Clean up utility functions.

[bdice]

Description

This PR removes unused utility functions and cleans up test coverage of the utility.py module.

Notes:

• The _query_yes_no function doesn't need test coverage (it's strictly for interactive use on the terminal).
• The _split_and_print_progress function can probably be simplified and replaced with tqdm, if it is needed at all. The function is used only once, to print info-level logging for updates to the in-memory state point cache. This should be investigated further, but I've made the function private for now.
• There was an important edge case of _nested_dicts_to_dotted_keys that wasn't being tested, when a value is an empty dict. I added a test that covers that edge case.

Motivation and Context

Cleanup for signac 2.0.

Types of Changes

• Documentation update
• Bug fix
• New feature
• Breaking change¹

¹The change breaks (or has the potential to break) existing functionality.

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• My code follows the code style guideline of this project.
• The changes introduced by this pull request are covered by existing or newly introduced tests.

If necessary:

• I have updated the API documentation as part of the package doc-strings.
• I have created a separate pull request to update the framework documentation on signac-docs and linked it here.
• I have updated the changelog and added all related issue and pull request numbers for future reference (if applicable). See example below.

[bdice]

This edge case was being missed until I added this test:

signac/signac/contrib/utility.py

Lines 339 to 340 in 257c931

	elif key is not None:
	yield key, t

[codecov]

Codecov Report

Merging #597 (c25bee2) into next (257c931) will increase coverage by 0.42%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             next     #597      +/-   ##
==========================================
+ Coverage   83.77%   84.20%   +0.42%     
==========================================
  Files          54       54              
  Lines        5535     5502      -33     
  Branches     1021     1014       -7     
==========================================
- Hits         4637     4633       -4     
+ Misses        668      641      -27     
+ Partials      230      228       -2     

Impacted Files	Coverage Δ
signac/__main__.py	75.17% <ø> (ø)
signac/contrib/project.py	85.91% <100.00%> (ø)
signac/contrib/utility.py	59.77% <100.00%> (+12.27%)	⬆️
signac/contrib/schema.py	96.24% <0.00%> (+0.75%)	⬆️

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[csadorf]

If I've had to guess the function was introduced prior to having the tqdm dependency or because there was some kind of threading issue or so with tqdm. But I agree, we should certainly try to replace it with tqdm if possible.