chore: deprecate getLastAtom and add a test

[stevenhua0320]

@sbillinge ready to review, note that there is no test for getLastAtom, but it is only a getter function, I add a very simple function to test this. Now the pytest would be shown like this:

(diffpy.structure) ~/dbs/diffpy.structure git:[deprecate-getLastAtom]
pytest
============================================================================================================== test session starts ==============================================================================================================
platform darwin -- Python 3.14.3, pytest-9.0.2, pluggy-1.6.0
rootdir: /Users/huarundong/dbs/diffpy.structure
configfile: pyproject.toml
collected 143 items                                                                                                                                                                                                                             

tests/test_atom.py ..                                                                                                                                                                                                                     [  1%]
tests/test_lattice.py ............                                                                                                                                                                                                        [  9%]
tests/test_loadstructure.py ......                                                                                                                                                                                                        [ 13%]
tests/test_p_cif.py .....................                                                                                                                                                                                                 [ 28%]
tests/test_p_discus.py .....                                                                                                                                                                                                              [ 32%]
tests/test_p_pdffit.py .........                                                                                                                                                                                                          [ 38%]
tests/test_parsers.py .............                                                                                                                                                                                                       [ 47%]
tests/test_spacegroups.py .....                                                                                                                                                                                                           [ 51%]
tests/test_structure.py .............................................                                                                                                                                                                     [ 82%]
tests/test_supercell.py ...                                                                                                                                                                                                               [ 84%]
tests/test_symmetryutilities.py .....................                                                                                                                                                                                     [ 99%]
tests/test_version.py .                                                                                                                                                                                                                   [100%]

=============================================================================================================== warnings summary ================================================================================================================
tests/test_structure.py::TestStructure::test_addNewAtom
  /Users/huarundong/dbs/diffpy.structure/tests/test_structure.py:149: DeprecationWarning: 'diffpy.structure.Structure.addNewAtom' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Structure.add_new_atom' instead.
    structure.addNewAtom(atype="C", xyz=[0.1, 0.2, 0.3])

tests/test_structure.py::TestStructure::test_getLastAtom
  /Users/huarundong/dbs/diffpy.structure/tests/test_structure.py:127: DeprecationWarning: 'diffpy.structure.Structure.getLastAtom' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Structure.get_last_atom' instead.
    actual = structure.getLastAtom()

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================================================================================== 143 passed, 2 warnings in 2.91s ========================================================================================================

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.95%. Comparing base (52c99e6) to head (793f5b0).
⚠️ Report is 3 commits behind head on v3.4.0.

Additional details and impacted files

@@           Coverage Diff           @@
##           v3.4.0     #159   +/-   ##
=======================================
  Coverage   98.95%   98.95%           
=======================================
  Files          13       13           
  Lines        1905     1919   +14     
=======================================
+ Hits         1885     1899   +14     
  Misses         20       20           

Files with missing lines	Coverage Δ
tests/test_structure.py	99.79% <100.00%> (+<0.01%)	⬆️

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• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[sbillinge]

This is perfect! Well, one thought, I am not sure why we are using build: as our prefix on the title. This has nothing to do with building the package. I think perhaps chore: might be better? But it is a small thing.

Now things are going smoothly, I think that it is ok to put more than one of these on each PR if that is easier. But please, not more than 3 or 4 as they become confusing to review.

Thanks so much for this @stevenhua0320