make the poetry installation work; add dalmatian as a package

[qinqian]

We have a working version of poetry for genepy python packages, while ignoring all R packages dependencies. We need to find the necessary functions for depmap_omics to add into that repo

[pgm]

Ah! I didn't fully understand what you meant when you said you added damination, but now that I've looked at the diff, I see you copied the damination into this repo.

I also see bumped the version of python to 3.11.

My guess of what's going on here is:

• you want to use python 3.11
• firecloud-damination is broken in python 3.11
• you copied the damination code into a folder into this repo and made some small fixes to allow it to work with python 3.11

Is that correct?

If so, I propose a slightly different workflow:

1. use github's "fork" function to make a clone of firecloud-damination called something like cds-firecloud-damination.
2. Make a branch in the cds-firecloud-damination repo with your python 3.11 fix.
3. update the dependencies to install dalmaition from that repo instead of from pypi.

this has advantages for maintenance in the future:

1. If firecloud-dalmatian is updated in the future, we'll be able to easily "merge" their changes into our patched version.
2. you can provide your 3.11 fix to them as a pull-request. The easier you make it for them to take, the more likely they might just merge it in.
3. it captures the history better where we'll be able to see that the only difference between our version and their version is just the changes you made. (As opposed to looking like these are entirely new files in this repo)

[qinqian]

Yes, it is correct. For the firecloud-damination pypi package used in genepy, it only supports Python 3.4. After a closer look at their latest commit at firecloud-damination github, they already corrected this.

I agree with you on the workflow that will easily update the damination with cds-firecloud-damination fork. I'll make a revision on this poetry pull request using this suggestion