- 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.

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

* build for py311
* update dependencies.csv

* 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

- 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 

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

* 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>

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

* 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.

* Add segment tree editing: join and split
* Add equivalence and equality on trees
* Apply isometries to trees
* Add raw loaders to NeuroLucida ASC and SWC that return segment trees instead of morphologies

Add functionality, docs, and examples on editing the connection table.  This is a first, small PR
on the topic, further functionality will come as requested.

Teaser example
```cxx
    // This recipe -- omitted -- implements a mutable connection table 
    // and returns it via the `connections_on` callback. New entries are
    // added using `add_connection` which makes one link from a central 
    // `spike_source_cell` to the given `gid`
    auto rec = recipe();
    rec.add_connection(1);

    auto sim = arb::simulation(rec, ctx);

    // Record spikes
    std::vector<arb::spike> spikes;
    sim.set_local_spike_callback([&spikes](const auto& s) { spikes.insert(spikes.end(), s.begin(), s.end()); });

    // Run and print all spikes per gid
    sim.run(0.25, 0.025);
    show_spikes(spikes);

    // Add a new connection
    rec.add_connection(2);
    sim.update_connections(rec);

    // Run and print all spikes per gid
    sim.run(0.5, 0.025);
    show_spikes(spikes);
```

# Update July '22

- added re-wiring of Event Generators
- implemented a split between a recipe and a recipe-update (cheekily dubbed `topping` until further notice)
- `recipes` are `toppings` via inheritance

**BREAKING** Remove access to time `t` in NMODL.

- Enhance `run_cpp_examples.sh` to do some very basic checking of spikes counts
- Add a script to check all releases
- The former must succeed for all commits to master

Here's the expected spike counts as of 0.7
- brunel 6998
- bench 972
- ring 94 (19 pre-v0.7)
- gap_junctions 30

Document use and care of spike detectors.

Functionality to
- delete ions from global properties
- peek into global properties
- expose painted, placed, and defaulted items
- expose voltage limit to python
- make voltage limit an optional to allow for arbitrary values.
- Add ion_settings view to python = (valence, ion_data, rev_pot_method)

Documentation
- cable cell properties in python

Closes #1578 
Closes #1577 
Closes #1607 

* Add find_private_gpu and arbor.env.

- Add stacktraces to
   1. arbor_exception (and all derived) as `where`
   2. arbor_internal_error as `where`
   3. arb_assert
- Propagate stacktraces to Python exceptions derived from the above.
- Expand dev/doc on debugging

- elaborate probing API
- add definitions for different kinds of probes (vector, scalar, set).
- add sketches and example for data layout

- It's actually a Github cache trick: https://github.com/actions/cache/issues/342#issuecomment-673371329
  - First run: 1h 7m 38s 
  - Second run: same duration. Hmm....
  - Third run: ~10 minutes!
  - 4th: ~7.5 min.
- Bump in configs: macos 10.15 will disappear in a month: https://github.com/actions/virtual-environments/issues/5583
  - Bump clang-max to 14, gcc-max to 11
  - macos-min to 11, macos-max to 12.

- Generate timestamped VERSION once, to properly group on Test.PyPI. Example:
  - https://github.com/arbor-sim/arbor/actions/runs/2696804929
  - https://test.pypi.org/project/arbor/0.7rc20220719101015/
- Update/simplify release documentation.
- Update to v0.7

* - Weekly CI Python wheel build pushes to Test.PyPI.org
    - Easy availability at https://test.pypi.org/project/arbor/
- Small change in documentation around VERSION
- Delete superfluous setup.py file.

Move Python build to `pyproject.toml`, bump Python minver to 3.7, fix macos wheel generation (#1916)

* Failing Macos Python wheel builds fixed.
* Macos Python wheels now come with dual-arch (x86-64 and arm64)
* Moved (nearly) all Python build instructions to `pyproject.toml`
  * Enables 'build isolation', and need to specify build-deps only once, no need for users or CI scripts to pre-install them.
  * Enables editable `pip` installs (`pip install -e ./arbor`)
  * Compatible with 'build frontends' `pip` and `build`.
  * Passing CMake options actually got shorter
* Drop Python 3.6 support.

- Fix line numbers in tutorials, fallout from #1906
- Mention arbor-contrib in a few relevant places
- Correct some fallout from #1904
- A new hardware and profiling tutorial, and covers things moved out of other examples in #1904
- Various other documentation fixes