Parameter estimation using censored data
This Notebook explains the use of censored data for parameter estimation of ODE models. An example model is provided in pypesto/doc/example/example_censored. The implementation supports all three censoring types of measurements:
Left censored: a datapoint is below a certain known value.
Right censored: a datapoint is above a certain known value.
Interval censored: a datapoint is on an interval between two known values.
In all three cases, the exact numerical value of the datapoint is unknown. For the integration of censored measurements, we employ the optimal scaling approach. In this approach, each datapoint is represented by a variable surrogate datapoint which is constrained to be in its respective category. Categories can be thought of as intervals with specific bounds.
For censored data, the category bounds are already known from the censoring value:
for left censored data the category bounds are (0, censoring value),
for right censored data the category bounds are (censoring value, infinity),
for interval censored data the category bounds are given by the interval bounds.
This makes the identification of surrogate data extremely simple, as it can be directly (analytically) calculated.
Details on the optimal scaling approach can be found in Shepard, 1962 (https://doi.org/10.1007/BF02289621). Details on the application of the gradient-based optimal scaling approach to mechanistic modeling with ordinal data can be found in Schmiester et al. 2020 (https://doi.org/10.1007/s00285-020-01522-w) and Schmiester et al. 2021 (https://doi.org/10.1093/bioinformatics/btab512).
Import model from the petab_problem
[1]:
import matplotlib.pyplot as plt
import numpy as np
import petab
import pypesto
import pypesto.logging
import pypesto.optimize as optimize
from pypesto.petab import PetabImporter
from pypesto.visualize import plot_categories_from_pypesto_result
To use censored data for parameter estimation, in pyPESTO we use the optimal scaling approach. Since the optimal scaling approach is implemented in the hierarchical manner, it requires us to specify hierarchical=True when importing the petab_problem:
[2]:
petab_folder = "./example_censored/"
yaml_file = "example_censored.yaml"
petab_problem = petab.Problem.from_yaml(petab_folder + yaml_file)
importer = PetabImporter(petab_problem, hierarchical=True)
Visualization table not available. Skipping.
The petab_problem has to be specified in the usual PEtab formulation. The censored measurements have to be specified in the measurement.tsv file by adding the censoring type in the measurementType column, where a censoring type can be:
left-censored,right-censored,or
interval-censored.
If the censoring type is not specified, the measurement will be considered as quantitative. Then, the censoring bound has to be specified in the censoringBounds column. For interval censored measurements the bounds should be separated with a semicolon:
[3]:
from pandas import option_context
with option_context("display.max_colwidth", 400):
display(petab_problem.measurement_df)
| observableId | preequilibrationConditionId | simulationConditionId | measurement | time | observableParameters | noiseParameters | observableTransformation | noiseDistribution | measurementType | censoringBounds | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | Activity | NaN | Inhibitor_0 | 0.000000 | 5 | NaN | 1 | lin | normal | interval-censored | 10.0;16.0 |
| 1 | Activity | NaN | Inhibitor_3 | 0.000000 | 5 | NaN | 1 | lin | normal | interval-censored | 10.0;16.0 |
| 2 | Activity | NaN | Inhibitor_10 | 17.892654 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 3 | Activity | NaN | Inhibitor_25 | 0.000000 | 5 | NaN | 1 | lin | normal | right-censored | 20.0 |
| 4 | Activity | NaN | Inhibitor_35 | 16.812104 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 5 | Activity | NaN | Inhibitor_50 | 9.173129 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 6 | Activity | NaN | Inhibitor_75 | 4.150928 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 7 | Activity | NaN | Inhibitor_100 | 0.000000 | 5 | NaN | 1 | lin | normal | left-censored | 3.0 |
| 8 | Activity | NaN | Inhibitor_300 | 0.000000 | 5 | NaN | 1 | lin | normal | left-censored | 3.0 |
| 9 | Ybar | NaN | Inhibitor_0 | 0.000000 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 10 | Ybar | NaN | Inhibitor_3 | 0.059999 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 11 | Ybar | NaN | Inhibitor_10 | 0.199994 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 12 | Ybar | NaN | Inhibitor_25 | 0.499043 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 13 | Ybar | NaN | Inhibitor_35 | 0.659169 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 14 | Ybar | NaN | Inhibitor_50 | 0.814954 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 15 | Ybar | NaN | Inhibitor_75 | 0.916383 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 16 | Ybar | NaN | Inhibitor_100 | 0.948981 | 5 | NaN | 1 | lin | normal | NaN | NaN |
| 17 | Ybar | NaN | Inhibitor_300 | 0.988130 | 5 | NaN | 1 | lin | normal | NaN | NaN |
For censored measurements, the measurement column will be ignored. For the Ybar observable we didn’t specify a measurement type, so those will be used as quantitative.
Note on inclusion of additional data types:
It is possible to include observables with different types of data to the same petab_problem. Refer to the notebooks on using semiquantitative data, relative data and ordinal data for details on integration of other data types. If the measurementType column is left empty for all measurements of an observable, the observable will be treated as quantitative.
Construct the objective and pypesto problem
Now when we construct the objective, it will construct all objects of the optimal scaling inner optimization:
OrdinalInnerSolverOrdinalCalculatorOrdinalProblem
As there are no censored data specific inner options, we will pass none to the constructor.
