Skip to content

Commit 0e793c1

Browse files
yurivictyurivict
committed
science/{,py-}avogadrolibs: Update 1.95.1 -> 1.97.0
1 parent e08eccc commit 0e793c1

5 files changed

Lines changed: 66 additions & 26 deletions

File tree

‎science/avogadrolibs/Makefile‎

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,5 @@
11
PORTNAME= avogadrolibs
2-
DISTVERSION= 1.95.1
3-
PORTREVISION= 3
2+
DISTVERSION= 1.97.0
43
CATEGORIES= science
54

65
MAINTAINER= yuri@FreeBSD.org
@@ -10,21 +9,22 @@ WWW= https://www.openchemistry.org/projects/avogadro2/
109
LICENSE= GPLv2
1110
LICENSE_FILE= ${WRKSRC}/LICENSE
1211

13-
TEST_DEPENDS= googletest>0:devel/googletest
12+
TEST_DEPENDS= googletest>0:devel/googletest \
13+
molequeue>0:misc/molequeue
1414

1515
USES= cmake:testing compiler:c++17-lang eigen:3,build,run # eigen needs to be 'run' because it is written into cmake files
1616
USE_LDCONFIG= yes
1717

1818
USE_GITHUB= yes
1919
GH_ACCOUNT= OpenChemistry
2020
GH_TUPLE= OpenChemistry:molecules:b1e16c5:molecules/../molecules \
21-
OpenChemistry:crystals:c3e2468:crystals/../crystals
21+
OpenChemistry:crystals:73a5bbc:crystals/../crystals
2222

2323
CMAKE_ON= BUILD_SHARED_LIBS
2424
CMAKE_TESTING_ON= ENABLE_TESTING
2525

2626
OPTIONS_DEFINE= HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB VTK
27-
OPTIONS_DEFAULT= LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB
27+
OPTIONS_DEFAULT= LIBARCHIVE LIBMSYM OPENGL QT5 SPGLIB # MMTF
2828
OPTIONS_SUB= yes
2929

3030
HDF5_CMAKE_BOOL= USE_HDF5
@@ -44,6 +44,7 @@ LIBMSYM_IMPLIES= QT5 # enables the 'symmetry' Qt plugin
4444
MMTF_DESC= Enable optional features using mmtf
4545
MMTF_CMAKE_BOOL= USE_MMTF
4646
MMTF_BUILD_DEPENDS= mmtf-cpp>0:science/mmtf-cpp
47+
MMTF_BROKEN= see https://github.com/OpenChemistry/avogadrolibs/issues/1185
4748

4849
OPENGL_CMAKE_BOOL= USE_OPENGL
4950
OPENGL_USES= gl
@@ -61,10 +62,13 @@ SPGLIB_LIB_DEPENDS= libsymspg.so:science/spglib
6162
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
6263

6364
VTK_DESC= Enable libraries that use VTK
65+
VTK_USES= xorg
66+
VTK_USE= QT=opengl XORG=x11
6467
VTK_CMAKE_BOOL= USE_VTK
65-
VTK_LIB_DEPENDS= libvtksys-8.2.so:math/vtk8
68+
VTK_LIB_DEPENDS= libvtksys-9.1.so:math/vtk9 \
69+
libfreetype.so:print/freetype2
6670
VTK_IMPLIES= QT5
67-
VTK_BROKEN= Needs https://github.com/psavery/genXrdPattern, etc
71+
VTK_BROKEN= Needs https://github.com/psavery/genXrdPattern, see https://github.com/OpenChemistry/avogadrolibs/issues/1186
6872

