Brion

* [250](https://github.com/BlueBrain/Brion/pull/250):
Added new overloads of brain::Simulation::getGIDs to get random GID sets.
* [249](https://github.com/BlueBrain/Brion/pull/249):
- brion::CompartmentReport::loadFrame changed to return brion::Frame
- Implemented missing brain::CompartmentReportView::getReport
* [239](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/226):
Read/write support for SONATA compartment reports. This file format replaces
the old file format when writing reports.
* [225](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/204):
Fixed brain::Circuit methods to not crash with empty gids lists.
* [191](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/176):
Removed the dependency on HDF5++ and use HighFive instead.
* [172](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/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.

* [159](https://github.com/BlueBrain/Brion/pull/159):
Changed mapping index according to Pandas requirements for indexing.
* [157](https://github.com/BlueBrain/Brion/pull/157):
- Add Synapse.gid() python wrapping
- Improve synapse attribute reading performance
* [154](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/153):
Updated Python wrapping of SpikeReportWriter to handle nympy arrays of spikes
* [152](https://github.com/BlueBrain/Brion/pull/152):
Added the function brain.neuron.compute_morphological_samples to help getting
sample positions from morphologies
* [151](https://github.com/BlueBrain/Brion/pull/151):
brain::Circuit accepts full paths to mvd files in CircuitPath
* [150](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/141):
Fixed documentation to specify that morphology section samples report
diameters and not radii.
* [130](https://github.com/BlueBrain/Brion/pull/130),[138](https://github.com/BlueBrain/Brion/pull/138):
Added brain::CompartmentReportReader and its Python wrapping
brain::CompartmentReport : python API v2
* [136](https://github.com/BlueBrain/Brion/pull/136):
Implement readable null:// compartment report for benchmarking
* [120](https://github.com/BlueBrain/Brion/pull/120), [131](https://github.com/BlueBrain/Brion/pull/131):
- New SpikeReport API.
- Reimplementation of the high level SpikeReportReader. The new implementation
uses numpy arrays to provide the requested spikes.
* [126](https://github.com/BlueBrain/Brion/pull/126):
Add erase for map compartment reports
* [122](https://github.com/BlueBrain/Brion/pull/122):
Support loading of individual neurons for binary and map compartment reports
* [121](https://github.com/BlueBrain/Brion/pull/121):
Performance optimizations for map and binary compartment reports, fix
sub target loading of map compartment reports
* [119](https://github.com/BlueBrain/Brion/pull/119):
Optimized brain::Circuit::loadMorphologies for slow stat'ing
filesystems (GPFS)

* [117](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/113):
Support for old circuits containing only synapse center positions
* [110](https://github.com/BlueBrain/Brion/pull/110):
Break PersistentMap out into keyv::Map
* [107](https://github.com/BlueBrain/Brion/pull/107):
Added Sphinx generated documentation of the brain python module
* [102](https://github.com/BlueBrain/Brion/pull/102):
Use PersistentMap for caching synapse positions loaded from brain::Circuit
* [94](https://github.com/BlueBrain/Brion/pull/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](https://github.com/BlueBrain/Brion/pull/89):
Python wrapping of brain classes
* [88](https://github.com/BlueBrain/Brion/pull/88):
- Brain namespace enums made strongly typed
- Fix for brain::Section::getSamples for sections where the first point
appears repeated
* [85](https://github.com/BlueBrain/Brion/pull/85):
Implement brain synapses specification
* [84](https://github.com/BlueBrain/Brion/pull/84):
Brain synapses specification
* [83](https://github.com/BlueBrain/Brion/pull/83):
Add brain::Circuit::getRandomGIDs()
* [82](https://github.com/BlueBrain/Brion/pull/82):
Improve performance when reading synapse attributes from non-merged files
* [81](https://github.com/BlueBrain/Brion/pull/81):
Fix GID out-of-bounds handling for MVD3 in brain::Circuit
* [79](https://github.com/BlueBrain/Brion/pull/79):
Use PersistentMap for cache in brain::Circuit::loadMorphologies(); add thread
safety w/ synapses cache