Now let’s construct the pyPESTO problem and optimizer. We’re going to use a gradient-based optimizer for a faster optimization, but gradient-free optimizers can be used in the same way:
[4]:
problem = importer.create_problem()
engine = pypesto.engine.MultiProcessEngine(n_procs=3)
optimizer = optimize.ScipyOptimizer(
method="L-BFGS-B",
options={"disp": None, "ftol": 2.220446049250313e-09, "gtol": 1e-5},
)
n_starts = 3
np.random.seed(n_starts)
Compiling amici model to folder /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.
2026-03-09 16:35:45.634 - amici.importers.petab.v1._sbml_import - INFO - Importing model ...
2026-03-09 16:35:45.634 - amici.importers.petab.v1._sbml_import - INFO - Validating PEtab problem ...
Visualization table not available. Skipping.
2026-03-09 16:35:45.650 - amici.importers.petab.v1._sbml_import - INFO - Model name is 'Raf_Mitra_NatCom2018OptimalScaling_3CatQual'.
Writing model code to '/home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual'.
2026-03-09 16:35:45.651 - amici.importers.petab.v1._sbml_import - INFO - Species: 6
2026-03-09 16:35:45.652 - amici.importers.petab.v1._sbml_import - INFO - Global parameters: 9
2026-03-09 16:35:45.653 - amici.importers.petab.v1._sbml_import - INFO - Reactions: 6
2026-03-09 16:35:45.686 - amici.importers.petab.v1._sbml_import - INFO - Number of observables: 2
2026-03-09 16:35:45.688 - amici.importers.petab.v1._sbml_import - DEBUG - Adding output parameters to model: ['noiseParameter1_Activity', 'noiseParameter1_Ybar']
2026-03-09 16:35:45.690 - amici.importers.petab.v1._sbml_import - DEBUG - Adding initial assignments for []
2026-03-09 16:35:45.694 - amici.importers.petab.v1._sbml_import - DEBUG - Fixed parameters are ['K1', 'K2', 'init_I']
2026-03-09 16:35:45.695 - amici.importers.petab.v1._sbml_import - INFO - Overall fixed parameters: 3
2026-03-09 16:35:45.696 - amici.importers.petab.v1._sbml_import - INFO - Variable parameters: 14
2026-03-09 16:35:45.710 - amici.importers.sbml - DEBUG - Finished processing SBML annotations ++ (4.29E-04s)
2026-03-09 16:35:45.724 - amici.importers.sbml - DEBUG - Finished gathering local SBML symbols ++ (7.05E-03s)
2026-03-09 16:35:45.733 - amici.importers.sbml - DEBUG - Finished processing SBML parameters ++ (9.61E-04s)
2026-03-09 16:35:45.740 - amici.importers.sbml - DEBUG - Finished processing SBML compartments ++ (8.14E-05s)
2026-03-09 16:35:45.755 - amici.importers.sbml - DEBUG - Finished processing SBML species initials+++ (1.49E-03s)
2026-03-09 16:35:45.762 - amici.importers.sbml - DEBUG - Finished processing SBML rate rules +++ (5.50E-05s)
2026-03-09 16:35:45.763 - amici.importers.sbml - DEBUG - Finished processing SBML species ++ (1.54E-02s)
2026-03-09 16:35:45.772 - amici.importers.sbml - DEBUG - Finished processing SBML reactions ++ (1.77E-03s)
2026-03-09 16:35:45.782 - amici.importers.sbml - DEBUG - Finished processing SBML rules ++ (4.11E-03s)
2026-03-09 16:35:45.789 - amici.importers.sbml - DEBUG - Finished processing SBML events ++ (6.96E-05s)
2026-03-09 16:35:45.797 - amici.importers.sbml - DEBUG - Finished processing SBML initial assignments++ (5.30E-05s)
2026-03-09 16:35:45.803 - amici.importers.sbml - DEBUG - Finished processing SBML species references++ (2.41E-04s)
2026-03-09 16:35:45.804 - amici.importers.sbml - DEBUG - Finished importing SBML + (1.00E-01s)
2026-03-09 16:35:45.821 - amici.importers.sbml - DEBUG - Finished processing observation model + (1.00E-02s)
2026-03-09 16:35:45.887 - amici._symbolic.de_model - DEBUG - Finished simplifying Jy ++++ (1.04E-02s)
2026-03-09 16:35:45.887 - amici._symbolic.de_model - DEBUG - Finished computing Jy +++ (1.80E-02s)
2026-03-09 16:35:45.929 - amici._symbolic.de_model - DEBUG - Finished simplifying y ++++ (2.11E-03s)
2026-03-09 16:35:45.930 - amici._symbolic.de_model - DEBUG - Finished computing y +++ (1.11E-02s)
2026-03-09 16:35:45.945 - amici._symbolic.de_model - DEBUG - Finished simplifying sigmay ++++ (5.97E-05s)
2026-03-09 16:35:45.946 - amici._symbolic.de_model - DEBUG - Finished computing sigmay +++ (7.67E-03s)
2026-03-09 16:35:45.947 - amici.exporters.sundials.de_export - DEBUG - Finished writing Jy.cpp ++ (8.35E-02s)
2026-03-09 16:35:45.995 - amici._symbolic.de_model - DEBUG - Finished simplifying dJydsigma ++++ (3.45E-03s)
2026-03-09 16:35:45.995 - amici._symbolic.de_model - DEBUG - Finished computing dJydsigma +++ (3.52E-02s)
2026-03-09 16:35:45.999 - amici.exporters.sundials.de_export - DEBUG - Finished writing dJydsigma.cpp++ (4.50E-02s)
2026-03-09 16:35:46.037 - amici._symbolic.de_model - DEBUG - Finished simplifying dJydy ++++ (3.34E-03s)
2026-03-09 16:35:46.038 - amici._symbolic.de_model - DEBUG - Finished computing dJydy +++ (2.44E-02s)
