Brain-indexer

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**October 2022**

**Breaking Changes**
* Implementation details w.r.t ``boost::serialize`` require a breaking change
in how indexes are stored. Old indexes cannot be loaded anymore and need to
be recreated.
* Remove MVD3 support. Only SONATA is supported. If you need MVD3 you must
convert the circuit to the new format.
* The keyword argument ``target_gids`` for ``MorphologyBuilder.from_sonata_file`` has been
renamed ``gids``. Please update your code before version 1.0 as the old name will be removed.
* The key ``gid`` for ``group_by`` has been renamed ``post_gid`` to reflect that the grouping is
happening according to the value of ``post_gid``. Please update your code
before version 1.0 as the old name will be removed.

**Features**
* ``accuracy="best_effort"`` is now the default.
* The radius of a segment is equal to the average of the radius at the two
endpoints.

**Improvements**
* Improves documentation.
* Improvements due to QA feedback.
* Bug fixes.
* Improve unit-testing with MPI.
* Improve CI: checking wheels and sdist.
* Improve integration tests: all usecases1-5

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**September 2022**

**Improvements**
* Improves documentation.

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**September 2022**

**Improvements**
* Improves documentation.
* Fixes OOM issue for synapse indexes that select by target GID.
* Fixes assert of `radii` during construction of morphology indexes.

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**September 2022**

**Improvements**
* Improves help and error messages.

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**September 2022**

**Features**
* Implemented multi-population support for indexes

**Improvements**
* Boxes are defined through any two opposing corners, not just the min- and max-corners.
* "window_query" and "vicinity_query" are now "box_query" and "sphere_query", respectively; and analogously for "{window,vicinity}_counts".
* "endpoints" are now exported as a tuples and not as two separate objects
* "kind" field has been replaced by "is_soma"
* Removed support for memory mapped files from the Python API
* The multi-index cache usage statistics report has been deactivated by default, available on-demand by setting the environment variable "SI_REPORT_USAGE_STATS" to "1" or "On"
* Consistency improvements for the code
* Bug fix for multi-index creation.

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**September 2022**

**Features**
* Overhaul of the Python APIs: API v2 (more info here: https://bbpteam.epfl.ch/project/spaces/x/MBStBg)
* Aligns internal identifier packing with TouchDetector. Requires rebuilding of existing indexes.
* Opening indexes from disk now requires a single command for every kind of index
* New Python logging infrastructure

**Improvements**
* Fixed issue in radius calculation
* Clean-up of the code base from unused code
* Improved validation using BluePy cross-checks
* Lots of bug fixes