Enabling virtual_packet_logging by default in the visualization folder

[atharva-2001]

This PR removes the symbolic link to tardis_example.yml in the visualization folder, and adds it with virtual_packet_logging enabled.

Description

To build the SDEC plot and the Line Info widget, one needs to enable virtual_packet_logging from the run_tardis function or edit the tardis_example.yml file in the docs folder. This enables virtual_packet_logging by default just for the visualization folder, easing the process for the user.

Motivation and context

#1665 (review)

How has this been tested?

• Testing pipeline.
• Other.

Examples

Type of change

• Bug fix.
• New feature.
• Breaking change.
• None of the above.

Checklist

• My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • (optional) I have built the documentation on my fork following the instructions.
• I have assigned and requested two reviewers for this pull request.

[tardis-bot]

Before a pull request is accepted, it must meet the following criteria:

• Is the necessary information provided?
• Is this a duplicate PR?
  • If a new PR is clearly a duplicate, ask how this PR is different from the original PR?
  • If this PR is about to be merged, close the original PR with a link to this new PR that solved the issue.
• Does it pass existing tests and are new tests provided if required?
  • The test coverage should not decrease, and for new features should be close to 100%.
• Is the code tidy?
  • No unnecessary print lines or code comments.

[tardis-bot]

Before a pull request is accepted, it must meet the following criteria:

• Is the necessary information provided?
• Is this a duplicate PR?
  • If a new PR is clearly a duplicate, ask how this PR is different from the original PR?
  • If this PR is about to be merged, close the original PR with a link to this new PR that solved the issue.
• Does it pass existing tests and are new tests provided if required?
  • The test coverage should not decrease, and for new features should be close to 100%.
• Is the code tidy?
  • No unnecessary print lines or code comments.

[codecov]

Codecov Report

Merging #1693 (4c5b405) into master (2c47baa) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1693   +/-   ##
=======================================
  Coverage   61.88%   61.88%           
=======================================
  Files          63       63           
  Lines        5851     5851           
=======================================
  Hits         3621     3621           
  Misses       2230     2230           

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[isaacgsmith]

Because of how we do things with symlinks, I think you should either:

• rename that file to something else besides tardis_example.yml

• add virtual packet logging to docs/tardis_example.yml and keep the file in docs/io/visualization as a symlink

[MarkMageeAstro]

We can probably change to something like tardis_example_SDEC? I guess this would also mean some notebooks need updated too

[MarkMageeAstro]

See previous comment...

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[yuyizheng1112]

just a suggestion: I used to add virtual_packet_logging option to run_tardis() function (see this pr). It seems that few people know this... Maybe you can set this option to True instead of adding new file.

[atharva-2001]

That sounds good to me too, maybe we could just set virtual_packet_logging to True in both notebooks in #1665?

[jaladh-singhal]

I think instead of adding new file, enabling virtual packet logging in run_tardis call will be better as suggested by @yuyizheng1112 .

And if you want to keep the new config file, name it as tardis_example_virt_logging.yml instead since it's not only for SDEC but also for Line info widget.

[andrewfullard]

Is this PR still relevant?