2026-03-09 16:35:46.046 - amici.exporters.sundials.de_export - DEBUG - Finished writing dJydy.cpp ++ (3.91E-02s)
2026-03-09 16:35:46.065 - amici._symbolic.de_model - DEBUG - Finished simplifying Jz ++++ (4.57E-05s)
2026-03-09 16:35:46.066 - amici._symbolic.de_model - DEBUG - Finished computing Jz +++ (7.22E-03s)
2026-03-09 16:35:46.067 - amici.exporters.sundials.de_export - DEBUG - Finished writing Jz.cpp ++ (1.37E-02s)
2026-03-09 16:35:46.095 - amici._symbolic.de_model - DEBUG - Finished simplifying dJzdsigma ++++ (6.34E-05s)
2026-03-09 16:35:46.095 - amici._symbolic.de_model - DEBUG - Finished computing dJzdsigma +++ (1.48E-02s)
2026-03-09 16:35:46.096 - amici.exporters.sundials.de_export - DEBUG - Finished writing dJzdsigma.cpp++ (2.23E-02s)
2026-03-09 16:35:46.123 - amici._symbolic.de_model - DEBUG - Finished simplifying dJzdz ++++ (6.83E-05s)
2026-03-09 16:35:46.124 - amici._symbolic.de_model - DEBUG - Finished computing dJzdz +++ (1.38E-02s)
2026-03-09 16:35:46.124 - amici.exporters.sundials.de_export - DEBUG - Finished writing dJzdz.cpp ++ (2.09E-02s)
2026-03-09 16:35:46.145 - amici._symbolic.de_model - DEBUG - Finished simplifying Jrz ++++ (6.00E-05s)
2026-03-09 16:35:46.146 - amici._symbolic.de_model - DEBUG - Finished computing Jrz +++ (7.77E-03s)
2026-03-09 16:35:46.147 - amici.exporters.sundials.de_export - DEBUG - Finished writing Jrz.cpp ++ (1.49E-02s)
2026-03-09 16:35:46.174 - amici._symbolic.de_model - DEBUG - Finished simplifying dJrzdsigma ++++ (5.18E-05s)
2026-03-09 16:35:46.174 - amici._symbolic.de_model - DEBUG - Finished computing dJrzdsigma +++ (1.38E-02s)
2026-03-09 16:35:46.175 - amici.exporters.sundials.de_export - DEBUG - Finished writing dJrzdsigma.cpp++ (2.00E-02s)
2026-03-09 16:35:46.203 - amici._symbolic.de_model - DEBUG - Finished simplifying dJrzdz ++++ (5.46E-05s)
2026-03-09 16:35:46.204 - amici._symbolic.de_model - DEBUG - Finished computing dJrzdz +++ (1.46E-02s)
2026-03-09 16:35:46.205 - amici.exporters.sundials.de_export - DEBUG - Finished writing dJrzdz.cpp++ (2.25E-02s)
2026-03-09 16:35:46.225 - amici._symbolic.de_model - DEBUG - Finished simplifying root ++++ (5.25E-05s)
2026-03-09 16:35:46.225 - amici._symbolic.de_model - DEBUG - Finished computing root +++ (7.40E-03s)
2026-03-09 16:35:46.226 - amici.exporters.sundials.de_export - DEBUG - Finished writing root.cpp ++ (1.35E-02s)
2026-03-09 16:35:46.260 - amici._symbolic.de_model - DEBUG - Finished simplifying w +++++ (6.15E-03s)
2026-03-09 16:35:46.261 - amici._symbolic.de_model - DEBUG - Finished computing w ++++ (1.53E-02s)
2026-03-09 16:35:46.296 - amici._symbolic.de_model - DEBUG - Finished simplifying dwdp ++++ (2.64E-03s)
2026-03-09 16:35:46.296 - amici._symbolic.de_model - DEBUG - Finished computing dwdp +++ (5.76E-02s)
2026-03-09 16:35:46.340 - amici._symbolic.de_model - DEBUG - Finished simplifying dwdx ++++ (3.47E-03s)
2026-03-09 16:35:46.341 - amici._symbolic.de_model - DEBUG - Finished computing dwdx +++ (3.39E-02s)
2026-03-09 16:35:46.370 - amici._symbolic.de_model - DEBUG - Finished simplifying dwdw ++++ (9.42E-04s)
2026-03-09 16:35:46.371 - amici._symbolic.de_model - DEBUG - Finished computing dwdw +++ (2.00E-02s)
2026-03-09 16:35:46.375 - amici.exporters.sundials.de_export - DEBUG - Finished writing dwdp.cpp ++ (1.42E-01s)
2026-03-09 16:35:46.386 - amici.exporters.sundials.de_export - DEBUG - Finished writing dwdx.cpp ++ (3.58E-03s)
2026-03-09 16:35:46.393 - amici.exporters.sundials.de_export - DEBUG - Finished writing create_splines.cpp++ (3.64E-04s)
2026-03-09 16:35:46.421 - amici._symbolic.de_model - DEBUG - Finished simplifying spline_values+++++ (6.24E-05s)
2026-03-09 16:35:46.422 - amici._symbolic.de_model - DEBUG - Finished computing spline_values ++++ (8.92E-03s)
2026-03-09 16:35:46.437 - amici._symbolic.de_model - DEBUG - Finished simplifying dspline_valuesdp++++ (4.83E-05s)
2026-03-09 16:35:46.437 - amici._symbolic.de_model - DEBUG - Finished computing dspline_valuesdp +++ (3.18E-02s)
2026-03-09 16:35:46.438 - amici.exporters.sundials.de_export - DEBUG - Finished writing dspline_valuesdp.cpp++ (3.78E-02s)
2026-03-09 16:35:46.464 - amici._symbolic.de_model - DEBUG - Finished simplifying spline_slopes+++++ (4.55E-05s)
2026-03-09 16:35:46.465 - amici._symbolic.de_model - DEBUG - Finished computing spline_slopes ++++ (7.74E-03s)
2026-03-09 16:35:46.481 - amici._symbolic.de_model - DEBUG - Finished simplifying dspline_slopesdp++++ (5.07E-05s)
2026-03-09 16:35:46.481 - amici._symbolic.de_model - DEBUG - Finished computing dspline_slopesdp +++ (3.08E-02s)
2026-03-09 16:35:46.482 - amici.exporters.sundials.de_export - DEBUG - Finished writing dspline_slopesdp.cpp++ (3.73E-02s)
