Netpyne

- Access to nested dictionaries via dot notation (secs.soma.geom) using new inherited classes Dict() and ODict() (issue 123)

- 'hSection' replaced with 'hSec'

- Added sim.popAvgRates() to calculate and optionally print population avg rates

- Functions to modify cells, conns or stims also update sim.allCells (issue 59)

- Fixed bug so can modify funcs now accept lists of strings (issue 59)

- Fixed bug when recording traces of relative cell indices of populations across multiple nodes

- Functions to modify parameters of cells, conns and stims in an instantiated network (issue 59)

- Added label of param rule used to create cells, conns and stims, so can modify later (issue 59)

- Ordered sim.net.allCells by gid

- Option to save figures with same name as data

- Added support for VClamp list params (issue 32)

- Fixed bug when creating pops consisiting of lists of cells

- Fixed bug that gave error since trying to import removed module default.py

- Easier and more consistent format for high-level specifications (issue 103):

- replaced default.py with specs.py which defines classes NetParams and SimConfig

- netParams and simConfig are now objects of class NetParams and SimConfig, respectively

- Can use object methods to add params, eg. netParams.addPopParams(label, params)

- All structures within netParams and simConfig are now OrderedDicts so can be referenced by label/key

- If no label is assigned, then an increasing number is automatically used as label

- Split netParams.stimParams into netParams.stimSourceParams and netParams.stimTargetParams (both OrderedDicts)

- Simplified/clarified keys: 'conditions' -> 'conds', 'sections' -> 'secs', 'preTags' -> 'preConds', 'postTags' -> 'postConds'

- Added netParams.importCellParams() to simplify

- Added sim wrappers and modified names of existing ones to make consistent

- Selectively save data to file: netParams, net, simConfig and/or simData (issue 30)

- Added functions to load netParams, net, simConfig and/or simData from file (issue 30)

- Added 'rerun' option to plotTraces()

- Added function to get cell object by gid, sim.cellByGid(gid)

- Fixed bug that was slowing down STDP by creating new h.Section() -- now uses existing.

- Fixed bug so vinit gets set for all segments in a section.

- Fixed bug related to readArgs() when running from IPYnotebook.

- Fixed bug related to plasticity in cells with V not in section (eg. Izhi2007a)

- Added option 'dataSaveInclude' to select what data to save to file (issue 30)

- Added sim.net.allPops which contains all cellGids of each when running on >1 nodes (issue 30)

- Connectivity matrix can now be grouped by numeric tags in intervals (eg. cortical depth y in 50 um intervals) (issue 92)

- Added support for all stims (VClamp, SEClamp, AlphaSynapse, etc) and can specify any of the stim params (amp, dur, delay,etc) as a function (eg. 'uniform(a,b)' or '2*post_ynorm') (issue 32)

- Fixed bugs so plotRaster() is identical when running on >1 nodes, and is ordered by gid correctly

- Fixed bug so can have multiple plot function calls even when one of them is False

- Modified format of simConfig analysis options to make it equivalent to calling analysis functions (issue 69)

- Improved plotRaster() function to add customizable options (select cells, time range, order, overlay histogram, and others) (issue 39)

- Improved plotTraces() function to add customizable options (select cells, time range, arrage by cell or trace, and others) (issue 39)

- Improved plot2Dnet() function to add customizable options (select cells, show connections, and others) (issue 39)

- Added spikeHist() function to plot spike histogram with customizable options (select cells, time range, bin size, and others) (issue 63)

- Added plotConn() function to plot spike histogram with multiple customizable options (select cells, feature, order, and others) (issue 39)

- Added option to save figure, save figure data, specify figure size, and show figure to all analysis/plotting functions (issue 39)

- Fixed bug when generating function-based random probability values -- made random stream independent

- Fixed bug when generating density-based random cell locations -- made random stream independent (issue 93)