Error running on Colab

[deebnrg]

Hi,
I tried running riptide o colab notebook after pip install riptide and pip install symengine.

On running the following code:
import riptide
import cobra
import symengine

my_model = cobra.io.read_sbml_model('genre.sbml')

transcript_abundances_1 = riptide.read_transcription_file('transcriptome1.tsv')
transcript_abundances_2 = riptide.read_transcription_file('transcriptome2.tsv') # has replicates

riptide_object_1_a = riptide.contextualize(model=my_model, transcriptome=transcript_abundances_1)
riptide_object_1_b = riptide.contextualize(model=my_model, transcriptome=transcript_abundances_1, tasks=['rxn1'], exclude=['rxn2','rxn3'])

riptide.save_output(riptide_obj=riptide_object_1_a, path='~/Desktop/example_riptide_output')

This is the error i get:

Initializing model and integrating transcriptomic data...
Pruning zero flux subnetworks...

AttributeError Traceback (most recent call last)
/tmp/ipython-input-575827912.py in <cell line: 0>()
8 transcript_abundances_2 = riptide.read_transcription_file('transcriptome2.tsv') # has replicates
9
---> 10 riptide_object_1_a = riptide.contextualize(model=my_model, transcriptome=transcript_abundances_1)
11 riptide_object_1_b = riptide.contextualize(model=my_model, transcriptome=transcript_abundances_1, tasks=['rxn1'], exclude=['rxn2','rxn3'])
12

4 frames
/usr/local/lib/python3.12/dist-packages/optlang/glpk_interface.py in objective(self, value)
626
627 for var, coef in coef_dict.items():
--> 628 glp_set_obj_coef(self.problem, var._index, float(coef))
629
630 glp_set_obj_dir(

AttributeError: 'symengine.lib.symengine_wrapper.Symbol' object has no attribute '_index'

Can you help me run riptide on colab notebook?
Thank you
Dee