Feature request: add virtual-packet-logging option to run_tardis()

[yuyizheng1112]

Description

This PR is to resolve #1356.

Motivation and Context

The virtual packet data is not enabled by default. Currently, we have to enable virtual_packet_logging by editing the configuration file to use visualization tools that require virtual packet data. Although offering instruction in the documentation can partly solve the problem, it is still inconvenient to edit configuration file every time.

The new feature allows us to enable virtual_packet_logging option while running TARDIS simulation by setting the parameter virtual_packet_logging=True. The default value of the parameter is False. Meanwhile, it still supports specifying the option in configuration files.

How Has This Been Tested?

• Testing pipeline
• Reference Data Comparison following these instructions
• Other (please describe)

Screenshots (if appropriate):

The output of virt_packet_last_interaction_type indicates whether the packet has been enabled.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• None of the above (please describe)

Checklist:

• My code follows the code style of this project
• My change requires a change to the documentation
• I have updated the documentation accordingly
• I have built the documentation on my fork following these instructions
• I have assigned and requested two reviewers for this pull request

[codecov]

Codecov Report

Merging #1498 (219c639) into master (47ed0ce) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1498   +/-   ##
=======================================
  Coverage   68.12%   68.12%           
=======================================
  Files          68       68           
  Lines        6040     6040           
=======================================
  Hits         4115     4115           
  Misses       1925     1925           

Impacted Files	Coverage Δ
tardis/tardis/base.py	5.55% <0.00%> (ø)
tardis/tardis/montecarlo/base.py	86.20% <0.00%> (ø)
tardis/tardis/simulation/base.py	85.71% <0.00%> (ø)

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[andrewfullard]

Thank you for this contribution! Please look at the results of failing checks and adjust appropriately. In particular, apply black formatting and add a docstring that informs the user of the new virtual packet logging option.

[yuyizheng1112]

Thank you for this contribution! Please look at the results of failing checks and adjust appropriately. In particular, apply black formatting and add a docstring that informs the user of the new virtual packet logging option.

Thanks for your kind reminder. I made some additions to the docstring and reformatted the files. Please review my work.

[jaladh-singhal]

@yuyizheng1112 this looks good. Just to make sure everything is alright, can you post output of sim.runner.virt_logging for both cases?

[yuyizheng1112]

@yuyizheng1112 this looks good. Just to make sure everything is alright, can you post output of sim.runner.virt_logging for both cases?

I've post the screenshot of new output. Please review it :)