finish book chapter move

[lazarusA]

continue #216

[gemini-code-assist]

Summary of Changes

Hello @lazarusA, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request finalizes the migration of the 'Synthetic Data Analysis' example from a standalone book chapter project into the core documentation as a new, accessible tutorial. This refactoring improves the organization of examples and ensures they are properly built and presented within the project's documentation. Additionally, it includes a minor update to project dependencies and a small code clarity improvement in an import statement.

Highlights

• Documentation Structure: The 'Synthetic Data Analysis' example, previously located in the projects/book_chapter directory, has been moved and integrated into the main documentation as a new tutorial.
• New Tutorial: A new tutorial titled 'Synthetic Respiration' has been added to the documentation, showcasing hybrid model training with Q10 temperature sensitivity.
• Dependency Management: The Statistics package has been added as a new dependency in the main Project.toml file.
• Code Refinement: The import statement for ComponentArrays in src/EasyHybrid.jl was refined for explicit module and type import.

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Changelog

• Project.toml
  • Added Statistics package as a dependency.
• docs/literate/tutorials/synthetic_respiration.jl
  • Introduced a new tutorial for synthetic data analysis, showcasing hybrid model training with Q10 temperature sensitivity.
• docs/make.jl
  • Integrated the new 'Synthetic Respiration' tutorial into the documentation's 'Research' section.
• projects/book_chapter/Project.toml
  • Deleted the Project.toml file previously associated with the book chapter project.
• projects/book_chapter/example_synthetic.jl
  • Eliminated the example_synthetic.jl script, as its content was moved to a new tutorial.
• src/EasyHybrid.jl
  • Modified the ComponentArrays import to be more specific, importing ComponentArrays and ComponentArray directly.

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[gemini-code-assist]

Code Review

This pull request moves a book chapter example into the main documentation as a tutorial. The changes include adding the new tutorial file, updating the documentation build configuration, removing the old project files, and adding a dependency compatibility entry.

My review focuses on the new tutorial file. I've suggested a few improvements for code clarity and quality, such as simplifying a redundant call, using more descriptive variable names, and adopting a more concise function syntax. I also noted the presence of TODO comments in the new tutorial, which should ideally be resolved or tracked as issues before being published as part of the documentation.

[gemini-code-assist]

The dimension names :col and :row are a bit generic. For better clarity and consistency with common practices in DimensionalData.jl, consider using more descriptive names like :variable and :observation. This would make the data structure's intent clearer to readers of the tutorial.

da = DimArray(mat, (Dim{:variable}(Symbol.(names(dfnot))), Dim{:observation}(1:size(dfnot, 1))));

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 50.31%. Comparing base (ea7f378) to head (c2da981).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #228   +/-   ##
=======================================
  Coverage   50.31%   50.31%           
=======================================
  Files          27       27           
  Lines        1932     1932           
=======================================
  Hits          972      972           
  Misses        960      960           

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[BernhardAhrens]

The bookchapter example should go under research as we try to replicate existing science

[lazarusA]

yes, currently in the menu bar is going there already.

Do you mean: we should create a new folder, research and put it there? make sense...

[BernhardAhrens]

Ah I did not see that it already goes there. I think the research folder is a good idea

[lazarusA]

I will do the new folder 📁.