Remove --doc-filter option from CLI.

[bdice]

Description

This PR resolves #613 by removing the --doc-filter argument from the signac CLI. Users who wish to search by a document filter should replace syntax as shown below:

Before (simple syntax):
$ signac find --doc-filter a 0
After (simple syntax):
$ signac find doc.a 0

Before (JSON syntax):
$ signac find --doc-filter '{"a": 0}'
After (JSON syntax):
$ signac find '{"doc.a": 0}'

Motivation and Context

The general feature of searching by document filters has been replaced by a generalized filter syntax that prefixes state point keys with sp. and document keys with doc.. This applies that change from #586 to the CLI.

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.
• The changes introduced by this pull request are covered by existing or newly introduced tests.
• The package documentation and framework documentation in signac-docs are up to date with these changes.
• I have updated the changelog and added any related issue and pull request numbers for future reference.

[codecov]

Codecov Report

Merging #795 (bda219a) into next (52ff017) will decrease coverage by 1.32%.
The diff coverage is 78.53%.

@@            Coverage Diff             @@
##             next     #795      +/-   ##
==========================================
- Coverage   86.32%   84.99%   -1.33%     
==========================================
  Files          51       54       +3     
  Lines        4687     4672      -15     
  Branches     1022     1011      -11     
==========================================
- Hits         4046     3971      -75     
- Misses        456      522      +66     
+ Partials      185      179       -6     

Impacted Files	Coverage Δ
signac/common/deprecation/__init__.py	0.00% <0.00%> (ø)
signac/common/errors.py	100.00% <ø> (ø)
signac/contrib/__init__.py	100.00% <ø> (ø)
signac/contrib/errors.py	94.11% <ø> (ø)
signac/synced_collections/_caching.py	0.00% <0.00%> (ø)
..._collections/buffers/memory_buffered_collection.py	100.00% <ø> (ø)
...ignac/synced_collections/data_types/synced_list.py	85.98% <ø> (ø)
signac/synced_collections/validators.py	91.48% <ø> (ø)
signac/testing.py	100.00% <ø> (ø)
signac/contrib/import_export.py	77.24% <71.42%> (-0.18%)	⬇️
... and 47 more

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[kidrahahjo]

Is it worth adding tests for these changes? I am not sure if we already have them or not. Also, I see a lot of lines not covered by us. Although not in scope for this PR, should we worry about this?

The changes looks good to me, if we decide to add tests, happy to re-review :)

[bdice]

@kidrahahjo Thanks for the questions! The new unified filter syntax is already testing document filters, just below where I deleted the tests for the old --doc-filter flag.

Codecov is extra noisy on this PR but I don’t think we are really missing anything new. The baseline coverage measurement for the next branch may be wrong because I just force-pushed some changes. I think this PR’s coverage is fine because we’re just removing a feature.

[vyasr]

I agree that we don't have to worry about the Codecov diff for now. Otherwise these changes LGTM.

[vyasr]

My guess is that _add_prefix can be removed entirely at this point. I can verify that and create a separate issue for that though.

[vyasr]

#810