CHANGES.rst

Change Log

Version 3.6.0

13 August 2024

New Features

• [BBPBGLIB-975] Improved "signal" shot noise parameterization (#187)

Improvements

• Read modifications list from libsonata API (#181)

Version 3.5.0

24 July 2024

New Features

• [BBPBGLIB-854] Implement a CLI option to run coreneuron in direct mode without writing model data to disk (#100)

Bug Fixes

• [BBPBGLIB-1175] Handle deleted sections correctly (#182)

Improvements

• Allow API configuration to preserve the axons during setup (#155)
• Update ngv test to use V10 emodels (#183)
• [BBPBGLIB-1167] Automatic balance loading and on-the-fly rebalance (#178)
• Replay with NetCons in CoreNEURON as in NEURON (#173)

Version 3.4.0

21 June 2024

New Features

• [BBPBGLIB-1152] Multi-cycle support for dry run estimate and instantiation (#171)

Improvements

• Remove VecStim to use the version in neurodamus-models (#177)
• Accurate synapse counts in dry-run (respect src target) (#169)
• Optimize Dockerfile a bit (#176)
• [BBPBGLIB-1141] Remove HDF5reader.mod which is already replaced by libsonata (#162)

Version 3.3.0

28 May 2024

New Features

• [BBPBGLIB-1137] Account for nonzero total current when using SEClamp; allow nonzero total

Bug Fixes

• Fix record_spikes for load balancing (#167)
• [BBPBGLIB-739] Override UTF-8 for logging (#147)

Improvements

• Removing legacy RNGs, leaving only Random123 (#136)
• [BBPBGLIB-1158] Add empirical mechanism to estimate simulation memory usage (#165)
• Tests with subprocess should capture streams (#164)
• Trigger workflow when pushing to main (#172)
• Avoid calling cleanup from destructor (#168)
• Add tests for python 3.9 to 3.12 (#124)
• Cache dependent packages in GH actions workflow (#166)

Version 3.2.1

30 April 2024

New Features

• [BBPBGLIB-1153] Allow disabling reports from SONATA config (#159)

Bug Fixes

• Fix dead link from CONTRIBUTING.md to README.rst (#160)
• Remove Report.hoc reference (#158)

Improvements

• [BBPBGLIB-1154] Add information about CORENEURONLIB in the Docker README (#161)

Version 3.2.0

17 April 2024

Bug Fixes

• [BBPBGLIB-1145] Write gids without offset in WholeCell LB complexity file (#148)
• [BBPGBLIB-1147] Fixes crashes with KeyError when running sonataconf-sscx-O1 circuit on dry run (#149)
• Hotfix to solve crashes when running on certain amount of ranks (#141)

Improvements

• [BBPBGLIB-1057] Replace Report.hoc by report.py (#145)
• [BBPGLIB-1148] Add support for gap junctions in dry run (#151)
• Update online-lfp.rst (#152)
• Update docker file with the new data location (#153)
• Replay with SONATA spikes files (#150)
• Clean up wheel contents. (#144)
• [BBPBGLIB-1139] Missing exception logging on configuration errors (#142)

Version 3.1.1

12 Mar 2024

Bug Fixes

• Fix fetching error in GH workflow triggered by tag

Version 3.1.0

12 Mar 2024

New Features

• [BBPBGLIB-1102] (Part two) Load memory balance from file (#129)
• [BBPBGLIB-1102] Add memory load balance export based on dry run estimate (#111)

Bug Fixes

• StrEnum not working with older python versions (#125)
• Fix unit tests (#119)

Improvements

• [BBPBGLIB-1125] GH forkflow for building a wheel (#121)
• On --debug install a hook for NGV to show neuro-glial "spikes" (#137)
• [BBPBGLIB-1132] Replace StimulusManager.hoc with the python classes (#132)
• [BBPBGLIB-1134] Move ShowProgress.hoc to python (#131)
• [BBPBGLIB-1135] Move CompartmentMapping to python (#133)
• [BBPBGLIB-1133] Remove ElectrodeManager.hoc and LookupTableV2.mod (#128)
• [BBPBGLIB-1121] Remove BlueConfig parser (#127)
• Use actions/checkout@v4 to use Node 20 (#126)
• [BBPBGLIB-1127] Remove SpikeWriter.mod and out.dat (#123)
• [BBPBGLIB-1110] Error now raised when executeConfigure is returned with errors (#120)
• Remove SynapseReader.mod and SynReaderNRN (#122)
• [BBPBGLIB-1124] Remove hoc targets related code (#118)
• [BBPBGLIB-1120] Remove node loaders for MVD3 and NCS (#117)

