memote
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opencobra
memote – the genome-scale metabolic model test suite
#### Problem description Without any markup at all a long description in the report is cumbersome to read. Perhaps consider automatically adding ``, `` or `` tags before merging the...
#### Problem description We should have one clearly defined and unit-tested function that runs basic FBA to find bugs faster and be able to set parameters centrally. - [ ]...
#### Problem description Despite #189 having been closed a long time ago, I had to remove the test for an infinite proton gradient i.e testing if the model can somehow...
The two functions share almost all variables and are run concurrently anyway. - [ ] Merge the two functions - [ ] Remove redundant `except` statement - [ ] Update...
#### Problem description - [ ] helpers.open_boundaries should set the default maximal bounds provided by the model i.e. those that we find with helpers.find_bounds() and not assume the standard cobra...
Many supporting functions could use some logging statements to help with debugging, refactoring or performance monitoring.
I've added both essentiality and growth screening data in the 'data' folder of my repo, but I only get an essentiality metric displayed in my memote reports. Both tests appear...
Tests that error (note: not fail) appear as "Errored" in the report but with no useful output to the user. The error message is only available when running memote manually...
At the moment, cobrapy changes identifiers when loading a model but reading in the medium does not apply the same transformation leading to mismatches.
#### Problem description > What about irreversible reactions that under the assumed conditions are pointing in the wrong direction? I think we should have a test for that, too. -...