* Bit of review on the copy of the mech abi docs.
* Convert api/abi docs to C Domain directives.

Implements #1376.

* Provide a common C linkage ABI for externally compiled mechanisms, for both CPU and GPU.
* Remove mechanism type hierarchy (`concrete_mechanism` etc.), and move corresponding functionality to the back-end shared state objects. Mechanism catalogue is no longer indexed by type id.
* Distinguish between SIMD optimal alignment and SIMD width with new `min_align` attribute. Mechanisms provide both pieces of information via ABI.

* added notes re literal_include to python examples
* merged changes in #1504 
* deduped and includified (https://github.com/arbor-sim/arbor/pull/1558) tutorials.
* First divergence of tutorial and code spotted!
* Added some contrib documentation for examples and docs.

- Minor fixes to python examples.
- Fix `mpi.py` to use new label API.
- Rename `mpi.py`.

- zenodo entry for v0.5.2
- minor formatting update to spack file

1. All s-exp parsing has migrated to `arborio`
2. CV policies can now be read from string as per #1334. This is needed for the GUI project.
2. No longer can `arb::locset` and `arb::region` be constructed from mere strings
2. We have `arborio::literals` to construct `region`s, `locset`s, and `cv_policy`s in the form of `_rg`, `_ls`, and `_cvp`.
3. The `_lab` suffix now constructs an object that converts to `named` morphologies, rather than a simple string.
4. Constructors of `region` and `locset` are now properly guarded
5. Consequently, a lot of missing inheritance from `region_tag` and `locset_tag` was retrofitted.

Closes #1334 
Closes #1419 

- Add an optional CMake option `ARB_CXX_FLAGS_TARGET` for setting target-specific flags to use when compiling for the target architecture (not applied to compilation of modcc).
- If `ARB_ARCH=="none"` CMake will not add architecture-specific `mtune/march/mcpu` flags
- Remove `ARB_CXXOPT_ARCH` from the installed `arbor-config.cmake`, and replace with more general `ARB_CXX_FLAGS_TARGET`.
- Update spack `package.py` to use this feature to pass custom flags.

Fixes #1519
Fixes #1522 

Replaces PR #1518 

New structs and types:
* `cell_tag_type` (std::string): for labelling placeable items on a cell. The label refers to a number of items placed on a locset, equal to the number of locations in a locset. The number of locations in not always known to the user, so the previous way of using indices for items was no longer sufficient. 
* `lid_selection_policy`: for allowing a user to select a single item from a group of items sharing a label. Currently only `round_robin` and `assert_univalent` are supported. 
* `cell_local_label_type` and `cell_global_label_type`: for identifying the target and source of a connection or gap_junction connection. 
* `cell_label_ranges`, and `cell_labels_and_gids`: for propagating information about the labelled items on the cell from the cell groups back to the simulation and communicator. 
* `label_resolution_map` and `resolver`: for selecting an item (and retaining state) from a labelled group of items on a cell according to a user-selected policy.

Changes to the model-initialization: 
* The `communicator` now needs `label_resolution_maps` constructed from the cell group data in order to build the `connections` vectors. 
* The `simulation_state` object handles the transfer of the information when it is constructed. 
* Spike exchange at runtime remains unchanged, because `communicator::connections` remains unchanged. 

Changes to cells, cell_groups and recipe:
* `decor::place` expects a third label parameter, no longer returns an `lid_range`.
* `lif`, `source`, and `benchmark` cells need source/target labels in their constructors. 
* A `cell_group` needs to save data about the gid/labels/lid_ranges of each cell, to propagate back to the `communicator` constructor. 
* Connections/gap junction connections are formed between {label, policy} pairs on cells instead of indices. 
* `num_sources`, `num_targets`, `num_gap_junction_sites` deleted from `recipe`.

Additional changes:
* Add MPI wrapper for exchanging vectors of strings. 
* Corresponding updates to unit tests, Python wrapper, C++ and Python examples, documentation.

Fixes #1394

* Sort collected spikes in Python API lfirst by time, then gid, then lid.
* Remove redundant old spike handling code from Python lib.

* Update URLs to arbor-sim.org
* update badge links

* Adapt CSS for the HTML5 transition in docutils 0.17
* Fix some reST markup errors
* Add meta-tag to enable indexation control at Google (current indexation appears at least a year old).

Fix mistakes reported by @Helveg in the Python tutorial docs. 

* fix mech_vec
* fix fvm_discretize
* small fixes

* Add Zenodo citation snippet.
* Correct Nora's last name, which is Abi Akar.
* Small css fix for change in docutils, see: https://github.com/readthedocs/sphinx_rtd_theme/issues/1115

Fixes #1297.

* `i_clamp` constructors take new optional phase argument.
* Pulse or box envelope clamps are now provided by the static method `i_clamp::box`, taking onset, duration, and amplitude parameters.
* Bump pybind11 version so we can have keyword-only arguments in the Python API.
* Make frequency and phase keyword-only arguments to Python `iclamp`.
* Change frequency units for clamps from Hz to kHz for consistency with other interfaces.

Fixes #1454.

* update and simplify the `load_swc_neuron` reader to match the simplified and more correct interpretation in NEURON 8
* update the documentation on the interpretation, and add details about how it still differs from the neuromorpho descriptions. 
* update unit tests to reflect new interpretation
* add a unit test that reproduces a complex case from the NEURON test suite.
* remove the `load_swc_allen` C++ and Python calls
* add links to NeuroMorpho site in the documention

Fixes #1445.

Always install Python module inside CMAKE_INSTALL_PREFIX, unless the user explicitly sets the ARB_PYTHON_LIB_PATH CMake variable.

Update documentation on installing and building the Python packing using CMake to have a detailed example of how to install the Python module inside a virtual env.

Fixes #1403

* Correct the installation page.
* Custom css is not supported by theme, so a css snippet improving table formatting was moved to the theme css.
* Non cable-cell concept docs were wrong, improved formatting
* Some typos

Co-authored-by: @clinssen 

* Implements parsers and writers in `arborio` for the s-expression based Arbor Cable-Cell Format defined in #1336.
* Moves `s_expr.hpp` to the public interface.
* Adds python wrappers to support the features in pyarb.  
* Adds unit tests.
* Adds docs.

Fixes #1336
Partially addresses #1233

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

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

* 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.

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