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

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Reported by:	portscout
This commit is contained in:
Yuri Victorovich 2024-02-12 07:27:04 -07:00
parent 3fad843b18
commit e2d8c2cf8a
11 changed files with 893 additions and 82 deletions
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16
science/avogadrolibs/Makefile
View file

@ -1,6 +1,5 @@
PORTNAME= avogadrolibs PORTNAME= avogadrolibs
DISTVERSION= 1.97.0 DISTVERSION= 1.99.0
PORTREVISION= 3
CATEGORIES= science CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org MAINTAINER= yuri@FreeBSD.org
@ -13,19 +12,20 @@ LICENSE_FILE= ${WRKSRC}/LICENSE
TEST_DEPENDS= googletest>0:devel/googletest \ TEST_DEPENDS= googletest>0:devel/googletest \
molequeue>0:misc/molequeue 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_LDCONFIG= yes
USE_GITHUB= yes USE_GITHUB= yes
GH_ACCOUNT= OpenChemistry GH_ACCOUNT= OpenChemistry
GH_TUPLE= OpenChemistry:molecules:b1e16c5:molecules/../molecules \ 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_ON= BUILD_SHARED_LIBS
CMAKE_TESTING_ON= ENABLE_TESTING CMAKE_TESTING_ON= ENABLE_TESTING
OPTIONS_DEFINE= HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB VTK 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 OPTIONS_SUB= yes
HDF5_CMAKE_BOOL= USE_HDF5 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_DESC= Enable optional features using mmtf
MMTF_CMAKE_BOOL= USE_MMTF MMTF_CMAKE_BOOL= USE_MMTF
MMTF_BUILD_DEPENDS= mmtf-cpp>0:science/mmtf-cpp MMTF_BUILD_DEPENDS= mmtf-cpp>0:science/mmtf-cpp \
MMTF_BROKEN= see https://github.com/OpenChemistry/avogadrolibs/issues/1185 ${LOCALBASE}/include/boost/predef/other/endian.h:devel/boost-libs # needed by /usr/local/include/msgpack/sysdep.hpp:102 while boost is an optional dependency there
OPENGL_CMAKE_BOOL= USE_OPENGL OPENGL_CMAKE_BOOL= USE_OPENGL
OPENGL_USES= gl OPENGL_USES= gl
@ -58,7 +58,7 @@ QT5_IMPLIES= OPENGL
SPGLIB_DESC= Enable optional features using spglib SPGLIB_DESC= Enable optional features using spglib
SPGLIB_CMAKE_BOOL= USE_SPGLIB SPGLIB_CMAKE_BOOL= USE_SPGLIB
SPGLIB_CMAKE_ON= -DSPGLIB_INCLUDE_DIR=${LOCALBASE}/include/spglib SPGLIB_CMAKE_ON= -DSPGLIB_INCLUDE_DIR=${LOCALBASE}/include
SPGLIB_LIB_DEPENDS= libsymspg.so:science/spglib SPGLIB_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 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

8
science/avogadrolibs/distinfo
View file

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

4
science/avogadrolibs/files/patch-CMakeLists.txt
View file

@ -1,8 +1,8 @@
- git is only needed when 'molecules' and 'crystals' aren't supplied by the caller - 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 +++ 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_PATCH "0")
set(AvogadroLibs_VERSION set(AvogadroLibs_VERSION
"${AvogadroLibs_VERSION_MAJOR}.${AvogadroLibs_VERSION_MINOR}.${AvogadroLibs_VERSION_PATCH}") "${AvogadroLibs_VERSION_MAJOR}.${AvogadroLibs_VERSION_MINOR}.${AvogadroLibs_VERSION_PATCH}")

13
science/avogadrolibs/files/patch-avogadro_qtplugins_templatetool_CMakeLists.txt Normal file
View file

@ -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}")

