Rework Reaction_Optimization notebook

[AVHopp]

This PR updates the Reaction_Optimization notebook.

Main changes are some more and different explanations as well as the usage of the RandomRecommender instead of the FPSRecommender. Using this recommender is now a task that people investigating the notebook can do.

Note that this PR is based on #7 and hence only the final commit is relevant.

[Copilot]

Pull request overview

This PR updates the Reaction_Optimization notebook to use BayBE version 0.14.2 instead of 0.13.0. The notebook has been reworked to use the RandomRecommender as the default instead of the FPSRecommender, with the latter now presented as a suggested task for users to explore. The changes also include improved explanations, reformatting of markdown sections, and updates to documentation links.

Changes:

• Updated BayBE version references from 0.13.0 to 0.14.2 across all notebooks
• Switched from FPSRecommender to RandomRecommender as the default initial recommender in the Reaction_Optimization notebook
• Removed unnecessary mode="MAX" parameters as maximization is now the default
• Updated documentation links and improved explanatory text throughout

Reviewed changes

Copilot reviewed 7 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
notebooks/Transfer_Learning.py	Updated version references, documentation links, and markdown formatting to align with BayBE 0.14.2
notebooks/Reaction_Optimization.py	Reworked to use RandomRecommender, improved explanations, added task section for FPSRecommender exploration
notebooks/Chemical_Encodings.py	Updated version references, documentation links, and markdown formatting consistency
additional_requirements/Transfer_Learning_requirements.txt	Removed requirements file (now consolidated)
additional_requirements/Chemical_Encodings_requirements.txt	Removed requirements file (now consolidated)
README.md	Updated Python version to 3.13, clarified installation instructions, added version tracking note
CHANGELOG.md	Documented the BayBE version update from 0.13.0 to 0.14.2

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[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 9 comments.

Comments suppressed due to low confidence (2)

notebooks/Reaction_Optimization.ipynb:1

• The narrative says the loop is repeated 5 times, but the code below runs 10 iterations. Either adjust the loop to 5 iterations or update the text so runtime/behavior matches the explanation.

{

notebooks/Reaction_Optimization.ipynb:1

• This executes 10 optimization iterations, which conflicts with the preceding explanation that says 5 iterations. Align code and narrative to avoid confusing readers and to keep notebook execution time predictable.

{

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