Mesh check error printout

[hajdik]

Purpose

This changes the logic for error printouts for boundary condition checks and topology errors so all errors present in the mesh will print out. The previous behavior was to exit on the first issue, making it hard to fix multiple errors at once.

I also changed the printout that shows up at the start of a case. Originally it printed the case name as the name of the input file, but when running pyHyp with patch input there's no input file. I changed this to print the output file when there isn't an input file.

Expected time until merged

None

Type of change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (non-backwards-compatible fix or feature)
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no API changes)
• Documentation update
• Maintenance update
• Other (please describe)

Testing

Run this with a broken mesh to see if all expected errors are printed out

Checklist

• I have run flake8 and black to make sure the Python code adheres to PEP-8 and is consistently formatted
• I have formatted the Fortran code with fprettify or C/C++ code with clang-format as applicable
• I have run unit and regression tests which pass locally with my changes
• I have added new tests that prove my fix is effective or that my feature works
• I have added necessary documentation

[codecov]

Codecov Report

Attention: Patch coverage is 50.00000% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 78.87%. Comparing base (71aa6c9) to head (fdbb4db).

Files	Patch %	Lines
pyhyp/pyHyp.py	50.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #81      +/-   ##
==========================================
- Coverage   79.48%   78.87%   -0.61%     
==========================================
  Files           4        4              
  Lines         424      426       +2     
==========================================
- Hits          337      336       -1     
- Misses         87       90       +3     

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[sseraj]

This needs some minor fixes and formatting with fprettify

[eirikurj]

From what I can tell, this looks good overall, although I dont have a case to test this. Just a few minor comments.

[eirikurj]

I realize that this was like this before, but since this is a parallel code, we should probably call mpi_abort to exit more gracefully. However, since there are other locations, we could also defer this to a separate PR.

[hajdik]

There are several places where the error handling isn't done properly in parallel and MPI gives wild errors, I could make an issue to address that.

[eirikurj]

For consistency, can you add ERROR here as well.

[eirikurj]

Sorry for the delay, couple of additional comments. BTW, do you have a mesh that we can add as tests that catch these cases?

[eirikurj]

For consistency, can you add ERROR here as well.

[eirikurj]

Is there ever a case you dont have either inputFile or outputFile specified?

[eirikurj]

The leading & with all the spaces will create a large gap in the string. For the line continuation to have consistent spacing, place the & right before See, i.e., &See.

[eirikurj]

Sorry for the delay, couple of additional comments. BTW, do you have a mesh that we can add as tests that catch these cases? Would also be good to add printout to the PR description. Create #92 to track that we should update to mpi_abort at some point.