What’s new?

0.1

Changelog

• Add ability to simulate multiple trials in parallel using joblibs, by Mainak Jas in #44

• Rhythmic inputs can now be turned off by setting their conductance weights to 0 instead of setting their start times to exceed the simulation stop time, by Ryan Thorpe in #105

• Reader for parameter files, by Blake Caldwell in #80

• Add plotting of voltage at soma to inspect firing pattern of cells, by Mainak Jas in #86

• Add ability to simulate a single trial in parallel across cores using MPI, by Blake Caldwell in #79

• Modify plot_dipole() to accept both lists and individual instances of Dipole object, by Nick Tolley in #145

• Update plot_hist_input to plot_spikes_hist() which can plot histogram of spikes for any cell type, by Nick Tolley in #157

• Add function to compute mean spike rates with user specified calculation type, by Nick Tolley and Mainak Jas in #155

• Add ability to record somatic voltages from all cells, by Nick Tolley in #190

• Add ability to instantiate external feed event times of a network prior to building it, by Christopher Bailey in #191

• Add ability to record somatic currents from all cells, by Nick Tolley in #199

• Add option to turn off dipole postprocessing, by Carmen Kohl in #188

• Add ability to add tonic inputs to cell types with add_tonic_bias(), by Mainak Jas in #209

• Modify plot_spikes_raster() to display individual cells, by Nick Tolley in #231

• Add copy() method for cloning a Network instance, by Christopher Bailey in #221

• Add methods for creating input drives and biases to network: add_evoked_drive(), add_poisson_drive(), add_bursty_drive() and add_tonic_bias(), by Christopher Bailey in #221

• Add functions for plotting power spectral density (plot_psd()) and Morlet time-frequency representations (plot_tfr_morlet()), by Christopher Bailey in #264

• Add y-label units (nAm) to all visualisation functions involving dipole moments, by Christopher Bailey in #264

• Add Savitzky-Golay filtering method savgol_filter() to Dipole; copied from mne-python savgol_filter(), by Christopher Bailey in #264

Bug

• Fix missing autapses in network construction, by Mainak Jas in #50

• Fix rhythmic input feed, by Ryan Thorpe in #98

• Fix bug introduced into rhythmic input feed and add test, by Christopher Bailey in #102

• Fix bug in amplitude of delay (for connection between L2 Basket and Gaussian feed) being passed incorrectly, by Mainak Jas in #146

• Connections now cannot be removed by setting the weights to 0., by Mainak Jas and Ryan Thorpe in #162

• MPI and Joblib backends now apply jitter across multiple trials identically, by Ryan Thorpe in #171

• Fix bug in Poisson input where the first spike was being missed after the start time, by Mainak Jas in #204

• Fix bug in network to add empty spike when empty file is read in, by Samika Kanekar and Ryan Thorpe in #207

API

• Make a context manager for Network class, by Mainak Jas and Blake Caldwell in #86

• Create Spikes class, add write methods and read functions for Spikes and Dipole classes, by Ryan Thorpe in #96

• Only specify n_jobs when instantiating the JoblibBackend, by Blake Caldwell in #79

• Make a context manager for parallel backends (JoblibBackend, MPIBackend), by Blake Caldwell in #79

• Add average_dipoles() function, by Blake Caldwell in #156

• New API for defining external drives and biases to network. By default, a Network is created without drives, which are added using class methods. The argument add_drives_from_params controls this behaviour, by Christopher Bailey in #221

• Examples apply random state seeds that reproduce the output of HNN GUI documentation, by Christopher Bailey in #221

• Force conversion to nAm (from fAm) for output of simulate_dipole() regardless of postproc-argument, which now only controls parameter file-based smoothing and scaling, by Christopher Bailey in #264

People who contributed to this release (in alphabetical order):

• Blake Caldwell

• Christopher Bailey

• Carmen Kohl

• Mainak Jas

• Nick Tolley

• Ryan Thorpe

• Samika Kanekar

• Stephanie Jones