* Used Sphinx glossary directive to create terms that can be referred to in `concepts/morphology.rst` and `concepts/labels.rst`.
* Added note box on difference with Neuron, add source for NEURON cylinder discretisation
* Parameters added to svg generation script: turn off colors, root
* Fix cpp TOC duplication, match ordering in other sections.
* State default cv policy
* center/re -> midpoints
* Clarify and remove compartment term

Introduce two minor changes to the Python API
to handle mechanism_catalogues idiomatically.

Instead of

import arbor as A

cat = A.default_catalogue()

if cat.has('hh'):
  print("Found HH.")

for mech in cat.keys():
   print("*", mech)

we can now write

import arbor as A

cat = A.default_catalogue()

if 'hh' in cat:
  print("Found HH.")

for mech in cat:
   print("*", mech)

which is closer to the expectations of Python users.

* Add docs tutorial page for single_cell_recipe.py example
* Adapted single_cell_recipe.py slightly
* Improved labels and fixed some broken cross-linking
* Fixed a typo here and there

* Set VERSION to 0.5.1-dev

* Add link to Zenodo entry for version 0.5 release.

Numpy is now explicitly required for use in the Python probes interface.

Fix some broken hyperlinks in the rst documentation.

* Add the ability to use json and pybind11 libraries installed on the system instead of the
  vesrsions of those libraries bundled as submodules in the Arbor repository
  * Turned on by default
  * Toggled using the new `ARB_USE_BUNDLED_LIBS` CMake flag
* Update documentation for installation
* Update CI and pip workflows to opt in to the bundled libraries

* Add unit test that checks the expected contribution of an
annulus to the embed_pwlin integrated area, when a zero-length segment
with differing radii exists in the segment tree.

Revert a change introduced in #1282 that required the python module for arbor to build the documentation.

This breaks the readthedocs build, where arbor is not available.

* Remove arbor dependence from `doc/conf.py`, reverting to the original "out of core" approach
* Fix other recently introduced issues that lead to CMake errors when configuring the documentation
  when the Python target is not configured.
  * The CMake variable `PYTHON_EXECUTABLE` wasn't set, but was required to make calls to the
     Python interpreter.
  * Instead of relying on pybind11 to find Python, explicitly detect it using `find_package(Python3 ...)`
  * Make Python3 a hard requirement when building the Python wrapper
  * And a soft requirement otherwise, that will fail only when the docs are built.

Update the PR licensing rules in the PR contribution guide.

Fix CMAKE to use PYTHON_EXECUTABLE that corresponds to the version of Python used to build the python module.

* Add 2 new examples to `python/examples` and their corresponding tutorials in the docs. 
    1. `single_cell_detailed.py` : a slightly more complex example using `single_cell_model`
    2. `single_cell_detailed_recipe.py`: equivalent to `single_cell_detailed.py` but using a recipe. 
* Change `load_swc`-> `load_swc_arbor` for consistency.
* Run Sphinx with specified PYTHON_EXECUTABLE.
* Set PYTHONPATH env var in doc/CMakeLists.txt, such that it propagates correctly, including locally.
* Build pyarb BEFORE html such that docs build can import arbor in Github Actions script.

Add API for `single_cell_model` and `label_dict`

* `concepts/cable_cell`: number subcategories to better illustrate document structure.
* `concepts/labels`: concretize -> thingify; more on label dictionaries.
* `concepts/mechanisms`: Some info on modcc, link to nmodl files in repo.
* `concepts/morphology`: NeuroML section and some notes on branches/segments

* Expose and document the (segment id) region expressions.
* gen-labels.py was not up to speed with decor #1235.
* The SWC example is read from disk and inserted into the docs verbatim.
* The same file is used to generate the image.
* The missing decor constructor has been added.
* Generating inputs.py on the fly when building docs. That should prevent this issue from coming up again.