Version 3.0.0

31 Jan 2024

New Features

• Deprecate BlueConfig part-1: Raise errors for BlueConfig configuration files (#101)
• Read synapse parameters in a collective safe manner. (#85)

Bug Fixes

• [BBPBGLIB-1115] Fix issue with summation reports and cell target in NEURON (#114)
• [BBPBGLIB-1114] Apply offset to the gids before reading node file (#113)

Improvements

• [BBPBGLIB-1111] Raise a proper error when missing "--configFile=" (#115)
• Remove dependency on mvdtool (#112)
• Transform setup.py to pyproject.toml (#110)

Version 2.17.0

22 Dec 2023

New Features

• Fast & lightweight dry run (#91)
• Implement chunking mechanism for loading synapses in dryrun mode (#88)

Bug Fixes

• CoreConfig: write_report_count() should always create a new report.conf (#107)
• Fix netstim_inhpoisson.mod for CoreNEURON direct mode (#94)
• Fix memory usage reporting on MacOS (#105)
• Fix call to trim_memory on non-GNU C libraries (#106)
• Fix unit test: new morphology test file to fulfil MorphIO change (#104)
• [BBPBGLIB-1027] Fix: Load Balance with multi-populations (#92)
• CI fix for python setup.py egg_info error (#95)
• Build recipe: remove shallow clone to meet the version requirement of latest setuptools (#90)
• Fix bug with duplicate count of synapses (#87)
• Fix docs (#84)

Improvements

• [BBPBGLIB-1093] Move scientific tests from blueconfigs (#103)
• Update documentation for new synapse estimate algorithm (#99)
• Modernize the setup infractructure slightly. (#98)
• [BBPBGLIB-1092] Add unit tests for CLI options (#86)
• [BBPBGLIB-1097] Reorganization of unit/integration tests (#83)
• Update build_neurodamus.sh with --only-neuron (#89)

Version 2.16.6

17 Nov 2023

Bug Fixes

• Use default dt value of NEURON in WholeCell load balancing (#81)
• Fix conversion from sonata parameter to neurodamus internal key : amp_cv -> AmpCV (#79)

Improvements

• CI and container improvements
• Protect numpy.concatenate empty tuple in get_local_gids (#53)
• [BBPP134-1022] Handling exceptions from NEURON during emodel loading (#80)

Version 2.16.5

1 Nov 2023

New Features

• [BBPBGLIB-1069] Dry-run node allocation suggestions (#64)
• [BBPBGLIB-1067] Implement 'node_sets_file' resolution order (#55)

Bug Fixes

• [BBPBGLIB-1076] Fix NGV offsetting with Sonata circuits (#69)
• [BBPBGLIB-1055] Support "<NONE>" as nrnPath (#65)

Improvements

• [BBPBGLIB-1044] Use libsonata to read the spikes (#70)
• [HPCTM-1824] Introducing a temporary set for faster lookup in the src_target gids (#63)
• [BBPBGLIB-556] Dry-run improvements, fixes with projections (#56, #60)
• [REP-68] Add report dt to the logging (#59)
• Remove ranks-cpus warning as can be inaccurate (#66)

Version 2.16.4

9 Oct 2023

New Features

• [BBPBGLIB-556] Full estimate of memory consumption (#32)

Bug Fixes

• [BBPBGLIB-1042] GapJunctionManager: filter source target by population (#42)
• [BBPBGLIB-1061] SONATA conf: Dont map to internal connectivity

Improvements

• Modernize ALU (#48)
• [HPCTM-1793] Add a Dockerfile for building Neurodamus

Version 2.16.3

21 Sep 2023

New Features

• Share GluSynapseHelper.hoc with public users (#47)
• Read 'electrodes_file' field from libsonata (#23)
• [BBPBGLIB-1060] Remove CoreConfig.mod and enable CoreNEURON execution via NEURON Python API (#41)

