Deprecate doc_filter parameters.

[vyasr]

Description

Deprecate doc_filter in favor of filters with a doc. prefix.

Motivation and Context

Simplifies the API and reduces duplication. The new combined queries are more general and will more naturally support encoding via URI, see #189.

I made a judgment call based on known usage patterns as to when different things will be deprecated. All doc_filter arguments to methods like find_jobs are quite old and I know they are used, so preserving them until a 3.0 release makes sense (see also the discussion on glotzerlab/signac-docs#115). I know very few users of the groupbydoc method, so I chose to deprecate that in 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.

[codecov]

Codecov Report

Merging #516 (b5f2e87) into master (7795dad) will increase coverage by 0.00%.
The diff coverage is 83.33%.

@@           Coverage Diff           @@
##           master     #516   +/-   ##
=======================================
  Coverage   78.16%   78.16%           
=======================================
  Files          65       65           
  Lines        7030     7036    +6     
  Branches     1310     1310           
=======================================
+ Hits         5495     5500    +5     
- Misses       1230     1231    +1     
  Partials      305      305           

Impacted Files	Coverage Δ
signac/contrib/project.py	85.06% <83.33%> (-0.02%)	⬇️

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[vyasr]

@bdice @pepak13 mind taking a look at this?

[bdice]

Seems fine to me.