CovertLab/arrow issues and pull requests

#52 - Rename arrow module to stochastic_arrow

Pull Request - State: closed - Opened by thalassemia over 1 year ago - 7 comments

#51 - Name conflict with Jupyter dependency

Issue - State: closed - Opened by thalassemia over 1 year ago - 9 comments

#50 - Release 0.5.1 for Python 3.11 compatibility

Pull Request - State: closed - Opened by 1fish2 almost 2 years ago

#49 - Avoid selection of 0 propensity reactions and negative counts

Pull Request - State: closed - Opened by tahorst almost 3 years ago - 4 comments

#48 - Arrow hangs wcEcoli complexation with certain sim seeds

Issue - State: closed - Opened by 1fish2 almost 3 years ago - 6 comments
Labels: bug

#47 - Serialize PRNG state

Pull Request - State: closed - Opened by U8NWXD about 3 years ago - 7 comments

#46 - consistent install even if installing numpy at the same time?

Issue - State: open - Opened by 1fish2 over 4 years ago
Labels: bug

#45 - Fix Build Failure by Including Numpy Include Dirs

Pull Request - State: closed - Opened by U8NWXD over 4 years ago - 11 comments

#44 - Bump psutil from 5.6.3 to 5.6.6

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#43 - Detecting when propensities overflow

Pull Request - State: closed - Opened by prismofeverything over 4 years ago - 9 comments

#42 - Adjustment to API to pass rates into evolve() instead of init()

Pull Request - State: closed - Opened by prismofeverything almost 5 years ago - 2 comments

#41 - Python 3 compatibility via Cython

Pull Request - State: closed - Opened by 1fish2 about 5 years ago - 3 comments

#40 - Python 3 compatibility [as needed by wcEcoli]

Issue - State: closed - Opened by 1fish2 about 5 years ago
Labels: enhancement

#39 - Negative counts from StochasticSystem

Issue - State: open - Opened by tahorst over 5 years ago - 5 comments

#38 - add a memory leak test

Issue - State: open - Opened by 1fish2 over 5 years ago - 2 comments

#37 - Decrement references to arrays before returning them

Pull Request - State: closed - Opened by prismofeverything over 5 years ago - 3 comments

#36 - Fix memory leak

Pull Request - State: closed - Opened by prismofeverything over 5 years ago - 2 comments

#35 - Forms of propensity calculations

Pull Request - State: open - Opened by heejochoi almost 6 years ago

#34 - Facilitating user-provided propensity calculations

Issue - State: open - Opened by heejochoi almost 6 years ago - 5 comments

#33 - Implement Gillespie in C and call from python

Pull Request - State: closed - Opened by prismofeverything almost 6 years ago - 6 comments

#32 - Precalculate and cache values outside of evolve()

Pull Request - State: closed - Opened by prismofeverything almost 6 years ago

#31 - Accelerating performance

Issue - State: open - Opened by jmason42 almost 6 years ago - 2 comments
Labels: enhancement, question

#30 - Switching between stochastic and ODE-based simulation

Issue - State: open - Opened by eagmon almost 6 years ago - 2 comments

#29 - Refactored propensity calculations and caching reaction stoichiometries

Pull Request - State: closed - Opened by jmason42 almost 6 years ago - 6 comments

#28 - Removed support for alternate forms, rearranging tests to allow for profiling

Pull Request - State: closed - Opened by prismofeverything almost 6 years ago - 4 comments

#27 - Suspend alternative propensity calculation 'form's

Issue - State: closed - Opened by jmason42 almost 6 years ago - 2 comments
Labels: question

#26 - Edge case: catalysts

Issue - State: open - Opened by jmason42 almost 6 years ago

#25 - Cached reaction dependencies

Pull Request - State: closed - Opened by jmason42 almost 6 years ago - 3 comments
Labels: enhancement

#24 - Profiling utilities and routine profiling

Issue - State: open - Opened by jmason42 almost 6 years ago - 3 comments

#23 - Returning which events occurred

Pull Request - State: closed - Opened by prismofeverything almost 6 years ago - 1 comment

#22 - Language and mathematical standardizations

Pull Request - State: closed - Opened by jmason42 almost 6 years ago - 2 comments

#21 - Release versioning

Issue - State: closed - Opened by jmason42 almost 6 years ago - 2 comments

#20 - Simplify complexation fixtures

Pull Request - State: closed - Opened by jmason42 almost 6 years ago - 2 comments

#19 - Transpose stoichiometry matrix

Issue - State: closed - Opened by jmason42 almost 6 years ago - 3 comments

#18 - Moving average utility - addresses #3

Pull Request - State: closed - Opened by jmason42 almost 6 years ago - 6 comments
Labels: enhancement

#17 - Adopt spaces over tabs

Issue - State: closed - Opened by jmason42 almost 6 years ago - 2 comments
Labels: enhancement, question

#16 - Cast time, counts to NumPy arrays after simulating

Issue - State: closed - Opened by jmason42 almost 6 years ago - 1 comment

#15 - Test different approaches for exponentially distributed random number generation

Issue - State: open - Opened by jmason42 almost 6 years ago - 1 comment

#14 - Store reaction dependencies for efficient propensity recalculation

Issue - State: closed - Opened by jmason42 almost 6 years ago - 1 comment

#13 - Utility for converting kinetic rate constants to stochastic rate constants

Issue - State: open - Opened by jmason42 almost 6 years ago
Labels: enhancement

#12 - Optionally return the number of times each event occurred

Issue - State: closed - Opened by jmason42 almost 6 years ago - 2 comments

#11 - Only return final state by default when running until a time

Issue - State: open - Opened by jmason42 almost 6 years ago
Labels: enhancement

#10 - Standardize output order and nomenclature

Issue - State: closed - Opened by jmason42 almost 6 years ago - 3 comments
Labels: enhancement

#9 - E. coli WCM complexation test system

Issue - State: closed - Opened by jmason42 almost 6 years ago - 5 comments

#8 - Compare sparse vs. full matrix representations

Issue - State: open - Opened by jmason42 almost 6 years ago - 4 comments

#7 - Document and contrast with other SSA packages

Issue - State: open - Opened by jmason42 almost 6 years ago - 1 comment

#6 - Classes for problem construction/interpretation

Issue - State: open - Opened by jmason42 almost 6 years ago - 2 comments
Labels: enhancement

#5 - PRNG determinism

Issue - State: open - Opened by jmason42 almost 6 years ago - 4 comments
Labels: enhancement, question

#4 - (Quasi) deterministic simulation option

Issue - State: open - Opened by jmason42 almost 6 years ago
Labels: enhancement

#3 - Moving distribution plots

Issue - State: closed - Opened by jmason42 almost 6 years ago - 2 comments
Labels: enhancement

#2 - Implement tau leaping

Issue - State: open - Opened by jmason42 almost 6 years ago - 4 comments
Labels: enhancement

#1 - Basic plotting function

Pull Request - State: closed - Opened by jmason42 almost 6 years ago - 2 comments
Labels: enhancement

GitHub / CovertLab/arrow issues and pull requests