Version 2.16.2

1 Sep 2023

Bug fixes

• Use 0-based gid for reading GlioVascular sonata edges file
• import h5py in the function call to filter numpy warnings
• Propagate the log level correctly from the CLI option to Neurodamus class
• Skip CORENEURON unit tests pending for a fix from NEURON (#38)

Version 2.16.1

25 Aug 2023

New Features

• [BBPBGLIB-1044] Sonata Replay
• [BBPBGLIB-712] Estimate memory usage for synapse and connection

Improvements

• Update CoreConfig.mod for latest CoreNEURON changes
• [BBPBGLIB-1030] Reject .sonata extenson for nodes and edges file
• Breaking enable_reports code into pieces
• [BBPBGLIB-851]Warning on cao_CR syn variable if not the same as extracellular_calcium
• Use libsonata API to read report secton keys in the sonata config file

Version 2.16.0

26 July 2023

New Features

• [BBPBGLIB-1036] Pure SONATA reader for gap junctions
• [BBPBGLIB-984] Option to keep Cell axon during init

Improvements

• [BBPBGLIB-1035] Drop Synapsetool. Migrate all synapses loading to libsonata (no syn2 support)

Version 2.15.3

14 July 2023

Improvements

• Replace sys.exit with h.quit to fix issue with MPI_Finalize

Version 2.15.2

13 July 2023

New Features

• [BBPBGLIB-1027] Enable load balance for Sonata config simulations
• [NRN-152] MorphIO API: morphio_read
• Support HDF5 morphology containers via MorphIO
• hocify: file mode
• [BBPBGLIB-711] Dry run for cells instantiation

Improvements

• [BBPBGLIB-795] Added documentation for how to install/develop/use a custom neurodamus-py
• Ncs with sonata
• [NSETM-1948] Log warning on SonataError from libsonata.NodeSets materialization
• Replace BlueConfig with SONATA config in ngv test

Version 2.15.1

13 June 2023

New Features

• [BBPBGLIB-706] Make all core mod files compatible with CoreNEURON/NMODL

Improvements

• Docs for the open source repo
• All usecase3 circuit files now are contained in neurodamus-py
• [HPCTM-1755] one morphio_wrapper.py in neurodamus

Bug fixes

• Fixed unit tests due to changes in common MOD files

Version 2.15.0

11 May 2023

New Features

• [BBPBGLIB-1008] Unify/Drop core submodule

Improvements

• [BBPBGLIB-988] Migrate to libsonata node reader
• [BBPBGLIB-1009] Remove utility.mod and replace checkDirectory with python function

Bug fixes

• [BBPBGLIB-1016] Read connection_overrides list insteamd of dict from libsonata
• CI dont rely on common submodule, Clone. Small fixes

Version 2.14.0

6 Apr 2023

New Features

• [BBPBGLIB-983] Remove Bin reports
• [BBPBGLIB-995] [BBPBGLIB-996] [BBPBGLIB-997] SONATA config: read "log_file" and report "file_name"
• Add support for on-line LFP calculations
• [BBPBGLIB-908] API to restrict features and populations

Improvements

• [BBPBGLIB-908] Scientific tests - Multi-population
• Control numpy subnormal flush to zero warnings
• Add test for projections connectivity
• [BBPBGLIB-908] Add spont-minis test
• [BBPP40-291] Improve Sonata configurations for ngv simulations

Bug fixes

• Force dtype during numpy.concatenate recarrays
• [HPCTM-1687]: fix error of checking np.recarray None or empty

Version 2.13.2

1 Mar 2023

Bug fixes

• Updates on sonata parsing to adapt changes from libsonata
• Don't handle SpikeLocation from Sonata conditions

Version 2.13.1

14 Feb 2023

Bug fixes

• Fix potential issues with freeing the NEURON event queues

Version 2.13.0

8 Feb 2023

New Features

• [BBPP40-275] Set endfeet R0pas based on vasculature.h5
• [BBPBGLIB-748]: neuromodulation with coreneuron

Improvements

• [BBPBGLIB-959] Clear bbss objects and SpontMini's random123 objects
• [BBPBGLIB-899] Improved Synapse instantiation memory and time
• Better warnings when synapses cannot be placed

