Removing my stale branches

[jmason42]

I have two stale branches that I think can be deleted but I'd like for @tahorst to take a look, as they both pertain to metabolism. They are:

• new_fba: Almost certainly not needed unless the cvxpy stuff is interesting.
• enzymeKinetics: Not as sure about this branch; I assume any relevant work on the kinetics has percolated its way into the main branch.

@tahorst Feel free to delete them yourself, or just give me the 👍 .

[tahorst]

I feel like there is a large diff here and not sure if it's worth it to really dig in. I think a lot of these old branches would be difficult to go through and there really isn't a way to know what we would be trying to get out of them unless the original authors had pointed something out. Looks like a majority of this stuff has been implemented so I'm fine deleting these branches. I don't think EnzymeKinetics is currently used anywhere in the model which seemed like the major diff with enzymeKinetics.

Are we planning on saving these old branches somewhere else just in case we decide to go back to them before we start removing? I don't think it's necessary and don't expect to go through other old branches but honestly don't know what is on them.

[jmason42]

Stashing the branch history is fine but I think some pruning wouldn't hurt either, particularly if a branch has been fully merged (presumably there are a few).

[1fish2]

GitHub has useful pages to list active and stale branches, see how many commits they have ahead & behind master, and delete them.

To handle stale branches that have unmerged changes, we talked about cloning the repo somewhere before deleting them. But here's a better technique: tag those branches in the repo before deleting them. Then it's easy to recover the branch if desired.

Each such tag could be named like archive/varTransRate and have an optional message about what's in the branch. A tag without a message or signature is considered a "lightweight tag" that will be ignored by some commands like git describe.

git tag -m 'varTransRate has plotting of active RNAP percentage' archive/varTransRate varTransRate
git push --tags

[tahorst]

I like the tag idea. Seems like a good alternative as long as it doesn't take too much time to go through and tag each branch. We'll just have to identify which ones are no longer active branches at this point, which I'd imagine is most of them

[1fish2]

The GitHub tool for viewing stale branches shows for each branch how old it is and how many commits it is ahead and behind master. Branches with 0 commits ahead of master are safe to delete.

The hardest part about tagging the rest is deciding what message to attach, if anything.

[jmason42]

Tagging sounds good to me. One stale tag seems OK but we could also try to lump them into broad categories, like stale-bugfix stale-enhancement stale-refactoring etc. I would guess that nearly all of the branches correspond to new features that were never good enough to get merged.

[1fish2]

The StackOverflow answer suggested using the prefix archive/, e.g. archive/wholecell-tutorial. That's visually clear.

If you know enough about the old branches to categorize them, that could look like archive/enhancement/wholecell-tutorial or archive-enhancement/wholecell-tutorial. I like the former.

[jmason42]

This has been resolved.