6973
post-install:
7074
@${RM} -r ${STAGEDIR}${PREFIX}/share/doc

‎science/avogadrolibs/distinfo‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
TIMESTAMP = 1644049029
2-
SHA256 (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 52817eebfc0cf700e5f6c0c4455b460618ec0dd7cb4ede5d8fabc5a2d73a7816
3-
SIZE (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 11015910
1+
TIMESTAMP = 1665902523
2+
SHA256 (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 46641504a1808c5ff6fb7d66be48d866848203899025fd386cc6e3dd5d9ec342
3+
SIZE (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 11456702
44
SHA256 (OpenChemistry-molecules-b1e16c5_GH0.tar.gz) = 9aa48dd94022e022d2c9eb9802ba72a4bfd69c04a08a36d562bfffc7d24bf99b
55
SIZE (OpenChemistry-molecules-b1e16c5_GH0.tar.gz) = 207309
6-
SHA256 (OpenChemistry-crystals-c3e2468_GH0.tar.gz) = db4ff16c3b5e6741914ae8b5e6e7b33b1f0e8b59d28916dab4e6fa9dd65fc633
7-
SIZE (OpenChemistry-crystals-c3e2468_GH0.tar.gz) = 151836
6+
SHA256 (OpenChemistry-crystals-73a5bbc_GH0.tar.gz) = f48a06bb9e4bdc1f7dbed22fe31b187b5aa490f5796f6927001228e9ced41a5e
7+
SIZE (OpenChemistry-crystals-73a5bbc_GH0.tar.gz) = 157627

