General quality check

[gnawin]

This PR does a quality check across the repo.

• update Project.toml
• improve workflow
• make plotting function optional
• consistency checks across the repo

Related issues

Closes #

Checklist

• I am following the contributing guidelines
• Tests are passing
• Lint workflow is passing
• Docs were updated and workflow is passing

[codecov]

Codecov Report

❌ Patch coverage is 27.77778% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 66.71%. Comparing base (be6922b) to head (322afba).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/main-analysis.jl	33.33%	10 Missing ⚠️
src/network-visualisation.jl	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #60      +/-   ##
==========================================
- Coverage   73.10%   66.71%   -6.40%     
==========================================
  Files          12       12              
  Lines         725      724       -1     
==========================================
- Hits          530      483      -47     
- Misses        195      241      +46     

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