fix: fix deprecation warning

[stevenhua0320]

@sbillinge ready to review. As followed by running pytest on the skpkg version, there is one deprecation warning as shown below:

(diffpy.structure) ~/dbs/diffpy.structure git:[main]
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%]

=============================================================================================================== warnings summary ================================================================================================================
tests/test_parsers.py::TestP_xyz::test_write_xyz
  /opt/miniconda3/envs/diffpy.structure/lib/python3.14/site-packages/diffpy/structure/structure.py:350: DeprecationWarning: codecs.open() is deprecated. Use open() instead.
    with codecs.open(filename, "w", encoding="UTF-8") as fp:

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================================================================================== 137 passed, 1 warning in 0.63s =========================================================================================================

After the fix done by this PR, I run the pip install -e . and then the pytest passed all tests without warnings as shown below:

(diffpy.structure) ~/dbs/diffpy.structure git:[fix-deprecation]
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 0.66s ==============================================================================================================

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.93%. Comparing base (25d6efd) to head (50380f5).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #153   +/-   ##
=======================================
  Coverage   98.93%   98.93%           
=======================================
  Files          13       13           
  Lines        1878     1878           
=======================================
  Hits         1858     1858           
  Misses         20       20           

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