Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>

* Fix the regular schedule generated in `single_cell_model::run`
* Adjust frequency of probes in python examples to the correct unit (KHz). 

Fixes #1457

Remove `gid` attribute of target of a connection, and local gap-junction site of a gap-junction connection (#1467)

* Change the type of the target of a `connection` from `cell_member_type` to `cell_lid_type`. The target cell's gid is always known in both the recipe and simulation.
* Change the type of the local site of a `gap_junction_connection` from `cell_member_type` to `cell_lid_type`, and make it such that the first argument of the connection is the peer site, and the second the local site. The local cell's gid is always known in both the recipe and simulation.
* Change the type of the target of an `event_generator` from `cell_member_type` to `cell_lid_type`. The target cell's gid is always known in both the recipe and simulation.
* New `cell_spike_events` and `cse_vector` for `simulation::inject_events`.
* Simplify recipe sanity checks and remove associated exception types. 
* Fix unit tests, examples, docs

* Adds a `neuroml_options` namespace with enum for use with `neuroml::morphology(...)` and `neuroml::cell_morphology(...)`.
* Add support for a 'spherical' root segment with option `neuroml_options;:allow_spherical_root`; a zero-length root segment with identical proximal and distal radius will then be converted into an area-equivalent cylinder in the resultant morphology.
* Amend `place_pwlin::all_at` so that locations on a zero-length segment with different radii at the endpoint will give an mpoint for either end.
* Add `allow_spherical_root` boolean optional parameter to Python NeuroML morphology methods.
* Update docs; C++ unit tests.

Fix orientation of ASC somas from along z axis to along the y axis.

As per the rules followed by Arbor's SWC parsers, and prescribed in:
http://neuromorpho.org/SomaFormat.html

Addresses #1445

* Fix semantic passes and error visitor expression coverage in modcc.

* Add a method to `event_generator` that returns all of its targets. 
* When the simulation is constructed, check the targets of each event generator, and throw an exception if an the `gid` or `lid` is invalid.
* Add corresponding unit tests.

* Make net_receive and post_event APIMethods in modcc.

* Add `nml_` prefix to NeuroML-related classes in arborio.
* Separate `arborio/xmlwrap` from NeuroML exceptions.
* Put xmlwrap functionality in its own namespace.
* Have xmlwrap property access errors returned by util::expected, so that the corresponding NeuroML exceptions are strictly the
responsibility of the NeuroML parsing code.
* Rename NeuroML implementation and support sources and headers.
* Place implementation classes for Neurolucida ASC parsing in an anonymous namespace.

Fixes #1441.

Fix bug attaching branches to the soma in ASCII file descriptions.

Branches in an ASCII description attached to the soma were incorrectly creating a segment
from the center of the soma to the first point in the branch.

Amend segment cables for zero length branches.

Ensure cables corresponding to segments cover even zero length branches, by setting the segment cables to (b, 0, 0) for all but the last segment in a zero-length branch b, and setting that last segment cable to (b, 0, 1).

Fixes #1442 

* Add on-components to label_parse.cpp, and to corresponding unit test.

Basic support for reading morphologies from Neurolucida ASCII (.asc) files.

Added to the arborio C++ library, and wrapped similarly to the other arborio features in Python.

Fixes #1429

* Add Python version of brunel.cpp example.
* Enforce consistency in units: both C++ and Python APIs use unit `kHz` for all frequencies.
* Align Python version `poisson_schedule` signature with C++ equivalent.
* Update unit tests to suit API changes.
* Update documentation to suit, along with minor additions related to networks and interconnectivity.
* Add `brunel.py` to `basic.yml` tests

- Add _running_ C++ examples to standard CI runs (compiling has been in since the start).
- Fix `bench.cpp` to set return value to 1 if exceptions are caught.

- Use parameter packs for multicore mechanisms.
- Adjust unit tests and modcc.
- CPU and GPU use the same mechanism_ppack_base.
- CPU code uses a split similar to GPU with `mech_XYZ_foo` and `kernel::mech_XYZ_foo.
- Make mechanism_ppack_base header public.
- Tracing macros for modcc code gen.

* Add start time to `epoch` struct, rename time fields to avoid confusion with tfinal parameter to `simulation_state::run()`. Default constructed epoch now has id -1.
* Replace `t_`, `epoch_`, `min_delay_` timekeeping in simulation_state with `epoch_` and `t_interval_`: `epoch_` holds most recently simulated interval.
* Split event_lane population out of exchange task.
* Document in code comments the sub-task dependencies in `simulation_state::run()`.
* Rewrite main simulation loop to abide by pre- and post-conditions that ensure correct behaviour from successive calls to
`simulation_state::run()`.
* Replace double buffer for `simulation::local_spikes_` with array, analogous to `event_lanes_`.
* Update cell groups, unit tests for new epoch interfaces.
* Remove `util::double_buffer` and test.
* Remove unnecessary includes in `mc_cell_group.hpp`.
* Add unit tests for simulation global spike callback and restart operations (i.e. successive calls to `simulat...