Bug fixes

• [BBPBGLIB-964] load additional cell properties to work when using Sonata nodesets
• [BBPBGLIB-964] Fix replay with virtual populations during coreneuron restore
• Fix CoreNeuron cleanup for re-running the same campaign with bbp-worfklow

Version 2.12.11

20 Dec 2022

Improvements

• [BBPBGLIB-954] Don't create hoc obj for nodeset targets
• [BBPBGLIB-937] Reduce memory consumption in Connection class
• [BBPBGLIB-954] Avoid flattening nodesets

Bug fixes

• Fix SHM File Transfer safety checks on large simulations
• Fix CI as tox got updated
• [BBPBGLIB-962] Fix and workaround for ngv test

Version 2.12.10

25 Nov 2022

New Features

• [BBPBGLIB-957] Added RSS printing in multiple places

Improvements

• Avoid writing --report-conf to the sim.conf if reports are disabled
• Load balancing improvements for multiple populations

Bug fixes

• Clear the model after calling savestate()

Version 2.12.9

09 Nov 2022

New Features

• [BBPBGLIB-938] Clean Random123 objects in synapses
• [BBPBGLIB-950] Call malloc_trim to return free pages back to the OS when clearing up the model
• Shrink NEURON ArrayPools and call Python garbage collect when clearing up the model

Version 2.12.8

07 Nov 2022

New Features

• [NRN-111] Add support for incoming Datum changes in 9.0.0

Version 2.12.7

04 Nov 2022

Improvements

• [BBPP134-14] Support node files with '.sonata' extension

Bug fixes

• [BBPBGLIB-945] Properly display the exception messages when the simulation crashes

Version 2.12.6

21 Oct 2022

New Features

• Enable model stats printing in CoreNEURON
• Read new sonata keys from libsonata
  • [BBPBGLIB-885] neuromodulation_dtc and neuromodulation_strength in connection_overrides
  • [BBPBGLIB-915] deprecate minis_single_vesicle key from conditions
  • [BBPBGLIB-913] deprecate forward_skip key
  • [BBPBGLIB-920] add keys in run for additional seedings: stimulus_seed, ionchannel_seed, minis_seed, synapse_seed
  • [BBPBGLIB-921] add series_resistance key in seclamp
  • [BBPBGLIB-919] parse modifications

Improvements

• [BBPBGLIB-934] LoadBalance refactoring for multiple circuits
• Enable reading sonata circuit config with empty edge

Bug fixes

• [BBPBGLIB-933] Fix coreneuron multi-cycle model building for multiple circuits
• Fix for conflict with SHM File Transfer and --keep-build

Version 2.12.5

07 Oct 2022

Improvements

• Add a GapJunction unit test to showcase how it could be tested
• Improved Cell Managers API with get_cell (python cell) and get_cellref (hoc cellref)
• Make Load balancer use the TargetManager Python class
• [HPCTM-1600] Set SHM File Transfer by default + Improve model memory consumption estimates

Version 2.12.4

23 Sep 2022

Improvements

• Add test for point to detailed neuron connectivity and vice versa
• [BBPBGLIB-904] Pytests refactoring and coverage + Have mini simulations run directly under pytest
• Add zero amplitude at start of new noise stimuli to allow stacking over time

Bug fixes

• [BBPBGLIB-888] Save populations_offset.dat in output directory to resolve issue in restore
• coreneuron restore: link populations_offset.dat only in rank0 and hold the other ranks
• [HPCTM-1584] Fix deletion of SHM coredat files when '--enable-shm' is not set

Version 2.12.3

29 Aug 2022

New Features

• Bump submodule past hpc/sim/neurodamus-core!12

Bug fixes

• [BBPBGLIB-887] Protect synapse reading: n_rrp_vesicles is required for SONATA circuits
• [REP-80] Call hoc in report initialization for synapse reports in CoreNEURON
• [BBPBGLIB-901] Fix corenrn input dir w sonata

Version 2.12.2

17 Aug 2022

Improvements

• CoreNEURON: Skip report initialization after creating report.conf in save/restore
• Improve report initialization time with CoreNEURON

