Example rework #737
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Example rework #737
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Updated Example folder. Example folder much much easier to navigate and understand
Changed all instances of .append in os path to .insert at position 1. Changed as many instances of "solver =" to "algorithm = "
Got rid of deprecated or removed functions calls. Model is precompiled on time comparisons to prevent massive performance hit due to running make each run. Light edits throughout examples folder as well.
JoshuaFisherC
requested review from
briandrawert,
jtcooper10 and
BryanRumsey
BryanRumsey
requested changes
Mar 8, 2022
There was a problem hiding this comment.
Remove all un-used solver imports and commented code
Dask worker space directory shouldn't be pushed up to github.
GillesPy2_photosynthesis_ex.pdf contians an image with a simulation error.
CLE_examples_convergence.ipynb
- Replace
solver=SSACSolverwithalgorithm=SSA - Replace
solver=ODECSolverwithalgorithm=ODE
- Reference to
BasicTauHybridSolverin code block 1. - Update the note in code block 1 to include
TauHybridCSolveras a viable solver for events.
Run GillesPy2 Simulations in Parallel.ipynb
- Notebook shouldn't contain a port warning.
- Replace deprecated
plot_std_dev_rangewithplot_mean_stdev.
- Download link for sbml file is broken. The correct link is
https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000028.2?filename=BIOMD0000000028_url.xml
TauHybridCSolveris missing from the notebook docs.- The final plot cell contains a simulation error.
hybrid_continuous_species.ipynb
- Reference to
Basic Tau Hybrid Solverin notebook header. - Plot contains a simulation error.
- Remove deprecated function call
plot_std_dev_range. - Remove deprecated function call
plotplotly_std_dev_range.
- Remove the incorrect comment:
#Default solver for model.run() is the VariableSSACSolver. For more information,
# checkout /examples/AdvancedFeatures/Variable_SSA_C_Example.ipynb
- Reference to
Basic Tau Leapingin notebook header. - Reference to deprecated
show_labelsin notebook docs forRun Model and plot.
- Replace
solver=SSACSolverwithalgorithm=SSA. - Replace
solver=ODESolverwithalgorithm=ODE.
TauSolverRunTimeComparison.ipynb
- initial_condition of
Vshould be set tonin for loop and should work with python and c solvers. - Instantiate
timing_dataas an empty dict.
- Needs to be updated to match the notebook or removed.
- Reference to deprecated
show_labelsin notebook docs forRun Model and plot.
- Reference to deprecated
show_labelsin notebook docs forRun Model and plot.
- Remove warnings import
- Remove cell with solver imports
BryanRumsey
requested changes
Mar 15, 2022
BryanRumsey
approved these changes
Mar 16, 2022
briandrawert
approved these changes
Mar 24, 2022
jtcooper10
approved these changes
Mar 24, 2022
Merged
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Extensive update to entire examples folder to make it more beginner friendly. Also updated deprecated functions in results.py to correctly display a deprecation warning.