Moved TODOs to Snakefile.

Snakefile

+# -*- coding: utf-8 -*-
+"""
+@author: Laura C. Kühle
+
+Discussion:
+TODO: Contemplate saving 5-CV split and evaluating models separately
+TODO: Contemplate separating cell average and reconstruction calculations
+    completely
+TODO: Contemplate removing Methods section from class docstring
+TODO: Contemplate containing the quadrature application for plots in Mesh
+TODO: Contemplate containing coarse mesh generation in Mesh
+TODO: Contemplate extracting boundary condition from InitialCondition
+TODO: Contemplate containing boundary condition in Mesh
+TODO: Ask whether all quadratures depend on freely chosen num_nodes
+TODO: Contemplate saving training data for each IC separately
+TODO: Contemplate removing TrainingDataGenerator class
+TODO: Ask why no fine mesh is used for calculate_coarse_projection()
+TODO: Discuss adding kwargs to attributes in documentation
+TODO: Discuss descriptions (matrices, cfl number, right-hand side,
+    limiting slope, basis, wavelet, etc.)
+TODO: Discuss referencing info on SSPRK3
+TODO: Discuss name for quadrature mesh (now: grid)
+
+Urgent:
+TODO: Build package for DG scheme -> Done
+TODO: Move scripts into separate directory -> Done
+TODO: Move TODOs to Snakefile -> Done
+TODO: Outsource run commands in SM rules into separate files
+TODO: Move plot_approximation_results() into plotting script
+TODO: Introduce env files for each SM rule
+
+Critical, but not urgent:
+TODO: Restructure 'calculate_approximate_solution()'
+TODO: Rework Theoretical TCD for efficiency
+TODO: Extract object initialization from DGScheme
+TODO: Replace loops with list comprehension if feasible
+TODO: Replace loops/list comprehension with vectorization if feasible
+TODO: Check whether 'projection' is always a ndarray
+TODO: Check whether ghost cells are handled/set correctly
+TODO: Enforce even number of ghost cells on each side on fine mesh (?)
+TODO: Check whether all instance variables are sensible
+TODO: Investigate g-mesh(?)
+TODO: Create g-mesh with Mesh class
+TODO: Combine ANN workflows if feasible
+TODO: Investigate profiling for speed up
+
+Currently not critical:
+TODO: Add an environment file for Snakemake
+TODO: Rename files according to standard
+TODO: Allow comparison between ANN training datasets
+TODO: Use full path for ANN model state
+TODO: Add a default model state
+TODO: Look into validators for variable checks
+
+Not feasible yet or doc-related:
+TODO: Replace pop() with get() for dictionary access
+TODO: Induce shift in IC class
+TODO: Force input_size for each ANN model to be stencil length
+TODO: Restructure directories
+TODO: Add images to report
+TODO: Add verbose output
+TODO: Adjust definitions of each IC to be dependent on domain
+TODO: Add README for ANN training
+TODO: Give detailed description of wavelet detection
+TODO: Use cfl_number for updating, not just time (equation-related?)
+TODO: Adjust code to allow classes for all equations
+    (Burger, linear advection, 1D Euler)
+TODO: Add ThresholdDetector
+TODO: Double-check everything! (also with pylint, pytype, pydoc,
+    pycodestyle, pydocstyle)
+TODO: Check whether documentation style is correct
+TODO: Check whether all types in doc are correct
+TODO: Add type annotations to function heads
+TODO: Clean up docstrings
+
+"""
+
 configfile: 'config.yaml'
 
 DIR = 'workflows'

scripts/tcd/DG_Approximation.py

@@ -2,77 +2,6 @@
 """
 @author: Laura C. Kühle
 
-Discussion:
-TODO: Contemplate saving 5-CV split and evaluating models separately
-TODO: Contemplate separating cell average and reconstruction calculations
-    completely
-TODO: Contemplate removing Methods section from class docstring
-TODO: Contemplate containing the quadrature application for plots in Mesh
-TODO: Contemplate containing coarse mesh generation in Mesh
-TODO: Contemplate extracting boundary condition from InitialCondition
-TODO: Contemplate containing boundary condition in Mesh
-TODO: Ask whether all quadratures depend on freely chosen num_nodes
-TODO: Contemplate saving training data for each IC separately
-TODO: Contemplate removing TrainingDataGenerator class
-TODO: Ask why no fine mesh is used for calculate_coarse_projection()
-TODO: Discuss adding kwargs to attributes in documentation
-TODO: Discuss descriptions (matrices, cfl number, right-hand side,
-    limiting slope, basis, wavelet, etc.)
-TODO: Discuss referencing info on SSPRK3
-TODO: Discuss name for quadrature mesh (now: grid)
-
-Urgent:
-TODO: Build package for DG scheme -> Done
-TODO: Move scripts into separate directory -> Done
-TODO: Move TODOs to Snakefile
-TODO: Outsource run commands in SM rules into separate files
-TODO: Move plot_approximation_results() into plotting script
-TODO: Introduce env files for each SM rule
-
-Critical, but not urgent:
-TODO: Restructure 'calculate_approximate_solution()'
-TODO: Rework Theoretical TCD for efficiency
-TODO: Extract object initialization from DGScheme
-TODO: Replace loops with list comprehension if feasible
-TODO: Replace loops/list comprehension with vectorization if feasible
-TODO: Check whether 'projection' is always a ndarray
-TODO: Check whether ghost cells are handled/set correctly
-TODO: Enforce even number of ghost cells on each side on fine mesh (?)
-TODO: Check whether all instance variables are sensible
-TODO: Investigate g-mesh(?)
-TODO: Create g-mesh with Mesh class
-TODO: Combine ANN workflows if feasible
-TODO: Investigate profiling for speed up
-
-Currently not critical:
-TODO: Add an environment file for Snakemake
-TODO: Rename files according to standard
-TODO: Allow comparison between ANN training datasets
-TODO: Use full path for ANN model state
-TODO: Add a default model state
-TODO: Look into validators for variable checks
-
-Not feasible yet or doc-related:
-TODO: Replace pop() with get() for dictionary access
-TODO: Induce shift in IC class
-TODO: Force input_size for each ANN model to be stencil length
-TODO: Restructure directories
-TODO: Add images to report
-TODO: Add verbose output
-TODO: Adjust definitions of each IC to be dependent on domain
-TODO: Add README for ANN training
-TODO: Give detailed description of wavelet detection
-TODO: Use cfl_number for updating, not just time (equation-related?)
-TODO: Adjust code to allow classes for all equations
-    (Burger, linear advection, 1D Euler)
-TODO: Add ThresholdDetector
-TODO: Double-check everything! (also with pylint, pytype, pydoc,
-    pycodestyle, pydocstyle)
-TODO: Check whether documentation style is correct
-TODO: Check whether all types in doc are correct
-TODO: Add type annotations to function heads
-TODO: Clean up docstrings
-
 """
 import json
 import numpy as np