* Docs: emphasised the option of having pip install a local copy of the Arbor source.
* CMake: default Python library install path to `${PYTHON_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_path('platlib'))"`. Fixes #1100.
* CMake: remove ARB_PYTHON_PREFIX option, added ARB_PYTHON_LIB_PATH option. We cannot know in general where in the prefix the packages are expected by Python.

Python tests were failing because pyarb was not built

First step of replacing Travis with GithubActions

Here, only a basic set of tests has been added

- Build arbor with MPI and Python
- Compile examples
- Run unit tests, incl distributed.
- Run python tests, incl distributed.
- Run python examples.
- Build documentation.

Wrap place_pwlin interface to allow querying rich geometry information from cell morphologies.

* Add Python bindings for the `place_pwlin` and `isometry` classes.
* Add equality test for Python `mpoint`.
* Add unit tests for new Python interfaces.
* Split C++ API morphology documentation into its own file.
* Add C++ API and Python API documentation for `place_pwlin` and `isometry`.

Extend Ptyhon recipe wrapper to support setting of global cell properties.

* Rename `pyrecipe::get_probes` to `py_recipe::probes`
* Remove `global_properties_shim` : It's easy to make mistakes with the class, as it holds a `mechanism_catalogue` and a `cable_cell_global_properties` which holds a pointer to the catalogue. This would likely have caused issues with the users.
* Expose `py_recipe::global_properties`

Make the `cable_cell` interface read only by passing the decorations
to its constructor in a new `decor` type.

C++ library
* Remove the paint/place/set_default interface from `cable_cell`
* Create a `decor` type that:
  * stores lists of paintings and placings
  * stores a set of cable cell parameters
  * uses the `paint`, `place`, `set_default` interface that was deprecated
    from `cable_cell`.
* Create `paintable`, `placeable` and `defaultable` variants that are sum types
  over the respective types that can be painted, placed and defaulted.
* Remove the overloaded `cable_cell::paint`, `cable_cell::place`,
  `cable_cell::set_default` methods to single methods that consume the sum types.

Unit Tests
* Many small changes because many many tests use cable cell API.
* There were no `cable_cell` unit tests! Not such a big deal, since cable_cell
  is tested implicitly in so many other tests
  * but I added cable_cell tests: not much at the moment but will quickly fill
    up as we work on reading, writing, etc.                                                            

Python
* Wrap the new decor type.
* Update cable cell type to reflect read only API.
* Wrap the cv_policy types and implement the same operator overloading.

Fix segfault in modcc when min/max used in net_receive.

* The error occurred when a synapse that use `max` or `min` expressions in the `net_receive` block: we test for linearity to check whether they can be coalesced; we cannot differentiate the expression; an error is raised but not reported; seg fault. 
* Fixes ` as_c_double` printing which does not print integers as doubles as intended. 

Fixes #1275 

Fix a latent bug in the Python wrapper that was triggered in pybind11 v2.6.1

These changes ensure that the GIL is acquired before calling functions in C++ that
may consume a Python object with reference count 1 as an argument, in which case
the object's destructor is called at the end of the function, after any GIL acquired inside
the function would have been released.

Fixes #1271.

* Move PR message instructions to 'Making a PR' section.
* Move coding instructions to 'Write code' section.

* Remove mention of the Copyright Transfer Agreement

* Fix pybind11 issues.

* Retract suspicious fix.

* Address comments.

Replace CMAKE_SOURCE_DIR with PROJECT_SOURCE_DIR to pick up the correct paths when used as a sub-module.

Fixes #1266.

Update CMake configure to look for svgwrite when building docs.

Fixes #1128.

Set up contribution guides.

Add a contribution guide, as well as 
* Added contribution section.
* Moved content here from the wiki regarding (contribution) processes.

Also added some incomplete / placeholder sections that can be improved later.
* How to write an example
* How to add a test
* Coding style guidelines

* An explanation of documentation structure.
* Added HBP/Ebrains to acknowledgements.