Remove bug workaround in tutorials #16
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kjohnsen
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kjohnsen
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* Update t_ms and interval_ms * updates t in other files * updated t * changed more _ms * added import * addes imports * fixed base.py and made changes to lfp - still failing 10 cases * Created jupyteer notebook for calculating ratios * added ratio into opsin library and added 2p action spectra into spectrum variables for all opsins * progress on all_optical fig * improve action spectrum extrapolation * start Newman 15 with alternate opsins * update Overview doc * finish newman15 validation w/ alternate opsins * Update paper plot style * style_plots_for_paper docstring * change Jupyter to Python for linguist * change OGB-1 name * add warning to scope when sensor not injected * add showcase to docs * implement LIOP reset in _base_reset * add showcase doc to index * add _base_reset to sim.reset * fresh run through of all-optical-fig notebook * add README to notebooks, env info to all_optical_fig.ipynb * bump to v0.15.0 * remove images [skip ci] * untrack images * more organizing notebook images * move Sridharan fig2 * use Brian units everywhere * reorganize ioproc tests * add firing_rate_estimate and pi_ctrl methods, revise PI_Ctrl notebook * ax ioproc folder * ax ProcessingBlock * upgrade nptyping, make sim.remove() private * fix more unit problems * get overview working * get tutorials working * use explicit units on Light * add units to SimpleOpsin gain * extend font stack * fix spike count problem * scope to_neo * 2p light to_neo * fix spiking test fail * Use utilities.rng * units on Light.values and other small tweaks * add version note to newman15 notebooks * add version note to opto val notebook * fix electrodes tutorial * fix opto tutorial * fix multi_opto notebook, add range to plot_spectra * fix on_off_ctrl notebook * update PI ctrl notebook * fix all_optical tutorial * fix video viz tutorial * fix Neo tutorial * fix advanced LFP notebook * rename firing_rate_estimate to exp_firing_rate_estimate * fix global set_seed * progress on lqr tutorial, before cutting adaptive control * revamp ldsCtrlEst tutorial * support numpy >= 2.0 * remove bug workaround (closes Remove bug workaround in tutorials #16) * fix light.to_neo * replace nptyping with jaxtyping * remove imported members from ioproc docs * mark lfp tests as slow * polish tutorial notebooks * tweak docstrings * add LatencyIOProcessor to base cleo import * clean up imports * fix lqr notebook, fresh rerun of all * polish video tutorial, exit if no ffmpeg * skip execution of video write cell * tweak overview docs, increase test cell timeout * simplify 4-state opsin model * eliminate warnings * rerun opto tutorial, increase timestep --------- Co-authored-by: Arnav Tripathi <atripathi83@gatech.edu>
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A bug between matplotlib 3.5.2 and Brian breaks some plotting. I used the workaround (converting VariableView to array via
mon.i[:]but this should be removed when the bug is fixed to teach users the simplest syntax possible.This is in the tutorials: two places in on_off_ctrl, two in PI_ctrl, and once in optogenetics
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