* Change implementation of current clamp from a builtin mechanism to
  functionality provided by the back-end shared state classes.
* Extend clamp functionality to cover more use cases: it now supports DC
  and AC stimuli governed by a piecewise-linear envelope.
* Update Python iclamp wrapper to suit; add unit test.
* Account for total applied stimulus currents separately, and remove
  their contribution to the reported transmembrane current and
  ionic (i.e. non-capacitive) transmembrane current.
* Add new probe specifically for tracking total current stimulus in a cell.
* Update docs, and add an entry for current clamps to the concepts doc.
* Remove entirely the builtin catalogue.

* Provide defines and variables for version string components: major
version; minor version; patch level version; development suffix.
* Change commit date format to strict ISO.
* Add define/variable for Arbor build configuration.
* Add usage/help info to `git-source-id` script.
* Add define/variable for a full build identification string,
incorporating source info, version, build configuration, feature
options.
* Add documentation for the version and build defines and variables.
* Extend version unit tests to suit.

* Remove parts of the C++ API which leaked into `doc/fileformat/neuroml.rst`
* Add links to the relevant C++ and Python API

* Correct some malformed YAML.

* Auto-generate binary Python wheels, triggered by git tags 'v*'.
  * Wheels are generated for Python versions 3.6-3.9, for Linux using the [PyPA manylinux-2014 image](https://github.com/pypa/manylinux) and MacOS using macos-latest (10.15 at time of writing).
  * The Action generates `sdist` for any other platforms.
  * The cibuildwheel action automatically prepares the wheels using [auditwheel](https://cibuildwheel.readthedocs.io/en/stable/options/#repair-wheel-command), which means bundling of external deps (e.g. libxml2 for NeuroML).
  * The output is all that's needed for publication of a new version to (Test)PyPI.
* `setup.py` defaults `neuroml` to on.
* A small change to `CMakeLists.txt` was required to build the wheels: based on this [Pybind hint](https://pybind11.readthedocs.io/en/stable/compiling.html#findpython-mode) `Development.Module`is now required, and not `Development` when CMake searches for Python. I confirm this change is needed to make Arbor build in the manylinux docker images, but I do not understand what the change implies, other than that we now don't link to `libpython`.

* Refactor Documentation layout. 
* Display Spack page.
* Display Extending catalogues page.

Fixes #1353.

Force nvcc to use the c++ compiler used to compile the c++ code.

* Fix a quite obvious ptr arithmetic bug.

* Clean-up to avoid similar issues.

* Const, my old friend.

* Test: refactor..

* Lambda capture.

* Clean up using append_chunk.

* Catch two escaped _.

Update `set_ion` method of `cable_global_properties` to allow the addition of new ions

* Remove redundant `initial_ion_data` specification.

* Use CMake check_cxx_source_compiles and check_cxx_source_runs to detect how std::filesystem
is enabled. The probes are executed first, if none succeeds, we use link-only to cover the possibility that we
are cross-compiling.

Preliminary work towards the mechanism ABI.

Unification of the `public` and `protected` interfaces of the mechanism classes.
These interfaces will be merged into the public API ('public' as in: exposed via `arbor/include/arbor`). 

Interface methods `nrn_` have been renamed
- `nrn_init`: `init` (would have preferred initialize, but that is taken)
- `deliver_events(event_stream)`: `apply_events` (to avoid a name clash)
- `nrn_state`: `advance_state`
- `nrn_current`: `compute_currents`

Additional changes:
  - Remove typedefs for index_type etc
  - Shuffle `ion_state_view` to public interface
  - Migrate `copy_extend` to a proper place out of `multicore/mechanism.hpp`. Maybe `memory` or `range_util`.
  - Remove `vec_t_to_`

* Update `README.md`: moved citation to `doc/index.rst`.
* Advertise Py3.9 compat PyPI in setup.py
* Fix typos.

* Tutorial ring network added. A few typos fixed, crosslinks fixed.
* MPI tutorial added.
* Improved SVG generation, added separate label scaling, increased default label size.
* Bugfix: didnt generate cable region in gen-labels.py used in `concepts/morphology.rst`.
* Termified Interconnectivity page.
* Termified probe nomenclature page. Will be moved in [this PR](https://github.com/arbor-sim/arbor/issues/1353) from python/simulation to concepts/probes_samplers.