2016 11 29

Participants

@cdiener, @hredestig, @pstjohn, @mmundy42, @phantomas1234

Agenda

Refactoring

Agreed generally a good idea, see notes in issue

Context manager for undo

• high priority, as dependency for refactoring cameo methods to cobrapy
• nested managers are good idea and the limited feature set is sufficient for cameo which can then be adjusted to use the new HistoryManager class

optlang interface

• possibility to make optlang lowlevel api lazy
• we need the dual model conversion from cameo moved to cobrapy. preferably not as a separate class.
• once context manager ready, time to start refactoring methods from cameo to cobra

Modelseed

• Slight preference to have the modelseed interaction functionality in a separate package.

Promotion / documentation / maintenance

• General agreement that the opencobra.github.io needs update and should link to the different projects.
• Thoughts on having a tagging system for functions / modules to indicate what topic they deal with so that we could build a table of which-function-does-what in all opencobra associated projects, also non-python
• cleanup action

Media manager

• CfB use media as list of compounds and concentrations
• Favour lightweight implementation with model.media being dict of dicts and that one can set model.medium to one of the entries to have bounds of exchange reactions updated