* [77](https://github.com/BlueBrain/Brion/pull/77):
Add brain::Circuit::getMorphologyTypes() and brain::Circuit::getElectrophysiologyTypes()
* [75](https://github.com/BlueBrain/Brion/pull/75):
Implement morphology version 1.1 specification
* [74](https://github.com/BlueBrain/Brion/pull/74):
Remove deprecated enums and functions:
- `CompartmentReport( const std::string&, const GIDSet& )` and
`CompartmentReport( const std::string&,
const brion::CompartmentReportFormat, const bool )` constructors; use
brion::CompartmentReport::CompartmentReport( const brion::URI&, int, const brion::GIDSet& )
instead
- `enum CompartmentReportFormat`; use brion::BlueConfig::getReportSource()
instead
* [71](https://github.com/BlueBrain/Brion/pull/71):
Transparent caching of Synapse loading. See
[Lunchbox263](https://github.com/Eyescale/Lunchbox/pull/263) for
configuration.
* [69](https://github.com/BlueBrain/Brion/pull/69):
Speedup brain::Circuit::getGIDs(), add brion::BlueConfig::getTargetSources()
* [63](https://github.com/BlueBrain/Brion/pull/63):
Moved old BBPSDK/Monsteer spike report to Brain (pending refactoring)

* [56](https://github.com/BlueBrain/Brion/pull/56):
Improved target parser
* [55](https://github.com/BlueBrain/Brion/pull/55):
Add basic provenance metadata for written HDF5 compartment reports
* [49](https://github.com/BlueBrain/Brion/pull/49):
Added the method brain::Circuit::getRotations
* [46](https://github.com/BlueBrain/Brion/pull/46):
Fixed a bug in enum to string conversions affecting morphologyConverter.
* [45](https://github.com/BlueBrain/Brion/pull/45):
Made targets optional.
- brain::Circuit::getGIDs() returns all GIDs handled by the circuit.
- brain::Circuit::getGIDs( target ) returns GIDS for a specified target.
- brain::Circuit::getNumNeurons() returns the total number of neurons in the
circuit.
* [43](https://github.com/BlueBrain/Brion/pull/43):
Add MVD3 support to brain::circuit
* [39](https://github.com/BlueBrain/Brion/pull/39):
Add compartment report converter tool
* [30](https://github.com/BlueBrain/Brion/pull/30),
[35](https://github.com/BlueBrain/Brion/pull/35):
Added a new library, Brain, to provide higher level functions and classes.
The library provides:
- A Circuit class to get basic information from cells and targets and load
morphologies at circuit level.
- A brain::cell namspace with a Morphology class plus other related classes
to access morphological data about neurons.
* [38](https://github.com/BlueBrain/Brion/pull/38):
Fix crash while reading more than `ulimit -Sn` (1024 default) morphologies
* [37](https://github.com/BlueBrain/Brion/pull/37):
Added support for synapse nrn_extra.h5 files.
* [31](https://github.com/BlueBrain/Brion/pull/31):
Fix crash while reading more than `ulimit -Sn` (1024 default) NEST gdf files
* [29](https://github.com/BlueBrain/Brion/pull/29):
New member functions in brion::BlueConfig to provide a semantic API.
* [28](https://github.com/BlueBrain/Brion/pull/28):
SpikeReport continues parsing files that have broken lines

* [24](https://github.com/BlueBrain/Brion/pull/24):
Add getURI() method in SpikeReport.
* [22](https://github.com/BlueBrain/Brion/pull/22):
spikeConverter can process spikes to and from stream-type SpikeReport plugins.
* [22](https://github.com/BlueBrain/Brion/pull/22):
SpikeReport DSO plugins in the LD_LIBRARY_PATH are loaded automatically.
* [12](https://github.com/BlueBrain/Brion/pull/12):
Extended brion::Synapse to also support non-merged synapse files
* [12](https://github.com/BlueBrain/Brion/pull/12):
Add brion::Target::parse() to resolve a given target name
* [9](https://github.com/BlueBrain/Brion/issues/9):
Extend SWC parser to support fork and end points and undefined section points.
The Brion::SectionType enum has not been extended to include end and fork
points, these types are translated into the most reasonable one based on the
point ancestors.