Fix usage of _convert_to_dict to avoid modifying nesting SyncedDict objects when calling items or values

[vyasr]

Description

A number of methods were calling _convert_to_dict on self._data rather than calling them on self. As a result, the member of the underlying dictionary was modified. Actually, we should be able to remove the dict branch of _convert_to_dict entirely, but that requires resolving #196 first (because that's the only way that branch is accessed). Further changes are probably worth postponing for when we address #249.

Motivation and Context

Resolves #234.

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.

Example for a changelog entry: Fix issue with launching rockets to the moon (#101, #212).

[bdice]

@vyasr Since the names of our CI checks changed with #266, you may need to merge master into this branch to make the required checks pass. I'm fine with you overriding the required checks if you want, since this PR is fairly small and doesn't touch anything altered in #266.

[codecov]

Codecov Report

Merging #269 into master will decrease coverage by 0.34%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #269      +/-   ##
==========================================
- Coverage   65.42%   65.07%   -0.35%     
==========================================
  Files          42       40       -2     
  Lines        5697     5629      -68     
==========================================
- Hits         3727     3663      -64     
+ Misses       1970     1966       -4

Impacted Files	Coverage Δ
signac/__main__.py	0% <ø> (ø)	⬆️
signac/contrib/__init__.py	92.59% <ø> (-0.27%)	⬇️
signac/core/json.py	72.72% <ø> (-0.61%)	⬇️
signac/contrib/utility.py	37.98% <ø> (-0.48%)	⬇️
signac/contrib/filterparse.py	82.25% <ø> (-0.29%)	⬇️
signac/contrib/project.py	90.86% <100%> (-0.02%)	⬇️
signac/contrib/import_export.py	84.89% <100%> (+0.15%)	⬆️
signac/contrib/job.py	90.63% <100%> (ø)	⬆️
signac/core/dict_manager.py	90.36% <100%> (ø)	⬆️
signac/core/h5store.py	90.45% <100%> (+0.17%)	⬆️
... and 1 more

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[tcmoore3]

👍

[csadorf]

@vyasr Can you update the name of this PR to be a bit more descriptive?

[vyasr]

Yes, sorry it was a single commit so it just autopopulated the title and I didn't change it.

[cbkerr]

Looks good!