Brain-indexer

-------------
**August 2022**

**Features**
* Introduced MultiIndex for parallel indexing
* Queries can now be performed in bounding box or best-effort mode
* Bulk return of values from queries as a dictionary of numpy arrays
* Support for .json file for CLI tools
* A full-fledged tutorial written in a Jupyter Notebook

**Improvements**
* Big improvements to CI
* Optimizations to collision detection
* C++ backend now upgraded to C++17
* Improved documentation
* Lots of bug fixes


Version 0.5.x
-------------
**April 2022**

**Features**
* Out-of-core support for node indexing
* Support for pre and post synaptic gids

**Improvements**
* Renamed NodeMorphIndexer to MorphIndexBuilder for clarity
* Introduced free space check for memory mapped files
* Improved documentation


Version 0.4.x
-------------
**November 2021**

**Features**
* Support for SONATA Selections for NodeMorphIndexer
* Add API to support counting elements and aggregate synapses by GID
* Chunked Synapse indexer feat progress monitor
* More flexible ranges: python-style (start, end, [step])

**Improvements**
* New CI (Gitlab): tests, wheels & docs, fix tox, drop custom setup.py docs
* Building and distributing wheels
* Added more examples and benchmarking scripts
* Added new classes to documentation API

-------------
**August 2021**

A major, and long waited, update since the previous release.
This is the first version effectively validated against FLAT index results.
It would take a lot of time to reconstruct everything that has changed from the first release so we'll just give a brief overview of the changes made in this new shiny version.

*Major changes*
* Morph object Indices are now tuples (gid, section, segment)
* New High level API/CLI for loading nodes and edges
* Initial IndexGrid and bindings, for future very large circuits

*Features*
* Added support for Section IDs
* Added support for Synapses Indexer
* Now supports CLI for indexing circuits
* Easier installation and interoperability with Sonata
* Gids, Section and Segment IDs are now ensured to be compliant with FLAT (0/1-based)
* Lots of validation fixes
* Improved installation experience
* Introduced IndexGrid/MultiIndex

*Improvements*
* Refactoring internal index intities, less inheritance
* Extensive validation against FLAT
* Many fixes for robustness and stability

-------------

*Features*
* Point API
* Support for window queries
* has_Soma flag (default=true) in add_neuron to allow the API to add segments only.

-------------

*Features*
* Support saving and loading dumps

*Improvements*
* Also some refactoring in the way we collect ids, automatic using `id_getter_for*`
* Docs and tests

-------------

*Features*
* Initial Spatial-Index based on boost.geometry.index.

* | IndexTree handling both generic geometries and boost variants implementing the protocol:
| - Base Geometries: Spheres and Cylinders.
| - Extended types: IndexedSphere, Soma and Segment.
| - Variant types: variant<Soma, Segment>

* | Created Python API for the two possibly most useful trees:
| - SphereIndex: IndexTree<IndexedSphere> - memory and cpu efficient.
| - MorphIndex: IndexTree<variant<Soma, Segment>> - capable of handling entire morphologies.