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