Fixing Plasma Graph to Allow .dot and .tex file Generation

[bartnikm]

Description

This reworks the code necessary to generate the .dot and .tex files for the plasma graph. The documentation regarding the graph has been changed to reflect this.

Motivation and context

The current way TARDIS builds the .dot file makes it raise errors upon attempting to build the .tex file, and the latex code within the .dot file, if written into a .tex file without using TARDIS, is displayed incorrectly.

How has this been tested?

• Testing pipeline.
• Other.

Examples

https://bartnikm.github.io/tardis-bartnikm/branch/plasma-graph/physics/setup/plasma/index.html#the-plasma-graph

Below are two graphs of the same configuration file. The first one had no entries passed into the args parameter:
Sample_Graph_no_args.pdf

The second one had the following passed:
[r"nodesep=1.0", r'edge[lblstyle="fill=white"]', r'margin=0', r'ratio="fill"', r'size="8.3,11.7!"']
Sample_Graph_with_args.pdf

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.

[codecov]

Codecov Report

Merging #1868 (5209738) into master (3471658) will increase coverage by 0.22%.
The diff coverage is n/a.

❗ Current head 5209738 differs from pull request most recent head 6c53e09. Consider uploading reports for the commit 6c53e09 to get more accurate results

@@            Coverage Diff             @@
##           master    #1868      +/-   ##
==========================================
+ Coverage   62.12%   62.34%   +0.22%     
==========================================
  Files          66       68       +2     
  Lines        6809     7149     +340     
==========================================
+ Hits         4230     4457     +227     
- Misses       2579     2692     +113     

Impacted Files	Coverage Δ
tardis/tardis/plasma/base.py	48.63% <0.00%> (-7.27%)	⬇️
tardis/tardis/io/parsers/arepo.py	69.04% <0.00%> (ø)
.../montecarlo/montecarlo_numba/r_packet_transport.py	16.45% <0.00%> (ø)
tardis/tardis/util/base.py	72.31% <0.00%> (+0.11%)	⬆️
tardis/tardis/model/base.py	88.96% <0.00%> (+0.66%)	⬆️
...rdis/tardis/montecarlo/montecarlo_numba/vpacket.py	19.19% <0.00%> (+0.82%)	⬆️
...montecarlo/montecarlo_numba/calculate_distances.py	25.00% <0.00%> (+1.31%)	⬆️
...dis/montecarlo/montecarlo_numba/numba_interface.py	36.92% <0.00%> (+1.45%)	⬆️
.../montecarlo/montecarlo_numba/single_packet_loop.py	31.25% <0.00%> (+1.46%)	⬆️
...dis/tardis/montecarlo/montecarlo_numba/r_packet.py	44.44% <0.00%> (+19.00%)	⬆️

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[wkerzendorf]

That looks interesting. Just a quick reminder - one PR one idea. In this PR there is the idea of fixing the old version and adding a new way of plotting this. Let's make a PR that fixes the old version first. Then we make a new PR that has the display_graph

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[bartnikm]

The failed black test flagged multiple files which I did not edit nor are a part of 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.