29
science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp
View file

@ -1,29 +0,0 @@
--- avogadro/rendering/ambientocclusionspheregeometry.cpp.orig 2018-10-16 22:25:02 UTC
+++ avogadro/rendering/ambientocclusionspheregeometry.cpp
@@ -930,7 +930,7 @@ public:
// draw
glDrawRangeElements(GL_TRIANGLES, 0, static_cast<GLuint>(m_numVertices),
static_cast<GLsizei>(m_numIndices), GL_UNSIGNED_INT,
- reinterpret_cast<const GLvoid*>(NULL));
+ (const GLvoid*)nullptr);
m_vbo.release();
m_ibo.release();
@@ -1004,7 +1004,7 @@ public:
// draw
glDrawRangeElements(GL_TRIANGLES, 0, static_cast<GLuint>(m_numVertices),
static_cast<GLsizei>(m_numIndices), GL_UNSIGNED_INT,
- reinterpret_cast<const GLvoid*>(NULL));
+ (const GLvoid*)nullptr);
m_vbo.release();
m_ibo.release();
@@ -1326,7 +1326,7 @@ void AmbientOcclusionSphereGeometry::ren
// Render the loaded spheres using the shader and bound VBO.
glDrawRangeElements(GL_TRIANGLES, 0, static_cast<GLuint>(d->numberOfVertices),
static_cast<GLsizei>(d->numberOfIndices), GL_UNSIGNED_INT,
- reinterpret_cast<const GLvoid*>(NULL));
+ (const GLvoid*)nullptr);
d->vbo.release();
d->ibo.release();

11
science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp
View file

@ -1,11 +0,0 @@
--- avogadro/rendering/spheregeometry.cpp.orig 2018-10-16 22:26:03 UTC
+++ avogadro/rendering/spheregeometry.cpp
@@ -196,7 +196,7 @@ void SphereGeometry::render(const Camera
// Render the loaded spheres using the shader and bound VBO.
glDrawRangeElements(GL_TRIANGLES, 0, static_cast<GLuint>(d->numberOfVertices),
static_cast<GLsizei>(d->numberOfIndices), GL_UNSIGNED_INT,
- reinterpret_cast<const GLvoid*>(NULL));
+ (const GLvoid*)nullptr);
d->vbo.release();
d->ibo.release();

