v1.15.3

Minor bug fixes including:

• shade kwarg added to plot for easier plotting of large numbers of neurons
• Motion model update to prevent rat escaping internal boxes (an edge case I'd never thought to consider but was brought to my attention by @romanpogodin)
• Better commenting of speed params in 2D
• Vector cell coloring bug

What's Changed

• Added shade_kwargs to utils.mountain_plot(). by @colleenjg in #122
• Resetting the colors of vector cells bugfix by @Alxec in #124
• Speed mean and std in 2D by @colleenjg in #126

Full Changelog: v1.15.2...v1.15.3

v1.15.2

@niksirbi fixed a bug causing the documentation website to fail. This has been patched.
@colleenjg changed how figures are saved so the folder does YYY_MM_DD
@colleenjg changed how BVCs are scaled with their max_fr

What's Changed

• Make save folders year first by default. by @colleenjg in #117
• Changed how firingrate is scaled to maximum for BVCs. by @colleenjg in #118
• Fix links in documentation build by @niksirbi in #119

New Contributors

• @niksirbi made their first contribution in #119

Full Changelog: v1.15.1...v1.15.2

v1.15.1

Just cleans up some API stuff for the SubAgent class introduced in version v1.15.0

v1.15.0

SubAgent contrib and minor QOL upgrades

This release adds save_fig() kwargs which aer passed directly to matplotlib.save_figure function so you can modify how figures are saved.

Also adds SubAgent class in the controls. SubAgents take as input, and are "subservient" to, another Agent (the LeadAgent). The key thing idea is that the SubAgent may have an update() function which relies heavily on the state of the LeadAgent. Examples included are:

• DumbAgent a noisy version of LeadAgent
• ThetaSequenceAgent theta sweeps around the LeadAgents position
• ReplayAgent occasional short replay events

The API is as follows

Env = Environment()
Ag = Agent(Env) # the lead agent
DumbAg = DumbAgent(LeadAgent=Ag, params = {'drift_distance':0.1})

while Ag.t < 60: 
    Ag.update()
    DumbAg.update()

DumbAg.animate_trajectory() then returns something like:

trajectory_1317.mp4

Full Changelog: v1.14.1...v1.15.0

v1.14.1

Minor interpolation bug fix as pointed out by #114. Also changed save_to_history() from using list(array) to array.tolist()

v1.14.0

numpy-2.0.0 compatibility

No substantial changes, I just fixed a few bugs to make compatible with numpy>=2.0.0

v1.13.0

Grids cell

• Grid cells work in 1D
• Grid cells have a width_ratio parameter which sets the ration of the width of the receptive field to the grid scale. It mist be between 0 (very sharp grid fields) and 1 (very diffuse grid fields) and only works for the rectified_cosines models.

• Minor api change (warning thrown, will not break) three_shifted_cosines --> shifted_cosines
• Default grid cells have been changed to 30 grid cells in three increasingly slightly rotated modules.

• Grid cell documentation on the readme has been improved

Plotting:

• Plotting the rate map of a single neuron in 1D can now be optimised using optimise_plot_for_single_neuron (without this it just does a mountain plot with a single line, which isn't ideal.

numpy pinned to versions <2.0.0

This will be unpinned as a soon as important associated packages (matplotlib, scipy etc.) support 2.0.0.

v1.12.6

BVC scaling bug fix

Thanks @colleenjg for minor bug fix relating to BVC firing rate scaling (see PR #109 and issue #108)

v1.12.5

Teeny tiny bug fixes....

Full Changelog: v1.12.3...v1.12.5

v1.12.3

Bug fix to maintain compatibility with python<=3.8.

We had been using list[str] (works in python>=3.9 only) and so have reverted back to from typing import List then List[str]. This fixes issue #105