2026-03-09 16:35:46.490 - amici.exporters.sundials.de_export - DEBUG - Finished writing dwdw.cpp ++ (1.11E-03s)
2026-03-09 16:35:46.519 - amici._symbolic.de_model - DEBUG - Finished simplifying xdot +++++ (1.52E-03s)
2026-03-09 16:35:46.520 - amici._symbolic.de_model - DEBUG - Finished computing xdot ++++ (9.22E-03s)
2026-03-09 16:35:46.539 - amici._symbolic.de_model - DEBUG - Finished simplifying dxdotdw ++++ (1.53E-04s)
2026-03-09 16:35:46.540 - amici._symbolic.de_model - DEBUG - Finished computing dxdotdw +++ (3.55E-02s)
2026-03-09 16:35:46.546 - amici.exporters.sundials.de_export - DEBUG - Finished writing dxdotdw.cpp++ (4.77E-02s)
2026-03-09 16:35:46.571 - amici._symbolic.de_model - DEBUG - Finished simplifying dxdotdx_explicit++++ (4.51E-05s)
2026-03-09 16:35:46.571 - amici._symbolic.de_model - DEBUG - Finished computing dxdotdx_explicit +++ (1.36E-02s)
2026-03-09 16:35:46.573 - amici.exporters.sundials.de_export - DEBUG - Finished writing dxdotdx_explicit.cpp++ (2.03E-02s)
2026-03-09 16:35:46.601 - amici._symbolic.de_model - DEBUG - Finished simplifying dxdotdp_explicit++++ (4.61E-05s)
2026-03-09 16:35:46.602 - amici._symbolic.de_model - DEBUG - Finished computing dxdotdp_explicit +++ (1.53E-02s)
2026-03-09 16:35:46.603 - amici.exporters.sundials.de_export - DEBUG - Finished writing dxdotdp_explicit.cpp++ (2.28E-02s)
2026-03-09 16:35:46.640 - amici._symbolic.de_model - DEBUG - Finished simplifying dydx +++++ (8.18E-04s)
2026-03-09 16:35:46.641 - amici._symbolic.de_model - DEBUG - Finished computing dydx ++++ (1.90E-02s)
2026-03-09 16:35:46.675 - amici._symbolic.de_model - DEBUG - Finished simplifying dydw +++++ (9.70E-04s)
2026-03-09 16:35:46.676 - amici._symbolic.de_model - DEBUG - Finished computing dydw ++++ (2.70E-02s)
2026-03-09 16:35:46.700 - amici._symbolic.de_model - DEBUG - Finished simplifying dydx ++++ (7.36E-03s)
2026-03-09 16:35:46.701 - amici._symbolic.de_model - DEBUG - Finished computing dydx +++ (8.61E-02s)
2026-03-09 16:35:46.706 - amici.exporters.sundials.de_export - DEBUG - Finished writing dydx.cpp ++ (9.65E-02s)
2026-03-09 16:35:46.750 - amici._symbolic.de_model - DEBUG - Finished simplifying dydp +++++ (5.42E-05s)
2026-03-09 16:35:46.751 - amici._symbolic.de_model - DEBUG - Finished computing dydp ++++ (1.64E-02s)
2026-03-09 16:35:46.767 - amici._symbolic.de_model - DEBUG - Finished simplifying dydp ++++ (5.60E-05s)
2026-03-09 16:35:46.768 - amici._symbolic.de_model - DEBUG - Finished computing dydp +++ (4.03E-02s)
2026-03-09 16:35:46.768 - amici.exporters.sundials.de_export - DEBUG - Finished writing dydp.cpp ++ (4.90E-02s)
2026-03-09 16:35:46.825 - amici._symbolic.de_model - DEBUG - Finished simplifying drootdt +++++++ (6.77E-05s)
2026-03-09 16:35:46.826 - amici._symbolic.de_model - DEBUG - Finished computing drootdt ++++++ (1.56E-02s)
2026-03-09 16:35:46.859 - amici._symbolic.de_model - DEBUG - Finished simplifying drootdw +++++++ (5.72E-05s)
2026-03-09 16:35:46.859 - amici._symbolic.de_model - DEBUG - Finished computing drootdw ++++++ (1.75E-02s)
2026-03-09 16:35:46.870 - amici._symbolic.de_model - DEBUG - Finished simplifying drootdt_total++++++ (6.90E-05s)
2026-03-09 16:35:46.871 - amici._symbolic.de_model - DEBUG - Finished computing drootdt_total +++++ (6.86E-02s)
2026-03-09 16:35:46.871 - amici._symbolic.de_model - DEBUG - Finished computing dtaudx ++++ (8.27E-02s)
2026-03-09 16:35:46.873 - amici._symbolic.de_model - DEBUG - Finished computing dzdx +++ (9.08E-02s)
2026-03-09 16:35:46.873 - amici.exporters.sundials.de_export - DEBUG - Finished writing dzdx.cpp ++ (9.69E-02s)
2026-03-09 16:35:46.889 - amici._symbolic.de_model - DEBUG - Finished computing dzdp +++ (1.51E-04s)
2026-03-09 16:35:46.890 - amici.exporters.sundials.de_export - DEBUG - Finished writing dzdp.cpp ++ (7.74E-03s)
2026-03-09 16:35:46.905 - amici._symbolic.de_model - DEBUG - Finished computing drzdx +++ (1.20E-04s)
2026-03-09 16:35:46.905 - amici.exporters.sundials.de_export - DEBUG - Finished writing drzdx.cpp ++ (6.94E-03s)
2026-03-09 16:35:46.923 - amici._symbolic.de_model - DEBUG - Finished computing drzdp +++ (1.23E-04s)
2026-03-09 16:35:46.923 - amici.exporters.sundials.de_export - DEBUG - Finished writing drzdp.cpp ++ (7.91E-03s)
2026-03-09 16:35:46.957 - amici._symbolic.de_model - DEBUG - Finished simplifying dsigmaydy ++++ (7.16E-05s)
2026-03-09 16:35:46.958 - amici._symbolic.de_model - DEBUG - Finished computing dsigmaydy +++ (1.77E-02s)
2026-03-09 16:35:46.959 - amici.exporters.sundials.de_export - DEBUG - Finished writing dsigmaydy.cpp++ (2.56E-02s)
2026-03-09 16:35:46.992 - amici._symbolic.de_model - DEBUG - Finished simplifying dsigmaydp ++++ (1.09E-04s)