853
science/avogadrolibs/pkg-plist
View file

@ -3,6 +3,9 @@ include/avogadro/calc/avogadrocalcexport.h
include/avogadro/calc/chargemanager.h include/avogadro/calc/chargemanager.h
include/avogadro/calc/chargemodel.h include/avogadro/calc/chargemodel.h
include/avogadro/calc/defaultmodel.h include/avogadro/calc/defaultmodel.h
include/avogadro/calc/energycalculator.h
include/avogadro/calc/energymanager.h
include/avogadro/calc/lennardjones.h
include/avogadro/core/angleiterator.h include/avogadro/core/angleiterator.h
include/avogadro/core/angletools.h include/avogadro/core/angletools.h
include/avogadro/core/array.h include/avogadro/core/array.h
@ -52,6 +55,7 @@ include/avogadro/core/version.h
include/avogadro/io/avogadroioexport.h include/avogadro/io/avogadroioexport.h
include/avogadro/io/cjsonformat.h include/avogadro/io/cjsonformat.h
include/avogadro/io/cmlformat.h include/avogadro/io/cmlformat.h
include/avogadro/io/cmsgpackformat.h
include/avogadro/io/dcdformat.h include/avogadro/io/dcdformat.h
include/avogadro/io/fileformat.h include/avogadro/io/fileformat.h
include/avogadro/io/fileformatmanager.h include/avogadro/io/fileformatmanager.h
@ -85,6 +89,7 @@ include/avogadro/io/xyzformat.h
%%QT5%%include/avogadro/qtgui/fileformatdialog.h %%QT5%%include/avogadro/qtgui/fileformatdialog.h
%%QT5%%include/avogadro/qtgui/generichighlighter.h %%QT5%%include/avogadro/qtgui/generichighlighter.h
%%QT5%%include/avogadro/qtgui/hydrogentools.h %%QT5%%include/avogadro/qtgui/hydrogentools.h
%%QT5%%include/avogadro/qtgui/insertfragmentdialog.h
%%QT5%%include/avogadro/qtgui/interfacescript.h %%QT5%%include/avogadro/qtgui/interfacescript.h
%%QT5%%include/avogadro/qtgui/interfacewidget.h %%QT5%%include/avogadro/qtgui/interfacewidget.h
%%QT5%%include/avogadro/qtgui/jsonwidget.h %%QT5%%include/avogadro/qtgui/jsonwidget.h
@ -103,6 +108,7 @@ include/avogadro/io/xyzformat.h
%%QT5%%include/avogadro/qtgui/sceneplugin.h %%QT5%%include/avogadro/qtgui/sceneplugin.h
%%QT5%%include/avogadro/qtgui/scenepluginmodel.h %%QT5%%include/avogadro/qtgui/scenepluginmodel.h
%%QT5%%include/avogadro/qtgui/scriptloader.h %%QT5%%include/avogadro/qtgui/scriptloader.h
%%QT5%%include/avogadro/qtgui/sortfiltertreeproxymodel.h
%%QT5%%include/avogadro/qtgui/toolplugin.h %%QT5%%include/avogadro/qtgui/toolplugin.h
%%QT5%%include/avogadro/qtgui/utilities.h %%QT5%%include/avogadro/qtgui/utilities.h
%%QT5%%include/avogadro/qtgui/viewfactory.h %%QT5%%include/avogadro/qtgui/viewfactory.h
@ -118,10 +124,14 @@ include/avogadro/quantumio/avogadroquantumioexport.h
include/avogadro/quantumio/gamessus.h include/avogadro/quantumio/gamessus.h
include/avogadro/quantumio/gaussiancube.h include/avogadro/quantumio/gaussiancube.h
include/avogadro/quantumio/gaussianfchk.h include/avogadro/quantumio/gaussianfchk.h
include/avogadro/quantumio/genericoutput.h
include/avogadro/quantumio/molden.h include/avogadro/quantumio/molden.h
