Moritz E. Beber

So you wouldn't even set it to zero if the absolute value was below tolerance? I agree that it's weird to not show anything when you request the summary of...

If you use the [get_solution](https://cobrapy.readthedocs.io/en/stable/autoapi/cobra/core/solution/index.html#cobra.core.solution.get_solution) function (it's admittedly hidden pretty deeply), you can extract fluxes for exactly the reactions and/or metabolites that you want. Maybe take a look if that...

Absolutely, but please don't feel the need to convert everything at the same time. I think one PR per module would be a good strategy. As the @opencobra/cobrapy-core team, we...

A check list of things to do as commented by @matthiaskoenig in https://github.com/opencobra/cobrapy/pull/975#issuecomment-663840911: > I would do all the python3.6 changes at once. I.e. > * [ ] fix imports...

One point where we should agree on a common style is logging strings. We can either also use f-strings or C-style string formatting. So either ```py greeting = "Hello" whom...

I agree, f-strings it is for logging, too. I will make an updated list with all the tasks at the top of this issue so it is clear what needs...

The original intent was that you can create different outputs from the same summary object. I would like to keep that behavior but the constructor arguments could certainly set the...

From my perspective it is desirable to have code that "upgrades" models (by moving information from notes to the correct fields) in libSBML directly. You can already read a level...

The PR #988 is still open. Lots of good stuff in there but unfortunately a bit dated by now and hard to review.

@cdiener is this something you'd still like to do? Otherwise I'd add a "help-wanted" label and advertise it.