https://github.com/bluebrain/brion - 3.3.14 Release

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

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Published by NadirRoGue about 5 years ago

https://github.com/bluebrain/brion - 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 PYTHON3ROOTDIR (wheel distribution)
307 Fixes version number typo
306 Fix for wrongly load check in synapse positions

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Published by NadirRoGue over 5 years ago

https://github.com/bluebrain/brion - 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.

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Published by NadirRoGue over 5 years ago

https://github.com/bluebrain/brion - 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.

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Published by NadirRoGue almost 6 years ago

https://github.com/bluebrain/brion - 3.1.0

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

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Published by NadirRoGue over 6 years ago

https://github.com/bluebrain/brion - 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

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Published by hernando about 7 years ago

https://github.com/bluebrain/brion - 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.computemorphologicalsamples 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)

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Published by hernando almost 9 years ago

https://github.com/bluebrain/brion - 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

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Published by tribal-tec over 9 years ago

https://github.com/bluebrain/brion - 1.8.0

77: Add brain::Circuit::getMorphologyTypes() and brain::Circuit::getElectrophysiologyTypes()
75: Implement morphology version 1.1 specification
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: Transparent caching of Synapse loading. See Lunchbox#263 for configuration.
69: Speedup brain::Circuit::getGIDs(), add brion::BlueConfig::getTargetSources()
63: Moved old BBPSDK/Monsteer spike report to Brain (pending refactoring

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Published by tribal-tec almost 10 years ago

https://github.com/bluebrain/brion - 1.7.0

56: Improved target parser
55: Add basic provenance metadata for written HDF5 compartment reports
49: Added the method brain::Circuit::getRotations
46: Fixed a bug in enum to string conversions affecting morphologyConverter.
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: Add MVD3 support to brain::circuit
39: Add compartment report converter tool
30, 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: Fix crash while reading more than ulimit -Sn (1024 default) morphologies
37: Added support for synapse nrn_extra.h5 files.
31: Fix crash while reading more than ulimit -Sn (1024 default) NEST gdf files
29: New member functions in brion::BlueConfig to provide a semantic API.
28: SpikeReport continues parsing files that have broken lines

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Published by chevtche about 10 years ago

https://github.com/bluebrain/brion - 1.6.0

Changelog: - 24: Add getURI() method in SpikeReport. - 22: spikeConverter can process spikes to and from stream-type SpikeReport plugins. - 22: SpikeReport DSO plugins in the LDLIBRARYPATH are loaded automatically. - 12: Extended brion::Synapse to also support non-merged synapse files - 12: Add brion::Target::parse() to resolve a given target name - 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.

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Published by hernando over 10 years ago

https://github.com/bluebrain/brion -

- C++
Published by tribal-tec almost 11 years ago

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