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Change Log

Version 2.1.0

Features
  • Support morphio.Collection to be able to also read from morphology containers.

Version 2.0.0

We've removed one method. It seems unlikely that users would be affected by this. Migration instructions are provided in the corresponding bullet point.

Features
  • CLI supports --verbose which prints log messages of any severity.
  • Infrastructure for creating indexes with randomly placed elements.
  • Support adding spheres to in-memory SphereIndex.
  • Support indexes of points PointIndex.
Improvements

  • Create in-memory indexes "in bulk". The internal structure of an R-tree is much better if all elements are known upfront; as opposed to being inserted one-by-one. This commit ensures that in-memory indexes are created via bulk creation.

    It optionally, old in-memory indexes should be recreated to benefit from this optimization. However, old indexes can still be read. Multi-indexes aren't affected at all by this change.

  • Use std::filesystem instead of boost::filesystem.

  • General restructuring of code and CI.

  • Added test to ensure consistency of morphology IDs between BrainIndexer and libsonata.

Deprecation
  • We've deprecated the certain constructors of core.MorphIndex and core.SynapseIndex. Users of BrainIndexer aren't expected to be using these classes directly.
Removal
  • We've removed a method add_sphere from the SphereBuilder. Instead please create all spheres upfront and then create the index. If upfront creation of all spheres doesn't work, the in-memory SphereIndex supports adding spheres interatively.
Fixes
  • Improved error message for missing files.
  • Warn if in-memory indexes are large.
  • Improved documentation.
  • Progress bar is only shown when in a TTY.

Version 1.2.1

December 2022

Improvements
  • Fix publishing documentation.

Version 1.2.0

December 2022

Features
  • Ability to optimize the order in which queries should be performed to improve cache reuse of multi-indexes.
Improvements
  • Document BrainIndexer environment variables.
  • Document important performance tricks.
  • Fix morphology builder to return SONATA enabled indexes.
  • Relax the minimum number of synapses in a multi-index.
  • Improvements to the overall code quality.

Version 1.1.0

November 2022

Features
  • Integrates section_type in index. This allows to retrieve information on the type of section (i.e. soma, axon, basal_dendrite, apical_dendrite) directly from the query.
  • Add box_empty and sphere_empty functions to check if a specific area is empty.
Improvements
  • Ignore virtual populations in circuit config files.
  • Populations with unsupported types are not allowed anymore.
  • Relaxed requirement on number of MPI ranks: now can be in the form 2**n * 3**m * 5**l + 1.
  • Workaround for BOOST_STATIC_CONSTANT build issue.
  • Multiple improvements to CI.
  • Removed memory mapped files support entirely.
  • Multiple fixes and improvements to the implementation.

Version 1.0.0

October 2022

No changes since version 0.9.0.

Version 0.9.0

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

Version 0.8.3

September 2022

Improvements
  • Improves documentation.

Version 0.8.2

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.

Version 0.8.1

September 2022

Improvements
  • Improves help and error messages.

Version 0.8.0

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.

Version 0.7.0

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

Version 0.6.0

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

Version 0.3.0

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

Version 0.2.0

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

Version 0.1.0

Features
  • Support saving and loading dumps
Improvements
  • Also some refactoring in the way we collect ids, automatic using id_getter_for*
  • Docs and tests

Version 0.0.1

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.