Annotate purpose of code files

[mih]

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 utils utils:

• [ ] analyse_model.py script that calls a plotting function, USED IN reaction_times_func.py
• [ ] analyse_nest.py python code USED IN analyse_model.py, model_fig_single.py, simulate_experiment.py
• [ ] analyses.py looks like a script that does a lot. It does interactive plotting, turning that off needs manual edit of the script. USED IN data_fig.py
• [ ] colors.py python code; defines some colors USED IN network_schematic.py
• [ ] cv_bias.py USED IN analyses.py, model_fig_single.py
• [ ] data_fig.py
• [ ] default.py USED IN NEST_Simulation.py, analyse_model.py, analyse_nest.py, model_fig_single.py, reservoir.py, sim_nest.py, simulate_experiment.py
• [ ] experimental_analysis_funcs.py USED IN reaction_times_func.py
• [ ] experiment.py USED IN simulate_experiment.py
• [ ] gamma_generator.py USED IN cv_bias.py
• [ ] general_func.py USED IN many places
• [ ] global_params.py USED IN many places
• [ ] joe_and_lili.py USED IN analyses.py, data_fig.py, experimental_analysis_funcs.py, reaction_times_func.py
• [ ] model_fig_single.py
• [ ] NEST_Simulation.py
• [ ] network_schematic.py script; interactive plotting
• [ ] organiser.py library; main function only runs tests USED IN many places
• [ ] plotting_functions.py library; main function only does some kind of demo USED IN data_fig.py, model_fig_single.py
• [ ] reaction_times_func.py
• [ ] reservoir.py
• [ ] sim_nest.py USED IN analyse_model.py, model_fig_single.py, simulate_experiment.py
• [ ] simulate_experiment.py USED IN analyse_model.py
• [ ] spiketools.py, Cspiketools.c, Cspiketools.pyx USED IN manyplaces

Code with evidence that it is not actually needed

• [ ] analyses_to_remove.py a lot of similarity with analyses.py -- the name suffix seems to suggest that this is NOT NEEDED
• [ ] cv_bias_to_remove.py suffix suggests NOTNEEDED
• [ ] data_fig_to_remove.py suffix suggests NOTNEEDED
• [ ] gamma_generator_to_remove.py suffix suggests NOTNEEDED
• [ ] NEST_Simulation_to_remove.py suffix suggests NOTNEEDED
• [ ] reservoir_to_remove.py suffix suggests NOTNEEDED
• [ ] simulation_analysis_funcs_to_remove.py suffix suggests NOTNEEDED
• [ ] utils/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 says

  a package for simulating binary balanced networks as described in e.g. VanVreeswijk 1998 or Renart 2010

• [ ] utils/Defaults/ some kind of python-based parameter files. Only used in utils/Helper (may also be obsolete, see there). Looks NOTNEEDED. comment says

  GIF-Parameters as similar as possible to lif model

• [ ] utils/Helper any import of this package outside the package is disabled. Looks NOTNEEDED

[schmitfe]

I 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.

[schmitfe]

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.