2026-03-09 16:35:46.993 - amici._symbolic.de_model - DEBUG - Finished computing dsigmaydp +++ (1.61E-02s)
2026-03-09 16:35:46.998 - amici.exporters.sundials.de_export - DEBUG - Finished writing dsigmaydp.cpp++ (2.84E-02s)
2026-03-09 16:35:47.009 - amici.exporters.sundials.de_export - DEBUG - Finished writing sigmay.cpp++ (4.89E-04s)
2026-03-09 16:35:47.042 - amici._symbolic.de_model - DEBUG - Finished simplifying sigmaz +++++ (6.91E-05s)
2026-03-09 16:35:47.043 - amici._symbolic.de_model - DEBUG - Finished computing sigmaz ++++ (1.02E-02s)
2026-03-09 16:35:47.061 - amici._symbolic.de_model - DEBUG - Finished simplifying dsigmazdp ++++ (6.77E-05s)
2026-03-09 16:35:47.061 - amici._symbolic.de_model - DEBUG - Finished computing dsigmazdp +++ (3.66E-02s)
2026-03-09 16:35:47.062 - amici.exporters.sundials.de_export - DEBUG - Finished writing dsigmazdp.cpp++ (4.31E-02s)
2026-03-09 16:35:47.071 - amici.exporters.sundials.de_export - DEBUG - Finished writing sigmaz.cpp++ (1.17E-05s)
2026-03-09 16:35:47.087 - amici._symbolic.de_model - DEBUG - Finished computing stau +++ (1.27E-04s)
2026-03-09 16:35:47.088 - amici.exporters.sundials.de_export - DEBUG - Finished writing stau.cpp ++ (8.11E-03s)
2026-03-09 16:35:47.105 - amici._symbolic.de_model - DEBUG - Finished computing deltax +++ (1.07E-04s)
2026-03-09 16:35:47.105 - amici.exporters.sundials.de_export - DEBUG - Finished writing deltax.cpp++ (9.22E-03s)
2026-03-09 16:35:47.125 - amici._symbolic.de_model - DEBUG - Finished computing deltasx +++ (1.35E-04s)
2026-03-09 16:35:47.126 - amici.exporters.sundials.de_export - DEBUG - Finished writing deltasx.cpp++ (9.16E-03s)
2026-03-09 16:35:47.145 - amici._symbolic.de_model - DEBUG - Finished computing deltaxB +++ (1.16E-04s)
2026-03-09 16:35:47.146 - amici.exporters.sundials.de_export - DEBUG - Finished writing deltaxB.cpp++ (8.86E-03s)
2026-03-09 16:35:47.165 - amici._symbolic.de_model - DEBUG - Finished computing deltaqB +++ (1.25E-04s)
2026-03-09 16:35:47.166 - amici.exporters.sundials.de_export - DEBUG - Finished writing deltaqB.cpp++ (9.28E-03s)
2026-03-09 16:35:47.181 - amici.exporters.sundials.de_export - DEBUG - Finished writing w.cpp ++ (3.75E-03s)
2026-03-09 16:35:47.204 - amici._symbolic.de_model - DEBUG - Finished simplifying x0 ++++ (1.72E-04s)
2026-03-09 16:35:47.205 - amici._symbolic.de_model - DEBUG - Finished computing x0 +++ (8.12E-03s)
2026-03-09 16:35:47.207 - amici.exporters.sundials.de_export - DEBUG - Finished writing x0.cpp ++ (1.60E-02s)
2026-03-09 16:35:47.230 - amici._symbolic.de_model - DEBUG - Finished simplifying x0_fixedParameters++++ (6.88E-05s)
2026-03-09 16:35:47.230 - amici._symbolic.de_model - DEBUG - Finished computing x0_fixedParameters+++ (8.15E-03s)
2026-03-09 16:35:47.232 - amici.exporters.sundials.de_export - DEBUG - Finished writing x0_fixedParameters.cpp++ (1.56E-02s)
2026-03-09 16:35:47.263 - amici._symbolic.de_model - DEBUG - Finished simplifying sx0 ++++ (6.64E-05s)
2026-03-09 16:35:47.264 - amici._symbolic.de_model - DEBUG - Finished computing sx0 +++ (1.53E-02s)
2026-03-09 16:35:47.266 - amici.exporters.sundials.de_export - DEBUG - Finished writing sx0.cpp ++ (2.40E-02s)
2026-03-09 16:35:47.320 - amici._symbolic.de_model - DEBUG - Finished simplifying sx0_fixedParameters++++ (7.51E-05s)
2026-03-09 16:35:47.321 - amici._symbolic.de_model - DEBUG - Finished computing sx0_fixedParameters+++ (3.30E-02s)
2026-03-09 16:35:47.322 - amici.exporters.sundials.de_export - DEBUG - Finished writing sx0_fixedParameters.cpp++ (4.45E-02s)
2026-03-09 16:35:47.336 - amici.exporters.sundials.de_export - DEBUG - Finished writing xdot.cpp ++ (2.74E-03s)
2026-03-09 16:35:47.351 - amici.exporters.sundials.de_export - DEBUG - Finished writing y.cpp ++ (1.24E-03s)
2026-03-09 16:35:47.384 - amici._symbolic.de_model - DEBUG - Finished simplifying x_rdata ++++ (1.07E-04s)
2026-03-09 16:35:47.385 - amici._symbolic.de_model - DEBUG - Finished computing x_rdata +++ (1.21E-02s)
2026-03-09 16:35:47.387 - amici.exporters.sundials.de_export - DEBUG - Finished writing x_rdata.cpp++ (2.40E-02s)
2026-03-09 16:35:47.418 - amici._symbolic.de_model - DEBUG - Finished simplifying total_cl ++++ (8.40E-05s)
2026-03-09 16:35:47.419 - amici._symbolic.de_model - DEBUG - Finished computing total_cl +++ (1.12E-02s)
2026-03-09 16:35:47.421 - amici.exporters.sundials.de_export - DEBUG - Finished writing total_cl.cpp++ (2.22E-02s)
2026-03-09 16:35:47.454 - amici._symbolic.de_model - DEBUG - Finished simplifying dtotal_cldp ++++ (7.55E-05s)
2026-03-09 16:35:47.455 - amici._symbolic.de_model - DEBUG - Finished computing dtotal_cldp +++ (1.52E-02s)
2026-03-09 16:35:47.456 - amici.exporters.sundials.de_export - DEBUG - Finished writing dtotal_cldp.cpp++ (2.47E-02s)
