build: deprecate addNewItem

[stevenhua0320]

@cadenmyers13 ready to review first. Note that this is the scenario that I described in the slack chat in the first case. We don't have any test for this function, so there will be no deprecation warning when we run pytest.

(diffpy.structure) ~/dbs/diffpy.structure git:[deprecate-addNewItem]
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 137 items                                                                                                                                                                                                                             

tests/test_atom.py ..                                                                                                                                                                                                                     [  1%]
tests/test_lattice.py ............                                                                                                                                                                                                        [ 10%]
tests/test_loadstructure.py ......                                                                                                                                                                                                        [ 14%]
tests/test_p_cif.py .....................                                                                                                                                                                                                 [ 29%]
tests/test_p_discus.py .....                                                                                                                                                                                                              [ 33%]
tests/test_p_pdffit.py .........                                                                                                                                                                                                          [ 40%]
tests/test_parsers.py .............                                                                                                                                                                                                       [ 49%]
tests/test_spacegroups.py .....                                                                                                                                                                                                           [ 53%]
tests/test_structure.py .......................................                                                                                                                                                                           [ 81%]
tests/test_supercell.py ...                                                                                                                                                                                                               [ 83%]
tests/test_symmetryutilities.py .....................                                                                                                                                                                                     [ 99%]
tests/test_version.py .                                                                                                                                                                                                                   [100%]

============================================================================================================== 137 passed in 0.61s ==============================================================================================================

[stevenhua0320]

Closed due to wrong commiting branch

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.93%. Comparing base (1b565c8) to head (9ed7fc6).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #156   +/-   ##
=======================================
  Coverage   98.93%   98.93%           
=======================================
  Files          13       13           
  Lines        1878     1878           
=======================================
  Hits         1858     1858           
  Misses         20       20           

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