Update dev requirements

[agladstein]

When I recently tried to follow the instructions on the dev docs to set up the environment to build docs locally, I ran into some problems. @benjeffery helped me get setup locally, but this needs to be applied to the requirements.yml (and requirements.txt?).

In order to setup locally (Apple M2, Sonoma 14.1.2), we:

Create a new env from python/development/requirements.txt

mamba create -n tskit_dev python=3.12
mamba activate tskit_dev
pip install -r python/requirements/development.txt
pip uninstall tskit msprime  # This is because pip didn't install tskit and msprime corectly with wheeles
mamba install tskit msprime 
pip install pandas
# Need to make tskit locally to use the local version
cd python; make clean; make 

[jeromekelleher]

Out of interest @agladstein, if you're working with mamba already, why not install all the requirements from there in the first place?

[benjeffery]

mamba was left installing for several hours without completing. We never got to the bottom of why.

[molpopgen]

This issue would seem to suggest not using anything in the conda/mamba world? Unless you 100% need some other tool only available that way, a regular venv will be much more reliable.

[hyanwong]

Is this just because of the msprime GSL requirement?

[jeromekelleher]

msprime has binary wheels including GSL built-in for some time now (although there is https://github.com/tskit-dev/msprime/issues/2343 )