2026-03-09 16:35:47.477 - amici._symbolic.de_model - DEBUG - Finished simplifying dtotal_cldx_rdata++++ (5.86E-05s)
2026-03-09 16:35:47.478 - amici._symbolic.de_model - DEBUG - Finished computing dtotal_cldx_rdata+++ (7.63E-03s)
2026-03-09 16:35:47.479 - amici.exporters.sundials.de_export - DEBUG - Finished writing dtotal_cldx_rdata.cpp++ (1.50E-02s)
2026-03-09 16:35:47.502 - amici._symbolic.de_model - DEBUG - Finished simplifying x_solver ++++ (1.02E-04s)
2026-03-09 16:35:47.503 - amici._symbolic.de_model - DEBUG - Finished computing x_solver +++ (7.77E-03s)
2026-03-09 16:35:47.505 - amici.exporters.sundials.de_export - DEBUG - Finished writing x_solver.cpp++ (1.63E-02s)
2026-03-09 16:35:47.528 - amici._symbolic.de_model - DEBUG - Finished simplifying dx_rdatadx_solver++++ (7.39E-05s)
2026-03-09 16:35:47.529 - amici._symbolic.de_model - DEBUG - Finished computing dx_rdatadx_solver+++ (8.50E-03s)
2026-03-09 16:35:47.530 - amici.exporters.sundials.de_export - DEBUG - Finished writing dx_rdatadx_solver.cpp++ (1.62E-02s)
2026-03-09 16:35:47.556 - amici._symbolic.de_model - DEBUG - Finished simplifying dx_rdatadp ++++ (7.69E-05s)
2026-03-09 16:35:47.557 - amici._symbolic.de_model - DEBUG - Finished computing dx_rdatadp +++ (8.70E-03s)
2026-03-09 16:35:47.557 - amici.exporters.sundials.de_export - DEBUG - Finished writing dx_rdatadp.cpp++ (1.67E-02s)
2026-03-09 16:35:47.600 - amici._symbolic.de_model - DEBUG - Finished simplifying dx_rdatadtcl ++++ (7.48E-05s)
2026-03-09 16:35:47.601 - amici._symbolic.de_model - DEBUG - Finished computing dx_rdatadtcl +++ (2.08E-02s)
2026-03-09 16:35:47.602 - amici.exporters.sundials.de_export - DEBUG - Finished writing dx_rdatadtcl.cpp++ (3.19E-02s)
2026-03-09 16:35:47.616 - amici._symbolic.de_model - DEBUG - Finished computing z +++ (1.20E-04s)
2026-03-09 16:35:47.616 - amici.exporters.sundials.de_export - DEBUG - Finished writing z.cpp ++ (6.40E-03s)
2026-03-09 16:35:47.631 - amici._symbolic.de_model - DEBUG - Finished computing rz +++ (1.25E-04s)
2026-03-09 16:35:47.632 - amici.exporters.sundials.de_export - DEBUG - Finished writing rz.cpp ++ (7.49E-03s)
2026-03-09 16:35:47.639 - amici.exporters.sundials.de_export - DEBUG - Finished writing explicit_roots.cpp++ (7.94E-05s)
2026-03-09 16:35:47.647 - amici.exporters.sundials.de_export - DEBUG - Finished generating cpp code+ (1.79E+00s)
2026-03-09 16:36:02.048 - amici.exporters.sundials.de_export - DEBUG - Finished compiling cpp code + (1.44E+01s)
2026-03-09 16:36:02.055 - amici.importers.petab.v1._sbml_import - INFO - Finished Importing PEtab model (1.64E+01s)
running build_ext
------------------------------ model_ext ------------------------------
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-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- CMAKE_CURRENT_SOURCE_DIR: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual
-- CMAKE_BINARY_DIR: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext
-- CMAKE_INSTALL_PREFIX: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/Raf_Mitra_NatCom2018OptimalScaling_3CatQual
-- CMAKE_VERSION: 4.2.3
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-- Performing Test CUR_FLAG_SUPPORTED - Success
-- Performing Test CUR_FLAG_SUPPORTED
-- Performing Test CUR_FLAG_SUPPORTED - Success
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-- Trying to find OpenBLAS in CONFIG mode (scipy-openblas64)
-- Found OpenBLAS in CONFIG mode (OpenBLAS_DIR=/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/cmake/openblas)
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5") found components: CXX
-- SuiteSparse_config version: 7.8.2
-- SuiteSparse_config include: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/suitesparse
-- SuiteSparse_config library: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsuitesparseconfig.a
-- SuiteSparse_config static: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsuitesparseconfig.a
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-- BTF include: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/suitesparse
-- BTF library: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libbtf.a
-- BTF static: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libbtf.a
-- AMD version: 3.3.3
-- AMD include: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/suitesparse
-- AMD library: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libamd.a
-- AMD static: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libamd.a
-- COLAMD version: 3.3.4
-- COLAMD include: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/suitesparse
-- COLAMD library: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libcolamd.a
-- COLAMD static: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libcolamd.a
