Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

clarify batch_load_from_files docstrings, variable names, and SBML/json checking #50

Open
gregmedlock opened this issue Jan 6, 2020 · 0 comments

Comments

@gregmedlock
Copy link
Member

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 files in a batch are json or SBML by checking for a .json or .xml suffix--because people often use different extensions (e.g., modelname.sbml is common rather than modelname.xml), we should use the built-in error handling capabilities of cobrapy to determine whether the file type was correct. This will also enable the SBML parser to read compressed SBML files without any additional modification of Medusa code. We will need to add an additional argument to the function for the user to specify json or sbml, or have separate functions a la cobrapy (I favor an additional argument).

@gregmedlock gregmedlock changed the title clarify batch_load_from_files docstrings, variable names, and SBML.json checking clarify batch_load_from_files docstrings, variable names, and SBML/json checking Jan 6, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

1 participant