Allow `__` in profiler names, now that we split on `:`.

`exprelr` was described all wrong, fixed.

Mechanism ids are assigned by iterating through an unordered map within `fvm_mechanism_data`. This changes the container in question to an ordered `std::map`.

See the same jobs fail, which turn out to execute using different Python
versions:
-
https://github.com/arbor-sim/arbor/actions/runs/3618204857/jobs/6097794385
-
https://github.com/arbor-sim/arbor/actions/runs/3630819640/jobs/6141257441

Implementation of stochastic calcium plasticity curves, originally
authored by Sebastian Schmitt @schmitts, and adapted here for Arbor
inclusion.
- python example plasticity_stdp.py
- stochastic mechanism calcium_based_synapse.mod
- tutorial

Closes #1987

* Actually set the compiler to the user provided `--cxx` or the scripts default.
* Have a fallback to `c++` in case `arbor.config()['CXX']` does not exist (typically true for pip installed wheels).
* Verbose mode for `a-b-c`

Switch XML parser to pugixml; one less runtime dependency and one less blocker to WASM via emscripten.

required for making an emscripten build of the arbor python library

* make ARB_MODCC functional again

* move add_subdir

* no modcc/CMakeLists.txt is needed also when external modcc is used.

* review

* Remove deprecated spike_detector.

added conditional variant for cuda builds to enable GPU-based random number generation

- unit tests and some examples build their own mechanism catalogue
- repeated logic for detecting GPUs, passing compile time flags
- leverage the cmake variables and targets which are already there since these catalogues are internal to arbor
- build a static library with mechanisms, which links to arbor-private-deps

Add the VOLTAGE_PROCESS mechanism kind to modcc, allowing for direct writing to the membrane voltage
Obviously these are extremely sharp tools and can break the cable model, so we add some constraints to their
use (see docs). Still, user discretion is required.

As a sneak peek for what this might be useful for

* implementing voltage clamps
* limiting membrane voltage (irritatingly also a kind of clamping)
* faking ABSTRACT_CELL like behaviour (although that might require a bit more work)

Closes #1343

Throw an informative error instead of `bad_optional_access` when we do not find a global or cell default for an ion's diffusivity.

Added common math functions which I came across in the wild quite frequently. Implementations may be more optimized than hand-rolled versions.

- sqrt: usual square root
- step_right: right-continuous heaviside step function
- step_left: left-continuous heaviside step function
- step: heaviside step function with half step at 0
- signum: sign bit function
- extended iexpr with the step_left, step_right variants

fix ornstein_uhlenbeck example on gpu:
- use make_catalogue instead of make_catalogue_standalone
- link to arbor-private-deps
- mark all files as c++ sources when using cuda-clang or hip-clang

- Correct `.gitmodules`
- Update all git submodules to latest released versions, except google-benchmark
- Have CHANGELOG
- Breaking changes since v0.7:
  - A change in API: `arbor.cable_cell` has the labels and decor arguments swapped. I.e.: `(tree, labels, decor)`
-> `(tree, decor, label)`. Labels are now optional.
  - Mechanism ABI version is bumped to 0.3.1. https://github.com/arbor-sim/arbor/pull/1884
  - Remove the `generate-catalogue` script.  `modcc` accepts now a list of NMODL files and is able to spit out a catalogue.cpp file
  - Rename spike detector -> threshold detector
  - Remove access to time `t` in NMODL.
- Major dependency version bumps:
  - GCC: 9 and up
  - CUDA: 11 and up
  - Clang: 10 and up

Addresses #1987

* reproducibility test for random number generator
* C++ example demonstrating Ornstein-Uhlenbeck process
* Python example featuring stochastic mechanism
* stochastic mechanism catalogue

The Python example is contributed by Jannik Luboeinski's (@jlubo): https://github.com/jlubo/arbor_ou_lif_example
and adapted to fit into Arbor.

* fix compiler warnings

* fix some more warnings

Co-authored-by: Brent Huisman <brenthuisman@users.noreply.github.com>

- Add (again) a reset voltage E_R that for V_m = E_R in the refractory period.
- Make V_m decay towards resting potential E_L instead of 0.
- Adjust docs and tests accordingly.
- Double check this against literature.
- Explain weight, add C++ API.

* Added fixture dev docs. Made fixtures more robust.

Co-authored-by: Brent Huisman <brenthuisman@users.noreply.github.com>

* Functionality
  * Add probes to LIF cells.
* Docs
  * Remove errorneous statement(s) about LIF cells (there never was an E_reset...)
  * Move probing chapter one level up (concepts/cable_cells -> concepts)
* Tests
  * Add tests for LIF probes

Closes #1861 
Closes #1783 

- arbor-build-catalogue (a-b-c) does no longer need to be in a fixed location
- nor do we statically fix the configuration for a-b-c
- instead, we rely on `arbor.config` to read the relevant default values
- each value can be overriden, if desired
- added many more values to the configuration
  - gpu type and arch
  - paths and prefix 
  - CXX
- report default settings for better diagnosis
- implement a fallback for prefix if that does not exist; in particular for the amazing skbuild.

In essence you can now use a-b-c as a standalone tool, as long as you have a properly 
configured py-arbor.

Example output after removing `_skbuild`
```
Warning: prefix '/Users/hater/src/arbor/_skbuild/macosx-11.0-x86_64-3.10/cmake-install' does not exist, falling back to '/Users/hater/src/arbor/.direnv/python-3.10.6'.
usage: arbor-build-catalogue catalogue_name mod_source_dir

Generate dynamic catalogue and build it into ...

* build for py311
* update dependencies.csv

- Use ninja instead of make.
- Use ccache with a per-config cache key.

* Support for exporting models with parameters optimized in BluePyOpt to a mixed JSON/ACC-format that can be loaded in Arbor (with faithful axon-replacement modelling)
* A tutorial and examples on how to run simulations with such models including a neocortical layer-5 pyramidal cell exported from BluePyOpt
* Support for using Arbor as a backend for single cell optimization in BluePyOpt

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

- GCC: goes up to 9 from 8, needed by CUDA 11
- CUDA: goes up to 11 from 10
- Clang: 10 up from 8

Closes #1815 

Add missing virtual destructors to some classes. Removes warnings and ensures correct behaviour.

- bump OpenMPI version in hope of fixing the intermittent memory corruption
- bump Ubuntu and clang versions in `sanitize.yml` workflow.

* Use HTTPS access instead of ssh/git for gtest.

* Make decor mandatory and labels optional.
* Sort morphology, decor, labels
* No more optional decor.

Fix clash betwenn Ninja build and CMake external_project