Code

OffLattice support#453

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kaizu merged 60 commits intomasterecell/ecell4_base:masterfrom offlatticeecell/ecell4_base:offlatticeCopy head branch name to clipboardFeb 9, 2020

+2,712-3,139

Commits

Commits on Oct 17, 2019

• 🔥 Remove alias functions used for Cython

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• 🚧 Add python apis for offlattice

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• ✅ Add a test for offlattice

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• 💥 Add SpatiocyteWorld.add_offlattice()

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Commits on Oct 24, 2019

• ✨ Add a class for generating OffLatticeSpace

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Commits on Oct 31, 2019

• ✨ Add an argument to add_offlattice()

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• ♻️ Refactor remove_voxel()

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Commits on Dec 12, 2019

• Merge pull request #431 from 0ncorhynchus/offlattice

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• ♻️ Remove some functions from VoxelSpaceBase

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• 🔥 Remove other functions from VoxelSpaceBase

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• 🔥 Remove VoxelSpaceBase::particle_at()

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• ♻️ Impl find_voxel() instead of find_particle()

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• 🎨 Format VoxelSpaceBase.[ch]pp

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• 🎨 Format spatiocyte codes

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• ♻️ Move get_value() and get_value_exact()

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• 🎨 Format LatticeSpaces

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• ♻️ Use ranged-for-loop instead of iterator

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• ♻️ Use auto for the return value of list_voxels()

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• Merge pull request #434 from 0ncorhynchus/refactor_spatiocyte

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• ♻️ Isolate push_voxels() from VoxelSpaceBase

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• 🐛 Make list_voxels() to show the real species

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• 💥 Modify SpatiocyteWorld::list_voxels()

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• 💥 Do not use radius, D and loc from ParticleVoxel

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• 💥 Modify VoxelSpaceBase::list_voxels()

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• 💥 Change the return type of find_voxel()

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• ♻️ Modify VoxelSpaceBase::get_voxel_at()

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• 💥 Remove radius and D from VoxelPool

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• ♻️ Remove VoxelSpaceBase::get_voxel_pool()

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• ♻️ Modify SpatiocyteWorld::update_voxel()

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• ♻️ Modify VoxelSpaceBase::update_voxel()

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• 🔥 Remove ParticleVoxel completely!

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Commits on Dec 26, 2019

• Merge pull request #435 from 0ncorhynchus/remove_particle_voxel

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• ♻️ Add Voxel::get_neighbor_randomly()

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• ♻️ Add another Voxel::get_neighbor_randomly()

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• ♻️ StepEvent2D uses Voxel::get_neighbor_randomly()

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Commits on Jan 9, 2020

• ♻️ Remove rng from args of get_neighbor_randomly()

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Commits on Jan 16, 2020

• ♻️ Move functions for neighbor to SpatiocyteWorld

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• ♻️ Change the types of intefaces_ and neighbors_

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• ♻️ Refactor add_structure() and remove is_inside()

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• ♻️ Change the arguments of gen_particle_from()

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• ♻️ Add find_space_and_voxel_pool()

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• ♻️ Add find_space_and_molecule_pool()

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• 🔥 Remove coordinate2voxel()

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• 🐛 Fix bug around locating molecules

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• 🔥 Remove SpatiocyteWorld::coordinate_type

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Commits on Jan 23, 2020

• 🐛 Fix num_voxels* and num_molecules*

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• 🐛 Fix the bug of SpatiocyteWorld::add_molecules()

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• ♻️ Refactor get_molecule_info()

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• 🐛 Get information from a model before add a space

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• ✅ Add test for get_molecule_info()

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• 🐛 Fix get_location() with a vacant voxel

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• 🐛 Fix SpatiocyteWorld::check_neighbor()

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• 🐛 Fix reactions with OffLatticeSpace

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Commits on Jan 30, 2020

• Merge pull request #445 from 0ncorhynchus/fix_offlattice

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• ♻️ Add a virtual function StepEvent::dimension()

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• ⚡ Use template for StepEvent and some functions

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• ♻️ Add a model to a python test

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Commits on Feb 6, 2020

• ✅ Add a test for OffLattice

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Commits on Feb 7, 2020

• 🔀 Cherry pick a commit for CircleCI

  

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