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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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2051105
Add find_active_reactions.py and test
shjchan Apr 19, 2019
b2b30f5
Simplify test
shjchan Apr 19, 2019
2ec5247
Small fix
shjchan Apr 19, 2019
a964fde
Use logger instead of print
shjchan Apr 19, 2019
f8f8b1d
Change zero_cutoff
shjchan Apr 19, 2019
c4a83ec
Add documentation for find_reactions_in_cycles
shjchan Apr 19, 2019
1a6beef
Fix math in doc, reorganize files and add loopless FVA options
shjchan Apr 21, 2019
bf4a04c
Add doc for new options in add_loopless
shjchan Apr 21, 2019
6b0526a
Fix small bugs, update docs and __init__.py
shjchan Apr 21, 2019
7b6ac4d
Use np.ndarray instead matrix
shjchan Apr 22, 2019
f1d5983
Update test_find_active_reactions.py
shjchan Apr 23, 2019
a02539f
Add exception for OptimizationError
shjchan Apr 30, 2019
315e286
Make the program flow more pythonic
shjchan Apr 30, 2019
0e21250
Handle unexpected zero optimal solutions
shjchan May 1, 2019
ee03892
Handle empty nullspace
shjchan May 1, 2019
410cc68
Test also solving MILP and Fast-SNP
shjchan May 1, 2019
900f132
Fix how tolerance is used
shjchan May 1, 2019
67f2863
Fix formatting
shjchan May 1, 2019
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5 changes: 4 additions & 1 deletion cobra/flux_analysis/__init__.py
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Expand Up @@ -4,9 +4,12 @@
double_gene_deletion, double_reaction_deletion, single_gene_deletion,
single_reaction_deletion)
from cobra.flux_analysis.fastcc import fastcc
from cobra.flux_analysis.find_active_reactions import (
find_active_reactions, find_reactions_in_cycles)
from cobra.flux_analysis.gapfilling import gapfill
from cobra.flux_analysis.geometric import geometric_fba
from cobra.flux_analysis.loopless import (loopless_solution, add_loopless)
from cobra.flux_analysis.loopless import (
loopless_solution, add_loopless, fastSNP)
from cobra.flux_analysis.moma import add_moma, moma
from cobra.flux_analysis.parsimonious import pfba
from cobra.flux_analysis.variability import (
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