Removed the deprecated --with-vpacket-logging flag

[antreev-brar]

This Pull request aims to resolve the issue #1342 Remove virtual packet logging compile flag as it was deprecated with the numba code.

Description

The changes made to the code are

• Removed add_command_option for the with-vpacket-logging in setup.py
• Removed a comment that described how to use full_hdf_properties with with-vpacket-logging flag in tardis/montecarlo/base.py
• Updated warning on properties virtual_packet_nu , virtual_packet_energy, virtual_packet_luminosity that worked with with-vpacket-logging flag in tardis/montecarlo/base.py

Motivation and Context

This pull request addresses the issue raised in #1342
Earlier there were several essential features of tardis that require compiling it with vpacket logging, but this was changed with numba-montecarlo as described in issue #1215 . I went through the code and removed instances of "with-vpacket-logging". I was unsure whether the properties must be removed but I ensured that they weren't called from anywhere in the code. Hence they were redundant as well.

How Has This Been Tested?

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

I checked it by running unit tests on it with python setup.py test that gave the following output on my local machine.

• 156 passed, 1254 skipped, 6 xpassed in 7.87s

I also ran python setup.py test --args="--tardis-refdata=/path/to/tardis-refdata/" test and gave the following log output

• 19 passed in 2.72s

Also the example notebook given in quickstart https://tardis-sn.github.io/tardis/quickstart/quickstart.html executed without any issues.

Screenshots (if appropriate):

N/A

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)

Removed deprecated segment from the code.

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 #1459 (f377b8c) into master (50f13ba) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1459   +/-   ##
=======================================
  Coverage   71.13%   71.13%           
=======================================
  Files          67       67           
  Lines        5523     5523           
=======================================
  Hits         3929     3929           
  Misses       1594     1594           

Impacted Files	Coverage Δ
tardis/tardis/io/util.py	72.09% <0.00%> (ø)
tardis/tardis/montecarlo/base.py	86.20% <0.00%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 50f13ba...730c20f. Read the comment docs.

[antreev-brar]

@wkerzendorf can you review this PR?

[wkerzendorf]

@antreev-brar There is additional vpacket code fragments left at https://github.com/tardis-sn/tardis/blob/master/tardis/montecarlo/setup_package.py

[antreev-brar]

@wkerzendorf Thanks for letting me know. From my point of view, the code fragment uses the "build", "install", and "develop" parameters of "with-vpacket-logging" from the setup.py ( which were already removed ). Therefore we should remove this code fragment as well.

I have changed this file.