2022-02-21 • Build jb toc automatically
Contents
2022-02-21 • Build jb toc automatically¶
show_startup_log()
Running `C:\Users\lpxtf3\.ipython\profile_default\startup\startup.py`
Imported some stdlib names: `sys`, `re`, `Path`, etc. See `dir()` for full list.
Regen current contents¶
cur = """
- file: index
- part: Notebooks
chapters:
- file: nb/2022-02-21b__FENS_abstract
- file: nb/2022-02-21__image_window_test
- file: nb/2022-02-20__vanilla_julia_fixed_dt_solver
- file: nb/2022-02-07__N_to_1_simulation
- file: nb/2022-01-08__lognormal_firing_rates
- file: nb/2021-12-08__biology_vs_Izh_subhtr
- file: nb/2021-12-06__local_HH_dV_shape
- file: nb/2021-12-02__LIF_vs_Izh_subthreshold
- file: nb/2021-11-11__vary_both_inh_strength_and_proportion
- file: nb/2021-11-05__vary_syncond_ratio
- file: nb/2021-09-16__vary_E_vs_I
- file: nb/2021-07-30__inhibitory
- file: nb/2021-01-13__multiple_ROC
- file: nb/2021-01-06__ROC
- file: nb/2021-01-01__vary_params
- file: nb/2020-12-30__test_all_connections
- file: nb/2020-12-11__KS_test_exponential_distribution
- file: nb/2020-11-27__permutation_test
- file: nb/2020-10-23__Delete_around_spike
- file: nb/2020-09-18__Clip_spikes_before_STA
- file: nb/2020-09-10__STA_for_different_PSP_shapes
- file: nb/2020-07-29__STA
- file: nb/2020-07-27__Synaptic_conductances
- file: nb/2020-07-06__Single_neuron_sim
- part: Unpolished Notebooks
chapters:
- file: unpolished_intro
- file: nb/2022-02-18__scale_up_N_and_duration
- file: nb/2022-01-04__Hello_Julia
- file: nb/2021-11-18__prototype_new_sim
- file: nb/2021-11-18__constant_input_spikes
- file: nb/2021-12-08__cortical_HH_vs_Izh_dV_shape
- file: nb/2021-11-04__control_for_output_rate
- file: nb/2021-03-10__cond_prob
- file: nb/2021-01-13__conntest_in_codebase
- file: nb/2021-01-02__full_network_sim_tryout
- file: nb/2021-01-01__debug_parallel_calc_STA
- file: nb/2020-11-30__speedup__spike_indices
- file: nb/2020-11-30__speedup
- file: nb/2020-11-27__factor_out_STA
- file: nb/2020-11-16__analytical_PSP
- file: nb/2020-07-28__Storing_in_base_units
- file: nb/2020-07-05__Izhikevich_paper_accomp
"""
import yaml
yaml.safe_load(cur)
[{'file': 'index'},
{'part': 'Notebooks',
'chapters': [{'file': 'nb/2022-02-21b__FENS_abstract'},
{'file': 'nb/2022-02-21__image_window_test'},
{'file': 'nb/2022-02-20__vanilla_julia_fixed_dt_solver'},
{'file': 'nb/2022-02-07__N_to_1_simulation'},
{'file': 'nb/2022-01-08__lognormal_firing_rates'},
{'file': 'nb/2021-12-08__biology_vs_Izh_subhtr'},
{'file': 'nb/2021-12-06__local_HH_dV_shape'},
{'file': 'nb/2021-12-02__LIF_vs_Izh_subthreshold'},
{'file': 'nb/2021-11-11__vary_both_inh_strength_and_proportion'},
{'file': 'nb/2021-11-05__vary_syncond_ratio'},
{'file': 'nb/2021-09-16__vary_E_vs_I'},
{'file': 'nb/2021-07-30__inhibitory'},
{'file': 'nb/2021-01-13__multiple_ROC'},
{'file': 'nb/2021-01-06__ROC'},
{'file': 'nb/2021-01-01__vary_params'},
{'file': 'nb/2020-12-30__test_all_connections'},
{'file': 'nb/2020-12-11__KS_test_exponential_distribution'},
{'file': 'nb/2020-11-27__permutation_test'},
