- Oct 01, 2020
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Brent Huisman authored
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- Sep 22, 2020
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Benjamin Cumming authored
* Move label and s-expr parsing code and unit tests from Python to arbor C++ library. * Update `locset` and `region` constructors that take string arguments to parse strings as s-expressions or "quoted" labels. * Modify the input stream modifier used to parse asc files to use a lookup table for substitutions, renamed it transmogrifier. * Replace `hopefully` type implemented in python headers with an `arb::util::expected`. * Add `ARBDEV_COLOR` CMake option that forces gcc and clang to always output color output. * Allow arbitrary strings in labels in region and locset expressions. * Add `parse_region_expression` and `parse_locset_expression` functions alongside the existing `parse_label_expression` function for use when a region or locset is expected. These calls will promote a quoted string `"label"` to `(region "label")` or `(locset "label")` respectively. * Ad...
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- Sep 18, 2020
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Sam Yates authored
* Replace usages of `util::any` with `std::any`. * Modify `util::any_cast` so that it forwards `std::any` arguments to `std::any_cast`; move into own header. * Prevent `std::unique_any` from implicitly encapsulating `std::any` objects. * Replace `test_any.cpp` unit tests with `test_any_cast.cpp` unit tests. * Replace some usages of `std::is_same<X, Y>::value` with `std::is_same_v<X, Y>` as part of general C++17ification. * Remove `util/variant.hpp`, `test_variant.cpp`. * Replace occurrences of `util::variant` with `std::variant`. * Replace `util::variant::get<N>` with `std::get<N>`. * Replace `util::get_if<N>` with `std::get_if<N>`, passing a pointer to variant instead of a ref or value. * Add some standard #includes where they were required in the source, but only included transitively. * Some minor comment tidying and fix-ups. * Update C++ API docs. Fixes #1144.
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- Jul 23, 2020
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Nora Abi Akar authored
Fix a Python example that was out of date.
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- Jul 13, 2020
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Benjamin Cumming authored
* 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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- Feb 04, 2020
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Benjamin Cumming authored
A big update that wraps over 90% of the public C++ API, with enough functionality to let Python users to perform useful modelling. Key features - wrapping of cable cell functionality - user-defined explicit compartmentalisation not supported - `single_cell_model` abstraction unique to the Python wrapper that simplifies developing and testing single cell models - one-dimensional cell builder for Python wrapper that simplfies building cells that - in and of itself limited in scope, but a very useful example of mapping a richer morphology builder onto `sample_tree`s. - parsing of region and location expressions from strings - implements a generic s-expression parser that we can use for other purposes later
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