include/avogadro/quantumio/mopacaux.h include/avogadro/quantumio/mopacaux.h
include/avogadro/quantumio/nwchemjson.h include/avogadro/quantumio/nwchemjson.h
include/avogadro/quantumio/nwchemlog.h %%OPENGL%%include/avogadro/quantumio/nwchemlog.h
%%OPENGL%%include/avogadro/quantumio/orca.h
%%OPENGL%%include/avogadro/rendering/arcsector.h
%%OPENGL%%include/avogadro/rendering/arcstrip.h
%%OPENGL%%include/avogadro/rendering/arrowgeometry.h %%OPENGL%%include/avogadro/rendering/arrowgeometry.h
%%OPENGL%%include/avogadro/rendering/avogadrogl.h %%OPENGL%%include/avogadro/rendering/avogadrogl.h
%%OPENGL%%include/avogadro/rendering/avogadrorendering.h %%OPENGL%%include/avogadro/rendering/avogadrorendering.h
@ -143,11 +153,15 @@ include/avogadro/quantumio/nwchemlog.h
%%OPENGL%%include/avogadro/rendering/linestripgeometry.h %%OPENGL%%include/avogadro/rendering/linestripgeometry.h
%%OPENGL%%include/avogadro/rendering/meshgeometry.h %%OPENGL%%include/avogadro/rendering/meshgeometry.h
%%OPENGL%%include/avogadro/rendering/node.h %%OPENGL%%include/avogadro/rendering/node.h
%%OPENGL%%include/avogadro/rendering/plyvisitor.h
%%OPENGL%%include/avogadro/rendering/povrayvisitor.h %%OPENGL%%include/avogadro/rendering/povrayvisitor.h
%%OPENGL%%include/avogadro/rendering/primitive.h %%OPENGL%%include/avogadro/rendering/primitive.h
%%OPENGL%%include/avogadro/rendering/quad.h
%%OPENGL%%include/avogadro/rendering/quadoutline.h
%%OPENGL%%include/avogadro/rendering/scene.h %%OPENGL%%include/avogadro/rendering/scene.h
%%OPENGL%%include/avogadro/rendering/shader.h %%OPENGL%%include/avogadro/rendering/shader.h
%%OPENGL%%include/avogadro/rendering/shaderprogram.h %%OPENGL%%include/avogadro/rendering/shaderprogram.h
%%OPENGL%%include/avogadro/rendering/solidpipeline.h
%%OPENGL%%include/avogadro/rendering/spheregeometry.h %%OPENGL%%include/avogadro/rendering/spheregeometry.h
%%OPENGL%%include/avogadro/rendering/textlabel2d.h %%OPENGL%%include/avogadro/rendering/textlabel2d.h
%%OPENGL%%include/avogadro/rendering/textlabel3d.h %%OPENGL%%include/avogadro/rendering/textlabel3d.h
@ -166,14 +180,24 @@ include/avogadro/quantumio/nwchemlog.h
%%QT5%%lib/avogadro2/libgwavi.a %%QT5%%lib/avogadro2/libgwavi.a
%%QT5%%lib/avogadro2/scripts/charges/antechamber.py %%QT5%%lib/avogadro2/scripts/charges/antechamber.py
%%QT5%%lib/avogadro2/scripts/charges/xtb.py %%QT5%%lib/avogadro2/scripts/charges/xtb.py
%%QT5%%lib/avogadro2/scripts/energy/ani2x.py
%%QT5%%lib/avogadro2/scripts/energy/gaff.py
%%QT5%%lib/avogadro2/scripts/energy/gfn1.py
%%QT5%%lib/avogadro2/scripts/energy/gfn2.py
%%QT5%%lib/avogadro2/scripts/energy/gfnff.py
%%QT5%%lib/avogadro2/scripts/energy/mmff94.py
%%QT5%%lib/avogadro2/scripts/energy/uff.py
%%QT5%%lib/avogadro2/scripts/formatScripts/zyx.py %%QT5%%lib/avogadro2/scripts/formatScripts/zyx.py
%%QT5%%lib/avogadro2/staticplugins/AlignTool.a
%%QT5%%lib/avogadro2/staticplugins/ApplyColors.a %%QT5%%lib/avogadro2/staticplugins/ApplyColors.a
