Netpyne

**New features**

- Added guiBlack and guiWhite themes, streamlined theming

- Updated iplots to avoid Bokeh deprecation

**New features**

- Added wrapper for distributed saving; can now simply replace 'sim.gatherData()' with 'sim.gatherDataFromNodes()'

- Added distributed saving/loading ability (save/load data by MPI node)

- Allowed to specify 'cellModel' and point neuron params in netParams.cellParams (not only in netParams.popParams)

- Added cellsVisualizationSpacingMultiplier property to netParams

- Improved Granger plot, renamed it plotGranger

- Added interactive Granger plot (iplotGranger)

- Implemented testing in GitHub Actions with pytest (thanks Daniel!)

- Improved sim.clearAll such that it works even before a sim is run

- Properly formatted all module docstrings

**Bug fixes**

- Fixed bug in TupleToStr function

- Fixed broken links in tutorials

- Bokeh update required changing options from None to 'auto'

**Bug fixes**

- Fixed gathering of dipoles when running on multiple cores (uncommented lines that had been commented for debugging)

**New features**

- Plot current source density (CSD) from local field potential (LFP) simulated data

- Additional customization of 3D shape plot: show voltage as color, change proportions, include axis labels

- Enable modifyConns based on properties of presynaptic neurons

- Replaced -np with -n so compatible for all commands: mpiexec/mpirun/srun

- Updated netrxd.py and network.py to include RxD's Parameter class, naming of States and Regions, and specification of Region geometries that do not require arguments like 'membrane' and 'inside'

- Improved recordTraces such that the cond 'gid' can accept a list of numbers as well as a single number

- Added a new tutorial going through use of NetPyNE with virtual environments and Jupyter notebooks

- Added cfg.use_fast_imem to enable recording membrane voltage via seg.i_membrane_

- Added swc import ability to importCell (and thus importCellParams)

- Batch now polls processes, prints their output and terminates them once completed

- Updated web documentation to explain importing SWC files and add Recording Configuration section

- Added link to Jupyter notebook tutorial and video to website front page

**Bug fixes**

- Made rate_b be positional instead of keyword argument in rxd multiCompartmentReaction

- Check if \_morphSegCoords exists in population before using

- Fixed bug to avoid recursive creating of synMechs when loading with cfg.oneSynPerNetcon=True

- Fixed an issue with running rxd code twice

- Wait until all subprocesses have ended before completing mpi_bulletin batches

- Fixed repeated rxd simulation issue for rates and reactions

- Fixed pointNeuron spikePattern 'sync' option

**New features**

- analysis.plotLFP can now be applied to external data

- Evolutionary and Optuna optimization can now read results from .pkl files

- Enabled recording of stimulus variables (e.g. SEClamp i)

- Added options in load func to avoid instantiating cells, conns, stims and/or rxd

- Analysis and plotting of rate vs current (f-I) curve for single cell tuning

- Recording and plotting of current dipoles in arbitrary subset of populations

- Added option to plot LFP spectrogram with log y-axis

- Added option to plot the log of connectivity in plotConn

- Enabled random distribution of multiple synapses with synsPerConn>1 and connRandomSecFromList=True

- Added lineWidth option to plot2Dnet (thanks Eric!)

- Updated Travis Continuous Integration to use NEURON 7.8.1 (from 7.6.2)

- Removed trailing white space from all Python files in the repository


**Bug fixes**

- Fixed bug when using index with recordTraces

- Fixed axes values in plotRxDConcentration and iplotRxDConcentration

- Added links to necessary mod files in the importing cell models tutorial

- Added aux_fun.inc to doc/source/code/mod as it's needed for some examples

- Blocked terminal output from Git when no repository is found (i.e. with pip install netpyne)

- Avoid adding section-based weightNorm values to point neurons (was affecting tut_import.py)

- Prevent error when loading pointCell params from json by converting Dict to dict

- Fixed bug in plotShape (thanks Eric!)

- Updated setup.py so PyPI website renders the README as markdown

- Fixed expected numSpikes in test of M1detailed example

- Merged GUI branch into development branch

- Fixed bug in iplotConn

- Fixed bug and coloring in iplotSpikeStats with different themes

**New features**

- Added optimization using Optuna (optuna.org)

- Simplified cellParams to use dict key as 'cellType' and make 'conds' optional

- Added netParams method addCellParamsTemplate() to create predefined cell templates

- Calculation of population avg rates now accepts multiple time intervals

- Optional index argument to record from synMech

- Added scale bar location option to plotTraces scalebar

- Added evolutionary optimization for cell

- Added support for reading pkl files in evol batches

- Added plotfI func to netpyne

- Added calculation of fI to gather.py

- Added module imports to netpyne import

- Added adaptive stochastic descent (ASD)

- Added ability to set theme and palette for iplots

- Added netParams method addCellParamsTemplate() to create predefined cell templates

- Added sizing-mode to iplots

- Added Bokeh to NetPyNE requirements

- Added theme for gui to analysis/utils, iplots can now use custom theme

- Added t variable to plotLFP output data

- Cleaned up plotRxD, added saving, added plot options, scalebar

- Added interactive plot: iplotRxDConcentration

- Added interactive plot: iplot2Dnet

- Added interactive plot: iplotRatePSD

- Added interactive plot: iplotSpikeStats

- Cleaned up iplotLFP and improved color-handling with themes


**Documentation improvements**

- Updated and tested online tutorials

- Changed all triple single-quoted docstrings to triple double-quoted

- Improved many docstrings

- Created a complete package index (http://netpyne.org/package_index.html) which is automatically generated from the human-readable docstrings in the codebase

- Documented the process to release a new version and automated the html building process

- Removed old unused Makefile for docs


**Bug fixes**

- Fixed bug importing cells (avoid reading __docstring__)

- Fixed bug when recording LFP with recordStep <1.0ms

- Fixed net_lfp.py example

- Fixed bug in plotSpikeStats

- Fixed bug in plotSpikeHist

- Fixed bugs in plotTraces scalebar

- Fixed travis test issues

- Fixed tut3 travis issue

- Fixed bug in spikes.py

- Fixed bug in plotRaster

- Fix minor bug in iplotRaster()

- Fixed problems with NeuroML