Sorted TODOs.

Snakefile

@@ -23,21 +23,35 @@ TODO: Contemplate allowing vector input for ICs
 TODO: Discuss how wavelet details should be plotted
 
 TODO: Ask after reasoning behind plotting approx for this specific Burgers case
-TODO: Ask what derivative basis represents
-TODO: Ask after Dirichlet boundary setup
-TODO: Ask after exact solution for different equations
-TODO: Ask where Euler 1D exact solution comes from
+ -> Done (maybe related to final time being after shock occurs, check what
+    happens)
+TODO: Ask what derivative basis represents -> Done (derivative of basis used
+    for stiffness matrix calculation; just derive from basis vector)
+TODO: Ask after Dirichlet boundary setup -> Done (fixed value for all cells
+    outside boundary in both directions; should NOT affect real cells at all)
+TODO: Ask after exact solution for different equations -> Done (in equation
+    class, then let's see)
+TODO: Ask where Euler 1D exact solution comes from -> Done (known reference
+    solution calculated by Thea)
 TODO: Discuss first calculating plotting data and then plotting in separate
-    step
+    step -> Done (no, because evaluation points might change)
 TODO: Ask whether the option of multiple ghost cells has any potential use
-    cases
-TODO: Discuss necessary object dependencies
+    cases -> Done (no)
+TODO: Discuss necessary object dependencies -> Done (extract as many as
+    possible)
 TODO: Contemplate extracting boundary condition from InitialCondition
-TODO: Contemplate containing boundary condition in Mesh
+    -> Done (yes)
+TODO: Contemplate containing boundary condition in Mesh -> Done (yes)
 TODO: Discuss extracting all objects from UpdateScheme and giving equation as
-    input instead
+    input instead -> Done (yes, do it)
 
 Urgent:
+TODO: Rename stiffness matrix to volume integral matrix
+TODO: Rename boundary matrix to flux matrix
+TODO: Change num_ghost_cells to be 1 for calc and 0 for other
+TODO: Move boundary condition to Mesh class
+TODO: Ensure exact solution is calculated in Equation class
+TODO: Extract objects from UpdateScheme
 TODO: Enforce num_ghost_cells to be positive integer for DG (not training)
 TODO: Add Burger class
 TODO: Use cfl_number for updating, not just time (equation-related?)