%%QT5%%lib/avogadro2/staticplugins/BallStick.a %%QT5%%lib/avogadro2/staticplugins/BallStick.a
%%QT5%%lib/avogadro2/staticplugins/BondCentric.a %%QT5%%lib/avogadro2/staticplugins/BondCentric.a
%%QT5%%lib/avogadro2/staticplugins/Bonding.a %%QT5%%lib/avogadro2/staticplugins/Bonding.a
%%QT5%%lib/avogadro2/staticplugins/Cartoons.a %%QT5%%lib/avogadro2/staticplugins/Cartoons.a
%%QT5%%lib/avogadro2/staticplugins/Centroid.a
%%QT5%%lib/avogadro2/staticplugins/CloseContacts.a %%QT5%%lib/avogadro2/staticplugins/CloseContacts.a
%%VTK%%lib/avogadro2/staticplugins/ColorOpacityMap.a %%VTK%%lib/avogadro2/staticplugins/ColorOpacityMap.a
%%QT5%%lib/avogadro2/staticplugins/ConfigurePython.a
%%QT5%%lib/avogadro2/staticplugins/CoordinateEditor.a %%QT5%%lib/avogadro2/staticplugins/CoordinateEditor.a
%%QT5%%lib/avogadro2/staticplugins/CopyPaste.a %%QT5%%lib/avogadro2/staticplugins/CopyPaste.a
%%QT5%%lib/avogadro2/staticplugins/Cp2kInput.a %%QT5%%lib/avogadro2/staticplugins/Cp2kInput.a
@ -184,6 +208,7 @@ include/avogadro/quantumio/nwchemlog.h
%%QT5%%lib/avogadro2/staticplugins/FetchPDB.a %%QT5%%lib/avogadro2/staticplugins/FetchPDB.a
%%QT5%%lib/avogadro2/staticplugins/Focus.a %%QT5%%lib/avogadro2/staticplugins/Focus.a
%%QT5%%lib/avogadro2/staticplugins/Force.a %%QT5%%lib/avogadro2/staticplugins/Force.a
%%QT5%%lib/avogadro2/staticplugins/Forcefield.a
%%QT5%%lib/avogadro2/staticplugins/GamessInput.a %%QT5%%lib/avogadro2/staticplugins/GamessInput.a
%%QT5%%lib/avogadro2/staticplugins/Hydrogens.a %%QT5%%lib/avogadro2/staticplugins/Hydrogens.a
%%QT5%%lib/avogadro2/staticplugins/ImportPQR.a %%QT5%%lib/avogadro2/staticplugins/ImportPQR.a
@ -197,7 +222,6 @@ include/avogadro/quantumio/nwchemlog.h
%%QT5%%lib/avogadro2/staticplugins/MeasureTool.a %%QT5%%lib/avogadro2/staticplugins/MeasureTool.a
%%QT5%%lib/avogadro2/staticplugins/Meshes.a %%QT5%%lib/avogadro2/staticplugins/Meshes.a
%%QT5%%lib/avogadro2/staticplugins/MolecularProperties.a %%QT5%%lib/avogadro2/staticplugins/MolecularProperties.a
%%QT5%%lib/avogadro2/staticplugins/MongoChem.a
%%QT5%%lib/avogadro2/staticplugins/Navigator.a %%QT5%%lib/avogadro2/staticplugins/Navigator.a
%%QT5%%lib/avogadro2/staticplugins/NetworkDatabases.a %%QT5%%lib/avogadro2/staticplugins/NetworkDatabases.a
%%QT5%%lib/avogadro2/staticplugins/NonCovalent.a %%QT5%%lib/avogadro2/staticplugins/NonCovalent.a
@ -205,6 +229,7 @@ include/avogadro/quantumio/nwchemlog.h
%%QT5%%lib/avogadro2/staticplugins/OpenBabel.a %%QT5%%lib/avogadro2/staticplugins/OpenBabel.a
%%QT5%%lib/avogadro2/staticplugins/OpenMMInput.a %%QT5%%lib/avogadro2/staticplugins/OpenMMInput.a
%%QT5%%lib/avogadro2/staticplugins/OverlayAxes.a %%QT5%%lib/avogadro2/staticplugins/OverlayAxes.a
%%QT5%%lib/avogadro2/staticplugins/PLY.a
%%QT5%%lib/avogadro2/staticplugins/POVRay.a %%QT5%%lib/avogadro2/staticplugins/POVRay.a
%%QT5%%lib/avogadro2/staticplugins/PlayerTool.a %%QT5%%lib/avogadro2/staticplugins/PlayerTool.a
