Rename PDF-specific smear option to --smear-pdf

[Sparks29032]

Closes #210.

The --smear-pdf option first converts the PDF to an RDF before applying the smear. The --smear option does not do such transformation. If both are enabled, the --smear-pdf option takes precedence.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.44%. Comparing base (ea41b24) to head (69d45ee).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #220      +/-   ##
==========================================
+ Coverage   97.36%   97.44%   +0.08%     
==========================================
  Files          20       20              
  Lines         947      978      +31     
==========================================
+ Hits          922      953      +31     
  Misses         25       25              

Files with missing lines	Coverage Δ
tests/test_morphapp.py	99.26% <100.00%> (+0.21%)	⬆️

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[sbillinge]

@Sparks29032 I am afraid this one has a conflict.

[Sparks29032]

@Sparks29032 I am afraid this one has a conflict.

Ah, probably from me fixing a typo on another PR. Should be resolved now.

[Sparks29032]

This code block also tests the default behavior if a user inputs both morphs. The pdf smear takes precedence.

[sbillinge]

I am merging this. I had one comment which is to please make all new tests as pytest tests, not unittest tests. We would gradually over time like to migrate back to pytest tests entirely, but at least, let's not make new unittest tests.

[Sparks29032]

Thanks for merging! I thought these tests were already migrated from unittest to Pytest in #83. These tests seem to follow the Pytest documentation.

[sbillinge]

Thanks for merging! I thought these tests were already migrated from unittest to Pytest in #83. These tests seem to follow the Pytest documentation.

maybe I didn't check well enough. It looked as if it was indented and part of a class and not a standalone function.

[Sparks29032]

They are classes, but I thought this is supported and encouraged by https://docs.pytest.org/en/stable/getting-started.html. I think I need the python tests presentation lol.

[sbillinge]

They are classes, but I thought this is supported and encouraged by https://docs.pytest.org/en/stable/getting-started.html. I think I need the python tests presentation lol.

Ah, I see. I don't really see any benefit unless tests are sharing a bunch of code or marks, but mostly I just assumed they were unittest tests (which are typically the only tests we write in classes.....)