CHANGELOG

# 3.7

## 3.7.5

* Cell IDs persistently increment across Python sessions.
* Added CONTRIBUTING & CODE_OF_CONDUCT
* NEST devices can be configured without targets, for manual targetting.
* NEST master seed is determined by clocktime but can be fixed.
* Added `bsb.core.Scaffold.get_connectivity_sets`


## 3.7.4

* Added raw config string to result files for reference.

## 3.7.3

* Bumped minimum nrn-patch to 3.0.0b3 to fix transfer variable stalling.

## 3.7.2

* Advertise compatible Python versions in `setup.py`
* Bumped minimum numpy to 1.19.0
* Bumped minimum nrn-patch to 3.0.0b1

## 3.7.1

* Fixed a bug with nest and MPI. (see #230)

## 3.7.0

* The NEURON adapter now supports source variables.
* Gap junctions were added to the model of the cerebellum.

# 3.6

## 3.6.7

* Altered NMDA channels.

## 3.6.6

* The return values of simulations are now the path to their result file.

## 3.6.5

* Fixed a bug with the NEURON adapter transmitter map causing loss of spike transmission.

## 3.6.4

* Slightly changed the `neuron` install workflow. NEURON is now pip installed

## 3.6.3

* Updated "Getting Started" guide.
* Changed default config to `network_configuration.json`

## 3.6.2

* New ionic recorder device for NEURON adapter.

## 3.6.0b1

* Added GC-GC, SC-SC & BC-BC GABA connections

## 3.6.0b0

* Morphology rework: they are now branch centric structures of arrays.
  * Backward compatible `compartments` system still available.

# 3.5.0

* Blender support

# 3.3.0

* FiberIntersection added.

# 3.2

## 3.2.13

* First version with a functional multicompartmental network.

## 3.2.1

* PlacementSets have been introduced (#303)
* Obfuscated setup uses scaffold version plus "rc0". (#301, #308)
* `placement.py` is now its own module. (#302)
* ConfigurableClasses can specify classes in the global namespace instead of only inside
  of modules. (#299)

## 3.2.0

* Added parallel neuron simulations

# 3.0

## 3.0.4

* Cilindrical targetting mechanism for devices.
* Fixed `scaffold simulate`

## 3.0.3

* Added changes for the hackathon.
* Fixed bugs that would have been encountered during the workshop.

## 3.0.2

* Added obfuscation scripts to create distributions that are obfuscated and
  expire after a certain date.

## 3.0.1

* Fixed particle placement for layers that don't originate in the coordinate
  system origin. (PR #150)
* Better NEST warnings/errors for module errors.
* CLI commands `compile` and `run` can resize the configuration with -x and -z.
* Switched to Travis CI
* Optimized AllToAll connectivity strategy.
* Sattelite placement strategy now respects simulation volume bounds.
* Addition of mossy fiber to glomerulus connectivity. (PR #167)
* Fixed some of the issues with ParticlePlacement.

## 3.0.0

* 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.

# 2.3
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.

# 2.2

## 2.2.2
* Changed dependency list for installs outside of Anaconda.

## 2.2.1
* Removed obsolete files transferred by bad merge.

## 2.2.0
* Released 2.1.3 as 2.2.0

# 2.1

## 2.1.3
* Removed dependency on pandas
* Added a list of dependencies to setup.py

## 2.1.2
* Reworked/fixed connectivity algorithm between Golgi and granule cells.

## 2.1.1
* CHANGELOG restructured to show newest first.
* Removed dependency on pint and quantulum3.

## 2.1.0
* README updated.
* Verbosity added.
* Command line interface added. (Linux version not tested)

# 2.0

## 2.0.1
* README updated.

## 2.0.0
* Complete rework of the codebase to ensure flexibility, scalability and
  adoption by the community.
* First steps of distribution as a Python package.