Bsb-core

* Multi-instancing

Alpha version 6
* Particle placement for IO
* EvalConfigurations

Alpha version 5
* Merged in the plasticity branch
* IO placement & connectivity
* DCN interneurons

Alpha version 4

Minor changes

* Fixed to a runnable state.

Alpha version 3

Major changes
* Merged touch detection branch
* 3D touch detection, can be reduced to 2 or 1 dimension cell intersection.
* Select from & to cell type & compartment type.
* Ability to auto-discover cell search radius or to specify it yourself.
Compartment needs to be specified (default 5µm)
* Configure amount of synapses with a constant or distribution

Alpha version 2

Major changes

* Cross-platform pip entry-points (console scripts such as `scaffold compile`)
* Merged in the plasticity branch
* Setting `"plastic": true` in a NestConnection configuration will set it up
as a plastic connection with volume transmitters attached
* Specifying to which receptor type a plastic connection is connected can be
done by providing a dictionary mapping the partner cell type to a receptor
type id in the configuration of cell types under `receptors`
* Removed dependency on archaic `matplotlib` and added `plotly`. Plotting
dependencies are optionally installed using `pip install
dbbs-scaffold[with-plotting]`
* NEST modules to load can be specified in the configuration.
* scipy.stats.distributions classes can be configured using
`DistributionConfiguration`s.
* Datasets in the `/cells/connections` group of an output HDF5 file can store
metadata on them
* The metadata keys `from_cell_types` and `to_cell_types` can help clarify
which cell_types are actually contained within the dataset when the
ConnectionStrategy has multiple types.
* Added a overloadable `boot` method to ConfigurableClass that is executed after
`__init__` and before `validate`

Minor changes

* NEST simulator resolution can be set
* Cells can be placed by an absolute amount instead of just densities.
* For very low amounts of cells to be placed there is a minimum of 1 per
sublayer.
* Renamed `addCellType` to `add_cell_type` in `configuration.py`.
* Added a `report` function to `scaffold.py` for verbosity compliant prints.
* IllegalConnection errors by NEST are now caught to display the device that
causes them.

Tests

* Added single and double cell type creation tests for NEST adapter.

This release is a prerelease of version 3.0 with finished simulator handling for
the NEST simulator and preliminary support for TreeCollections, tree pickling,
MorphologyRepositories, morphologies, voxelization and touch detection.

* Added MorphologyRepositories to preprocess and store morphologies before they
are used in the placement/connectivity.
* Added TreeCollections to load, cache and store trees. OutputFormatters should
know how to handle trees.
* HDF5Formatter can pickle trees.
* Simulations can be configured through SimulatorAdapters, should provide
ConfigurableClasses to configure `cell_models`, `connection_models` and
`devices`.
* Implemented a NestAdapter with NestCells, NestConnections and NestDevices.

* Changed dependency list for installs outside of Anaconda.

* Removed obsolete files transferred by bad merge.