Bug fixes

• Fix for race-condition when reading sim.conf
• [BBPBGLIB-894] Fix spike train handling

Version 2.12.1

28 Jul 2022

New Features

• Add support for SHM file transfer in CoreNEURON

Version 2.12.0

15 Jul 2022

New Features

• [BBPBGLIB-816] Complete Baseline support for SONATA configuration
• New CLI options for save-restore, run mode and dump cell state
• Documentation for running a SONATA simulation

Improvements

• Avoid creating out.dat when running simulations with SONATA config file
• Read sonata config parameters from libsonata parser
• Replace calculation of U scale_factors calculation by a single function

Bug fixes

• Resolve nodes and edges paths according to circuit_config.json location
• [BBPBGLIB-856] Fixes for hoc targets w offset and nodes extra properties
• Expect same behavior when connection delay is not present and when is 0

Version 2.11.3

25 May 2022

New Features

• Load extended cell properties from SONATA [BBPBGLIB-806]

Improvements

• Core mods compatibility across Nrn8.0..9.x
• Added synapses test [BBPBGLIB-826]

Version 2.11.2

12 May 2022

Improvements

• Improved target intersection for nodesets addressed in BBPBGLIB-823

Version 2.11.1

2 May 2022

Improvements

• Use libsonata API parser for sonata config

Version 2.11.0

28 Apr 2022

Improvements

• No eager caching of synaptic parameters
• Sonata nodesets to be able to cross multiple populations
• Adding test with patched delays after ModOverride

Version 2.10.3

30 Mar 2022

New Features

• Support sonata configurations for ngv

Improvements

• BBPBGLIB-805 Allow independent scaling fields
• Configurable scaling between I_thresh and invRin

Bug fixes

• Summation report fixes

Version 2.10.2

4 Mar 2022

New Features

• Suport multi-population compartment report
• Suport sonata configuration and sonata NodeSetTarget
• Implement RelativeOrnsteinUhlenbeck stimulus
• New-gen stimuli injected as Current or Conductance
• Implement StochasticConductance stimulus
• Implement ConductanceSource(SignalSource) using an SEClamp
• Implement Ornstein-Uhlenbeck process signal generation

Improvements

• Control display of unhandled exceptions

Bug fixes

• Store reference to rs-driving signal (fix CELLS-79)

Version 2.8.0

October 21, 2021

New Features

• Addition of PointNeuron Engine for supporting Point neuron simulations
• Reading extra parameters for GluSynapses ffrom SONATA edges file
• Allow ConfigureAllSections modifications

Improvements

• Handle reports for multiple populations adapting new features of libsonata-report
• Add warning when synapse targets invalid point
• Refactoring Targets for Nodeset compat
• Differenciate between cell target and section soma
• NGV endpoint id: Fallback to global synapse id

Bug fixes

• Fix stims for new target API. Make API compat old usage
• Fix regression: pass nodesets file as BC TargetFile
• Offset fixes for replay with multiple circuits
• Fix bug with SynConfigure and multipopulation

Version 2.7.0

July 7, 2021

New Features

• Initial Framework for Python modifications + TTX
• Implement python helpers for common stim
• V6 cells provide API (local_to_global_coord_mapping) to move cell points to absolute position

Improvements

• BBPBGLIB-675 Neurodamus to re-launch using special
• MorphIO lazy loading to avoid issue #316
• Validation of report configuration
• [NGVDISS-89] glia_2013 superseded by mcd

Bug fixes

• local_nodes to handle case of 0 count

Version 2.6.0

May 11, 2021

New Features

• NGV
  • [NGVDISS-1] Astrocyte Endoplasmic Reticulum
  • [NGVDISS-73] Astrocyte perimeters & cross-sectional areas
  • [NGVDISS-74] Endfeet handling
  • [NGVDISS-229] Spec update for neuroglial synapse parameters
• SONATA reports node_ids offsetting
• post-stdinit callback support in Node

Improvements

• Checks for non-negative config params
• Don't raise exception if replay file is empty

Version 2.5.3

Fixes

• Attach source netconns in additional populations and CoreNeuron [critical c/53194]
• Type field in StimulusInject to select the proper cell manager

