sys-bio/roadrunner

Issues

• Simulations with negative start times handle math with csymbol `time` incorrectly

  #1211 opened 3 months ago by matthiaskoenig
  3

• Saving and loading state does not work across python interpreter sessions

  #1210 opened 3 months ago by matthiaskoenig
  2

• Not possible to set seed for deterministic distrib model

  #1173 opened 6 months ago by matthiaskoenig
  14

• addX functions not wrapped well in Python

  #1205 opened 3 months ago by luciansmith
  0

• Fix doc building so python-only functions make it to the docs

  #1197 opened 3 months ago by luciansmith
  0

• removeInitialAssignment results in many variables changing

  #1195 opened 4 months ago by dalbabur
  3

• Changing initial values should change SBML export

  #1193 opened 4 months ago by luciansmith
  0

• Missing initial assignments after loading model

  #1189 opened 4 months ago by dalbabur
  8

• Support python 3.12

  #1171 opened 5 months ago by matthiaskoenig
  8

• Segmentation Fault error when running in cluster

  #1183 opened 5 months ago by dalbabur
  2

• No doc string for setValues method

  #1172 opened 5 months ago by hsauro
  1

• Turning on and off conservedMoietyAnalysis doesn't reset total mass.

  #1146 opened 8 months ago by luciansmith
  5

• Julia bindings for libroadrunner 2.5.0

  #1179 opened 5 months ago by matthiaskoenig
  15

• How to access species values as defined via the hasOnlySubstanceUnit flag (amount/concentration)?

  #1090 opened 5 months ago by matthiaskoenig
  2

• Latest version 2.4.0 not available for Mac M1, python 3.10 on pypi

  #1147 opened 8 months ago by matthiaskoenig
  9

• Broken Intel Mac wheels

  #1177 opened 5 months ago by FFroehlich
  6

• libroadrunner 2.5.0 not available for python 3.9

  #1174 opened 6 months ago by matthiaskoenig
  1

• Update for Compatibility with MacOS 12.6.8 (Intel) and Python 3.11.5

  #1167 opened 7 months ago by AlexanderSimWS
  1

• Calculating steady state changes the selection vector

  #1148 opened 7 months ago by luciansmith
  0

• Reset not quite working as expected

  #1037 opened 8 months ago by luciansmith
  2

• Numpy exception PyDataMem_UserFREE when using pd.melt with simulation results.

  #1073 opened 8 months ago by kaisengit
  6

• Flux control coefficients that are zero calculated as near-zero

  #1150 opened 8 months ago by luciansmith
  2

• Setting a init value overwrites parameter changes

  #1078 opened 8 months ago by matthiaskoenig
  5

• Clearer error message when trying to read non-SBML file

  #1048 opened 8 months ago by luciansmith
  0

• Tell people who try to load qual models what to do

  #1036 opened 8 months ago by luciansmith
  1

• getValue('time') returns 0

  #1142 opened 8 months ago by luciansmith
  1

• Different trajectories for equivalent models using gillespie integrator

  #1135 opened 8 months ago by leon9812
  2

• removeInitialAssignment; removeRule shouldn't remove variable as well

  #1136 opened 8 months ago by luciansmith
  0

• Allow setting "init(k1)" when k1 has an initial assignment.

  #1137 opened 8 months ago by luciansmith
  0

• r.getCurrentSBML() should set all values to current values, including those with initial assignments.

  #1138 opened 8 months ago by luciansmith
  0

• order of metabolites in stoichiometric matrix not consistent depending on where it is run

  #1143 opened 10 months ago by janisshin
  5

• Add macos arm-64 to azure build

  #1141 opened a year ago by luciansmith
  0

• Expat Error while trying to install roadrunner from Source

  #1140 opened a year ago by Jan-Piotraschke
  4

• Problem compiling roadrunner C++ version

  #1133 opened a year ago by matthiaskoenig
  4

• Allow calculation of fluxes even when there are initial assignments

  #1132 opened a year ago by luciansmith
  0

• Support LLVM large code model

  #1091 opened a year ago by matthiaskoenig
  11

• Building newer version in C++

  #1099 opened a year ago by steffenger
  2

• building and linking in C++

  #1054 opened a year ago by steffenger
  1

• Inconsistent results with varying number of points in `Roadrunner.simulate`.

  #1092 opened a year ago by ahalev
  26

• Investigate potential memory leaks

  #1095 opened a year ago by luciansmith
  0

• Loading models failing in python>=3.8 on Mac M1

  #1052 opened a year ago by ahalev
  3

• roadrunner.testing does not exist

  #1041 opened a year ago by hsauro
  4

• Roadrunner allows L2 events to fire at t0.

  #1074 opened a year ago by eltix
  6

• Support python 3.11

  #1064 opened a year ago by matthiaskoenig
  7

• Importing rrplugins results in an error

  #1056 opened 2 years ago by kirichoi
  0

• Anaconda x86 distro on Mac M1: numpy.core.multiarray failed to import

  #1053 opened 2 years ago by rheiland
  3

• ncols not working quite right in plotTimeSeriesSens

  #1042 opened 2 years ago by hsauro
  1

• Similar to #1042, possibly the same bug

  #1043 opened 2 years ago by hsauro
  1

• Change availability section to....

  #1039 opened 2 years ago by hsauro
  2

• Add link to the roadrunner readthedocs in the docs section of readme.md

  #1038 opened 2 years ago by hsauro
  1