Add Spell Checker

[bpaul4]

Summary/Motivation:

Adds spell checker to CI test runs.

Changes proposed in this PR:

• Add CI setup necessary to run spell checker on PR runs

• Initial configuration file with some known file type exceptions; comments lists all other (included) file types for reference

• Open questions: 1) what file types should be included/excluded? 2) what known "misspellings" should be excepted, e.g. "IDAES"? 3) should we mandate that the pylint and docs checks wait on the spell-check and code-formatting (black), like pytest does?

• Locally, navigating to the FOQUS/ directory, installing typos and running typos --files will list all files that are checked. Running typos --config ./.github/workflows/typos.toml will run the spell check using the configuration file.

• Note: the Check Spelling test will fail for now, as we haven't actually corrected the spelling errors yet

Legal Acknowledgement

By contributing to this software project, I agree to the following terms and conditions for my contribution:

1. I agree my contributions are submitted under the copyright and license terms described in the LICENSE.md file at the top level of this directory.
2. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer.

[lbianchi-lbl]

@sotorrio1 the one remaining word flagged as an error is an instance of "ghostOuput" here:

FOQUS/foqus_lib/framework/uq/ExperimentalDesign.py

Line 80 in 5334847

names = ["ghostOuput"]

That part seems to be related to PSUADE (i.e. writing the PSUADE input file), so I wanted to double-check if "ghostOuput" is a misspelling of "ghostOutput", or it's actually the correct string in the context of the PSUADE input file syntax.

[sotorrio1]

@lbianchi-lbl I'm pretty sure this is just a misspelling of "ghostOutput". It's only naming that variable "ghostOuput" in the case there are no outputs (all the variables are inputs). I've even tested the method generateSamples changing it to the correct spelling (ghostOutput) and it works fine. PSUADE is not looking for that specific (and wrong) string lol

[codecov]

Codecov Report

Attention: 42 lines in your changes are missing coverage. Please review.

Comparison is base (5334847) 37.25% compared to head (143fec1) 37.10%.

Files	Patch %	Lines
foqus_lib/framework/surrogate/ALAMO.py	0.00%	7 Missing ⚠️
foqus_lib/framework/uq/RSAnalyzer.py	0.00%	5 Missing ⚠️
foqus_lib/framework/optimizer/NLopt.py	0.00%	4 Missing ⚠️
foqus_lib/framework/optimizer/Snobfit.py	0.00%	4 Missing ⚠️
foqus_lib/framework/optimizer/SM_Optimizer.py	0.00%	3 Missing ⚠️
foqus_lib/framework/pymodel/heat_integration.py	0.00%	3 Missing ⚠️
foqus_lib/framework/sim/turbineConfiguration.py	0.00%	3 Missing ⚠️
foqus_lib/framework/graph/nodeVars.py	0.00%	2 Missing ⚠️
foqus_lib/foqus.py	0.00%	1 Missing ⚠️
foqus_lib/framework/graph/graph.py	50.00%	1 Missing ⚠️
... and 9 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1168      +/-   ##
==========================================
- Coverage   37.25%   37.10%   -0.15%     
==========================================
  Files         160      160              
  Lines       36396    36396              
  Branches     5956     5956              
==========================================
- Hits        13558    13504      -54     
- Misses      21750    21794      +44     
- Partials     1088     1098      +10     

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