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!
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!