Another round of atom mapping fixes

[kfir4444]

Finally, no more reactions in work in progress

[codecov[bot]]

Codecov Report

Merging #680 (6bd562b) into main (b0182c5) will increase coverage by 0.24%. The diff coverage is 95.83%.

@@            Coverage Diff             @@
##             main     #680      +/-   ##
==========================================
+ Coverage   73.23%   73.47%   +0.24%     
==========================================
  Files          99       99              
  Lines       26456    26477      +21     
  Branches     5538     5540       +2     
==========================================
+ Hits        19374    19455      +81     
+ Misses       5716     5659      -57     
+ Partials     1366     1363       -3     

Flag	Coverage Δ
unittests	73.47% <95.83%> (+0.24%)	:arrow_up:

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Impacted Files	Coverage Δ
arc/mapping/engine.py	88.14% <75.00%> (-0.73%)	:arrow_down:
arc/mapping/driver.py	74.31% <80.00%> (+0.48%)	:arrow_up:
arc/reaction_test.py	99.71% <100.00%> (+8.76%)	:arrow_up:

... and 4 files with indirect coverage changes

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