-- KLU version: 2.3.4
-- KLU include: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/suitesparse
-- KLU library: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libklu.a
-- KLU static: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libklu.a
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.10") found components: C HL CXX
-- Found AMICI /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/cmake/Amici
CMake Warning at CMakeLists.txt:122 (find_package):
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Add the installation prefix of "Boost" to CMAKE_PREFIX_PATH or set
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-- Found SWIG: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/bin/swig4.0 (found version "4.4.1")
-- Found Python3: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/bin/python (found version "3.11.12") found components: Interpreter Development Development.Module Development.Embed
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-- Build files have been written to: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext
Change Dir: '/home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext'
Run Build Command(s): /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/bin/ninja -v
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[22/25] : && /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/cmake/data/bin/cmake -E rm -f libRaf_Mitra_NatCom2018OptimalScaling_3CatQual.a && /usr/bin/ar qc libRaf_Mitra_NatCom2018OptimalScaling_3CatQual.a CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/Jy.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/create_splines.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dJydsigma.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dJydy.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dsigmaydp.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dwdp.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dwdw.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dwdx.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dxdotdw.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/dydx.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/sigmay.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/sx0_fixedParameters.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/w.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/wrapfunctions.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/x0.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/x0_fixedParameters.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/x_rdata.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/x_solver.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/xdot.cpp.o CMakeFiles/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/y.cpp.o && /usr/bin/ranlib libRaf_Mitra_NatCom2018OptimalScaling_3CatQual.a && :
[23/25] cd /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext/swig && /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/cmake/data/bin/cmake -E make_directory /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext/swig/CMakeFiles/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext/swig /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext/swig/CMakeFiles/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir && /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/cmake/data/bin/cmake -E env SWIG_LIB=/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/swig/data/share/swig/4.4.1 /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/bin/swig4.0 -python -I/home/docs/.asdf/installs/python/3.11.12/include/python3.11 -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/share/amici/swig -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/swig/.. -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/../swig -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual -I/usr/include/hdf5/serial -outdir /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext/swig -c++ -interface _Raf_Mitra_NatCom2018OptimalScaling_3CatQual -I/home/docs/.asdf/installs/python/3.11.12/include/python3.11 -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/share/amici/swig -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/swig/.. -I/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/include/../swig -o /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext/swig/CMakeFiles/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/Raf_Mitra_NatCom2018OptimalScaling_3CatQualPYTHON_wrap.cxx /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/swig/Raf_Mitra_NatCom2018OptimalScaling_3CatQual.i
