flexible cable-based cable_cell representation (#1083)
* Remove spherical root/soma from morphology representations and logic. * Replace `sample_tree` with `segment_tree`, which represents sample points in pairs and allows the representation of detached branches and cable segments. * Remove sample point properties and predicates. * Remove `cv_policy_flag::single_root_cv` as somata with a single attached dendrite will have a representation in the morphology of a single branch. * Remove `arb::math::{volume/area}_sphere`, which are no longer being used. * Remove spherical root special cases from `embed_pwlin` and `place_pwlin` objects. * Add textual representation of `mnpos` in morphology exception text. * Rename `sample_tree_from_swc` to `segement_tree_from_swc` and remove any special casing for one point somata. * Remove `msample` and `mbranch` types. * Update unit tests and python wrapper to reflect the changes.
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- arbor/CMakeLists.txt 1 addition, 2 deletionsarbor/CMakeLists.txt
- arbor/cv_policy.cpp 4 additions, 11 deletionsarbor/cv_policy.cpp
- arbor/include/arbor/cv_policy.hpp 3 additions, 4 deletionsarbor/include/arbor/cv_policy.hpp
- arbor/include/arbor/math.hpp 0 additions, 12 deletionsarbor/include/arbor/math.hpp
- arbor/include/arbor/morph/embed_pwlin.hpp 10 additions, 4 deletionsarbor/include/arbor/morph/embed_pwlin.hpp
- arbor/include/arbor/morph/locset.hpp 3 additions, 3 deletionsarbor/include/arbor/morph/locset.hpp
- arbor/include/arbor/morph/morphexcept.hpp 7 additions, 2 deletionsarbor/include/arbor/morph/morphexcept.hpp
- arbor/include/arbor/morph/morphology.hpp 4 additions, 22 deletionsarbor/include/arbor/morph/morphology.hpp
- arbor/include/arbor/morph/primitives.hpp 7 additions, 40 deletionsarbor/include/arbor/morph/primitives.hpp
- arbor/include/arbor/morph/sample_tree.hpp 0 additions, 56 deletionsarbor/include/arbor/morph/sample_tree.hpp
- arbor/include/arbor/morph/segment_tree.hpp 62 additions, 0 deletionsarbor/include/arbor/morph/segment_tree.hpp
- arbor/morph/embed_pwlin.cpp 64 additions, 81 deletionsarbor/morph/embed_pwlin.cpp
- arbor/morph/locset.cpp 17 additions, 19 deletionsarbor/morph/locset.cpp
- arbor/morph/mbranch.cpp 0 additions, 29 deletionsarbor/morph/mbranch.cpp
- arbor/morph/mbranch.hpp 0 additions, 38 deletionsarbor/morph/mbranch.hpp
- arbor/morph/morphexcept.cpp 18 additions, 8 deletionsarbor/morph/morphexcept.cpp
- arbor/morph/morphology.cpp 64 additions, 125 deletionsarbor/morph/morphology.cpp
- arbor/morph/place_pwlin.cpp 34 additions, 91 deletionsarbor/morph/place_pwlin.cpp
- arbor/morph/primitives.cpp 6 additions, 10 deletionsarbor/morph/primitives.cpp
- arbor/morph/region.cpp 10 additions, 22 deletionsarbor/morph/region.cpp
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