Cleaned up top-level directory, document run_sims

[elaine-ran]

1. cleaned up the top-level directory
2. added pyproject.toml in order to ensure notebooks ran smoothly
3. changed load_vars to load in a dictionary instead of multiple variables
4. Added descriptions to parts of run_sims (not yet done)
5. added paper folder for PR between joss-paper branch and dev-massdist
6. added code to .github/workflows to update paper on push
7. changed read_yaml, load_vars, make_sz_cluster to accurately work with new system

should resolve issues #168 #167 #163 #110
Issue #114 still in progress

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[samueldmcdermott]

@elaine-ran I'll do a first pass on this review

• it looks like the paper action needs some contents in order to run (it's not sufficient to have a blank paper.md file). There should be sample files on the joss website, or of course feel free to use the files in deepcmbsim. Apologies for having given you bad guidance here!
• the second fail is from pytest. I think there are multiple errors: some from syntax (unexpected line breaks in the assert command) and some from an import error (saying that there is no simsz package; seems only to be happening in test_utils for some reason). Try correcting the first and we can go from there

[evavagiakis]

There should be a populated paper.md file in the joss paper branch of the directory, did you find that @elaine-ran? I am currently seeing some conflicting files here:
make_sz_cluster.py
massdist.h5
run_sims.ipynb
tests/test_simtools.py
tests/test_szcluster.py
tests/test_utils.py

[elaine-ran]

There should be a populated paper.md file in the joss paper branch of the directory, did you find that @elaine-ran? I am currently seeing some conflicting files here: make_sz_cluster.py massdist.h5 run_sims.ipynb tests/test_simtools.py tests/test_szcluster.py tests/test_utils.py

I copied the paper.md file from the joss-paper branch into this one, and I think that resolved the issue? Since the .github/worksflows/paper.yml check is successful.

[samueldmcdermott]

the paper action seems to be fine, but the tests actions still seem to be failing, and there are additional conflicts related to files that you’ve changed @elaine-ran — essentially, github doesn’t know how to reconcile changes you’ve introduced in several files (the ones that @evavagiakis points to). This might be most effectively resolved synchronously — I’m happy to meet tomorrow AM or Friday PM if you want to have a co-coding session

[samueldmcdermott]

there were still errors in tests but we can fix those downstream