Netpyne

**New features**

- Introducing `batchtools` subpackage for parameters exploration and optimization

- Added progress-bar indicating network creation progress. Toggle the progress bar with cfg.progressBar

- cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be overriden in individual conn rule

- Added ability to use `sec`, `loc`, `preSec` and `preLoc` from list in connList-type connParams

- Updated tests.examples.utils to allow for dynamic pathing

- Dropped python2 support

**Bug fixes**

- Better handling of exceptions in `importCellParams()` (incl. `h.load_file()` - issue 782)

- Pandas deprecated parameter fix

- Fixed pointer id overflow on MPI (e.g. for gap junctions)

- preSec and preLoc are no longer lost for inverse pointer connection

- Fixed crash due to use of matplotlib.TextArea deprecated param (credit: Christian O'Reilly)

- syncLines in rasterPlot restored

- Fixed a bug in `gatherDataFromFiles()` where cellGids for node 0 were lost

- Fixed generating rhythmic spiking pattern with 'uniform' option

- Fixed misleading console output when cfg.recordStims is On

- The colors in CSD plots are now properly aligned vertically with the CSD time-series overlays (credit: Sam Neymotin)

- Update mkdir to makedirs (credit: Jacob Sprouse)

**New features**

- Raster plot colored by phase

- Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster

- API for loading .mod files selectively

- Ability to specify custom executor to run batch with (defaults to `sh`)

**Bug fixes**

- Fixed loading point cell params from legacy models (issue 607)

- Fix voltage movie tutorial

- Fix to automatically include netstims in the sim.allSimData object when plotRaster 'include' selects 'all'

- Fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)

- Fix of `plotRaster` pops coloring if ordered not by gid

- Made cells diversity work with popParams based on `cellsList` and `gridSpacing`

- Fixed handling of output of `sim.create()` - was wrong order (credit: Kate Doxey)

- Fixed undeclared var `dpi` in `plotShape()`

- Fixes in batch utils

- Added some missing math functions to use with 'Functions as string' functionality

- Switch file copying method to shutil to be compatible over all operating systems (credit: Henrik Podeus)

**New features**

- Time series and PSD plots for current source density (CSD)

- Added colorbar to CSD plot

- Support for Sun Grid Engine HPC

- Extended sim.gatherData() with more optional arguments for flexibility

- Specify linear/log scale in `plotRatePSD()`

- Print more info about exceptions in plotting functions

- Check RxD specification for potential syntax issues

- Prevent zero population size in scaled-down models

- Better messages for validation errors

**Bug fixes**

- Fixed errors in plotting with sim.cfg.gatherOnlySimData=True

- Support saving and loading data in .mat and .hdf5 formats

- Multiple fixes in `plotRatePSD()` - popColors, fft, minFreq

- Fixed sync lines in `plotRaster()`

- Fixed performance issue in `plotConn()` with `groupBy='pop'` (default)

- Fixed `recordTraces` to not require more presicion than segment size (for stim and synMech)

**Bug fixes**

- Unpin matplotlib version (params copying issue fixed)

**New features**

- Added env variable to define head model placement

**New features**

- Added 'linewidth' as argument of plotting.plotSpikeHist()

- More detailed validation of netParams

- Save and load model in native NetPyNE format

- Converted most of examples to new NetPyNE model structure

- Complex stimulation ('rhythmic', 'evoked', 'poisson' and 'gauss') for VecStim created as pointCell (as a population rule)

- Codebase brought into compliance with PEP8 conventions

- Updates in NeuroML examples and tests

**Bug fixes**

- fixed handling filenames with multiple dots in `MetaFigure.saveFig()`

- Fixed readCmdLimeArgs() default arguments for backward-compatibility

- Cleaned up example models to drop some legacy/irrelevant params

- RxD module: Parameters defined before reactions + names given by default when missing (by the key)

- Analysis: try ... except call in plotDipole

- Save hObj of gap junction to connParams

- Removed duplicated or unused code from gridSearch()

- Fixes in batch utilities to make OS-agnostic