Maintenance task

[daico007]

PR Summary:

Attempt to address some maintenance related issue, including the flakey test test_save_residue_map in test_compound.py and deprecated warnings in github actions (#1122).

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[codecov]

Codecov Report

Patch and project coverage have no change.

Comparison is base (d83e341) 87.13% compared to head (e25f36f) 87.13%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1123   +/-   ##
=======================================
  Coverage   87.13%   87.13%           
=======================================
  Files          62       62           
  Lines        6420     6420           
=======================================
  Hits         5594     5594           
  Misses        826      826           

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