%%VTK%%lib/avogadro2/staticplugins/PlotPdf.a %%VTK%%lib/avogadro2/staticplugins/PlotPdf.a
@ -220,14 +245,14 @@ include/avogadro/quantumio/nwchemlog.h
%%QT5%%lib/avogadro2/staticplugins/Select.a %%QT5%%lib/avogadro2/staticplugins/Select.a
%%QT5%%lib/avogadro2/staticplugins/Selection.a %%QT5%%lib/avogadro2/staticplugins/Selection.a
%%SPGLIB%%lib/avogadro2/staticplugins/SpaceGroup.a %%SPGLIB%%lib/avogadro2/staticplugins/SpaceGroup.a
%%QT5%%lib/avogadro2/staticplugins/Spectra.a
%%QT5%%lib/avogadro2/staticplugins/Surfaces.a %%QT5%%lib/avogadro2/staticplugins/Surfaces.a
%%LIBMSYM%%lib/avogadro2/staticplugins/Symmetry.a %%LIBMSYM%%lib/avogadro2/staticplugins/Symmetry.a
%%LIBMSYM%%lib/avogadro2/staticplugins/SymmetryScene.a %%LIBMSYM%%lib/avogadro2/staticplugins/SymmetryScene.a
%%QT5%%lib/avogadro2/staticplugins/TemplateTool.a
%%QT5%%lib/avogadro2/staticplugins/ThreeDMol.a %%QT5%%lib/avogadro2/staticplugins/ThreeDMol.a
%%QT5%%lib/avogadro2/staticplugins/VRML.a %%QT5%%lib/avogadro2/staticplugins/VRML.a
%%QT5%%lib/avogadro2/staticplugins/VanDerWaals.a %%QT5%%lib/avogadro2/staticplugins/VanDerWaals.a
%%QT5%%lib/avogadro2/staticplugins/VanDerWaalsAO.a %%QT5%%lib/avogadro2/staticplugins/Vibrations.a
%%QT5%%lib/avogadro2/staticplugins/Wireframe.a %%QT5%%lib/avogadro2/staticplugins/Wireframe.a
%%QT5%%lib/avogadro2/staticplugins/apbs.a %%QT5%%lib/avogadro2/staticplugins/apbs.a
%%QT5%%lib/avogadro2/staticplugins/commands.a %%QT5%%lib/avogadro2/staticplugins/commands.a
@ -236,39 +261,37 @@ lib/cmake/avogadrolibs/AvogadroLibsConfigVersion.cmake
lib/cmake/avogadrolibs/AvogadroLibsTargets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/avogadrolibs/AvogadroLibsTargets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/avogadrolibs/AvogadroLibsTargets.cmake lib/cmake/avogadrolibs/AvogadroLibsTargets.cmake
lib/cmake/avogadrolibs/FindEigen3.cmake lib/cmake/avogadrolibs/FindEigen3.cmake
lib/cmake/avogadrolibs/FindGLEW.cmake
lib/cmake/avogadrolibs/FindLibArchive.cmake
lib/cmake/avogadrolibs/Findlibmsym.cmake lib/cmake/avogadrolibs/Findlibmsym.cmake
lib/libAvogadroCalc.so lib/libAvogadroCalc.so
lib/libAvogadroCalc.so.1 lib/libAvogadroCalc.so.1
lib/libAvogadroCalc.so.1.97.0 lib/libAvogadroCalc.so.1.99.0
lib/libAvogadroCore.so lib/libAvogadroCore.so
lib/libAvogadroCore.so.1 lib/libAvogadroCore.so.1
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%%QT5%%share/avogadro2/fragments/scripts/requirements.txt
%%QT5%%share/avogadro2/fragments/scripts/svg2png.py
%%QT5%%share/avogadro2/fragments/scripts/test_depict_ligands.smi
%%QT5%%share/avogadro2/fragments/thiocyanate.png
%%QT5%%share/avogadro2/molecules/LICENSE %%QT5%%share/avogadro2/molecules/LICENSE
%%QT5%%share/avogadro2/molecules/README.md %%QT5%%share/avogadro2/molecules/README.md
%%QT5%%share/avogadro2/molecules/alcohols/2-aminoethanol.cml %%QT5%%share/avogadro2/molecules/alcohols/2-aminoethanol.cml