‎science/avogadrolibs/pkg-plist‎

Lines changed: 46 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,21 @@
1+
%%VTK%%bin/genXrdPattern
2+
include/avogadro/calc/avogadrocalcexport.h
3+
include/avogadro/calc/chargemanager.h
4+
include/avogadro/calc/chargemodel.h
5+
include/avogadro/calc/defaultmodel.h
16
include/avogadro/core/angleiterator.h
27
include/avogadro/core/angletools.h
38
include/avogadro/core/array.h
49
include/avogadro/core/atom.h
510
include/avogadro/core/atomtyper-inline.h
611
include/avogadro/core/atomtyper.h
12+
include/avogadro/core/atomutilities.h
713
include/avogadro/core/avogadrocore.h
814
include/avogadro/core/avogadrocoreexport.h
915
%%SPGLIB%%include/avogadro/core/avospglib.h
1016
include/avogadro/core/basisset.h
1117
include/avogadro/core/bond.h
1218
include/avogadro/core/color3f.h
13-
include/avogadro/core/connectedgroup.h
1419
include/avogadro/core/coordinateblockgenerator.h
1520
include/avogadro/core/coordinateset.h
1621
include/avogadro/core/crystaltools.h
@@ -27,6 +32,7 @@ include/avogadro/core/mesh.h
2732
include/avogadro/core/molecule.h
2833
include/avogadro/core/mutex.h
2934
include/avogadro/core/nameatomtyper.h
35+
include/avogadro/core/neighborperceiver.h
3036
include/avogadro/core/residue.h
3137
include/avogadro/core/ringperceiver.h
3238
include/avogadro/core/secondarystructure.h
@@ -56,6 +62,7 @@ include/avogadro/io/mdlformat.h
5662
%%MMTF%%include/avogadro/io/mmtfformat.h
5763
include/avogadro/io/pdbformat.h
5864
include/avogadro/io/trrformat.h
65+
include/avogadro/io/turbomoleformat.h
5966
include/avogadro/io/vaspformat.h
6067
include/avogadro/io/xyzformat.h
6168
%%QT5%%include/avogadro/molequeue/avogadromolequeueexport.h
@@ -126,6 +133,7 @@ include/avogadro/quantumio/nwchemlog.h
126133
%%OPENGL%%include/avogadro/rendering/cartoongeometry.h
127134
%%OPENGL%%include/avogadro/rendering/curvegeometry.h
128135
%%OPENGL%%include/avogadro/rendering/cylindergeometry.h
136+
%%OPENGL%%include/avogadro/rendering/dashedlinegeometry.h
129137
%%OPENGL%%include/avogadro/rendering/drawable.h
130138
%%OPENGL%%include/avogadro/rendering/geometrynode.h
131139
%%OPENGL%%include/avogadro/rendering/geometryvisitor.h
@@ -151,14 +159,21 @@ include/avogadro/quantumio/nwchemlog.h
151159
%%OPENGL%%include/avogadro/rendering/visitor.h
152160
%%OPENGL%%include/avogadro/rendering/volumegeometry.h
153161
%%OPENGL%%include/avogadro/rendering/vrmlvisitor.h
162+
%%VTK%%include/avogadro/vtk/avogadrovtkexport.h
163+
%%VTK%%include/avogadro/vtk/vtkAvogadroActor.h
164+
%%VTK%%include/avogadro/vtk/vtkglwidget.h
165+
%%VTK%%include/avogadro/vtk/vtkplot.h
154166
%%QT5%%lib/avogadro2/libgwavi.a
155-
%%QT5%%lib/avogadro2/scripts/commands/scale.py
167+
%%QT5%%lib/avogadro2/scripts/charges/antechamber.py
168+
%%QT5%%lib/avogadro2/scripts/charges/xtb.py
156169
%%QT5%%lib/avogadro2/scripts/formatScripts/zyx.py
157170
%%QT5%%lib/avogadro2/staticplugins/ApplyColors.a
158171
%%QT5%%lib/avogadro2/staticplugins/BallStick.a
159172
%%QT5%%lib/avogadro2/staticplugins/BondCentric.a
160173
%%QT5%%lib/avogadro2/staticplugins/Bonding.a
161174
%%QT5%%lib/avogadro2/staticplugins/Cartoons.a
175+
%%QT5%%lib/avogadro2/staticplugins/CloseContacts.a
176+
%%VTK%%lib/avogadro2/staticplugins/ColorOpacityMap.a
162177
%%QT5%%lib/avogadro2/staticplugins/CoordinateEditor.a
163178
%%QT5%%lib/avogadro2/staticplugins/CopyPaste.a
164179
%%QT5%%lib/avogadro2/staticplugins/Cp2kInput.a
@@ -167,12 +182,14 @@ include/avogadro/quantumio/nwchemlog.h
167182
%%QT5%%lib/avogadro2/staticplugins/CustomElements.a
168183
%%QT5%%lib/avogadro2/staticplugins/Editor.a
169184
%%QT5%%lib/avogadro2/staticplugins/FetchPDB.a
185+
%%QT5%%lib/avogadro2/staticplugins/Focus.a
170186
