Fix The Usage Section in Docs

[zhuchcn]

Description

The usage section in docs has mkdocs instead of moPepGen (see below). Fixed it to show the correct command name.

Also fixed grammar issues in documentations.

Closes #...

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• I have read the code review guidelines and the code review best practice on GitHub check-list.
• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• All test cases passed locally.

[zhuchcn]

@nwiltsie Hi Nick, help is needed! I just updated the cicd docker image from docker hub to ghcr. Didn't realize this until today. Why is my .pylintrc config file not recognized? I specifically disabled some warnings but they are still raised by pylint.

[lydiayliu]

This is taking some time to review, I'll keep at it!

[nwiltsie]

Your .pylintrc file is being recognized - your changes in cec7b27 reduced the warnings from 28 to 12.

We updated the version of pylint when we migrated from the old container registry and I think there are a few new checks in there.

[zhuchcn]

Thanks Nick! I think when I clicked on the github action output link, it redirected me to an old run which has all the error messages that are supposed to be fixed. It's probably just GitHub being laggy. So now I only have the Cyclic import left. The old pylint doesn't complain about it. Should we just disable it, too? If there is a cyclic import, the problem won't run anyway, right?

[nwiltsie]

You can also test the CICD process locally with the bllint script (https://github.com/uclahs-cds/docker-CICD-base?tab=readme-ov-file#how-to-run-locally). In order for that to work you'll need to make a .cicd-env file (you can literally duplicate this PR, it had the same change).

[nwiltsie]

So now I only have the Cyclic import left. The old pylint doesn't complain about it. Should we just disable it, too? If there is a cyclic import, the problem won't run anyway, right?

I don't think it's a good idea to blindly disable, but fixing that code is out-of-scope for this PR. I'd recommend disabling it now but adding an issue (linking back here) to re-enable that check and fix the offending code.

[zhuchcn]

It's a lot of work to fix them all. But since the program is running, and the tests are all passed, would you say it's a relatively small issue for now?

Also, do you know why they were not caught by the old pylint?

[nwiltsie]

For the purposes of this PR, things are golden! I don't know enough about the code in question to prioritize the new issue relative to other work, so I don't want to call it a "small issue", but at the very least the code is in the same state it was yesterday.

The old pylint didn't catch these circular imports because we were previously linting each file individually, but now we are linting them all simultaneously. That's also why the duplicate code checker is triggering - it could never see both files at once before.

[zhuchcn]

I think I incorporated all your suggested changes. I also updated the repo name in all occurrences. @lydiayliu

[lydiayliu]

I don't want to go through this again XD just merge