Version 2.5.2

Apr. 20, 2021

Fixes

• Reset ShotNoise.stimCount for multi-cycle builds
• Enable getting target from hoc via TargetManager
• Initialization improvements. Always NEURON_INIT_MPI

Version 2.5.1

Improvements

• Summation reports support for CoreNeuron
• Prepend /scatter to out.dat after CoreNEURON simulation
• Local to global transformation in METype
• ShotNoise and RelativeShotNoise stimuli

Version 2.5.0

Mar. 26, 2021

New Features

• Support for Multi-Circuit
• Connection configurations override checks
• NGV Engine

Improvements

• reading src/dst population from edges meta
• Support for Sonata Edges with mvd3 nodes
• Detection of node file type: support for arbitrary mvd3

Version 2.4.0

Feb. 2, 2021

New features

• Read additional attributes from new emodel hoc template and pass to metype constructor
• New key SynDelayOverride in Connection block to modify synaptic delays
• New key SYNAPSES__init_depleted in Conditions block to initialize synapses in depleted state

Improvements

• Read CoreNeuron data version dynamically than hard coded number in case of more ranks than cells
• Full debug logging only for src-dst
• Fixes related to Engines
• Refactoring Node and Engine for multi-circuit
• Pass population ids to override_helper

Version 2.3.1

Jan. 29, 2021

Fixes

• Issue when launching CoreNEURON sim with more ranks than cells

Version 2.3.0

Dec. 22, 2020

New features

• Implement global options block in BlueConfig

Improvements

• Attach to src cell when not offset and CoreNeuron
• Save load balance data to folder sim_conf

Version 2.2.1

Dec. 10, 2020

New features

• Support for Section target reports

Improvements

• Completely drop hoc ParallelNetManager
• Refactoring cell distribution: explicit V5 and V6 cells, gid offset, unified finalize
• Refactoring Sim-Config: New config validation framework

Version 2.1.2

Nov. 27, 2020

New Features

• Support for MinisSingleVesicle BlueConfig option (BBPBGLIB-660)
• Added options for setting SpikeLocation, SpikeThreshold, temperature and initial voltage

Fixes

• Fixing call to write sim config
• Flush SONATA reports at the end of the simulation
• Documentation: launch notes
• Throw error when report tstart > tend

Improvements

• CellDistributor: Refactoring cell loading

Version 2.0.2

Oct. 28, 2020

Fixes

• Fix skipping synapse creation when weight is 0 (BBPBGLIB-673)
• Fix deadlock when an exception is thrown from NEURON (BBPBGLIB-678)
• Ensure data dir when skipping model build
• SONATA: Replay to work with multiple populations
• Logging colors only for terminal devices

Vesion 2.0.0

New Features

• Full delayed connection implementation mechanisms.
• SONATA: Computig PopulationIDs from Edge population names
• SONATA: Connection blocks to handle target populations
• Support for setting SecondOrder in BlueConfig

Improvements

• Improved delayed connections, setup before finalize
• New behavior of relative paths. Set CurrentDir

Fixes

• Fix spike with negative time (BBPBGLIB-367)
• CoreNeuron processes with 0-cells
• Single spike in SynapseReplay (BBPBGLIB-661)
• Fixing replay to work with multiple populations

Version 1.3.1

Aug. 26, 2020

Improvements

• Calcium scaling via new BlueConfig key "ExtracellularCalcium"
• Pass Baseseed to Coreneuron

Fixes

• GJ Offset calculation only for nrn
• Fix for nrn when sgids are not ascending

Version 1.2.1

July 27, 2020

New features

• Support for multipopulation edge files, for circuit and projections
• Support for SONATA reports
• Support for nodes "exc_mini_frequency" and "inh_mini_frequency"

Version 1.1.0

May 28, 2020

New features

• BBPBGLIB-618 Add Time Measurements featuring support for nested routines
• BBPBGLIB-555 Heuristic to auto select the Load Balance mode

Improvements

• Simplify cell loaders API/implementation using numpy exclusively

Bug fixes

• Delayed connections: Handle simultaneous events. Avoid last delayed connection from overriding previous ones (late binding issue)