%%QT5%%lib/avogadro2/staticplugins/Force.a
171187
%%QT5%%lib/avogadro2/staticplugins/GamessInput.a
172188
%%QT5%%lib/avogadro2/staticplugins/Hydrogens.a
173189
%%QT5%%lib/avogadro2/staticplugins/ImportPQR.a
174190
%%QT5%%lib/avogadro2/staticplugins/InsertFragment.a
175191
%%QT5%%lib/avogadro2/staticplugins/Label.a
192+
%%QT5%%lib/avogadro2/staticplugins/LabelEditor.a
176193
%%QT5%%lib/avogadro2/staticplugins/LammpsInput.a
177194
%%QT5%%lib/avogadro2/staticplugins/Licorice.a
178195
%%QT5%%lib/avogadro2/staticplugins/LineFormatInput.a
@@ -183,16 +200,22 @@ include/avogadro/quantumio/nwchemlog.h
183200
%%QT5%%lib/avogadro2/staticplugins/MongoChem.a
184201
%%QT5%%lib/avogadro2/staticplugins/Navigator.a
185202
%%QT5%%lib/avogadro2/staticplugins/NetworkDatabases.a
203+
%%QT5%%lib/avogadro2/staticplugins/NonCovalent.a
204+
%%QT5%%lib/avogadro2/staticplugins/NucleicInput.a
186205
%%QT5%%lib/avogadro2/staticplugins/OpenBabel.a
187206
%%QT5%%lib/avogadro2/staticplugins/OpenMMInput.a
188207
%%QT5%%lib/avogadro2/staticplugins/OverlayAxes.a
189208
%%QT5%%lib/avogadro2/staticplugins/POVRay.a
190209
%%QT5%%lib/avogadro2/staticplugins/PlayerTool.a
210+
%%VTK%%lib/avogadro2/staticplugins/PlotPdf.a
211+
%%VTK%%lib/avogadro2/staticplugins/PlotRmsd.a
212+
%%VTK%%lib/avogadro2/staticplugins/PlotXrd.a
191213
%%LIBARCHIVE%%lib/avogadro2/staticplugins/PluginDownloader.a
192214
%%QT5%%lib/avogadro2/staticplugins/PropertyTables.a
193215
%%QT5%%lib/avogadro2/staticplugins/QuantumInput.a
194216
%%QT5%%lib/avogadro2/staticplugins/ResetView.a
195217
%%QT5%%lib/avogadro2/staticplugins/SVG.a
218+
%%QT5%%lib/avogadro2/staticplugins/ScriptCharges.a
196219
%%QT5%%lib/avogadro2/staticplugins/ScriptFileFormats.a
197220
%%QT5%%lib/avogadro2/staticplugins/Select.a
198221
%%QT5%%lib/avogadro2/staticplugins/Selection.a
@@ -216,30 +239,36 @@ lib/cmake/avogadrolibs/FindEigen3.cmake
216239
lib/cmake/avogadrolibs/FindGLEW.cmake
217240
lib/cmake/avogadrolibs/FindLibArchive.cmake
218241
lib/cmake/avogadrolibs/Findlibmsym.cmake
242+
lib/libAvogadroCalc.so
243+
lib/libAvogadroCalc.so.1
244+
lib/libAvogadroCalc.so.1.97.0
219245
lib/libAvogadroCore.so
220246
lib/libAvogadroCore.so.1
221-
lib/libAvogadroCore.so.1.95.1
247+
lib/libAvogadroCore.so.1.97.0
222248
lib/libAvogadroIO.so
223249
lib/libAvogadroIO.so.1
224-
lib/libAvogadroIO.so.1.95.1
250+
lib/libAvogadroIO.so.1.97.0
225251
%%QT5%%lib/libAvogadroMoleQueue.so
226252
%%QT5%%lib/libAvogadroMoleQueue.so.1
227-
%%QT5%%lib/libAvogadroMoleQueue.so.1.95.1
253+
%%QT5%%lib/libAvogadroMoleQueue.so.1.97.0
228254
%%QT5%%lib/libAvogadroQtGui.so
229255
%%QT5%%lib/libAvogadroQtGui.so.1
230-
%%QT5%%lib/libAvogadroQtGui.so.1.95.1
256+
%%QT5%%lib/libAvogadroQtGui.so.1.97.0
231257
%%QT5%%lib/libAvogadroQtOpenGL.so
232258
%%QT5%%lib/libAvogadroQtOpenGL.so.1
233-
%%QT5%%lib/libAvogadroQtOpenGL.so.1.95.1
259+
%%QT5%%lib/libAvogadroQtOpenGL.so.1.97.0
234260
%%QT5%%lib/libAvogadroQtPlugins.so
235261
%%QT5%%lib/libAvogadroQtPlugins.so.1
236-
%%QT5%%lib/libAvogadroQtPlugins.so.1.95.1
262+
%%QT5%%lib/libAvogadroQtPlugins.so.1.97.0
237263
lib/libAvogadroQuantumIO.so
238264
lib/libAvogadroQuantumIO.so.1
239-
lib/libAvogadroQuantumIO.so.1.95.1
265+
lib/libAvogadroQuantumIO.so.1.97.0
240266
%%OPENGL%%lib/libAvogadroRendering.so
241267
%%OPENGL%%lib/libAvogadroRendering.so.1
242-
%%OPENGL%%lib/libAvogadroRendering.so.1.95.1
268+
%%OPENGL%%lib/libAvogadroRendering.so.1.97.0
269+
%%VTK%%lib/libAvogadroVtk.so
270+
%%VTK%%lib/libAvogadroVtk.so.1
271+
%%VTK%%lib/libAvogadroVtk.so.1.97.0
243272
%%QT5%%share/avogadro2/crystals/README.md
244273
%%QT5%%share/avogadro2/crystals/antimonides/AlSb.cif
245274
%%QT5%%share/avogadro2/crystals/antimonides/GaSb.cif
@@ -260,9 +289,11 @@ lib/libAvogadroQuantumIO.so.1.95.1
