All pull requests

Pull requests

• fix: orient FASTCC constraints for negative-only reactions

  #1500·ArtificialZeng opened Oct 26, 2026·

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• fix: handle empty internal selections in loopless analysis

  #1499·ArtificialZeng opened Oct 26, 2026·3 tasks done·

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• Fix write_sbml_model TypeError for numpy-typed bounds and stoichiometries

  #1496·Mohit-Ak opened Oct 5, 2026Contributor·4 tasks done·

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  1

• feat: add the SPECTRA consistency check (spectra_cc)

  #1495·pavan-kumar-s opened Oct 2, 2026·4 tasks done·

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  2

• feat: add raise_error to pfba and geometric_fba

  #1494·RonitBStudent opened Sep 18, 2026·4 tasks done·

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  2

• Keep SBML-named exchanges when filling boundary species

  #1493·shaneraphel opened Sep 16, 2026·4 tasks done·

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  4

• Fix build_reaction_from_string clobbering user-set bounds

  #1481·Mohit-Ak opened Aug 1, 2026Contributor·

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  4

• feat: add loopless blocked reactions search + new "potentials" loopless constraints

  #1472·isaf27 opened Apr 28, 2026Contributor·3 of 5 tasks·

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  4

• Added fast gapfilling flag. All tests pass with fast_gapfill=True

  #1450·djinnome opened Jun 27, 2025·5 tasks done·

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  7

• Metadata FBC3

  #1440·pascalaldo opened Apr 29, 2025·

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  23

• Direct gene.id modification warning message.

  #1424·mdziurzynski opened Jan 13, 2025·

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• feat: add progress to fva

  stale
  #1283·achillesrasquinha opened Sep 20, 2022Contributor·4 tasks done·

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  12

• feat: add embl gems repository

  stale
  #1282·achillesrasquinha opened Sep 20, 2022Contributor·4 tasks done·

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  10

• feat: add repr to dictlist

  stale
  #1278·achillesrasquinha opened Sep 19, 2022Contributor·2 of 4 tasks·

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  6

• Fix 673

  stale
  #1264·akaviaLab opened Aug 10, 2022Contributor·4 tasks done·

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  16

• type hint changes in dictlist.py

  stale
  #1256·akaviaLab opened Jul 26, 2022Contributor·2 of 4 tasks·

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• Metadata fbc3

  stale
  #1237·akaviaLab opened Jun 19, 2022Contributor·1 task·

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  73

• add compare.py which contains functions for comparing.

  stale
  #1206·akaviaLab opened Apr 25, 2022Contributor·1 of 3 tasks·

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• initial attempt at compartments

  stale
  #1193·akaviaLab opened Mar 25, 2022Contributor·

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  16

• User defined constraints

  stale
  #996·Hemant27031999 opened Aug 28, 2020Contributor·

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  2

• Metadata fbc3 group

  enhancementreadystale
  #988·Hemant27031999 opened Aug 15, 2020Contributor·8 of 9 tasks·

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  21

• Consistent list annotation

  stale
  #959·Hemant27031999 opened Jun 4, 2020Contributor·

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  2

• Gap-filling multi-strain workflow

  cookbookstale
  #873·yseif opened Jul 11, 2019·

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  2

• Add find_active_reactions.py to find active reactions quicker

  staleWIP
  #841·shjchan opened Apr 19, 2019·

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  53

  

• refactor: turn compartments into objects

  staleWIP
  #725·Midnighter opened Jun 13, 2018Member·

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  35