Transition tutorial examples from Associations to Links

[Copilot]

The tutorial and example macros were still using the legacy EICrecon association naming while the current tree layout exposes link-based branches and index arrays. This left the examples out of sync with the actual data products and their naming conventions.

• Scope

  • Updated the lesson text, analysis snippets, and pruning utilities to use the *_Links_* branch names instead of the legacy *_Associations_* names.
  • Switched the reader arrays to TTreeReaderArray<unsigned int> and aligned the from/to index branches with the current EICrecon schema.
  • Normalized the narrative language from “association” to “link” throughout the docs and examples.

• Examples updated

  • "_ReconstructedChargedParticleAssociations_rec.index" → "_ReconstructedChargedParticleLinks_from.index"
  • "_ReconstructedChargedParticleAssociations_sim.index" → "_ReconstructedChargedParticleLinks_to.index"
  • TTreeReaderArray<int> → TTreeReaderArray<unsigned int>

 // Get Links Between MCParticles and ReconstructedChargedParticles
 TTreeReaderArray<unsigned int> recoAssoc(tree_reader, "_ReconstructedChargedParticleLinks_from.index");
 TTreeReaderArray<unsigned int> simuAssoc(tree_reader, "_ReconstructedChargedParticleLinks_to.index");

• Notes

  • The migration was applied consistently across the tutorial, exercise scripts, and pruning examples rather than only to the highlighted instance.
  • A few copy-paste typos and a stray Python syntax issue in the exercise script were corrected in the same pass to keep the examples usable as written.

• Fixes Transition from Associations to Links #11

[github-actions]

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Rendered Changes

🔍 Inspect the changes: https://github.com/eic/tutorial-analysis/compare/md-outputs..md-outputs-PR-12

The following changes were observed in the rendered markdown documents:

 03-analysis.md         |  66 ++++++++++++------------
 branch-dictionary.md   |   8 +--
 exercise-scripts.md    | 136 ++++++++++++++++++++++++-------------------------
 files/TreePrune.C      |   4 +-
 md5sum.txt             |   8 +--
 tree-pruning-script.md |   4 +-
 6 files changed, 113 insertions(+), 113 deletions(-)

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⏱️ Updated at 2026-08-30 16:20:39 +0000

[Copilot]

Pull request overview

This PR updates the tutorial documentation and example macros to align with the current EICrecon output schema by replacing legacy *_Associations_* usage with *_Links_* branches and updating related narrative text.

Changes:

• Updated pruning examples to keep link-related branches instead of association branches.
• Updated C++ (TTreeReader) and Python examples to use _ReconstructedChargedParticleLinks_{from,to}.index and TTreeReaderArray<unsigned int>.
• Reworded tutorial text from “association” to “link” across the lesson and learner docs.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
learners/tree-pruning-script.md	Updates the pruning script snippet to retain *Links* branches.
learners/files/TreePrune.C	Updates the actual ROOT pruning macro to keep link branches (needs a small pattern fix).
learners/exercise-scripts.md	Migrates multiple exercise code templates (C++/Python/RDF) from associations to links.
learners/branch-dictionary.md	Renames branch sections and updates explanatory text to “links” (needs a wording correction).
episodes/03-analysis.md	Updates Episode 3 tutorial narrative and code blocks to use link-based branches and unsigned indices.

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[wdconinc]

This looks good to me.

[sjdkay]

Looks good, even a typo fix to boot.