[med-svn] [ecell] 13/14: Update upstream source from tag 'upstream/4.1.2'
Andreas Tille
tille at debian.org
Tue Dec 5 14:18:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ecell.
commit 60b2ec8dfe8e8beab2fae8a2149af209acef7456
Merge: 7039993 893c88d
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 5 15:15:19 2017 +0100
Update upstream source from tag 'upstream/4.1.2'
Update to upstream version '4.1.2'
with Debian dir 62c7f442e8aca52bf8c82ee73ed585f099e5feb3
.gitignore | 13 +
.gitmodules | 0
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AUTHORS | 14 +
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ecell4/CMakeLists.txt | 11 +
ecell4/bd/BDFactory.hpp | 119 +
ecell4/bd/BDPropagator.cpp | 304 +
ecell4/bd/BDPropagator.hpp | 152 +
ecell4/bd/BDSimulator.cpp | 54 +
ecell4/bd/BDSimulator.hpp | 128 +
ecell4/bd/BDWorld.hpp | 420 +
ecell4/bd/CMakeLists.txt | 20 +
ecell4/bd/functions3d.cpp | 154 +
ecell4/bd/functions3d.hpp | 57 +
ecell4/bd/samples/CMakeLists.txt | 2 +
ecell4/bd/samples/hardbody.cpp | 68 +
ecell4/bd/tests/BDSimulator_test.cpp | 61 +
ecell4/bd/tests/BDWorld_test.cpp | 41 +
ecell4/bd/tests/CMakeLists.txt | 16 +
ecell4/core/AABB.cpp | 46 +
ecell4/core/AABB.hpp | 96 +
ecell4/core/AABBSurface.cpp | 138 +
ecell4/core/AABBSurface.hpp | 105 +
ecell4/core/CMakeLists.txt | 63 +
ecell4/core/CompartmentSpace.cpp | 159 +
ecell4/core/CompartmentSpace.hpp | 261 +
ecell4/core/CompartmentSpaceHDF5Writer.hpp | 253 +
ecell4/core/Context.cpp | 791 +
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ecell4/core/Cylinder.cpp | 142 +
ecell4/core/Cylinder.hpp | 119 +
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ecell4/core/DynamicPriorityQueue.hpp | 585 +
ecell4/core/EventScheduler.hpp | 168 +
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ecell4/core/Integer3.cpp | 65 +
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ecell4/core/InterfaceType.hpp | 53 +
ecell4/core/Journal.cpp | 83 +
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ecell4/core/LatticeSpace.cpp | 86 +
ecell4/core/LatticeSpace.hpp | 280 +
ecell4/core/LatticeSpaceBase.cpp | 51 +
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ecell4/core/LatticeSpaceCellListImpl.cpp | 419 +
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ecell4/core/LatticeSpaceHDF5Writer.hpp | 320 +
ecell4/core/LatticeSpaceVectorImpl.cpp | 1088 +
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ecell4/core/Mesh.cpp | 150 +
ecell4/core/Mesh.hpp | 80 +
ecell4/core/Model.cpp | 68 +
ecell4/core/Model.hpp | 224 +
ecell4/core/ModelWrapper.hpp | 129 +
ecell4/core/MolecularType.hpp | 62 +
ecell4/core/NetfreeModel.cpp | 575 +
ecell4/core/NetfreeModel.hpp | 148 +
ecell4/core/NetworkModel.cpp | 258 +
ecell4/core/NetworkModel.hpp | 137 +
ecell4/core/OffLatticeSpace.cpp | 476 +
ecell4/core/OffLatticeSpace.hpp | 102 +
ecell4/core/Particle.hpp | 171 +
ecell4/core/ParticleSpace.cpp | 233 +
ecell4/core/ParticleSpace.hpp | 434 +
ecell4/core/ParticleSpaceCellListImpl.cpp | 346 +
ecell4/core/ParticleSpaceCellListImpl.hpp | 500 +
ecell4/core/ParticleSpaceHDF5Writer.hpp | 274 +
ecell4/core/PlanarSurface.cpp | 84 +
ecell4/core/PlanarSurface.hpp | 71 +
ecell4/core/RandomNumberGenerator.cpp | 121 +
ecell4/core/RandomNumberGenerator.hpp | 135 +
ecell4/core/ReactionRule.cpp | 107 +
ecell4/core/ReactionRule.hpp | 180 +
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ecell4/core/SerialIDGenerator.hpp | 360 +
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ecell4/core/SimulatorBase.hpp | 250 +
