Migrate to UV for Package Management

[ktehranchi]

Feature Request

I started a branch to migrate to UV for our package management (kt/uv), but found there are issues with installing a few of our dependencies with UV. They have been identified to the UV developers in the following tickets (astral-sh/uv#8429) , (astral-sh/uv#7525).

The issue is associated with installing snakemake (snakemake/snakemake-executor-plugin-slurm#157) so there wouldnt be a good workaround besides using mamba for snakemake. They identify one workaround to get around the datrie dependency but I found that there are other installation issues as well after that.

The bug was identified only a few weeks ago so I imagine they'll patch it soon. Let's just keep an eye on those tickets to see when they are fixed.... we can switch then, since it is so dang fast.

[ktehranchi]

I can't find a distribution for coin-or-cbc that works with UV, so when running snakemake we'll need to specify the solver used to solve the rule scheduling ... options are 'GLPK_CMD', 'GUROBI_CMD', 'PULP_CBC_CMD', 'COIN_CMD'

[ktehranchi]

Dependencies which gave errors with UV:

• cyipopt # doesn't work

Dependencies I am not adding since I don't this we actually need them locked-in:

• memory_profiler==0.61.0 # not adding
• yaml==0.2.5 ## added pyyaml instead
• pytables==3.9.1 ### not-used??
• lxml==4.9.3 ### not used
• flake8
• tqdm==4.66.1
• country_converter==1.0.0
• ipython==8.16.1
• jupyter==1.0.0
• notebook==7.0.6
• ipykernel==6.25.2