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Add find_active_reactions.py to find active reactions quicker #841

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Add find_active_reactions.py to find active reactions quicker #841

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Commits on May 1, 2019

  1. Add find_active_reactions.py and test

    @shjchan
    shjchan committed May 1, 2019
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  2. Simplify test

    @shjchan
    shjchan committed May 1, 2019
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  3. Small fix

    @shjchan
    shjchan committed May 1, 2019
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  4. Use logger instead of print

    @shjchan
    shjchan committed May 1, 2019
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  5. Change zero_cutoff

    @shjchan
    shjchan committed May 1, 2019
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  6. Add documentation for find_reactions_in_cycles

    @shjchan
    shjchan committed May 1, 2019
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  7. Fix math in doc, reorganize files and add loopless FVA options

    @shjchan
    shjchan committed May 1, 2019
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  8. Add doc for new options in add_loopless

    @shjchan
    shjchan committed May 1, 2019
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  9. Fix small bugs, update docs and __init__.py

    @shjchan
    shjchan committed May 1, 2019
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  10. Use np.ndarray instead matrix

    @shjchan
    shjchan committed May 1, 2019
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  11. Update test_find_active_reactions.py

    @shjchan
    shjchan committed May 1, 2019
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  12. Add exception for OptimizationError

    @shjchan
    shjchan committed May 1, 2019
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  13. Make the program flow more pythonic

    @shjchan
    shjchan committed May 1, 2019
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  14. Handle unexpected zero optimal solutions

    @shjchan
    shjchan committed May 1, 2019
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  15. Handle empty nullspace

    @shjchan
    shjchan committed May 1, 2019
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  16. Test also solving MILP and Fast-SNP

    @shjchan
    shjchan committed May 1, 2019
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  17. Fix how tolerance is used

    @shjchan
    shjchan committed May 1, 2019
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  18. Fix formatting

    @shjchan
    shjchan committed May 1, 2019
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