Move cmd and with_job to FlowProject.operation

[b-butler]

Description

Does not break current behavior.

• refactor: Deprecate cmd and with_job decorators.
• feat: Add cmd and with_job keyword only arguments for @operation
• test: Add tests for new keyword only arguments of FlowProject.operation

Motivation and Context

Closes #669
and replaces #671.

I had large suggestions to the way the code should be changed. I think this is much simpler to get the desired behavior.

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.

[bdice]

LGTM. In the future, it can be helpful to do something like this instead:

def _func(...):
    # do stuff

def func(...):
    warnings.warn(FutureWarning, "func is deprecated")
    _func(...)

and then call _func internally, instead of using a warnings.catch_warnings + warnings.simplefilter.

[b-butler]

@bdice I agree and it is generally what I do. Here, I think the solution is different in that I think we should remove the implementations in flow/operations.py and put them in operation register.

[codecov]

Codecov Report

Merging #679 (30405b7) into master (7a33919) will increase coverage by 0.08%.
The diff coverage is 96.29%.

@@            Coverage Diff             @@
##           master     #679      +/-   ##
==========================================
+ Coverage   80.15%   80.24%   +0.08%     
==========================================
  Files          32       32              
  Lines        3165     3189      +24     
  Branches      674      682       +8     
==========================================
+ Hits         2537     2559      +22     
- Misses        497      498       +1     
- Partials      131      132       +1     

Impacted Files	Coverage Δ
flow/aggregates.py	87.55% <ø> (ø)
flow/operations.py	80.70% <90.00%> (-0.55%)	⬇️
flow/project.py	82.69% <100.00%> (+0.16%)	⬆️

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