3.3.4

• 327
  3.3.4 Release preparation
• 326
  Add extra checks to choose the appropriate synapse handling class

3.3.3

• 325
  3.3.3 Release preparation
• 324
  Sort returned SONATA report values by node ID
• 323
  Adds warning message about using Brion to read SONATA format
• 322
  Update copyright and funding notice

3.3.2

• 321
  3.3.2 Release preparation
• 320
  Allow tabs '\t' as key - value separator in BlueConfig
• 319
  Fix wrong frame index calculation from report timestamp, drop support for python < 3.6
• 318
  General submodule update
• 317
  Custom BlueConfig file support for multipopulation
• 316
  Fix BlueConfig class to follow documentation about morphology type

3.3.1

• 314
  3.3.1 Release preparation
• 313
  Improve error message for GIDs out of range in report
• 312
  Handling MorphologyType from BlueConfig
• 311
  Handle 0 based GIDs on sonata files
• 310
  Miscelaneous fixes and updates
• 309
  Use env vars for setting PYTHON3_ROOT_DIR (wheel distribution)
• 307
  Fixes version number typo
• 306
  Fix for wrongly load check in synapse positions

3.3.0

• 305
  Preparation for 3.3.0 release.
• 304
  Rename brain python package to brion.
• 303
  Improve SONATA syanapse support.
• 302
  Fix glm targets not installed properly.
• 300
  Initial commit for python wheel distribution package support.
• 299
  Removing unused functions from old SONATA circuit implementation.
• 298
  Support for relative paths in BlueConfig/CircuitConfig.
• 297
  SONATA circuit support.
• 295
  Misc. fixes and updates.
• 293
  Fix mvdtool bug when mecombo file is empty.
• 290
  Replacing morphology readers and tests with MorphIO.
• 289
  Update README.md.
• 288
  Update MVDTool submodule.

3.2.0

This release enables the use of DOI through Zenodo

• 281
  Strips Pydoxygen, Servus and CMake/common.
• 280
  Bumps libsonata submodule
• 279
  Strips lunchbox library.
• 278
  Strips vmmlib library. Replaces it with GLM.
• 275
  Strips key-value library.

3.1.0

• 269:
  Introduce SONATA support
• 263:
  Detect start.target in CircuitPath
• 255:
  Adding Python 3.7 and removing 3.4 from wheels

3.0.0

• 250:
  Added new overloads of brain::Simulation::getGIDs to get random GID sets.
• 249:
  • brion::CompartmentReport::loadFrame changed to return brion::Frame
  • Implemented missing brain::CompartmentReportView::getReport
• 239:
  • Added two query options to configure chunking and chunk cache size when
    opening/creating SONATA compartment reports.
  • Added a new overload of brion::CompartmentReport::write to allow
    optimizations for full frame writes.
• 229:
  • Added a method to brain::Circuit to retrive custom node attributes. This is
    only supported in C++ for SONATA circuits.
  • Implemented morphology recentering for SONATA circuits.
• 227:
  Read/write support for SONATA compartment reports. This file format replaces
  the old file format when writing reports.
• 225:
  Addition of some new methods and classes:
  • Added the class Simulation for accesing the contents of simulation
    configurations
  • Circuit::getSource
  • Circuit::getMorphologyNames
  • Made CompartmentReport and SpikeReporReader movable
  • Soma::getMaxRadius
  • neuron::Section::getNumSamples
  • neuron::Section::operator[]
  • Support morphologies with single point somas
  • Added default Synapses::iterator constructor
  • Changed Synapses and Synapse memory magement implementation to allow
    use in Python wrappings of client code.
• 222:
  Implemented basic support for reading circuit in SONATA file format
  • The implementation is limited to node, no edges are read
  • Only one population and one node group are read, the rest are ignored.
• 204:
  Fixed brain::Circuit methods to not crash with empty gids lists.
• 191:
  • Optimizations in brain::CompartmentReport opening, only the metadata is
    read.
  • Removed compartmentCount and cellCount from brain::CompartmentReportMetadata
    because they can't be figured out efficiently in all report types.
  • New function getFrameSize added to CompartmentReportMapping to replace
    compartmentCount.
  • New function getCellCount added to CompartmentReport to replace cellCount.
• 180:
  Bugfixes in compartment reports:
  • The report converter was messing up the order of the data when writing to
    .h5 from an out-of-order binary.
  • Timestamps reported were wrong for reports not starting at 0.
  • Read time and data unit attributes from H5 reports is they exist.
  • Do not assume the first section is always present post-processing the
    mapping in H5 reports.
  • Avoid crashing when calling getNumCompartments from Python with and out of
    bounds index.
  • Corrections in compartmentReport comparison code.
• 176:
  Removed the dependency on HDF5++ and use HighFive instead.
• 172:
  • zeroeq::Server/Client based morphology loader.
  • New brion::Morphology read API and removed write API (see doc/feature/morphologyRead.md)
  • Removed apical point API
  • morphologyConverter can only write H5 V1.1 morphologies
• 171:
  Ban obsolete morphology repair stage from API: The stage parameter from
  certain Morphology methods has been removed. In the case of h5v2 morphologies,
  the implementation will pick the most complete repair stage.
• Performance optimizations in compartment reports and synapses
• Python-wheel generation for Linux and Mac OS/X (versions 3.5, 3.6 and 3.7): scripts and CMake fixes
• Use gitsubmodule for Pydoxine
• Make ZeroEQ optional and off by default

