Feature templates

[beykyle]

Pending PR tasks

• Consistent use of type hints based on clear developer guidelines
• Get bfrescox tests passing. Please document and justify all test design decisions in TestData/README (e.g., adjusting threshold test value)
• Update bfrescoxpro testing to run the same tests as bfrescox
• Get all code passing standard adherence check (flake8 / check tox task)
• Since this is a large PR, some clean-up efforts could be skipped in this PR to keep manageable. Determine what will be skipped and create an Issue for each distinct task and add these as tasks in alpha release Issue

PR Self-review

• Review all changes
• Confirm all tox tasks running locally
• Build source distribution for both and universal wheel for bfrescox and confirm that contents are correct and minimal.
• Assess if code coverage levels are acceptable and assess test update needs to address insufficiencies
  • Is it acceptable that a test file not have 100% coverage?
• Confirm all actions passing

@jared321 PR Review

• Review all changes
• Confirm all tox tasks running locally and, for bfrescoxpro, on a variety of different machines with modules and different MPI implementations
• Confirm correct synchronization with main
• Confirm all actions passing

[codecov-commenter]

Codecov Report

❌ Patch coverage is 81.06952% with 177 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.45%. Comparing base (2e69dc9) to head (151c208).

Files with missing lines	Patch %	Lines
common/parse_parallelization_setup.py	6.25%	60 Missing ⚠️
common/parse_performance_results.py	12.82%	34 Missing ⚠️
common/Configuration.py	67.50%	13 Missing ⚠️
common/generate_inelastic_template.py	82.75%	10 Missing ⚠️
common/_parsing.py	36.36%	7 Missing ⚠️
...src/bfrescox/tests/TestRunUserProvidedTemplates.py	91.52%	5 Missing ⚠️
.../bfrescoxpro/tests/TestRunUserProvidedTemplates.py	92.64%	5 Missing ⚠️
common/generate_elastic_template.py	82.75%	5 Missing ⚠️
common/parse_fort16.py	88.37%	5 Missing ⚠️
...escox_pypkg/src/bfrescox/tests/TestElasticSuite.py	93.93%	4 Missing ⚠️
... and 13 more

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #19       +/-   ##
===========================================
+ Coverage   58.75%   78.45%   +19.70%     
===========================================
  Files          17       35       +18     
  Lines         320     1193      +873     
===========================================
+ Hits          188      936      +748     
- Misses        132      257      +125     

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[beykyle]

At this point, tests are passing for user defined templates, including tests which run a simulation and compare cross sections parsed from the output to expected values. See bfrescox_pypkg/src/bfrescox/tests/TestRunUserProvidedTemplates.py.

It should be fairly simple to copy and modify this test file to apply to a new test suite. We need test suites for problems with the template types that can be generated in bfrescox:

• elastic
• inelastic

There is an additional remaining task:

• get GH actions to pass

[beykyle]

Also, we could probably simplify testing with https://docs.python.org/3/library/tempfile.html

[beykyle]

Final self review:

• tested open mpi implementations with bfrescoxpro install and test
• Final cleanup up book and docs

[wildsm]

Will this PR be addressed before bandframework/bandframework#181 ?

[beykyle]

Will this PR be addressed before bandframework/bandframework#181 ?

v0.0.1-alpha is based on this branch, not main. This can be merged into main after v0.5 release.

[wildsm]

I suggest deleting all of the DS_Store files.

Also, in v0.0.1-alpha,
bfrescox.version
produced '0.0.0'