Annotate purpose of code files #10
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We have a sizeable number of code files for generating intermediate outcomes. There is no documentation or defined entrypoint. Let's annotate what they do
> ls -1R utilsutils:
analyse_model.pyscript that calls a plotting function, USED INreaction_times_func.pyanalyse_nest.pypython code USED INanalyse_model.py,model_fig_single.py,simulate_experiment.pyanalyses.pylooks like a script that does a lot. It does interactive plotting, turning that off needs manual edit of the script. USED INdata_fig.pycolors.pypython code; defines some colors USED INnetwork_schematic.pycv_bias.pyUSED INanalyses.py,model_fig_single.pydata_fig.pydefault.pyUSED INNEST_Simulation.py,analyse_model.py,analyse_nest.py,model_fig_single.py,reservoir.py,sim_nest.py,simulate_experiment.pyexperimental_analysis_funcs.pyUSED INreaction_times_func.pyexperiment.pyUSED INsimulate_experiment.pygamma_generator.pyUSED INcv_bias.pygeneral_func.pyUSED IN many placesglobal_params.pyUSED IN many placesjoe_and_lili.pyUSED INanalyses.py,data_fig.py,experimental_analysis_funcs.py,reaction_times_func.pymodel_fig_single.pyNEST_Simulation.pynetwork_schematic.pyscript; interactive plottingorganiser.pylibrary; main function only runs tests USED IN many placesplotting_functions.pylibrary; main function only does some kind of demo USED INdata_fig.py,model_fig_single.pyreaction_times_func.pyreservoir.pysim_nest.pyUSED INanalyse_model.py,model_fig_single.py,simulate_experiment.pysimulate_experiment.pyUSED INanalyse_model.pyspiketools.py,Cspiketools.c,Cspiketools.pyxUSED IN manyplacesCode with evidence that it is not actually needed
analyses_to_remove.pya lot of similarity withanalyses.py-- the name suffix seems to suggest that this is NOT NEEDEDcv_bias_to_remove.pysuffix suggests NOTNEEDEDdata_fig_to_remove.pysuffix suggests NOTNEEDEDgamma_generator_to_remove.pysuffix suggests NOTNEEDEDNEST_Simulation_to_remove.pysuffix suggests NOTNEEDEDreservoir_to_remove.pysuffix suggests NOTNEEDEDsimulation_analysis_funcs_to_remove.pysuffix suggests NOTNEEDEDutils/BiNet/this could be an (external) utility package. Any import of this package is commented out, though. So likely this is Looks NOTNEEDED. Only comment saysutils/Defaults/some kind of python-based parameter files. Only used inutils/Helper(may also be obsolete, see there). Looks NOTNEEDED. comment saysutils/Helperany import of this package outside the package is disabled. Looks NOTNEEDEDI think the Code you identified as not needed is actually not needed. utils/Helper and utils/Defaults are alternative implementations with NEST3 for the sim_nest.py and default.py.
utils/Binet is likely not used anymore. I think it was used in an early version.
Furthermore, NEST_Simulation.py and reservoir.py are also not used in the current version to my knowledge.
To generate the results, functions from analyses.py, analyse_model.py or functions which rely on sim_nest.py are called by the corresponding figX.py in fig_codes.