Greg Medlock
Using mackinac 0.8.0, When attempting the following: mackinac.gapfill_modelseed_model('97138.3',likelihood=True) my system returns the following error: Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python3.5/site-packages/mackinac-0.8.0-py3.5.egg/mackinac/modelseed.py", line 105, in gapfill_modelseed_model...
### Is there an existing issue for this? - [X] I have searched the existing issues ### Problem description The stable release of the documentation is broken and returns a...
Some utility functions that have come up as potentially useful so far: * getting a list of all reactions that vary across an ensemble, rather than iterating over all features...
The docstrings and variable names for the batch_load_from_files function suggest that only json files are accepted as input, rather than both json and SBML. The function currently checks whether the...
The last cobrapy version since exhaustive testing/usage was 0.13. Things seemed to work fine in practice for newer versions, but we should update the version used on TravisCI to 0.17.1.
It's time for some cleanup--we need to remove unnecessary imports, check for PEP compliance, and do some review of function documentation.
Several tests can and should take advantage of purest parametrization (https://docs.pytest.org/en/latest/parametrize.html). This will greatly reduce the size of the test code and should lead to fewer copy/paste errors where the...
When performing FVA in cobrapy, a dataframe is returned with the minimum and maximum flux values, each taking up a column. Currently, ensemble FVA has the column order hardcoded, but...
This may be difficult or memory-intensive due to serialization/deserialization of large universal models, but could get the total runtime for iterative gapfilling to a more reasonable range.
The current examples have a few too many steps to serve as good introductions to the software. Add at least the following examples, each with some simple matplotlib-based visualization: *...