Add initial 3d dune-copasi simulation support #937
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Additional details and impacted files@@ Coverage Diff @@
## main #937 +/- ##
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+ Coverage 89.06% 89.17% +0.11%
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Files 143 151 +8
Lines 13854 14120 +266
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+ Hits 12339 12592 +253
- Misses 1515 1528 +13
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- add `Mesh3d` class - Uses CGAL to convert segmented ImageStack to tetrahedral mesh - Provides vectors of vertices and tetrahedra for each compartment - Provides grid in gmsh .msh version 2 format that dune can import - setCompartmentMaxCellVolume allows the max size of tetrahedra to be set for each compartment - ModelGeometry - Now has both a Mesh and a Mesh3d - With 1 z-slice, Mesh is used and Mesh3d is null - With >1 z-slices, Mesh3d is used and Mesh is null - add `getIsMeshValid()` which tells you if the model has a valid mesh - DuneGrid - makeDuneGrid now templated on MeshType which can be Mesh or Mesh3d - generates a 2d dune grid of triangles from a Mesh as before - generates a 3d dune grid of tetrahedrons from a Mesh3d - DuneFunction - extend to 3d - re-enable 2d tiff part of dunefunction test - DuneConverter - Uses mesh3d & 3d ini file if mesh3d is not null, otherwise previous 2d ini file & mesh - DuneSim - move most dune-copasi code into impl header and template on number of dimensions - Add 3d example models - very-simple-model-3d - gray-scott-3d - Update build system - ensure scotch libs are linked in the correct order in core/CMakeLists.txt - add scotch to installed core dependencies - make dune::copasi a public dependency of core - add `-fvisibility=hidden` to compile flags - update codecov cli & explicitly pass token - sme_deps -> 2024.02.01 - manylinux -> 2024.02.01 - use Python 3.12 in CI
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This was referenced Feb 15, 2024
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Mesh3dclassgetIsMeshValid()which tells you if the model has a valid mesh-fvisibility=hiddento compile flags