Command line options moved to input file

[willGraham01]

Closes #261, closes #217 | Hence also closes #208

Important files with changes

• README.md
• developers.md
• input_flags.h
• Nearly everything else is renaming variables, updating the input files, and deleting now-redundant code blocks.

Moves command-line flags to the input file

• ArgumentParser no longer reads the -c and -fd flags
• The option to pass these flags via the command line has been removed, and the CLI -h help does not say anything about them
• InputFlags class created to handle reading (possibly non-existent) names from the input files. This is a counterpart to InputMatrices, which requires that all the datastructures it searches for in the input file exist.
• Simplifies some of the initialisation methods for SimulationManager and ObjectsFromInfile
• Removes duplicate InterpolationMethods enum
• Namespaces flag-related variables and enums. Flag-related enums are weakly typed to bools indicating whether or not they are on/off
• usecd has been replaced with use_pstd and intmethod has been replaced with use_bli as per Names of flag variables in the input file #261

Updates system tests accordingly

• There is another Zenodo update required for the system test data, since the config files no longer need to provide command-line options to TDMS and the input files correspondingly need to provide this information.
• Portions of code that add ow-redundant flags to TDMS executable calls have been removed.

[samcunliffe]

As discussed in our meeting 2023-04-13, when this guy is merged we will tag v1.0.0 (following semver it can't be v0.anything).

Conveniently, this would also coincide with a stable trustworthy version.

[samcunliffe]

Just a note for when we get here. There are some slightly different lines to be deleted in the README now. And a little bit of the unit-tests can be deleted with this merge.

[codecov]

Codecov Report

Patch coverage: 45% and project coverage change: -1 ⚠️

Comparison is base (bf6eaeb) 48% compared to head (40df6da) 48%.

❗ Current head 40df6da differs from pull request most recent head b5ad930. Consider uploading reports for the commit b5ad930 to get more accurate results

Additional details and impacted files

@@         Coverage Diff         @@
##           main   #262   +/-   ##
===================================
- Coverage    48%    48%   -1%     
===================================
  Files        63     65    +2     
  Lines      7826   7792   -34     
===================================
- Hits       3783   3712   -71     
- Misses     4043   4080   +37     

Impacted Files	Coverage Δ
tdms/include/field.h	0% <0%> (ø)
tdms/include/input_flags.h	0% <0%> (ø)
tdms/include/interpolation_methods.h	0% <ø> (ø)
tdms/include/output_matrices/output_matrices.h	0% <0%> (ø)
...s/include/simulation_manager/objects_from_infile.h	0% <ø> (ø)
...ms/include/simulation_manager/simulation_manager.h	0% <ø> (ø)
tdms/include/simulation_parameters.h	100% <ø> (ø)
tdms/src/argument_parser.cpp	74% <ø> (+6%)	⬆️
tdms/src/simulation_manager/execute_simulation.cpp	5% <ø> (-<1%)	⬇️
...src/simulation_manager/execute_update_Ex_split.cpp	35% <ø> (-1%)	⬇️
... and 8 more

... and 19 files with indirect coverage changes

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[samcunliffe]

Patch coverage: 58% and no project coverage change.

So why did you fail?

codecov/project — 48% (-0%) compared to b510b06

[samcunliffe]

Nice. Sorry for being slow.

A few docs suggestions, and I'd plop some of the implementation stuff into a .cpp file rather than the header.

Whats with 6?

[samcunliffe]

Requesting changes explicitly because: automerge is on.

[samcunliffe]

🍉

[samcunliffe]

I doubled the merge queue runtime max. So it's now 120 mins (for instances where we need to flush the cache this makes sense and should be in the minority).

• Enable merge queues for PRs to main. #287

If this still doesn't work, then we revert IMHO.

[samcunliffe]

🥳