search

yaml2sbml-dev / yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.
https://yaml2sbml.readthedocs.io/en/latest/
Other
12 stars 7 forks source link

Error in creation of PEtab tables for the model #138

Open aidinbii opened 1 year ago

aidinbii commented 1 year ago

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 

yaml_file_petab = 'ODEs_HuImm_PKN3_MM1_timeDep.yml'
PEtab_dir = './PKN3_MM1_PETAB/'
PEtab_yaml_name = 'problem.yml'
measurement_table_name = 'measurement_table.tsv'
model_name = 'PKN3_MM1_model'

yaml2sbml.yaml2petab(yaml_file_petab,
                     PEtab_dir,
                     model_name,
                     PEtab_yaml_name,
                     measurement_table_name,
                    )

I get the following error:

File ~/miniconda3/envs/amici_env/lib/python3.10/site-packages/yaml2sbml/yaml2PEtab.py:287, in validate_petab_tables(sbml_dir, output_dir)
    283 if os.path.exists(condition_table_dir):
    284     condition_df = pd.read_csv(condition_table_dir,
    285                                sep='\t',
    286                                index_col='conditionId')
--> 287     petab.lint.check_condition_df(condition_df, model)
    289 # check parameter table
    290 parameter_df = pd.read_csv(parameter_file_dir,
    291                            sep='\t',
    292                            index_col='parameterId')

File ~/miniconda3/envs/amici_env/lib/python3.10/site-packages/petab/lint.py:123, in check_condition_df(df, model, observable_df)
    119         assert_no_leading_trailing_whitespace(
    120             df[column_name].values, column_name)
    122 if model is not None:
--> 123     allowed_cols = set(model.get_valid_ids_for_condition_table())
    124     if observable_df is not None:
    125         allowed_cols |= set(petab.get_output_parameters(
    126             model=model, observable_df=observable_df))

AttributeError: 'Model' object has no attribute 'get_valid_ids_for_condition_table'

The model instance was created:

model = model_module.getModel()

Could you please help me out and explain this error

Thanks!

jvanhoefer commented 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?

jvanhoefer commented 1 year ago

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?

aidinbii commented 1 year ago

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

jvanhoefer commented 1 year ago

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?

jvanhoefer commented 1 year ago

so ignoring the fact, that the linter complains...

aidinbii commented 1 year ago

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
yannikschaelte commented 1 year ago

I believe we can reproduce this error here https://github.com/yaml2sbml-dev/yaml2sbml/pull/139

aidinbii commented 1 year ago

@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

jvanhoefer commented 1 year ago

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... :)

shoepfl commented 1 year ago

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