260289
%%QT5%%share/avogadro2/crystals/carbides/WC.cif
261290
%%QT5%%share/avogadro2/crystals/carbonates/CaCO3-Calcite.cif
262291
%%QT5%%share/avogadro2/crystals/carbonates/CaMgC2O6-Dolomite.cif
292+
%%QT5%%share/avogadro2/crystals/carbonates/FeCO3-Siderte.cif
263293
%%QT5%%share/avogadro2/crystals/carbonates/Li2CO3-Zabuyelite.cif
264294
%%QT5%%share/avogadro2/crystals/carbonates/MgCO3-Magnesite.cif
265295
%%QT5%%share/avogadro2/crystals/carbonates/Na2CO3-Natrite.cif
296+
%%QT5%%share/avogadro2/crystals/carbonates/NaHCO3-Nahcolite.cif
266297
%%QT5%%share/avogadro2/crystals/clays/Al2Si2O9H4-Dickite.cif
267298
%%QT5%%share/avogadro2/crystals/clays/Al2Si2O9H4-Kaolinite.cif
268299
%%QT5%%share/avogadro2/crystals/clays/Al2Si2O9H4-Nacrite.cif
@@ -385,6 +416,7 @@ lib/libAvogadroQuantumIO.so.1.95.1
385416
%%QT5%%share/avogadro2/crystals/halides/AgCl-Chlorargyrite.cif
386417
%%QT5%%share/avogadro2/crystals/halides/AlCl3.cif
387418
%%QT5%%share/avogadro2/crystals/halides/AlNa3F6-Cryolite.cif
419+
%%QT5%%share/avogadro2/crystals/halides/CaCl2-Hydrophilite.cif
388420
%%QT5%%share/avogadro2/crystals/halides/CaF2-Fluorite.cif
389421
%%QT5%%share/avogadro2/crystals/halides/CdCl2.cif
390422
%%QT5%%share/avogadro2/crystals/halides/CdI2.cif
@@ -395,6 +427,7 @@ lib/libAvogadroQuantumIO.so.1.95.1
395427
%%QT5%%share/avogadro2/crystals/halides/HgCl-Calomel.cif
396428
%%QT5%%share/avogadro2/crystals/halides/KBr.cif
397429
%%QT5%%share/avogadro2/crystals/halides/KCl-Sylvite.cif
430+
%%QT5%%share/avogadro2/crystals/halides/LiCl.cif
398431
%%QT5%%share/avogadro2/crystals/halides/NaCl-Halite.cif
399432
%%QT5%%share/avogadro2/crystals/halides/PbFCl-Matlockite.cif
400433
%%QT5%%share/avogadro2/crystals/hydrides/KH.cif
@@ -427,6 +460,7 @@ lib/libAvogadroQuantumIO.so.1.95.1
427460
%%QT5%%share/avogadro2/crystals/nitrides/GaN.cif
428461
%%QT5%%share/avogadro2/crystals/nitrides/InN.cif
429462
%%QT5%%share/avogadro2/crystals/nitrides/Si3N4-beta.cif
463+
%%QT5%%share/avogadro2/crystals/nitrides/TiN-Osbornite.cif
430464
%%QT5%%share/avogadro2/crystals/other/(NH4)MgPO4-6(H2O)-Struvite.cif
431465
%%QT5%%share/avogadro2/crystals/other/C10H10Fe-Ferrocene.cif
432466
%%QT5%%share/avogadro2/crystals/other/Ca2C4O10H2.57-Oxalate-Whewellite.cif
@@ -527,7 +561,9 @@ lib/libAvogadroQuantumIO.so.1.95.1
527561
%%QT5%%share/avogadro2/crystals/sulfates/CaSO4-Anhydrite.cif
528562
%%QT5%%share/avogadro2/crystals/sulfates/CoSO4.cif
529563
%%QT5%%share/avogadro2/crystals/sulfates/CuSO4.cif
564+
%%QT5%%share/avogadro2/crystals/sulfates/H4SO5.cif
530565
%%QT5%%share/avogadro2/crystals/sulfates/MgSO4.cif
566+
%%QT5%%share/avogadro2/crystals/sulfates/Na2SO4.cif
531567
%%QT5%%share/avogadro2/crystals/sulfates/PbSO4-Anglesite.cif
532568
%%QT5%%share/avogadro2/crystals/sulfates/SrSO4-Celestine.cif
533569
%%QT5%%share/avogadro2/crystals/sulfides/Bi2S3-Bismuthinite.cif

‎science/py-avogadrolibs/Makefile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
PORTNAME= avogadrolibs
2-
DISTVERSION= 1.95.1
2+
DISTVERSION= 1.97.0
33
CATEGORIES= science
44
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
55

‎science/py-avogadrolibs/distinfo‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
1-
TIMESTAMP = 1644050284
2-
SHA256 (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 52817eebfc0cf700e5f6c0c4455b460618ec0dd7cb4ede5d8fabc5a2d73a7816
3-
SIZE (OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz) = 11015910
1+
TIMESTAMP = 1665903668
2+
SHA256 (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 46641504a1808c5ff6fb7d66be48d866848203899025fd386cc6e3dd5d9ec342
3+
SIZE (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 11456702

0 commit comments

Comments
 (0)