- 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

- 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>

* Discuss q10 pattern in NMODL docs.

Adds the Heaviside step function to Arbor's iexpr

Co-authored-by: boeschf <48126478+boeschf@users.noreply.github.com>

1. Fix Python bindings for `recipe::update`
   - *drop* the GIL before handing off to C++
   - tighten exception safety
2. Run plasticity examples with threads; both C++ and Python.
   - C++: Guard against I/O interleaving.
   - Py: Drop spikes from source, prettify reporting.
   - C++: use decor chaining.
3. Modernise PYBIND11_OVERLOAD -> *RIDE (advised since 2.6).
4. No longer do we initialise connectivity twice.
   - Simplify communicator construction.
   - Fix unit tests that needed to two-phase init communicator.

Inline NMODL `PROCEDURE`s into their callers.

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

* remove storage of RHS and face-conductance in solvers
* elide copy RHS->U and RHS->Xd respectively
  -> solve will now directly mangly U and Xd
* fix tests accordingly
* Introduce wrapper macro for __restrict__ to Isolate against compiler specifics.

use std variants of sqrt and move (removes warnings, and is safer)

Fix a typo preventing the generation of GPU mechs.

* Add pybind11 version to config.
* Add version check for PB11.
* Bump CMake a tiny bit.

This is prep for meson in addition to simplifying (ie reducing) the amount of scripting
we have. In the long run, I'd like to remove `BuildModules.cmake` too, but this might
be superseded by meson and this PR is self-contained.

# Changes
- `modcc` accepts now a list of NMODL files
- likewise, `modcc` is now able to spit out a catalogue.cpp file
- remove the `generate-catalogue` script, simplify a-b-c
- remove some options from `modcc` we never use
- No longer allow external modcc

- BREAKING: Rename spike detector -> threshold detector in Python
- `spike_detector` is still around, will throw a deprecation error; will be removed 0.9
- this brings Python closer to the C++ API and removes lots of ambiguities in the docs.