Ratinabox

BVC scaling bug fix

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

Teeny tiny bug fixes....

**Full Changelog**: https://github.com/RatInABox-Lab/RatInABox/compare/v1.12.3...v1.12.5

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

Bug fixes and very minor changes from 1.12.1

Faster animations and bug fixes

* New `Agent._history_arrays` dataframe. This is identical to `Agent.history` except for two things (same for `Neurons` too):
* It is dictionary of arrays, not lists.
* It should only be accessed via its getter-function `_history_arrays = self.get_history_arrays()`
For now this API is intended to be mostly internal. We don't recommend users use this and instead should stuck to using `self.history` as before. But it speeds up animation internally a lot because it _checks_ a cache to see if the list-->array conversion has been done recently and only repeats it if it hasn't.
* Plotting rate maps via the `history` method now shows the regions where the Agent never went as grey rather than black (i.e. zero firing rate). This is more realistic, shows the data more honestly and closer to how experimentalists do it (i.e. by shooting spikes and dividing by position occupancy).
* Additionally users can specify the discretisation of the rate mat smoothing

PlaceCells.plot_rate_map(method="history", bin_size=0.06) defaults of 0.04, i.e. 4 cm

* Bug fixes relating to 104 and some other minor stuff I hadn't spotted in 1.12.

**Full Changelog**: https://github.com/RatInABox-Lab/RatInABox/compare/1.12.0...v1.12.1

Main charges include:

* Significantly modularised `Agent.update()` function. It is now more readable. This should be fully backwards compatible for conventional users of RiaB. For power users a few internal variables were renamed e.g. `save_velocity`-->`measured_velocity` but really very few. It also accepts (but doesn't recommend) users just _forcing_ the next position of the `Agent` via
python
Agent.update(forced_next_position = <next_pos>)

This should be fully backwards compatible for conventional users of RiaB. For power users a few internal variables were renamed e.g. `save_velocity`-->`measured_velocity` but really very few.
* Small bug fixes for colleenjg to do with warning when params['n']` is incompatible with the specific class.
* Bug fix from gsivori to make position sampling acknowledge and account for the existence of holes in the Environment more naturally than was done before.
* Minor changes to some plotting functions. More params have been moved from `args` to `kwargs` to clean up the doctoring and some (previously fixed) constants have been exposed as via letting `kwargs` define them. This both simplifies and improves plotting.
*
What's Changed
* Position sampling in Environments with holes. by gsivori in https://github.com/RatInABox-Lab/RatInABox/pull/100
* Small fixes and new warning for Neurons classes. by colleenjg in https://github.com/RatInABox-Lab/RatInABox/pull/101
* Fixes spurious warning raised when initializing VectorCells objects. by colleenjg in https://github.com/RatInABox-Lab/RatInABox/pull/103
* For spike rasters, or rate maps plotted via the `'history'` method there is a hidden option (via a `kwarg`) to set a _different_ `Agent` from which you draw position data from. In case, say, you want to plot the spikes from `Neurons1` against the positions of `Agent2`.

New Contributors
* gsivori made their first contribution in https://github.com/RatInABox-Lab/RatInABox/pull/100

**Full Changelog**: https://github.com/RatInABox-Lab/RatInABox/compare/v1.11.4...v1.12.0