Replace logging with warnings

[pllim]

Description

In trying to figure out why deprecating warning is thrown when I do specviz = Specviz(), I found out that it is from logging. The use of logging in Jdaviz does not quite make sense because we do not have a custom logger to begin with. Looks like all we use logging for is to emit deprecation warning and unit warning. I think this is better done by just using warnings directly, which we then can control directly either from Python proper or pytest.

While I am at it, also did some isort because I cannot help myself.

Change log entry

• Is a change log needed? If yes, is it added to CHANGES.rst? If you want to avoid merge conflicts,
  list the proposed change log here for review and add to CHANGES.rst before merge. If no, maintainer
  should add a no-changelog-entry-needed label.

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

• Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
• Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
• Do the proposed changes follow the STScI Style Guides?
• Are tests added/updated as required? If so, do they follow the STScI Style Guides?
• Are docs added/updated as required? If so, do they follow the STScI Style Guides?
• Did the CI pass? If not, are the failures related?
• Is a milestone set? Set this to bugfix milestone if this is a bug fix and needs to be released ASAP; otherwise, set this to the next major release milestone. Bugfix milestone also needs an accompanying backport label.
• After merge, any internal documentations need updating (e.g., JIRA, Innerspace)? 🐱

[pllim]

devdeps failures are unrelated

[pllim]

Hmm the SOURCE_ID isn't a problem here... Why is it flaky? Nvm it is there after all.

[kecnry]

LGTM - thanks for the cleanup!

[kecnry]

(is any of this worth backporting?)

[pllim]

Re: backport -- You didn't deprecate any plugin thingy in v4.1.x, did you? Even if you did, I don't think the stuff is showing up in the notebook anyway because your API refactor stuff isn't backported, right? So, no, I don't think this needs backporting.

[pllim]

Gah looks like I have to rebase after #3400 is merged.