Implement feature to search jobs with a sp- and doc-integrated filter

[vishav1771]

Description

This patch enables the search for jobs with a statepoint- and document-
combined filter. To specify whether a key is a statepoint- or a
document-key use prefixes 'sp.' and 'doc.' respectively. No prefix is
equivalent to the 'sp.' prefix.

This patch is backwards compatible with the exception that the index
scheme was slightly modified.

Related to issue glotzerlab/signac-dashboard#25 .

Minimal example

This patch enables queries such as this one:

 >>> project.find_jobs({'foo': 0, 'doc.bar': True})
 signac.contrib.project.JobsCursor({'project': 'project', 'filter': '{'sp.foo': 0, 'doc.bar': True}'})
 >>> # equivalent to:
 >>> project.find_jobs({'foo': 0}, {'bar': True})
 signac.contrib.project.JobsCursor({'project': 'project', 'filter': '{'sp.foo': 0, 'doc.bar': True}'})

Equivalently on the command line:

$ signac find foo 0 doc.bar true

All keys without a prefix are automatically interpreted as having the sp. prefix.

Motivation and Context

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).

[vishav1771]

@csadorf @vyasr I have updated the PR according to the master.
I have some doubts about the warning. I think it should warn while setting the root key as doc in statepoint and sp in document. Please guide.

[codecov]

Codecov Report

Merging #332 (b81817c) into master (e1de895) will decrease coverage by 0.06%.
The diff coverage is 89.10%.

@@            Coverage Diff             @@
##           master     #332      +/-   ##
==========================================
- Coverage   77.19%   77.12%   -0.07%     
==========================================
  Files          42       42              
  Lines        5770     5828      +58     
  Branches     1130     1151      +21     
==========================================
+ Hits         4454     4495      +41     
- Misses       1030     1047      +17     
  Partials      286      286              

Impacted Files	Coverage Δ
signac/contrib/filterparse.py	84.53% <87.23%> (+9.93%)	⬆️
signac/contrib/project.py	85.58% <90.00%> (-1.39%)	⬇️
signac/contrib/import_export.py	77.89% <100.00%> (ø)
signac/contrib/linked_view.py	83.91% <100.00%> (ø)
signac/contrib/schema.py	95.48% <100.00%> (ø)
signac/__main__.py	71.89% <0.00%> (-0.45%)	⬇️

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[vyasr]

@vishav1771 could you clarify what you mean? What warning are you referring to?

[csadorf]

@vishav1771 I'm also not sure what you are referring to, could you clarify, please?

[vishav1771]

Sorry for the misunderstanding. Actually, I was referring to the task defined in the PR #188

Add warning about the use of sp and doc as root-level keys in documents.

[csadorf]

#188

The reasoning was that users should generally avoid those keys in both cases, because otherwise it is difficult to know what they are actually referring to. I don't think it's a huge issue, because if you use doc or sp as a key in either one of them, you could always refer to them as sp.doc: .. or sp.sp: ... etc. So it's more of an issue of creating misleading structures, but I think the best thing is to probably just ignore this for now.

[vishav1771]

Okay, I understand 👍 .

[vishav1771]

I've changed all the functions, but still, if there's anything missing please do tell!

[csadorf]

I have a few questions and suggestions.

[mikemhenry]

Looks pretty good, mostly just need a few more tests and I just had some minor points to improve clarity!

[vyasr]

@mikemhenry is going to work on adding a few more of these tests.