Fix double gene deletion

[Midnighter]

• fix Knockout vs. deletion results #1102
• Even in double deletion, genes were checked individually for their effect, thus missing synthetically lethal combinations.
• tests added/passed
• add an entry to the next release

[codecov-commenter]

Codecov Report

Merging #1103 (afb7623) into devel (0b15120) will decrease coverage by 0.00%.
The diff coverage is 100.00%.

❗ Current head afb7623 differs from pull request most recent head 4eaa5f6. Consider uploading reports for the commit 4eaa5f6 to get more accurate results

@@            Coverage Diff             @@
##            devel    #1103      +/-   ##
==========================================
- Coverage   84.29%   84.29%   -0.01%     
==========================================
  Files          65       65              
  Lines        5210     5207       -3     
  Branches     1118     1116       -2     
==========================================
- Hits         4392     4389       -3     
  Misses        528      528              
  Partials      290      290              

Impacted Files	Coverage Δ
src/cobra/flux_analysis/deletion.py	91.07% <100.00%> (-0.24%)	⬇️

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[cdiener]

Looks good. Much more explicit as well. Looks like find_gene_knockout_reactions can be deprecated in the future.

[Midnighter]

Looks good. Much more explicit as well. Looks like find_gene_knockout_reactions can be deprecated in the future.

Thank you for the quick review 🙂 Good call, I will add a deprecation warning.