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ecell4/core/Species.cpp | 375 +
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ecell4/core/Sphere.cpp | 139 +
ecell4/core/Sphere.hpp | 96 +
ecell4/core/StructureType.hpp | 53 +
ecell4/core/SubvolumeSpace.cpp | 401 +
ecell4/core/SubvolumeSpace.hpp | 562 +
ecell4/core/SubvolumeSpaceHDF5Writer.hpp | 316 +
ecell4/core/UnitSpecies.cpp | 264 +
ecell4/core/UnitSpecies.hpp | 163 +
ecell4/core/VacantType.hpp | 53 +
ecell4/core/Voxel.hpp | 86 +
ecell4/core/VoxelPool.hpp | 435 +
ecell4/core/VoxelSpaceBase.cpp | 228 +
ecell4/core/VoxelSpaceBase.hpp | 86 +
ecell4/core/collision.cpp | 388 +
ecell4/core/collision.hpp | 105 +
ecell4/core/comparators.hpp | 95 +
ecell4/core/config.h.in | 31 +
ecell4/core/exceptions.hpp | 192 +
ecell4/core/extras.cpp | 133 +
ecell4/core/extras.hpp | 112 +
ecell4/core/functions.hpp | 116 +
ecell4/core/get_mapper_mf.hpp | 60 +
ecell4/core/hash.hpp | 29 +
ecell4/core/linear_algebra.hpp | 48 +
ecell4/core/observers.cpp | 629 +
ecell4/core/observers.hpp | 1096 +
ecell4/core/shape_operators.hpp | 441 +
ecell4/core/swap.hpp | 23 +
ecell4/core/tests/CMakeLists.txt | 19 +
ecell4/core/tests/CompartmentSpace_test.cpp | 68 +
ecell4/core/tests/EventScheduler_test.cpp | 19 +
ecell4/core/tests/LatticeSpace_test.cpp | 617 +
ecell4/core/tests/NetfreeModel_test.cpp | 256 +
ecell4/core/tests/NetworkModel_test.cpp | 106 +
ecell4/core/tests/OffLatticeSpace_test.cpp | 178 +
ecell4/core/tests/ParticleSpace_test.cpp | 150 +
ecell4/core/tests/RandomNumberGenerator_test.cpp | 49 +
ecell4/core/tests/ReactionRule_test.cpp | 298 +
ecell4/core/tests/Real3_test.cpp | 34 +
ecell4/core/tests/Shape_test.cpp | 89 +
ecell4/core/tests/Species_test.cpp | 102 +
ecell4/core/tests/SubvolumeSpace_test.cpp | 72 +
ecell4/core/tests/extras_test.cpp | 23 +
ecell4/core/tests/get_mapper_mf_test.cpp | 65 +
ecell4/core/types.hpp | 22 +
ecell4/egfrd/.gitignore | 63 +
ecell4/egfrd/.hgignore | 60 +
ecell4/egfrd/AUTHORS | 4 +
ecell4/egfrd/AnalyticalPair.hpp | 198 +
ecell4/egfrd/AnalyticalSingle.hpp | 109 +
ecell4/egfrd/BDPropagator.hpp | 423 +
ecell4/egfrd/BDSimulator.hpp | 253 +
ecell4/egfrd/CMakeLists.txt | 77 +
ecell4/egfrd/COPYING | 340 +
ecell4/egfrd/ChangeLog | 0
ecell4/egfrd/ConsoleAppender.cpp | 24 +
ecell4/egfrd/ConsoleAppender.hpp | 21 +
ecell4/egfrd/CylindricalBesselGenerator.cpp | 187 +
ecell4/egfrd/CylindricalBesselGenerator.hpp | 109 +
ecell4/egfrd/Defs.hpp | 29 +
ecell4/egfrd/Domain.hpp | 112 +
ecell4/egfrd/DomainFactory.hpp | 33 +
ecell4/egfrd/DomainID.hpp | 40 +
ecell4/egfrd/DomainUtils.hpp | 116 +
ecell4/egfrd/EGFRDSimulator.hpp | 4243 ++
ecell4/egfrd/FaceTriangle.hpp | 149 +
ecell4/egfrd/GreensFunction.hpp | 30 +
ecell4/egfrd/GreensFunction1DAbsAbs.cpp | 708 +
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ecell4/egfrd/GreensFunction1DRadAbs.cpp | 703 +
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ecell4/egfrd/GreensFunction3D.cpp | 275 +
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ecell4/egfrd/GreensFunction3DAbsSym.cpp | 411 +
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ecell4/egfrd/HalfOrderBesselGenerator.hpp | 134 +
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ecell4/egfrd/Logger.cpp | 270 +
ecell4/egfrd/Logger.hpp | 163 +
ecell4/egfrd/MatrixSpace.hpp | 642 +
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ecell4/egfrd/NEWS | 0
ecell4/egfrd/NetworkRulesAdapter.hpp | 207 +
ecell4/egfrd/OldDefs.hpp | 46 +
ecell4/egfrd/Pair.hpp | 55 +
ecell4/egfrd/PairGreensFunction.cpp | 7 +
ecell4/egfrd/PairGreensFunction.hpp | 52 +
