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Fixed bug and typos in Ch_advanced_spikes_input notebook
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beaherrera committed Oct 24, 2024
1 parent 5160fd4 commit 93de306
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3 changes: 3 additions & 0 deletions .gitignore
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.cache/
.tox
**/*.DS_Store
**/components/mechanisms/x86_64/
**/components/mechanisms/arm64/
**/*.nwb
build/
dist/
docs/autodocs/source/bmtk/
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123,225 changes: 123,225 additions & 0 deletions docs/tutorial/03_opt_advanced_spiking_inputs/ecephys_cache_dir/channels.csv

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