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[25/25] : && /usr/bin/c++ -fPIC -Wall -Wno-unused-function -Wno-unused-variable -Wno-unused-but-set-variable -O3 -DNDEBUG -shared -Wl,--dependency-file=swig/CMakeFiles/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/link.d -o swig/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.cpython-311-x86_64-linux-gnu.so swig/CMakeFiles/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/CMakeFiles/_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.dir/Raf_Mitra_NatCom2018OptimalScaling_3CatQualPYTHON_wrap.cxx.o -Wl,-rpath,/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib:/usr/lib/x86_64-linux-gnu/hdf5/serial libRaf_Mitra_NatCom2018OptimalScaling_3CatQual.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libamici.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_nvecserial.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolspbcgs.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolspfgmr.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolspgmr.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolsptfqmr.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_cvodes.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_idas.a /usr/lib/gcc/x86_64-linux-gnu/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -ldl /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libscipy_openblas64_.so /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunnonlinsolnewton.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunnonlinsolfixedpoint.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolklu.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunmatrixsparse.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libklu.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libamd.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libcolamd.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsuitesparseconfig.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libbtf.a -lm /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolband.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunmatrixband.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsoldense.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunmatrixdense.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_sunlinsolpcg.a /home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation/lib/libsundials_core.a -lm /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so && :
-- Installing: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/./Raf_Mitra_NatCom2018OptimalScaling_3CatQual.py
-- Installing: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/./_Raf_Mitra_NatCom2018OptimalScaling_3CatQual.cpython-311-x86_64-linux-gnu.so
-- Installing: /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/lib/libRaf_Mitra_NatCom2018OptimalScaling_3CatQual.a
------------------------------ model_ext ------------------------------
running AmiciBuildCMakeExtension
==> Configuring:
$ cmake -S /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual -B /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext -G Ninja -DCMAKE_MAKE_PROGRAM=/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/bin/ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=/home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/Raf_Mitra_NatCom2018OptimalScaling_3CatQual -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH='/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation;/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/amici/_installation' -DAMICI_PYTHON_BUILD_EXT_ONLY=ON -DPython3_EXECUTABLE=/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/bin/python
==> Building:
$ cmake --build /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext --config Release
==> Installing:
$ cmake --install /home/docs/checkouts/readthedocs.org/user_builds/pypesto/checkouts/1652/doc/example/amici_models/1.0.0/Raf_Mitra_NatCom2018OptimalScaling_3CatQual/build_model_ext --config Release
Run optimization using optimal scaling approach
[5]:
np.random.seed(n_starts)
res = optimize.minimize(
problem, n_starts=n_starts, optimizer=optimizer, engine=engine
)
Visualizing the result
[6]:
from pypesto.visualize import waterfall
waterfall(res)
[6]:
<Axes: title={'center': 'Waterfall plot'}, xlabel='Ordered optimizer run', ylabel='Objective value (offset=-1.554e+01)'>
We can plot the censoring categories using the plot_categories_from_pypesto_result plotting function.
[7]:
plot_categories_from_pypesto_result(res, figsize=(15, 10))
plt.show()
/home/docs/checkouts/readthedocs.org/user_builds/pypesto/envs/1652/lib/python3.11/site-packages/pypesto/visualize/ordinal_categories.py:91: RuntimeWarning: The following problem parameters were not used: {'K2', 'K1'}
fill_in_parameters(
