Progress: Clean-ups.

Documentation.org

 #+TITLE: Documentation
 
 * NOTE
-This code documentation will be updated throughout the coming weeks (July 2020).
-
 ** WAIT Improve project structure :noexport:crypt:
 -----BEGIN PGP MESSAGE-----
 
@@ -643,7 +641,7 @@ filepath = Plotter.plot_density(stan_results,
 #+END_SRC
 
 #+NAME: c1_stan_ppc
-#+begin_src python :exports code :results file :tangle ./Scripts/c1_stan_ppc.py :noweb yes :return filepath
+#+begin_src python :exports none :results file :tangle ./Scripts/c1_stan_ppc.py :noweb yes :return filepath
 import numpy as np
 <<paper_plotting_header>>
 import arviz as az
@@ -756,7 +754,7 @@ The code blocks in this section represent the Stan models with increasing comple
 - =sindyc_stan_code_1234.stan= :: Stan model with active terms 1, 2, 3 and 4.
 
 #+NAME: sindyc_stan_code_12
-#+begin_src stan :exports code :results none :tangle ./Scripts/sindyc_stan_code_12.stan
+#+begin_src stan :exports none :results none :tangle ./Scripts/sindyc_stan_code_12.stan
 functions {
 real[] dy_dt(real t, real[] y, real[] xi, real[] params, int[] ncupoly) {
   vector[ncupoly[1]] poly;
@@ -1337,10 +1335,12 @@ generated quantities {
  #+end_src
 
 * TODO General code blocks
-** Header :noexport:
+** Header
+
+This code block provides defaults to all other code blocks.
 
 #+NAME: paper_simulation_header
-#+begin_src python
+#+begin_src python :results none :exports none
 from collections import OrderedDict
 import numpy as np
 import pandas as pd
@@ -1388,7 +1388,7 @@ def read_from_disc(filename="save.pkl"):
 
 ** Modeling
 
-*** Prosumer dynamics
+*** TODO Prosumer dynamics
 
 Common prosumer response dynamics.
 
@@ -1494,10 +1494,10 @@ class Prosumer:
 
 *** TODO SINDyc identification
 
-
+Identification routines.
 
 #+NAME: code_identification
-#+begin_src python
+#+begin_src python :exports none :results none
 class Identification:
     def __init__(self, data, **kwargs):
         """
@@ -1573,10 +1573,15 @@ class Identification:
 
 #+end_src
 
+#+RESULTS: code_identification
+: None
+
 *** TODO Stan identification
 
+Stan related identification routines.
+
 #+NAME: code_stan_fitModel
-#+begin_src python :results none :exports code
+#+begin_src python :results none :exports none
 import pystan
 
 
@@ -1968,12 +1973,10 @@ y_init_rep[1] = normal_rng(z_init[1], sigma[1]);
 
 *** TODO Signal generator
 
-Signal generation:
-
-- ...
+Signal generation routines.
 
 #+NAME: code_signal_generator
-#+begin_src python
+#+begin_src python :results none :exports none
 class SignalGenerator:
     def __init__(self, random=False, filter=None, **kwargs):
         """
@@ -2083,12 +2086,10 @@ class SignalGenerator:
 
 *** Evaluation
 
-Model performance evaluation routines:
-
-- ...
+Model performance evaluation routines.
 
 #+NAME: code_evaluate_fit
-#+begin_src python :exports code :results none
+#+begin_src python :exports none :results none
 def evaluate(systraj, modeltraj, method='nrmse', n=None, t=5):
     """Evaluate the model trajectory `modeltraj` against the system
     trajectory `systraj` using one of the following evaluation metrics:..
@@ -2183,10 +2184,10 @@ def evaluate(systraj, modeltraj, method='nrmse', n=None, t=5):
 
 ** Simulation
 
-A common simulation header:
+A common simulation header.
 
 #+NAME: paper_simulation
-#+begin_src python :noweb strip-export :exports code
+#+begin_src python :noweb strip-export :exports none
 <<paper_simulation_header>>
 <<code_signal_generator>>
 <<code_identification>>
@@ -2200,12 +2201,10 @@ simulator = Simulator(simspec, mp)  # Initialize simulation
 
 *** TODO System simulation
 
-General system simulation routines:
-
-- ...
+General system simulation routines.
 
 #+NAME: code_system_simulator
-#+begin_src python
+#+begin_src python :exports none :results none
 class SystemSimulator:
 
     def __init__(self, Tsim, D=None, **kwargs):
@@ -2554,9 +2553,7 @@ class SystemSimulator:
 
 *** TODO Simulator class
 
-SINDyc system simulation routines:
-
-- ...
+SINDyc system simulation routines.
 
 #+NAME: paper_simulation_class
 #+begin_src python :noweb strip-export :exports none
@@ -3541,7 +3538,7 @@ class Simulator(SystemSimulator):
 
 #+end_src
 
-** WAIT Plotting
+** Plotting
 
 Common plotting routines: