Conversation
|
Here a first draft. @FFroehlich @dilpath: Would that work for you? Any better suggestions? |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #2963 +/- ##
==========================================
- Coverage 76.51% 74.46% -2.05%
==========================================
Files 307 302 -5
Lines 19992 19849 -143
Branches 1500 1500
==========================================
- Hits 15296 14781 -515
- Misses 4683 5055 +372
Partials 13 13
Flags with carried forward coverage won't be shown. Click here to find out more.
🚀 New features to boost your workflow:
|
dilpath
left a comment
dilpath
left a comment
There was a problem hiding this comment.
Works for me 👍 I would also be fine with removing Model.simulate_multiple and instead adapting Model.simulate to support edatas = ExpData | list[ExpData].
| solver.setSensitivityOrder(amici.SensitivityOrder.first) | ||
| solver.setSensitivityMethod(amici.SensitivityMethod.forward) | ||
| rdata = amici.runAmiciSimulation(model, solver) | ||
| rdata = model.simulate(sensi_order="first", sensi_method="forward") |
There was a problem hiding this comment.
| rdata = model.simulate(sensi_order="first", sensi_method="forward") | |
| rdata = model.simulate(sensi_order=amici.SensitivityOrder.first, sensi_method=amici.SensitivityMethod.forward) |
There was a problem hiding this comment.
Both are supported. I like the former, because it's less verbose, in particular for interactive use.
Thanks. Yeah, I am divided on that one. |
I think my concerns are easily addressable by two |
dweindl
force-pushed
the
gh-2944-simulate
branch
from
bf1cdb6 to
75fba39
Compare
yes looks great! |
dweindl
force-pushed
the
gh-2944-simulate
branch
2 times, most recently
from
d9d4017 to
addf172
Compare
dweindl
changed the title
amici.runAmiciSimulation -> Model.simulateModel.simulate
dweindl
force-pushed
the
gh-2944-simulate
branch
from
addf172 to
bd60500
Compare
Add `Model.simulate()` as a convenience function to run simulations without having to create a `Solver` object explicitly. This is a wrapper for both `amici.run_simulation` and `amici.run_simulations`, depending on the type of the `edata` argument. It also supports passing some `Solver` options as keyword arguments.
dweindl
force-pushed
the
gh-2944-simulate
branch
from
bd60500 to
6c2d9cc
Compare
3 participants
ReplaceComplement the oldamici.runAmiciSimulation,amici.runAmiciSimulationsbywith something more convenient.Related to #2944.