update base notebook to hub-2.2.2

[rpwagner]

Builds, but not tested

• replaced louvain and python-igraph with leidenalg
• removed all version pinning
• removed bento-tools because of incompatibility with Python 3.10

@byee4 can you find out if bento-tools can support Python 3.10? I believe the developer is in your group.

[byee4]

Sure, I think he's testing it now. Should have an answer by tomorrow

[byee4]

I think one of bento's dependencies hasn't been updated: https://github.com/ckmah/bento-tools/runs/7116902834?check_suite_focus=true#step:4:99

He's taking a look right now, but alternatively, would another option be to use a conda py39 environment?

[rpwagner]

Bento has astropy pinned at 4.9.*, but there's a 5.0 release. Can you ask him to try the more recent version of astropy?

[rpwagner]

I put some time into trying to sort out the dependencies to try and get Bento to work with Python 3.10. In short, I'll look at what version of the hub and notebook servers we can run at Python 3.9 as you suggested.

If Clarence is open for input, I'd suggest that he looks at a few things to make his code more portable across environments and able to be installed alongside other packages. This is natural step when releasing code from a personal development environment to the community:

• Review package imports to check for dependencies. For example, I think xgboost isn't used. Pylint and Pyflakes are good tools to help with this.
• Actually, I'd suggest running reviewing the pylint output as part of the regular CI process that's set up.
• Reconsider the version requirements for dependencies. Right now, there are several dependencies and they all have a version statement. This can be a problem when the version needs conflict. Like if packages want different versions of numpy.
• I'm not sure if poetry.lock should be kept in the repo.

[byee4]

Oh, awesome. Thanks! I’ll forward to Clarence. Right now, I do see an open PR for python3.10 compatibility, so if bento is the only package that requires 3.9 still, there may still be hope to get the version bumped to 3.10.

SECURE: MESSAGE FROM Rick Wagner ON 6/29/22, 1:23 PM

I put some time into trying to sort out the dependencies to try and get Bento to work with Python 3.10. In short, I'll look at what version of the hub and notebook servers we can run at Python 3.9 as you suggested.

If Clarence is open for input, I'd suggest that he looks at a few things to make his code more portable across environments and able to be installed alongside other packages. This is natural step when releasing code from a personal development environment to the community:

• Review package imports to check for dependencies. For example, I think xgboost isn't used. Pylint and Pyflakes are good tools to help with this.
• Actually, I'd suggest running reviewing the pylint output as part of the regular CI process that's set up.
• Reconsider the version requirements for dependencies. Right now, there are several dependencies and they all have a version statement. This can be a problem when the version needs conflict. Like if packages want different versions of numpy.
• I'm not sure if poetry.lock should be kept in the repo.

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[rpwagner]

There's now a working build that I was able to test locally. @byee4 when you get a chance, can you do a build from this branch and tag it hub-2.2.2 in Docker Hub? Then later today I'll snapshot the hub instance and try and upgrade JupyterHub. It should be a quick a quick test and we can roll back if it doesn't work.

[byee4]

@rpwagner Pushed! https://hub.docker.com/repository/docker/brianyee/spatial-tx

[rpwagner]

Excellent, I'll start the update test. The hub will restart in about 30 minutes. I won't spend too long if something goes wrong, I'm sure you're in the middle of getting things going. The Globus server will still be up so you can keep moving things that way.

[rpwagner]

Hub is running at version 2.2.2. I tested Bento and got the same results. The notebook is in the shared-data folder if you want to run it. It's good at loading the CPUs.

Right now, the config pulls the hub-2.2.2 tag. We can set the back to latest when you've tested and want to stick with this build.

[rpwagner]

@byee4 the test image option is now on the hub, which will use brianyee/spatial-tx:latest. I'd say let's merge this PR since it's now the "stable" version. Then you can try out updates by pushing to the latest tag.