cdiener
commented
4 years ago Hi, thanks for providing a reproducible example. That helped a lot. Micom makes some adjustments to the IDs and that did not work for the models you provided. I fixed that in version 0.9.13, and updating to that version will make your setup work. You will see some SBML errors and the micom logs since your models are invalid SBML (missing a model ID), but it will read anyways. Those message will disappear if you set a model id in your SBML.
Anyways it will build the community and can obtain solutions.
Test run
```python
In [1]: import micom
In [2]: import pandas as pd
In [3]: tax = pd.read_csv("pandas_metacyc.csv", sep="\t")
In [4]: com = micom.Community(tax)
0%| | 0/4 [00:00
In [7]: sol.members
Out[7]:
abundance growth_rate reactions metabolites
compartments
eclAA4 0.6 7.359998 3246 1531
hfrAA6 0.2 2.453333 3411 1538
medium NaN NaN 22 22
ppuAA7 0.1 1.226668 3051 1493
smaAA1 0.1 1.226667 2626 1262
```
mostueve
When trying to build a community, I always get a ValueError similar to the one below.
ValueError: ('The model already contains a reaction with the id:', 'ABC_RXN__smaAA1')
Files causing this can be found at https://gitlab.com/mostueve/micom-error-files