Open aidinbii opened 1 year ago
Hey Aidin,
sure, could you maybe share the petab
version you are using? And the part regarding conditions of your yaml-file?
As the error is thrown in the last step of the PEtab
generation, when basically all the tables have been generated and stored and only are validated: Could you have a look into the PEtab model? There should a condition sable be stored somewhere? How does this look? As expected?
Of course, petab version: 0.1.30
My problem.yml file:
format_version: 1
parameter_file: parameters_PKN3_MM1_model.tsv
problems:
- condition_files:
- experimental_conditions_PKN3_MM1_model.tsv
measurement_files:
- measurement_table.tsv
observable_files:
- observables_PKN3_MM1_model.tsv
sbml_files:
- PKN3_MM1_model.xml
and ODEs_HuImm_PKN3_MM1_timeDep.yml
conditions:
- conditionId: condition1
You mean the .xml file (PKN3_MM1_model.xml)?
Yes, the generated experimental_conditions_PKN3_MM1_model.tsv file has a single row and column (conditionId) with value: condition1
In general this looks good, this is similar to the standard one-condition table, e.g. by Crust 2017: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/master/Benchmark-Models/Crauste_CellSystems2017/experimentalCondition_Crauste_CellSystems2017.tsv
Probably importing your model into pypesto in the following section fails, right?
so ignoring the fact, that the linter complains...
In general this looks good, this is similar to the standard one-condition table, e.g. by Crust 2017: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/master/Benchmark-Models/Crauste_CellSystems2017/experimentalCondition_Crauste_CellSystems2017.tsv
Probably importing your model into pypesto in the following section fails, right?
No, not exactly. I have only one column
conditionId
1 condition1
When importing the model it returns:
Measurement table not available. Skipping.
Parameter table not available. Skipping.
Not all files of the PEtab problem definition could be checked.
running AmiciInstall
Adding OpenMP flags...
running build_ext
Changed extra_compile_args for unix to ['-fopenmp', '-std=c++14']
Building model extension in /home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model
building 'PKN3_MM1_model._PKN3_MM1_model' extension
Testing SWIG executable swig4.0... FAILED.
Testing SWIG executable swig3.0... FAILED.
Testing SWIG executable swig... SUCCEEDED.
swigging swig/PKN3_MM1_model.i to swig/PKN3_MM1_model_wrap.cpp
swig -python -c++ -modern -outdir PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/swig -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -o swig/PKN3_MM1_model_wrap.cpp swig/PKN3_MM1_model.i
Deprecated command line option: -modern. This option is now always on.
creating build
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/swig
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_Jy.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_Jy.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dJydsigma.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydsigma.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dJydy.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydy.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dJydy_colptrs.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydy_colptrs.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dJydy_rowvals.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydy_rowvals.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dsigmaydp.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dsigmaydp.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dxdotdp_explicit.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdp_explicit.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dxdotdp_explicit_colptrs.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdp_explicit_colptrs.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dxdotdp_explicit_rowvals.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdp_explicit_rowvals.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dxdotdx_explicit.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdx_explicit.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dxdotdx_explicit_colptrs.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdx_explicit_colptrs.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dxdotdx_explicit_rowvals.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdx_explicit_rowvals.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dydp.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dydp.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_dydx.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dydx.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_sigmay.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_sigmay.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_x0.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_x0.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_x_rdata.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_x_rdata.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_x_solver.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_x_solver.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_xdot.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_xdot.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c PKN3_MM1_model_y.cpp -o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_y.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c swig/PKN3_MM1_model_wrap.cpp -o build/temp.linux-x86_64-cpython-310/swig/PKN3_MM1_model_wrap.o -fopenmp -std=c++14
gcc -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -O2 -isystem /home/aidin/miniconda3/envs/amici_env/include -fPIC -I/home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/gsl -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/sundials/include -I/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/ThirdParty/SuiteSparse/include -I/home/aidin/miniconda3/envs/amici_env/include/python3.10 -c wrapfunctions.cpp -o build/temp.linux-x86_64-cpython-310/wrapfunctions.o -fopenmp -std=c++14
g++ -pthread -B /home/aidin/miniconda3/envs/amici_env/compiler_compat -shared -Wl,-rpath,/home/aidin/miniconda3/envs/amici_env/lib -Wl,-rpath-link,/home/aidin/miniconda3/envs/amici_env/lib -L/home/aidin/miniconda3/envs/amici_env/lib -Wl,-rpath,/home/aidin/miniconda3/envs/amici_env/lib -Wl,-rpath-link,/home/aidin/miniconda3/envs/amici_env/lib -L/home/aidin/miniconda3/envs/amici_env/lib build/temp.linux-x86_64-cpython-310/PKN3_MM1_model.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_Jy.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydsigma.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydy.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydy_colptrs.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dJydy_rowvals.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dsigmaydp.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdp_explicit.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdp_explicit_colptrs.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdp_explicit_rowvals.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdx_explicit.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdx_explicit_colptrs.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dxdotdx_explicit_rowvals.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dydp.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_dydx.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_sigmay.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_x0.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_x_rdata.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_x_solver.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_xdot.o build/temp.linux-x86_64-cpython-310/PKN3_MM1_model_y.o build/temp.linux-x86_64-cpython-310/swig/PKN3_MM1_model_wrap.o build/temp.linux-x86_64-cpython-310/wrapfunctions.o -L/home/aidin/miniconda3/envs/amici_env/lib/python3.10/site-packages/amici/libs -lamici -lsundials -lsuitesparse -lcblas -o /home/aidin/Documents/tum_courses/hiwi_Atefeh/alivexbiotech/projects/huimmb/repo/python/amici_simulations/PKN3_MM1/amici_models/PKN3_MM1_model/PKN3_MM1_model/_PKN3_MM1_model.cpython-310-x86_64-linux-gnu.so -fopenmp -lcblas
I believe we can reproduce this error here https://github.com/yaml2sbml-dev/yaml2sbml/pull/139
@jvanhoefer, btw I also get the same error while running the example notebook: https://github.com/yaml2sbml-dev/yaml2sbml/blob/main/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb
So, now I am also able to reproduce the issue locally at my laptop. Seems like something broke in recent PEtab updatdes. Meaning two things:
1) @aidinbii A pragmatic quick fix for you might be downgrading to PEtab 0.1.26 for which I didn't have the issues yet.
2) Find out if this is maybe not rather a PEtab issue (given that it happens deeper in the PEtab linter...) and propose a fix either in PEtab or yaml2sbml. This might take some days, until I have this fixed... :)
Hi there,
I encountered the same problem for my model. However, downgrading is in my eyes not a good option and ignoring the error is also not nice as I would like to have calculations afterwards in the same script. Is there a possibility to deactivate linting?
Thanks in advance
Hi, I'm following this notebook: https://github.com/yaml2sbml-dev/yaml2sbml/blob/main/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb
After running
I get the following error:
The model instance was created:
Could you please help me out and explain this error
Thanks!