Ahh, just got internet.

OK, so for the github stuff I’ve been moving items from git.kbase.us to github once there is a License file in the git.kbase.us based repo. I’ve put a license in some repos for ANL folks, per Rick’s approval, however, those repos that are predominately LBL should have a license placed in them by a LBL person. Shane, I think you would be the best person to do this, but that’s up to you guys.

When I create a repo at github, say assembly, i also create an assembly_team. I give that team administrative access to that repo. I put into that team the repo owner and anyone he requests. So for assembly, the assembly_team is fang fang as the owner. The team owner can then add everyone (the kbase group) or can just accept pull requests. We leave that up to the repo owner.

The owner is already defined for most repos in the git.kbase.us system, and I’m just going with that, and some common sense on who is the owner in case it is not specified in git.kbase.us config files.

Finally, there is a small group who are owners of the kbase organization. These folks have permission across all teams and repos. This is basically the same set of folks who have gitosis admin privileges on gitosis.conf.

I should be done with this by mid next week depending on how quickly the License gets committed to the repos.


On May 16, 2014, at 1:30 PM, Brettin, Thomas S. <brettin@anl.gov> wrote:

Hey Shane. Can u do me a favor and grab the license out of the assembly repo at gtihub and either pass it around the LBL team or just commit it in their repos?

I'll migrate repos once the license has been committed. I'm almost done with the mostly ANL repos. But still some more to do.

I'll be working on this more in a few hrs.

Thanks

Sent from my Verizon Wireless 4G LTE DROID


Shane Canon <scanon@lbl.gov> wrote:


Nomi,

I’ll leave the disk image discussion to others.

Dan and I talked about the version feature this morning.  We think it is useful for several purposes and we (the project) should just commit to it.

Regarding redeploys, I’ve been buried this week and I’m hesitant to start something major that could destabilize things on a Friday.  So Dan and I plan to tackle this first thing Monday.  Just to be clear, redploying the FBA service itself is easy.  The part that concerns me is redeploying the updates for IRIS and getting that all correct.  We’ve also seen some cases where we did a redeploy thinking it would be fairly contained and it wound up breaking something.  Just one more reason for why we need the CI.

—Shane




On May 15, 2014, at 9:34 AM, Nomi Harris <nlharris@lbl.gov> wrote:

Since I won’t be able to attend the release meeting today (I’m available tomorrow, but Dan doesn’t work Fridays), here are some of my thoughts about releases and disk images. I’m including below a message I wrote on the topic in December, most of which still applies. I would again encourage you to weigh the benefit of producing the disk images against the human effort required to build them. I know Rick uses the DMG, and it is also useful for testing. Also, the process of creating and testing the images often exposes (and motivates us to fix) issues in the build/deploy process and/or with individual services. I have asked Erik if we can determine from the website analytics how many times the disk images were downloaded; I will let you know what he finds.

It’s very important that we start attaching version information to every service, and making it available in a standardized way (via the API and via a command-line arg, e.g. —version). This is important both for internal development and particularly if we want outside developers to integrate services. Every service should also describe the input/output formats it uses, so that services can be chained together in workflows.

Every more pressing is that we need to do a new deploy of some services ASAP, particularly FBA modeling, which I believe has fixes that Chris has made recently that address issues that many users have complained about. I think workspace may need to be redeployed as well. We have tutorials in which everything worked back in October that have since broken; we need to get back to at least the level of functionality we had in October.

Also, the renewal proposal referred to some new services that are not yet publicly deployed, so we need to get those deployed as soon as we can (e.g., Bambi, MAK). That may be more involved than redeploying our existing services, since it will be the first deploy of these new services.

I hope someone will take meeting notes today. Sorry I can’t attend.

Nomi

Begin forwarded message:

From: Nomi Harris <nlharris@lbl.gov>
Subject: Release products: services, dmg (?), Iris
Date: December 3, 2013 at 11:03:48 AM PST
To: "Tom S. Brettin" <Brettin@mcs.anl.gov>, Adam Arkin <aparkin@lbl.gov>
Cc: Nomi Harris <nlharris@lbl.gov>

Hi Tom,
As you noted, there is a lack of clarity about what it means to have a release. In my view, right now there are three categories of release product:
1. Services. From a user perspective, it is hard to tell when a service has been updated. I would suggest that there should be a client command that asks the server its version number/datestamp. This would be particularly useful in cases where a change to a service API might break some methods in the client—the client might want to interrogate the service about what version it is.
2. DMG/Ubuntu image. You mentioned that some people don’t think it’s worth the time and effort to put these together, but I wasn’t clear which side of the fence you fell on. I can definitely see both sides of this. I think these images are used by a small minority of power users, and that most people who use them either should be sticking with Iris, or, if they are developers, going the next step to using the Magellan images. It’s also clear that creating these images still requires significant human time—it would be nice if one could just type “make dmg” and it would all magically happen, but I gather there’s a fair amount of tinkering that’s necessary to make that work, and it might not be worth the effort. On the other hand, the dmg and ubuntu image are possibly the most visible release products, and that does count for something.
3. Iris. Until the Narrative is publicly available, it seems to me that Iris is the most visible measure of progress. Jim has made Iris show a version number and datestamp, so that users can tell when it was updated and what’s new:
<Screen Shot 2013-12-03 at 10.34.25 AM.png>

This makes it clear that Iris indeed has not been redeployed—not even in October. 
Do you want me to ask Dan (and Jim) about that, so we can figure out what’s holding that up?

4. There’s a fourth thing that might be viewed as a release “product”, which is the data. It would be great if we could put something on our website after each data build that says the date of the data build and what’s new (N new data types [list], X new genomes, etc.).

In summary, I would propose that a (software) release consists of:
- Release team does an integrity check on services to be (re)deployed—passes tests, has appropriate documentation (including release notes)
- Redeployment of updated services and deployment of new services
- Iris updated on public site
- Internal announcement from the release team that the release has happened, including a list of which services are new and which are changed in this release (and presumably the info about what’s changed is included in the service release notes)
- Public announcement (which I am happy to put together, given the info about what’s new/changed) to be posted to kbase.us

I think the dmg/ubuntu images are optional in this process.

Does this seem reasonable?

Nomi


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