{'file': 'nb/2020-10-23__Delete_around_spike'},
{'file': 'nb/2020-09-18__Clip_spikes_before_STA'},
{'file': 'nb/2020-09-10__STA_for_different_PSP_shapes'},
{'file': 'nb/2020-07-29__STA'},
{'file': 'nb/2020-07-27__Synaptic_conductances'},
{'file': 'nb/2020-07-06__Single_neuron_sim'}]},
{'part': 'Unpolished Notebooks',
'chapters': [{'file': 'unpolished_intro'},
{'file': 'nb/2022-02-18__scale_up_N_and_duration'},
{'file': 'nb/2022-01-04__Hello_Julia'},
{'file': 'nb/2021-11-18__prototype_new_sim'},
{'file': 'nb/2021-11-18__constant_input_spikes'},
{'file': 'nb/2021-12-08__cortical_HH_vs_Izh_dV_shape'},
{'file': 'nb/2021-11-04__control_for_output_rate'},
{'file': 'nb/2021-03-10__cond_prob'},
{'file': 'nb/2021-01-13__conntest_in_codebase'},
{'file': 'nb/2021-01-02__full_network_sim_tryout'},
{'file': 'nb/2021-01-01__debug_parallel_calc_STA'},
{'file': 'nb/2020-11-30__speedup__spike_indices'},
{'file': 'nb/2020-11-30__speedup'},
{'file': 'nb/2020-11-27__factor_out_STA'},
{'file': 'nb/2020-11-16__analytical_PSP'},
{'file': 'nb/2020-07-28__Storing_in_base_units'},
{'file': 'nb/2020-07-05__Izhikevich_paper_accomp'}]}]
Polished nb names¶
polished_nb_names = (
"2022-02-21b__FENS_abstract",
"2022-02-21__image_window_test",
"2022-02-20__vanilla_julia_fixed_dt_solver",
"2022-02-07__N_to_1_simulation",
"2022-01-08__lognormal_firing_rates",
"2021-12-08__biology_vs_Izh_subhtr",
"2021-12-06__local_HH_dV_shape",
"2021-12-02__LIF_vs_Izh_subthreshold",
"2021-11-11__vary_both_inh_strength_and_proportion",
"2021-11-05__vary_syncond_ratio",
"2021-09-16__vary_E_vs_I",
"2021-07-30__inhibitory",
"2021-01-13__multiple_ROC",
"2021-01-06__ROC",
"2021-01-01__vary_params",
"2020-12-30__test_all_connections",
"2020-12-11__KS_test_exponential_distribution",
"2020-11-27__permutation_test",
"2020-10-23__Delete_around_spike",
"2020-09-18__Clip_spikes_before_STA",
"2020-09-10__STA_for_different_PSP_shapes",
"2020-07-29__STA",
"2020-07-27__Synaptic_conductances",
"2020-07-06__Single_neuron_sim",
)
Read nb dir¶
from pathlib import Path
all_nb = list(Path(".").glob("*.ipynb"))
all_nb
[WindowsPath('2020-07-05__Izhikevich_paper_accomp.ipynb'),
WindowsPath('2020-07-06__Single_neuron_sim.ipynb'),
WindowsPath('2020-07-27__Synaptic_conductances.ipynb'),
WindowsPath('2020-07-28__Storing_in_base_units.ipynb'),
WindowsPath('2020-07-29__STA.ipynb'),
WindowsPath('2020-09-10__STA_for_different_PSP_shapes.ipynb'),
WindowsPath('2020-09-18__Clip_spikes_before_STA.ipynb'),
WindowsPath('2020-10-23__Delete_around_spike.ipynb'),
WindowsPath('2020-11-16__analytical_PSP.ipynb'),
WindowsPath('2020-11-27__factor_out_STA.ipynb'),
WindowsPath('2020-11-27__permutation_test.ipynb'),
WindowsPath('2020-11-30__speedup.ipynb'),
WindowsPath('2020-11-30__speedup__spike_indices.ipynb'),
WindowsPath('2020-12-11__KS_test_exponential_distribution.ipynb'),
WindowsPath('2020-12-30__test_all_connections.ipynb'),
WindowsPath('2021-01-01__debug_parallel_calc_STA.ipynb'),
WindowsPath('2021-01-01__vary_params.ipynb'),