ecell4/egfrd/ParticleContainer.hpp | 140 +
ecell4/egfrd/ParticleContainerBase.hpp | 332 +
ecell4/egfrd/ParticleSimulator.hpp | 201 +
ecell4/egfrd/ParticleTraits.hpp | 153 +
ecell4/egfrd/Polygon.hpp | 215 +
ecell4/egfrd/README | 95 +
ecell4/egfrd/ReactionRecord.hpp | 137 +
ecell4/egfrd/ReactionRecorder.hpp | 16 +
ecell4/egfrd/ReactionRecorderWrapper.hpp | 134 +
ecell4/egfrd/ReactionRuleInfo.hpp | 112 +
ecell4/egfrd/Real3Type.hpp | 58 +
ecell4/egfrd/ShapedDomain.hpp | 31 +
ecell4/egfrd/Shell.hpp | 111 +
ecell4/egfrd/ShellID.hpp | 40 +
ecell4/egfrd/Single.hpp | 45 +
ecell4/egfrd/SphericalBesselGenerator.cpp | 271 +
ecell4/egfrd/SphericalBesselGenerator.hpp | 109 +
ecell4/egfrd/StlFileReader.hpp | 270 +
ecell4/egfrd/Transaction.hpp | 290 +
ecell4/egfrd/TriangleOperation.hpp | 187 +
ecell4/egfrd/VolumeClearer.hpp | 19 +
ecell4/egfrd/World.hpp | 1083 +
ecell4/egfrd/abstract_set.hpp | 91 +
ecell4/egfrd/compat.h | 47 +
ecell4/egfrd/config.h.in | 21 +
ecell4/egfrd/egfrd.hpp | 289 +
ecell4/egfrd/exceptions.hpp | 201 +
ecell4/egfrd/factorial.hpp | 443 +
ecell4/egfrd/filters.hpp | 74 +
ecell4/egfrd/findRoot.cpp | 51 +
ecell4/egfrd/findRoot.hpp | 12 +
ecell4/egfrd/freeFunctions.hpp | 436 +
ecell4/egfrd/funcSum.cpp | 154 +
ecell4/egfrd/funcSum.hpp | 20 +
ecell4/egfrd/generator.hpp | 555 +
ecell4/egfrd/geometry.hpp | 234 +
ecell4/egfrd/legacy/BDSimulator.hpp | 125 +
ecell4/egfrd/legacy/BasicNetworkRulesImpl.cpp | 59 +
ecell4/egfrd/legacy/BasicNetworkRulesImpl.hpp | 33 +
ecell4/egfrd/legacy/BasicReactionRecorderImpl.hpp | 24 +
ecell4/egfrd/legacy/Box.hpp | 369 +
ecell4/egfrd/legacy/CuboidalRegion.hpp | 62 +
ecell4/egfrd/legacy/Cylinder.hpp | 285 +
ecell4/egfrd/legacy/CylindricalSurface.hpp | 64 +
ecell4/egfrd/legacy/DynamicPriorityQueue.hpp | 578 +
ecell4/egfrd/legacy/EGFRDSimulatorFactory.hpp | 89 +
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ecell4/egfrd/legacy/ParticleModel.cpp | 51 +
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ecell4/egfrd/legacy/ParticleSimulatorFactory.hpp | 22 +
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ecell4/egfrd/legacy/SpeciesInfo.hpp | 97 +
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ecell4/egfrd/legacy/SpeciesTypeID.hpp | 57 +
ecell4/egfrd/legacy/Sphere.hpp | 184 +
ecell4/egfrd/legacy/SphericalSurface.hpp | 54 +
ecell4/egfrd/legacy/Structure.hpp | 114 +
ecell4/egfrd/legacy/StructureType.cpp | 32 +
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ecell4/egfrd/legacy/StructureUtils.hpp | 111 +
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ecell4/egfrd/legacy/greens_functions.cpp | 213 +
ecell4/egfrd/legacy/gui/renderParticles.py | 167 +
ecell4/egfrd/legacy/gui/vtk_particles.py | 148 +
ecell4/egfrd/legacy/m4/ac_prog_pdflatex.m4 | 22 +
ecell4/egfrd/legacy/m4/ax_boost_base.m4 | 248 +
ecell4/egfrd/legacy/misc/from_camel_case.sed | 114 +
ecell4/egfrd/legacy/misc/strip-spaces.hs | 247 +
ecell4/egfrd/legacy/misc/unroller.py | 29 +
ecell4/egfrd/legacy/peer/compat.h | 38 +
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ecell4/egfrd/legacy/peer/converters/iterator.hpp | 16 +
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ecell4/egfrd/legacy/peer/pickle_support.hpp | 85 +
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readthedocs/old/Spatiocyte.md | 859 +
readthedocs/old/WorldSimBasics.md | 202 +
readthedocs/old/license.md | 12 +
readthedocs/old/tutorials.md | 63 +
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requirements.txt | 5 +
860 files changed, 294054 insertions(+)
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