- Bump CI actions to latest (cache, checkout, cmake)
- Bump mimimal compiler versions
- Bump minimal test OS to Ubuntu 20.04 LTS
- gtest as submodule (version 1.12.1)
- fixes heap corruptions
- update gtest macros, include paths

Co-authored-by: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>

Main changes
- uncorrelated and independently distributed white noise generation for point and density mechanisms
- enabled by extending nmodl dialect and adjusting modcc (WHITE_NOISE block, stochastic solver method)
- SDEs are solved by Euler-Maruyama method (synapse collapsing disabled in this case)
- CPU and GPU backends responsible for creating random numbers using random123
- simulation takes a seed value
- bumped ABI due to addition of random numbers in ppack
Incidental changes
- builder pattern for simulation
- pimpl idiom supported by util classes

Exports all symbols so arbor can be compiled as set of shared libraries. 

In order to export all symbols correctly, one macro per library and one global macro are added. The content of the macros is determined at configure time depending on build variant (static/shared), compiler, and platforms (linux, mac os) and goes into the library's include directory as `export.hpp` when installed (at build time it resides at cmake's temporary build directory). The per-library macro is named `ARB_LIBNAME_API` and goes in front of to-be-exported symbols. The global macro is `ARB_SYMBOL_VISIBLE`. 

This PR adds the annotation in all of the places where it is required. Most of them are in the public headers (and corresponding sources) but some are also added in internal headers, which were required for the unit tests to link properly.

Fixes #1752

- Bump CMake to 3.18 for better CUDA support.
- Clean-up our use of said support.
- Remove old cruft and workarounds.
- Maintenance in CI: enable MacOS 11; bump CMake versions to 3.18 / 3.22; bump bors CMake to 3.18

Fixes #1790 

* Make access to `segment`s in a `cable_cell` read only
* Change cell constructor to require morphology and label dictionary; `make_cable_cell` no longer required.
* Consolidate paint/place functionality on `cable_cell`.
* Add simple cell builder wrapping new API for use in unit tests.
* Remove validation test code: appropriate validation tests will need to be implemented in nsuite.

Fixes #871 

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

Fixes #618 and fixes #617.

*  Add convenience targets: 'examples' for all examples; 'tests' for all tests.
* Add support for component-testing in installed CMake package.
* Allow test for MPI support via find_package via component.
* Remove REQUIRED specification from `find_dependency()` commands in generated config.
* Update `mech_vec.cpp` to match new `fvm_lowered_cell_impl` constructor.

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.