Fix topology tests

[Midnighter]

• [x] fix #519
• [x] description of feature/fix
• [x] tests added/passed
• [x] add an entry to the next release

Metabolites with irreversible exchange reactions were falsely identified as orphans. Not consumed and not produced metabolites were detected opening all boundary reactions. This has changed to only opening exchanges.

• Orphans are now a complete subset of not produced compounds.
• Dead-ends are now a complete subset of not consumed compounds.

[codecov[bot]]

Codecov Report

Merging #589 into develop will increase coverage by 0.03%. The diff coverage is 100%.

@@             Coverage Diff             @@
##           develop     #589      +/-   ##
===========================================
+ Coverage    80.04%   80.07%   +0.03%     
===========================================
  Files           57       57              
  Lines         2926     2931       +5     
  Branches       385      386       +1     
===========================================
+ Hits          2342     2347       +5     
  Misses         518      518              
  Partials        66       66

Impacted Files	Coverage Δ
memote/suite/tests/test_consistency.py	95.29% <ø> (ø)	:arrow_up:
memote/support/consistency.py	97.07% <100%> (+0.03%)	:arrow_up:
memote/suite/tests/test_basic.py	100% <100%> (ø)	:arrow_up:
memote/support/helpers.py	94% <100%> (+0.09%)	:arrow_up:

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