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python interface should be able to continue existing simulations #514

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lkeegan opened this issue Apr 28, 2021 · 0 comments · Fixed by #515
Closed

python interface should be able to continue existing simulations #514

lkeegan opened this issue Apr 28, 2021 · 0 comments · Fixed by #515
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enhancement New feature or request python Python library

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@lkeegan
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lkeegan commented Apr 28, 2021

  • both the GUI and CLI can import an existing simulation from an sme file and continue the simulation
  • currently this is not possible in sme: any existing simulation results are first cleared before simulating
  • also the results are returned by simulate(), and constructed at each timestep using the simulator concentrations, so existing simulation results are also currently missing from the python interface
@lkeegan lkeegan added enhancement New feature or request python Python library labels Apr 28, 2021
lkeegan added a commit that referenced this issue Apr 29, 2021
@lkeegan
add support for continuing existing simulations in python lib
21edca5 
- add `continue_existing_simulation` arg to `Model.simulate()`
  - default value `False` to avoid changing existing default behaviour of `simulate()`
- `simulate()` now returns all simulation results (not just the ones it generated)
  - `species_dcdt` is now only provided for pixel simulations and for the last timepoint
  - this is not part of `SimulationData`, but is currently used for steady-state python fitting
- add `Model.export_sme_file()` and `sme.import_file()` to allow import/export of sme files
- add `simulate()` overload that takes strings instead of floats for lengths/intervals
  - allows comma-delimited lists of lengths&intervals as in GUI & CLI
- resolves #514
@lkeegan lkeegan mentioned this issue Apr 29, 2021
Merged
lkeegan added a commit that referenced this issue Apr 29, 2021
@lkeegan
add support for continuing existing simulations in python lib
4287006 
- add `continue_existing_simulation` arg to `Model.simulate()`
  - default value `False` to avoid changing existing default behaviour of `simulate()`
- `simulate()` now returns all simulation results (not just the ones it generated)
  - `species_dcdt` is now only provided for pixel simulations and for the last timepoint
  - this is not part of `SimulationData`, but is currently used for steady-state python fitting
- add `Model.export_sme_file()` and `sme.import_file()` to allow import/export of sme files
- add `simulate()` overload that takes strings instead of floats for lengths/intervals
  - allows comma-delimited lists of lengths&intervals as in GUI & CLI
- resolves #514
lkeegan added a commit that referenced this issue Apr 29, 2021
@lkeegan
add support for continuing existing simulations in python lib (#515)
77ad0cd 
- add `continue_existing_simulation` arg to `Model.simulate()`
  - default value `False` to avoid changing existing default behaviour of `simulate()`
- `simulate()` now returns all simulation results (not just the ones it generated)
  - `species_dcdt` is now only provided for pixel simulations and for the last timepoint
  - this is not part of `SimulationData`, but is currently used for steady-state python fitting
- add `Model.export_sme_file()` and `sme.import_file()` to allow import/export of sme files
- add `simulate()` overload that takes strings instead of floats for lengths/intervals
  - allows comma-delimited lists of lengths&intervals as in GUI & CLI
- resolves #514
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@lkeegan