Retooling T3 Environment

[calvinp0]

This PR makes the following changes to T3:

• Updates the environment.yml file to remove unnecessary packages and update the MKL package to the 2023 version.
• Fixes the importing of the settings files, which were previously imported from the .arc folder. The settings files have now been renamed to t3_settings.
• Fixes an index error that occurred when attempting to get the value_range of concentrations of species.
• Fixes a syntax error that occurred when attempting to set variables.
• Updates the .gitignore file to now include VSCode files.

These changes make T3 a more stable and reliable tool for generating chemical reaction mechanisms.

Here are some additional details about the changes:

• The update to the environment.yml file removes unnecessary packages and updates the MKL package to the 2023 version.
• The fix to the importing of the settings files makes it easier for users to set the configuration options for T3.
• The fix to the index error that occurred when attempting to get the value_range of concentrations of species makes it possible to get the correct values for the concentrations.
• The fix to the syntax error that occurred when attempting to set variables makes it possible to set variables correctly.
• The update to the .gitignore file ensures that VSCode files are not tracked by Git. This will prevent accidental changes to VSCode files from being committed to the repository.

[codecov-commenter]

Codecov Report

Merging #125 (324c126) into main (2de3b76) will decrease coverage by 0.07%. The diff coverage is 18.18%.

@@            Coverage Diff             @@
##             main     #125      +/-   ##
==========================================
- Coverage   73.46%   73.40%   -0.07%     
==========================================
  Files          22       22              
  Lines        2891     2891              
  Branches      762      725      -37     
==========================================
- Hits         2124     2122       -2     
- Misses        552      553       +1     
- Partials      215      216       +1     

Flag	Coverage Δ
unittests	73.40% <18.18%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
t3/runners/rmg_runner.py	34.37% <0.00%> (ø)
t3/settings/t3_settings.py	100.00% <ø> (ø)
t3/settings/t3_submit.py	100.00% <ø> (ø)
t3/simulate/rmg_constantTP.py	58.41% <0.00%> (ø)
t3/imports.py	30.00% <40.00%> (ø)

... and 1 file with indirect coverage changes

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[alongd]

Thanks! T3 can spawn RMG as a job on a server or "incore". I think these changes will not allow T3 to execute RMG incore. Perhaps we should spawn RMG in a subprocess within its own env when "incore" is requested? see here and here