13
science/kalzium/files/patch-compoundviewer_CMakeLists.txt Normal file
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@ -0,0 +1,13 @@
- fix linking with avogadrolibs: it fails w/out the lib specification
- cmake's link_directories doesn't work for some reason
--- compoundviewer/CMakeLists.txt.orig 2023-11-30 16:56:21 UTC
+++ compoundviewer/CMakeLists.txt
@@ -30,6 +30,7 @@ target_link_libraries(compoundviewer
AvogadroQtOpenGL
AvogadroQtPlugins
Eigen3::Eigen
+ -L${CMAKE_INSTALL_PREFIX}/lib
)
target_include_directories(compoundviewer PRIVATE

7
science/py-avogadrolibs/Makefile
View file

@ -1,12 +1,11 @@
PORTNAME= avogadrolibs PORTNAME= avogadrolibs
DISTVERSION= 1.97.0 DISTVERSION= 1.99.0
PORTREVISION= 1
CATEGORIES= science CATEGORIES= science
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org MAINTAINER= yuri@FreeBSD.org
COMMENT= Python bindings for Avogadro2 chemistry libraries COMMENT= Python bindings for Avogadro2 chemistry libraries
WWW= https://www.openchemistry.org/projects/avogadro2/ WWW= https://two.avogadro.cc/
LICENSE= GPLv2 LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/../LICENSE LICENSE_FILE= ${WRKSRC}/../LICENSE
@ -25,6 +24,8 @@ WRKSRC_SUBDIR= python
CMAKE_ARGS= -DINSTALL_LIBRARY_DIR:STRING=${PYTHON_SITELIBDIR} CMAKE_ARGS= -DINSTALL_LIBRARY_DIR:STRING=${PYTHON_SITELIBDIR}
PLIST_FILES= ${PYTHON_SITELIBDIR}/avogadro/__init__.py \ PLIST_FILES= ${PYTHON_SITELIBDIR}/avogadro/__init__.py \
${PYTHON_SITELIBDIR}/avogadro/cjson.py \
${PYTHON_SITELIBDIR}/avogadro/connect.py \
${PYTHON_SITELIBDIR}/avogadro/core${PYTHON_EXT_SUFFIX}.so \ ${PYTHON_SITELIBDIR}/avogadro/core${PYTHON_EXT_SUFFIX}.so \
${PYTHON_SITELIBDIR}/avogadro/io${PYTHON_EXT_SUFFIX}.so ${PYTHON_SITELIBDIR}/avogadro/io${PYTHON_EXT_SUFFIX}.so

6
science/py-avogadrolibs/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1665903668 TIMESTAMP = 1707762010
SHA256 (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 46641504a1808c5ff6fb7d66be48d866848203899025fd386cc6e3dd5d9ec342 SHA256 (OpenChemistry-avogadrolibs-1.99.0_GH0.tar.gz) = 34808e3c602b0f60f3c160ff0220832aee777db86e962e3f958c6327fb434063
SIZE (OpenChemistry-avogadrolibs-1.97.0_GH0.tar.gz) = 11456702 SIZE (OpenChemistry-avogadrolibs-1.99.0_GH0.tar.gz) = 4858298

15
science/py-avogadrolibs/files/patch-CMakeLists.txt
View file

@ -1,9 +1,10 @@
--- CMakeLists.txt.orig 2022-07-21 15:20:28 UTC --- CMakeLists.txt.orig 2024-02-12 18:24:36 UTC
+++ CMakeLists.txt +++ CMakeLists.txt
@@ -1,3 +1,6 @@ @@ -1,5 +1,7 @@ cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR) cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+find_package (Eigen3 3.3 REQUIRED NO_MODULE)
+ +
+find_package(AvogadroLibs REQUIRED) if (NOT TARGET Avogadro::Core)
find_package(PythonInterp 3 REQUIRED) find_package(AvogadroLibs REQUIRED)
find_package(PythonLibs 3 REQUIRED) endif()
set(PYBIND11_PYTHON_VERSION "3" CACHE STRING "")