fix: fix Structure loading with close-duplicate atom

[stevenhua0320]

@sbillinge ready to review. This is the potential solution proposed by @Tieqiong last summer diffpy/diffpy.pdfgui#291. We change the order of the source that we trust most as the priority. After this is merged and released, we could ask whether this fix would solve this by asking people to test it.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.19%. Comparing base (991889b) to head (dc1b007).
⚠️ Report is 5 commits behind head on v3.4.0.

Additional details and impacted files

@@            Coverage Diff             @@
##           v3.4.0     #183      +/-   ##
==========================================
+ Coverage   99.17%   99.19%   +0.01%     
==========================================
  Files          15       15              
  Lines        2439     2489      +50     
==========================================
+ Hits         2419     2469      +50     
  Misses         20       20              

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[sbillinge]

I think we need good tests for this. @stevenhua0320 we may want to work with Tieqiong to get a cif file that is not working currently so we can test that it works correctly after the fix.

[sbillinge]

@stevenhua0320 I am moving this to the 3.5.0 release as I want this to be fixed carefully and with excellent tests. Actually, it is an important fix, so it would be good if you were interested in working with @cadenmyers13 to write good tests and then to put in a fix, but we don't need to hold up 3.4.0 for this.

[cadenmyers13]

@stevenhua0320 Im happy to help with writing a test for this. LMK when you want to