Convert Matrix to a strided vector

[willGraham01]

Concerns #285:

• Completes the Matrix and CCoefficientMatrix tasks
• Moves towards the derived class objectives too.
• Also detaches Pupil from MATLAB

Description

Converts the Matrix template class to a wrapper for strided vector storage.
Derived class behaviour changes:

• CCoefficientMatrix is now just a typedef for Matrix<double>.
• Pupil is a struct that inherits from Matrix<double>.
• Vertices & GratingStructure are structs that inherit from Matrix<int>.

Although the only thing the derived "structs" now add is a unique way to read these classes via MATLAB. Once they have their MATLAB dependency removed, we can probably just typedef them all to Matrix<double/int>.

Testing

Tests are preserved for all existing classes.

[codecov]

Codecov Report

Patch coverage: 43% and no project coverage change.

Comparison is base (18840c0) 27% compared to head (97c7fae) 27%.

Additional details and impacted files

@@         Coverage Diff         @@
##           main   #307   +/-   ##
===================================
- Coverage    27%    27%   -0%     
===================================
  Files        75     77    +2     
  Lines      3699   3690    -9     
===================================
- Hits        992    981   -11     
- Misses     2707   2709    +2     

Impacted Files	Coverage Δ
tdms/include/arrays.h	45% <ø> (+12%)	⬆️
tdms/include/hdf5_io/hdf5_reader.h	0% <0%> (ø)
...s/include/simulation_manager/objects_from_infile.h	0% <ø> (ø)
tdms/include/simulation_manager/pstd_variables.h	0% <ø> (ø)
tdms/include/vertex_phasors.h	0% <ø> (ø)
tdms/src/arrays.cpp	91% <ø> (-1%)	⬇️
...mulation_manager/execute_detector_subfunctions.cpp	0% <0%> (ø)
tdms/src/simulation_manager/execute_simulation.cpp	0% <ø> (ø)
...src/simulation_manager/execute_update_Ex_split.cpp	0% <0%> (ø)
...dms/src/simulation_manager/objects_from_infile.cpp	0% <0%> (ø)
... and 4 more

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