Morphfuncxy

[Sparks29032]

Current being used at APS for applying pdfgetx3.

In progress:

• More robust tests
• Tutorial documentation
• Change funcxy docstring example

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.22%. Comparing base (af80472) to head (783f6f7).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@ Coverage Diff @@## main #239 +/- ##
==========================================
+ Coverage 99.13% 99.22% +0.08% 
==========================================
Files 21 23 +2 Lines 1154 1285 +131 ==========================================
+ Hits 1144 1275 +131 
Misses 10 10 

Files with missing lines	Coverage Δ
tests/test_morph_func.py	100.00% <100.00%> (ø)
tests/test_morphfuncx.py	100.00% <100.00%> (ø)
tests/test_morphfuncxy.py	100.00% <100.00%> (ø)
tests/test_morphfuncy.py	100.00% <100.00%> (ø)
tests/test_morphpy.py	100.00% <100.00%> (ø)
tests/test_refine.py	100.00% <100.00%> (ø)

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[sbillinge]

lookin good

[Sparks29032]

Long PR, but a lot of the code has to be changed with the introduction of MorphFuncx, and we cannot test those changes without the implementation of MorphFuncx. As such, changes in non-MorphFuncx files are not put into a separate PR.

[Sparks29032]

Force push to remove 3 accidental commits. See changes on the force push compare. Only updates should be merging with upstream main.

[Sparks29032]

Here's a breakdown of the changes in each of the files:

• Documentation (docs/source/morphpy.rst): Added tutorial examples for MorphFuncx and MorphFuncxy.
• News: Standard news updates
• Source (src/diffpy/morph): Changed name of function parameter in the MorphFuncy function to funcy function.
  • morph_api.py: function -> funcy function
  • morph_io.py: Implement printing of MorphFuncx, MorphFuncxy morph outputs.
  • morphapp.py: Implement the MorphFuncx and MorphFuncxy functions.
  • morphpy.py: Implement the MorphFuncx and MorphFuncxy functions.
  • refine.py: The refiner originally assumes a fixed grid length. However, the MorphFuncx morph can shift and scale the grid. This behavior is desirable as the output grid may be vastly different from the original grid, so simply interpolating onto the new grid (what stretch, squeeze do) is insufficient. The MorphFuncx example in docs/source/morphpy.rst demonstrates this. New tests are added to tests/test_refine.py to check this.
  • morphs/morphrgrid.py: The morphed r-grid due to MorphFuncx may not have equal spacing. We adjust for that. Furthermore, while the previous implementation assumes the morph and target grids are fixed, we add new variables tagged _origin to account for the possibility of a dynamic grid. These satisfy previous tests in tests/test_morphrgrid.py. The new behavior is tested in the tests/test_morphfuncx.py tests as no other morphs will trigger this behavior.
• New morphs (src/diffpy/morph/morphs): Implement new MorphFuncx, MorphFuncxy morphs.
• New tests (tests): Mostly to test the new morphing functions in the CLI and Python implementations. Also some tests for the new refiner changes due to MorphFuncx.

[sbillinge]

LGTM