHA256 (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 46641504a1808c5ff6fb7d66be48d866848203899025fd386cc6e3dd5d9ec342
+SIZE (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 11456702