* Substitute `std::optional<T>` for `arb::util::optional<T>` for non-reference types T.
* Remove reference-deducing `util::value_by_key`; replace usages with new function `util::ptr_by_key`.
* Add some missing header includes that were required but included only transitively.
* Remove `operator<<` overload for optional in python/strprintf.hpp; replace with utility wrapper class that catches `std::optional<T>`.
* Wrap some `std::optional` values with `to_string` in ostream output in python lib.

Fixes #1154.

Switch `arb::util::either` to `arb::util::variant` in the Python wrapper.

Fixes #1133 

Update core library:
* support derivation of named mechanisms in catalogue from a string description of the parent.
* fix bug in radois_ge region expression that was finding region_lt.
* fix test for radius_ge region expression

Add support for mechanism, global properties and catalogue shenanigans to python wrapper

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

akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

Domain decomposition in python wrapper
* functions: `partition_load_balance`
*  types: `group_description` and `domain_decomposition`

Also includes
* remove comment that `gid` in a `group_description` must be sorted.
* a host of small clean ups of python wrapper

Fixes #761

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

This time we're moving `recipe.hpp` and `simulation.hpp`, plus the requirements they bring.

Code changes:
* Pimplize `simulation`.
* Consolidate arbor exceptions: all non-cell kind specific exceptions that might be expected to reach user code now have consistent messages and fit in an exception hierarchy based at `arb::arbor_exception`. Internal errors throw an `arb::arbor_internal_error` exception.
* Renamed `postsynaptic_spike_event` to `spike_event`. (Note: `pse_vector` name is unchanged.)
* Repurposed `pprintf` and moved it into `strprintf.h` — further consolidation is a TODO.
* Made a generic `util::to_string` to avoid redundancy of `operator<<` overloads and other `to_string` definitions. Defaults to ADL `to_string`, `std::to_string`, and finally tries using `operator<<`.

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

CMake and build refactoring

*   Use CUDA as first-class language (leading to CMake 3.9 minimum version requirement).

*   Use 'modern CMake' interface libraries for compiler options, include file and library dependency tracking. Interface library targets:
    * `arbor-deps`: compiler options and library requirements for the `libarbor.a` static library, as governed by configure-time options and environment.
    * `arbor-private-headers`: include path for non-installed headers, as required by unit tests and arbor itself.
    * `arbor-aux`: helper classes and utilities used across tests and examples.
    * `ext-json`, `ext-tclap`, `ext-tbb`, `ext-benchmark`, `ext-sphinx_rtd_theme`: externally maintained software that we include (directly or via submodule) in the `ext/` subdirectory.
 
*   Single static library `libarbor.a` includes all built-in modules and CUDA objects.

*   Simply configuration options:
    *  `ARB_WITH_TRACE`, `ARB_AUTORUN_MODCC_ON_CHANGES` `ARB_SYSTEM_TYPE` removed.
    * External `modcc` is provided by `ARB_MODCC` configuration option; if provided `modcc` is still buildable, but is not included in the default target.
    * `ARB_PRIVATE_TBBLIB`, defaulting to `OFF`, instructs the build to make TBB from the included submodule.

*   Extend `ErrorTarget` functionality to provide a dummy target or an error target based on a condition.
*   Generate header version defines and library version variables based on git status and project version, via new script `include/git-source-id`.
*   All generated binaries now placed in `bin/` subdirectory at build.
*   Install targets installs: public headers (incomplete); static library; `modcc` tool; `lmorpho` executable; `html` documentation (examples, tests and validation data are currently not installed).
*   Executable targets have had the `.exe` suffix removed; unit tests are labelled `unit` (arbor unit tests), `unit-modcc` (modcc unit tests), `unit-local` (distributed tests with local context), `unit-mpi` (distributed tests with MPI context).
*   More graceful handling of configure-time detection of `nrniv`, Julia and required Julia modules for validation data generation.
*   Add `cmake/FindJulia.cmake`, `cmake/FindTBB.cmake`  package finders, and adjust `cmake/FindUnwind.cmake` to use link library-style properties.
*  Adjust travis script to test `unit-local` and `unit-mpi` if appropriate.
*  Simply documentation `conf.py`.

Source relocation and reorganization

* All external project sources and files moved to `ext/`.
* Source code refactoring to decouple library-using code from the configure-time definitions that govern arbor behaviour: removes conditional code in public headers that depends upon `ARB_WITH_X`-type definitions at compile time. Affected code is is in the public interfaces for MPI, the threading implementation, and the profiler.
* Remove `util/debug.hpp`; split out functionality for pretty-printing from assertion handling.
* Make FVM cell non-physical voltage check a run-time cell-group parameter.
* Move spike double buffer implementation to `simulation.cpp`.
* Make timer utility wrap POSIX `clock_gettime` independent of threading configuration.
* Make `mpi_error` derive from `system_error` and follow C++11 `system_error` semantics.
* `EXPECTS` macro replaced by `arb_assert` macro.
* JSON dependency removed from `libarbor.a` and header files: moved to auxiliary library.
* Publicly visible macros garner an `ARB_` prefix as required.
* Move SWC test file to `test/unit` directory.
* Work-in-progress splitting of public from private includes: as a convention not entirely adhered to as yet, private headers within arbor source are included with `""`, public headers with `<>`.

Modcc interface changes

* Expose via `--namespace` option the functionality that sets the namespace in generated code.
* Use `--profile` option to add profiler hooks to generated code; uses public function interface directly rather than `PE/PL` macros in order to avoid public `PE` and `PL` defines.

Change nest::mc namespaces to arb

Fixes #245.

    Add missing header <system_error> to src/util/strprintf.hpp
    Remove redundant const in cell_kind returns.

Move string-printf utility from lmorpho into util.

* Add `util::strprintf` printf-alike function that returns a `std::string` result.
* Include simple adaptors for `std::string` and standard smart pointer arguments fot `util::strprintf` (i.e. `std::string` arguments can be used with `%s`, smart pointers with `%p`).
* Add unit tests to suit.