Bump base image + use environment.yml

[yuvipanda]

• Pin to latest dated version of the base image, to bring in new package versions. We should work on establishing an automated cadence for this somehow.
• Specifying environment.yml file for conda packages is more standard, and allows users not familiar with Dockerfile syntax to also add & edit packages. Also paves the way for conda-lock in the future.
• Remove a couple packages that were upgraded in the base image anyway.

[yuvipanda]

Thank you for listing our your concerns, Erik! I will sort those out over the next few days!

[yuvipanda]

@consideRatio gh-scoped-creds is no longer installed as part of this repo, as it's now present in the base image. As such, I don't think a comment about that is relevant here anymore. The env config is part of the hub configuration, so I think it's ok it's just present in the infrastructure config.

I'll tackle the other items slowly over the course of this week.

[yuvipanda]

With qgis, my goal is to replicate the work from https://github.com/CryoInTheCloud/hub-image here to the extent possible, as a lot of debugging and fine tuning went into that.

[yuvipanda]

@consideRatio after spending some more time stepping back and thinking about it, I've come to conclude that maintaining huge all-in-one images is an antipattern I want to move away from. As such, I've opened https://github.com/2i2c-org/infrastructure/pull/2683 which provides more image choices for JMTE, and hopefully can deprecate this once I figure out how to provide missing functionality in other ways.

I'm going to close this PR now.

[yuvipanda]

https://github.com/2i2c-org/infrastructure/issues/2583 is also related, on doing this systematically.