improved bash scripting for conda setup

[ryan-tock]

No description provided.

[shankari]

@ryan-tock this largely copying over the setup from e-mission-server to mobilitynet. But that ends up changing the conda version, and more importantly the set of packages installed. Note that the original environment.yml had shapely and copied over environments don't.

That's because we use shapely for spatial trajectory evaluation in mobilitynet, but not (yet?) in production. As I said, we should really stick with the old conda version, at least initially, for better reproducibility. If that doesn't work, we can upgrade the conda version as well, but I would then expect the rationale for doing so to be documented (e.g. what was the error with the old version)

[shankari]

glad to see that you excluded this!

[ryan-tock]

I have now downgraded to the previously used conda version with the previous environment

[shankari]

You can also rebase your changes (git rebase -i HEAD~3 or similar) instead of creating new commits to keep the commit history a bit cleaner.

[shankari]

Suggested change

	conda deactivate && conda env remove --name emission
	conda deactivate && conda env remove --name emissioneval

Those of us who also write server code already have an emission environment set up and we don't want to mess it up with a different set of dependencies

[shankari]

Suggested change

	conda env update --name emission --file setup/environment.yml
	conda env update --name emissioneval --file setup/environment.yml

Ditto

[ryan-tock]

I found all instances of emission and replaced them with emissioneval as well as doing a rebase. It should be ready now

[shankari]

Please submit another PR to update the README! You can improve the documentation and and fix the broken links at the same time

[shankari]

I noticed that you no longer activate right after the setup here.

But then I noticed that you do set this up as part of the new activate_conda.sh script
https://github.com/MobilityNet/mobilitynet-analysis-scripts/pull/72/files#diff-b6b89814c0d70733151b062c77846d8546d726d07548236ee6a5bacff96b1f5eR7

I am merging this now to unblock @KG2468, but note that you need to update the README to match
https://github.com/MobilityNet/mobilitynet-analysis-scripts/tree/master?tab=readme-ov-file#running-existing-notebooks

[shankari]

when I try to run the new setup script, I get an error

$ bash setup/setup.sh 
For conda, found 23.1.0, expected 23.1.0, all is good!
Installing using conda now

CondaValueError: You have chosen a non-default solver backend (libmamba) but it was not recognized. Choose one of: classic

[shankari]

This is because I had a prior partial install of miniconda that did not have mamba installed BUT was configured to use mamba by the previous run of the setup script. After re-running, it was able to install properly