Generate/update derivative files in preparation for packaging the schema

[eecavanna]

These files were generated/updated by running this one-liner, when on the tip of main (i.e. at commit 36e5db9), with a clean working directory:

$ docker compose run --rm app \
  sh -c 'poetry install && make squeaky-clean all test'

The file nmdc.py was already being tracked by Git. The other 4 files were not. I ran git add {path/to/file} for each of those 4 files in order to make it so Git tracks them.

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://microbiomedata.github.io/berkeley-schema-fy24/pr-preview/pr-252/
on branch gh-pages at 2024-09-12 01:25 UTC

[eecavanna]

Hi @turbomam, during today's metadata meeting, I said I'd try to make a release of the Berkeley schema, including generating the derivative files. I did generate the files (they are in this PR). Then, I ran into a blocker related to GitHub permissions: I do not have permission to merge this PR into the main branch. Will you take over from here; i.e. merge this into main and generate a GitHub Release?

[eecavanna]

I find the title (which I wrote) of this PR to be misleading. The GitHub Actions workflow will run make squeaky-clean all (here), so the resulting PyPI package will contain the same files as this PR (albeit, different instances of the files). So, the "added value" of this PR—from my perspective—is that it puts those files into the GitHub repo.

I would still prefer that this be merged in before the GitHub Release gets created, so that the commit associated with the Release includes these files. (Longer term, I don't want the repo to contain derivative files—a GHA workflow can generate them and either attach them to the GitHub Release or publish them to GitHub Pages. Related: microbiomedata#1960.)

[turbomam]

do you think those git add operations will be remembered now as tracked files?

[turbomam]

What permissions would have allowed you to do more of this task, if you wanted to? Here's a current permission table. I think some of those are inherited form "Base role" . I don't understand how that's different from inheriting from the Organization access.

echo -e "login\tadmin\tmaintain\tpull\tpush\ttriage" > berkeley-schema-fy24_permissions.tsv ; \
gh api repos/microbiomedata/berkeley-schema-fy24/collaborators \
--jq '.[] | "\(.login)\t\(.permissions.admin)\t\(.permissions.maintain)\t\(.permissions.pull)\t\(.permissions.push)\t\(.permissions.triage)"' >> berkeley-schema-fy24_permissions.tsv

login	admin	maintain	pull	push	triage
cmungall	true	true	true	true	true
kfagnan	true	true	true	true	true
scanon	true	true	true	true	true
shreddd	true	true	true	true	true
sierra-moxon	true	true	true	true	true
turbomam	true	true	true	true	true
aclum	false	false	true	true	true
chienchi	false	false	true	true	true
corilo	false	false	true	true	true
dwinston	false	false	true	true	true
GrantFujimoto	false	false	true	true	true
hubin-keio	false	false	true	true	true
jeffbaumes	false	false	true	true	true
kaijli	false	false	true	true	true
kfox1111	false	false	true	true	true
kheal	false	false	true	true	true
lamccue	false	false	true	true	true
mflynn-lanl	false	false	true	true	true
mhuntemann	false	false	true	true	true
mshakya	false	false	true	true	true
naglepuff	false	false	true	true	true
patrickchain	false	false	true	true	true
PeopleMakeCulture	false	false	true	true	true
picowatt	false	false	true	true	true
poeli	false	false	true	true	true
SamuelPurvine	false	false	true	true	true
Shalsh23	false	false	true	true	true
simroux	false	false	true	true	true
smcolby	false	false	true	true	true
sujaypatil96	false	false	true	true	true

[turbomam]

I still have some potentially irrational discomfort with omitting generated files form the repo. That has probably played a role in making it hard to make a schema release for a long time now, so as long as you, @pkalita-lbl, @sierra-moxon , @sujaypatil96 can a shared vision on building and deploying, I'll go along with it.

I may have some scripts that pick some of that stuff up from git raw URLs, but we'll deal with that as it arises.

[eecavanna]

do you think those git add operations will be remembered now as tracked files?

I think so. They are not currently listed in any .gitignore files in the repo. I didn't have to do anything more than git add {filename} in order to add each one (i.e. no --force).

[eecavanna]

What permissions would have allowed you to do more of this task, if you wanted to?

Because I was working after hours, I was blocked by my inability to merge a PR without review. So, being able to override that requirement would have allowed me to do more of this task.

[eecavanna]

Closing in favor of #253 (ready for review).