WindowsPath('2021-01-02__full_network_sim_tryout.ipynb'),
WindowsPath('2021-01-06__ROC.ipynb'),
WindowsPath('2021-01-13__conntest_in_codebase.ipynb'),
WindowsPath('2021-01-13__multiple_ROC.ipynb'),
WindowsPath('2021-02-22__spikes_only_conntests.ipynb'),
WindowsPath('2021-03-10__cond_prob.ipynb'),
WindowsPath('2021-05-25__PGR_conf.ipynb'),
WindowsPath('2021-07-30__inhibitory.ipynb'),
WindowsPath('2021-09-16__vary_E_vs_I.ipynb'),
WindowsPath('2021-11-04__control_for_output_rate.ipynb'),
WindowsPath('2021-11-05__vary_syncond_ratio.ipynb'),
WindowsPath('2021-11-11__vary_both_inh_strength_and_proportion.ipynb'),
WindowsPath('2021-11-18__constant_input_spikes.ipynb'),
WindowsPath('2021-11-18__prototype_new_sim.ipynb'),
WindowsPath('2021-12-02__LIF_vs_Izh_subthreshold.ipynb'),
WindowsPath('2021-12-06__local_HH_dV_shape.ipynb'),
WindowsPath('2021-12-08__biology_vs_Izh_subhtr.ipynb'),
WindowsPath('2021-12-08__cortical_HH_vs_Izh_dV_shape.ipynb'),
WindowsPath('2022-01-04__Hello_Julia.ipynb'),
WindowsPath('2022-01-08__lognormal_firing_rates.ipynb'),
WindowsPath('2022-02-07__N_to_1_simulation.ipynb'),
WindowsPath('2022-02-18__scale_up_N_and_duration.ipynb'),
WindowsPath('2022-02-20__vanilla_julia_fixed_dt_solver.ipynb'),
WindowsPath('2022-02-21b__FENS_abstract.ipynb'),
WindowsPath('2022-02-21__autobuild_jb_toc.ipynb'),
WindowsPath('2022-02-21__image_window_test.ipynb'),
WindowsPath('2022-03-02__factor_out_conntest_eval.ipynb')]
Get all nb not in polished list¶
We can ignore jupytext pairs (.jl), as only .ipynb’s are rendered.
all_nb[0].name
'2020-07-05__Izhikevich_paper_accomp.ipynb'
polished_nb = [Path(name + ".ipynb") for name in polished_nb_names]
polished_nb
[WindowsPath('2022-02-21b__FENS_abstract.ipynb'),
WindowsPath('2022-02-21__image_window_test.ipynb'),
WindowsPath('2022-02-20__vanilla_julia_fixed_dt_solver.ipynb'),
WindowsPath('2022-02-07__N_to_1_simulation.ipynb'),
WindowsPath('2022-01-08__lognormal_firing_rates.ipynb'),
WindowsPath('2021-12-08__biology_vs_Izh_subhtr.ipynb'),
WindowsPath('2021-12-06__local_HH_dV_shape.ipynb'),
WindowsPath('2021-12-02__LIF_vs_Izh_subthreshold.ipynb'),
WindowsPath('2021-11-11__vary_both_inh_strength_and_proportion.ipynb'),
WindowsPath('2021-11-05__vary_syncond_ratio.ipynb'),
WindowsPath('2021-09-16__vary_E_vs_I.ipynb'),
WindowsPath('2021-07-30__inhibitory.ipynb'),
WindowsPath('2021-01-13__multiple_ROC.ipynb'),
WindowsPath('2021-01-06__ROC.ipynb'),
WindowsPath('2021-01-01__vary_params.ipynb'),
WindowsPath('2020-12-30__test_all_connections.ipynb'),
WindowsPath('2020-12-11__KS_test_exponential_distribution.ipynb'),
WindowsPath('2020-11-27__permutation_test.ipynb'),
WindowsPath('2020-10-23__Delete_around_spike.ipynb'),
WindowsPath('2020-09-18__Clip_spikes_before_STA.ipynb'),
WindowsPath('2020-09-10__STA_for_different_PSP_shapes.ipynb'),
WindowsPath('2020-07-29__STA.ipynb'),
WindowsPath('2020-07-27__Synaptic_conductances.ipynb'),
WindowsPath('2020-07-06__Single_neuron_sim.ipynb')]
get_ipython().profile_dir.startup_dir
'C:\\Users\\lpxtf3\\.ipython\\profile_default\\startup'