Version 1.0.0

Apr 21, 2020

New features / Major changes

• Add xopen morphology generation and loading feature
• Reusing previously calculated LoadBalance
• Dropped Python 2.x support (simplified deps)

Improvements

• Refactoring of ConnectionManager wrt instantiation of SpontMinis and Replay
• Make SimConfig global singleton
• Refactoring CellDistributor

Version 0.9.0

Feb 27, 2020

New features

• New loader to support Sonata nodes
• Initial support for Sonata node populations, specified via the target pop:target_name
• Added CLI option --modelbuilding-steps to set the number of steps for the model building
• BBPBGLIB-567 Filter Instantiated projections

Improvements

• Refactoring replay for compat with save-restore and CoreNeuron
• Refactoring connection_manager for dedicated ConnectionSet structure

Version 0.8.1

Feb 20, 2020

Improvements

• Refactoring for ConnectionSet class
• Documentation

Bug fixes

• Cached Hoc values were not being updated
• Resume w CoreNeuron: dont init circuit

Version 0.8.0

Jan. 14, 2020

New features

• Allow selecting which phases to run with --build-model --simulate-model --output-path
• Will delete intermediate CoreNeuron files, unless --keep-build option is set
• Ability to load multiple mod libraries. NRNMECH_LIBRARY_PATH should point to a library containing at least the neurodamus aux mods. Libraries of cell mechanisms alone shall go into BGLIBPY_MOD_LIBRARY_PATH (multiple accepted)

Bug Fixes

• BBPBGLIB-554 Finalize connections only at init() time

Version 0.7.2

Dec. 19, 2019

Improvements

• Support loading of several mech lib (: separated)
• Fixed & cleanup options to detect build model

Version 0.7.1

Nov. 22, 2019

Improvements

• Adding option to initialize later
• Refactor for Single configure step, allowing for split-file conections

Version 0.7.0

Nov. 19, 2019

New Features

• Multi-Cycle model building
• src- dst- seed popuplation IDs
• New circuit paths (start.target and edges location)

Bug Fixes

• Spont minis was not being updated correctly (c/46614)

Improvements

• MPI auto-detection
• targets printCellCounts()
• Automatic project version & documentation

Version 0.6.0

Aug. 15, 2019

New Features

• Support to launch with CoreNeuron with Reports and Replay
• Support mixed projection file types
• Nice API for Step-by-step run
• Replay like in save-state, support for delay and shift

Bug Fixes

• MultiSplit fixed

Improvements

• SpontMiniRate independent of the Connection definition order
• General improvements after MG review
• Refactoring on connection.py
• Refactored LoadBalance
• Refactored neurodamus.prepare_run()
• Cell Readers spinned off cell distributor.
• PEP8 / doctrings...
• Better integration with SynapseTool
• Deployment improv for pip-install compat
• Documentation

Version 0.5.0

Nov. 3, 2018

Bug Fixes

• Instantiate synapses/GJs in reverse, mimicking HOC
• Always Instantiate ElectrodeManager
• More GJ fixes
• OSError lock err for MVD3 file

Improvements

• Detection of circuit file types
• Enabling other configFiles via --configFile=

Version 0.4.0

Oct. 1, 2018

New Features

• Support of SynapseTool for Syn2/SONATA

fixes

• GapJunctions
• Progressbar for streams

Version 0.3.0

Aug. 14, 2018

New Features

• Synapse Replay and Projections

Improvements

• connection_configure implemented in a fast hoc routine
• Pep8

Version 0.2.2

July 31, 2018

New Features

• Added init.py
• V6 circuit loading
• V6 circuit stim apply

Improvements

• Sync Hoc files with latest neurodamus master
• Better output for multi-cpu runs

Version 0.2.1

July 26, 2018

New Python API

• ConnectionManager
• GapJuntionsManager
• METype
• Enable/Disable connections

Improvements

• Replays using a new OrderedMap structure
• Cleaned and Refactored: Creation of .core subpackage
• Refactoring CellDistributor
• Remove mpi4y dependency

Version 0.1.0

June 5, 2018

New Features

• Initial version of Neurodamus Python
• Node.hoc API 100% in Python
• High-Level Neuron implementation
  • Neuron Bridge, Cell, Stimuli
  • Examples on how to implement Neuron full tutorials in a few lines