2.0.0

• 157:
  • Add Synapse.gid() python wrapping
  • Improve synapse attribute reading performance
• 156:
  Performance improvements in compartment report mapping handling
• 154:
  • Improved help and command line inverface for spikeConverter and
    compartmentConverter.
  • Timestamps in brion::CompartmentReport changed from float to double.
  • New implementation of binary compartment report reader using POSIX AIO.
• 153:
  Updated Python wrapping of SpikeReportWriter to handle nympy arrays of spikes
• 152:
  Added the function brain.neuron.compute_morphological_samples to help getting
  sample positions from morphologies
• 151:
  brain::Circuit accepts full paths to mvd files in CircuitPath
• 150:
  • Added a new method in brain::Circuit to obtain synapses for afferent
    projections from outside the circuit (e.g. thalamocortical projections).
  • Support for Projections sections in brion::BlueConfig
• 141:
  Fixed documentation to specify that morphology section samples report
  diameters and not radii.
• 130,138:
  Added brain::CompartmentReportReader and its Python wrapping
  brain::CompartmentReport : python API v2
• 136:
  Implement readable null:// compartment report for benchmarking
• 120, 131:
  • New SpikeReport API.
  • Reimplementation of the high level SpikeReportReader. The new implementation
    uses numpy arrays to provide the requested spikes.
• 126:
  Add erase for map compartment reports
• 122:
  Support loading of individual neurons for binary and map compartment reports
• 121:
  Performance optimizations for map and binary compartment reports, fix
  sub target loading of map compartment reports
• 119:
  Optimized brain::Circuit::loadMorphologies for slow stat'ing
  filesystems (GPFS)

1.9.0

• 117:
  Changes and fixes in Brain Python module:
  • Functions that take gids now preserve the iteration order of the input in
    the output arrays/lists.
  • Replaced Python sets with numpy arrays in functions returning GID sets.
  • Circuit::getXYZNames functions renamed to Circuit::getXYZTypeNames.
• 113:
  Support for old circuits containing only synapse center positions.
• 110:
  Break PersistentMap out into keyv::Map
• 107:
  Added Sphinx generated documentation of the brain python module.
• 102:
  Use PersistentMap for caching synapse positions loaded from brain::Circuit
• 94:
  Fixed SWC morphology parser for morphologies with soma contour. The parser was
  creating invalid soma sections when the first order sections where connected
  to arbitrary soma sample points.
• 89:
  Python wrapping of brain classes.
• 88:
  • Brain namespace enums made strongly typed.
  • Fix for brain::Section::getSamples for sections where the first point
    appears repeated.
• 85:
  Implement brain synapses specification
• 84:
  Brain synapses specification
• 83:
  Add brain::Circuit::getRandomGIDs()
• 82:
  Improve performance when reading synapse attributes from non-merged files
• 81:
  Fix GID out-of-bounds handling for MVD3 in brain::Circuit
• 79:
  Use PersistentMap for cache in brain::Circuit::loadMorphologies(); add thread
  safety w/ synapses cache