CovertLab arrow issues - Githubissues

CovertLab / arrow

Stochastic simulations in python

MIT License

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Rename arrow module to stochastic_arrow

#52 thalassemia closed 1 year ago
7
Name conflict with Jupyter dependency

#51 thalassemia closed 1 year ago
9
Release 0.5.1 for Python 3.11 compatibility

#50 1fish2 closed 1 year ago
0
Avoid selection of 0 propensity reactions and negative counts

#49 tahorst closed 2 years ago
4
Arrow hangs wcEcoli complexation with certain sim seeds

#48 1fish2 closed 2 years ago
6
Serialize PRNG state

#47 U8NWXD closed 3 years ago
7
consistent install even if installing numpy at the same time?

#46 1fish2 opened 4 years ago
0
Fix Build Failure by Including Numpy Include Dirs

#45 U8NWXD closed 4 years ago
11
Bump psutil from 5.6.3 to 5.6.6

#44 dependabot[bot] closed 4 years ago
0
Detecting when propensities overflow

#43 prismofeverything closed 4 years ago
9
Adjustment to API to pass rates into evolve() instead of __init__()

#42 prismofeverything closed 4 years ago
2
Python 3 compatibility via Cython

#41 1fish2 closed 5 years ago
3
Python 3 compatibility [as needed by wcEcoli]

#40 1fish2 closed 2 years ago
0
Negative counts from StochasticSystem

#39 tahorst opened 5 years ago
5
add a memory leak test

#38 1fish2 opened 5 years ago
2
Decrement references to arrays before returning them

#37 prismofeverything closed 5 years ago
3
Fix memory leak

#36 prismofeverything closed 5 years ago
2
Forms of propensity calculations

#35 heejochoi opened 5 years ago
0
Facilitating user-provided propensity calculations

#34 heejochoi opened 5 years ago
5
Implement Gillespie in C and call from python

#33 prismofeverything closed 5 years ago
6
Precalculate and cache values outside of evolve()

#32 prismofeverything closed 5 years ago
0
Accelerating performance

#31 jmason42 opened 5 years ago
2
Switching between stochastic and ODE-based simulation

#30 eagmon opened 5 years ago
2
Refactored propensity calculations and caching reaction stoichiometries

#29 jmason42 closed 5 years ago
6
Removed support for alternate forms, rearranging tests to allow for profiling

#28 prismofeverything closed 5 years ago
4
Suspend alternative propensity calculation 'form's

#27 jmason42 closed 5 years ago
2
Edge case: catalysts

#26 jmason42 opened 5 years ago
0
Cached reaction dependencies

#25 jmason42 closed 5 years ago
3
Profiling utilities and routine profiling

#24 jmason42 opened 5 years ago
3
Returning which events occurred

#23 prismofeverything closed 5 years ago
1
Language and mathematical standardizations

#22 jmason42 closed 5 years ago
2
Release versioning

#21 jmason42 closed 2 years ago
2
Simplify complexation fixtures

#20 jmason42 closed 5 years ago
2
Transpose stoichiometry matrix

#19 jmason42 closed 5 years ago
3
Moving average utility - addresses #3

#18 jmason42 closed 5 years ago
6
Adopt spaces over tabs

#17 jmason42 closed 5 years ago
2
Cast time, counts to NumPy arrays after simulating

#16 jmason42 closed 5 years ago
1
Test different approaches for exponentially distributed random number generation

#15 jmason42 opened 5 years ago
1
Store reaction dependencies for efficient propensity recalculation

#14 jmason42 closed 5 years ago
1
Utility for converting kinetic rate constants to stochastic rate constants

#13 jmason42 opened 5 years ago
0
Optionally return the number of times each event occurred

#12 jmason42 closed 5 years ago
2
Only return final state by default when running until a time

#11 jmason42 opened 5 years ago
0
Standardize output order and nomenclature

#10 jmason42 closed 5 years ago
3
E. coli WCM complexation test system

#9 jmason42 closed 5 years ago
5
Compare sparse vs. full matrix representations

#8 jmason42 opened 5 years ago
4
Document and contrast with other SSA packages

#7 jmason42 opened 5 years ago
1
Classes for problem construction/interpretation

#6 jmason42 opened 5 years ago
2
PRNG determinism

#5 jmason42 opened 5 years ago
4
(Quasi) deterministic simulation option

#4 jmason42 opened 5 years ago
0
Moving distribution plots

#3 jmason42 closed 5 years ago
2