DiODeProject/MuMoT

Issues

• Controllers broken on MyBinder

  #414 opened 3 years ago by jarmarshall
  1

• Add CFF file to make it easier for others to cite MuMoT

  #412 opened 3 years ago by willfurnass
  1

• bifurcation() causes TypeError: cannot determine truth value of Relational

  #411 opened 4 years ago by joefresna
  2

• Intermittently hitting cell execution timeout of 120 seconds

  #407 opened 4 years ago by willfurnass
  2

• Changing visualisation type of MuMoTstochasticSimulationViews through GUI causes plot deformations (squeezing)

  #409 opened 4 years ago by joefresna
  0

• Unpin package dependencies

  #349 opened 4 years ago by jarmarshall
  9

• Automatic build and deploy process for releases not working

  #374 opened 4 years ago by willfurnass
  1

• Test suite: run all notebooks in one or more dirs rather than explicitly named notebooks

  #325 opened 5 years ago by willfurnass
  9

• model2.showODEs(method='vanKampen') -> IndexError: list index out of range

  #377 opened 4 years ago by willfurnass
  7

• Erroneous line breaks before some (not all) in-line LaTeX in Markdown cells (Safari only)

  #397 opened 4 years ago by willfurnass
  6

• Possible issue with ipykernel or tornado event loop

  #361 opened 4 years ago by willfurnass
  2

• Upgrade nbval when new version released

  #378 opened 4 years ago by willfurnass
  1

• Only define versions in one place (using setuptools-scm)

  #393 opened 4 years ago by willfurnass
  1

• runtime plot update for multiagent within multicontrollers disables runtime update

  #395 opened 4 years ago by jarmarshall
  0

• MuMoTstochasticSimulationView should support the graphical keywords as other views do

  #389 opened 4 years ago by joefresna
  0

• TkAgg error on MyBinder

  #391 opened 4 years ago by jarmarshall
  0

• ANTLR runtime and generated code versions disagree: 4.8!=4.7.1

  #386 opened 4 years ago by willfurnass
  2

• Test new release of pydstool

  #375 opened 4 years ago by willfurnass
  1

• Incompat with Python 3.8: changing dictionary keys during iteration now results in a RuntimeError

  #379 opened 4 years ago by willfurnass
  0

• Use of bare 'except:' is bad

  #387 opened 4 years ago by willfurnass
  1

• Multicontroller do not accept some of the plotting parameters that normal controllers support

  #385 opened 4 years ago by joefresna
  0

• Do not suppress tracebacks when running 'test' notebooks via nbval

  #384 opened 4 years ago by willfurnass
  3

• Configure logging via 'logging' module

  #383 opened 4 years ago by willfurnass
  0

• Switch to using matplotlib's object-oriented API

  #367 opened 5 years ago by willfurnass
  1

• Configure ReadTheDocs so serves the latest tagged release by default...

  #370 opened 5 years ago by willfurnass
  2

• Consider pointing binder icon to latest release branch

  #320 opened 5 years ago by jarmarshall
  2

• Reduce runtime of CI jobs?

  #366 opened 5 years ago by willfurnass
  0

• Update contributors

  #327 opened 5 years ago by jarmarshall
  2

• ipywidgets erroneously removed from list of deps (was: RTD builds are failing with v1.1.0)

  #368 opened 5 years ago by willfurnass
  2

• Increase notebook message rate limit

  #359 opened 5 years ago by jarmarshall
  0

• tox: pytest bails due to spaces in one of its args not being escaped

  #356 opened 5 years ago by willfurnass
  0

• Consider DOI release assignment strategy

  #319 opened 5 years ago by jarmarshall
  1

• Muticontroller plot warning

  #355 opened 5 years ago by jarmarshall
  1

• SSA/multiagent force initial state widgets to sum to 1 even if system size is not constant

  #318 opened 5 years ago by jarmarshall
  16

• initial state widgets forced to sum to 1 even if not appropriate / incorrect error message methodology used

  #317 opened 5 years ago by jarmarshall
  1

• Clean exceptions

  #352 opened 5 years ago by joefresna
  3

• Greek letters should be used consistently in all functions

  #324 opened 5 years ago by joefresna
  2

• Multicontrollers missing some advanced options

  #353 opened 5 years ago by jarmarshall
  0

• Some rates are not properly handled in some models... probably a parser issue

  #321 opened 5 years ago by joefresna
  1

• Type error in SSA after substitution of rates

  #322 opened 5 years ago by tbose1
  18

• SSA computation is not correct for reactions with multiple occurrences of the same rate

  #346 opened 5 years ago by joefresna
  0

• Add unit tests

  #339 opened 5 years ago by willfurnass
  0

• Replace global var figcounter with matplotlib.pyplot.get_fignums()?

  #333 opened 5 years ago by willfurnass
  1

• Visualise noise in 3d stream plot

  #336 opened 5 years ago by jarmarshall
  0

• Document 1d and 3d stream plots

  #335 opened 5 years ago by jarmarshall
  0

• 1d stream plot does not appear in full after re-generation using sliders

  #329 opened 5 years ago by tbose1
  0

• Add type hints

  #328 opened 5 years ago by willfurnass
  0

• Enhance random walk computation

  #326 opened 5 years ago by jarmarshall
  0

• Update release deployment instructions / configuration

  #316 opened 5 years ago by jarmarshall
  2

• Note that need to explicitly push tags in docs on making releases

  #315 opened 5 years ago by willfurnass
  4