CLI options - Githubissues

CovertLab / vEcoli

Whole cell model of E. coli implemented with Vivarium

https://covertlab.github.io/vEcoli/

MIT License

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CLI options #29

Closed Robotato closed 4 months ago

Robotato commented 3 years ago

This list represents options that are intended to be added to the command line interface for vivarium-ecoli.

Options taken from wcEcoli:

[x] random seed (-seed SEED)
[x] number of generations (-g GENERATIONS)
[x] length of simulation in seconds (--length-sec LENGTH_SEC)
[ ] variant (-?)
[ ] whether to enable growth rate noise (--growth-rate-noise)
[ ] environmental perturbation timeline (-t TIMELINE)
[x] path to sim_data ([SIM_DIR])

New in vivarium-ecoli:

[x] database emitter (-?)
[x] modifying parameter values (possibly - PARAMETER_PATH PARAMETER_VALUE ?)
[x] model customization and swapping (details subject to change)
- inclusion/removal: (-models MODEL_NAMES) (-exclude MODEL_NAMES)
- swapping (- VARIANT_NAME)

thalassemia commented 4 months ago

De-prioritized CLI in favor of unified JSON configuration interface.