[jucordero]

Description

This PR introduces new pipeline management utilities, and fixes to existing datablock manipulation functions:

• ability to set skip flags for new nodes, and control skip flags of existing nodes, either by node index or name
• ability to set node parameters on existing nodes by index or name
• print_datablock and copy_datablock node functions not use the right dictionary manipulation utilities to correctly take datablock path tuples as inputs.

Checklist

• Follow the Contributor Guidelines
• Write unit tests
• Write documentation strings

[Copilot]

Copilot review overview

🟡 Changes recommended

A critical tuple-path loading defect and several moderate pipeline behavior issues remain unresolved.

Review effort: Lite
Findings: 1 · 1 · 1

Open (3)

• Fix standalone tuple-path dataset lookup · New
• Preserve one-based numbering for skipped nodes · New
• Add execution tests for configured and name-based node skipping · New

What changed in this PR

This PR adds pipeline node controls and tuple-path support for datablock utilities, while consolidating utility tests.

Changes:

• Adds persistent skip flags and node parameter setters by index or name.
• Supports nested datablock paths in utility nodes.
• Consolidates utility tests and updates documentation.

File	Summary
agrifoodpy/​utils/​tests/​test_write_to_disk.py	Reviewed consolidated utility test coverage.
agrifoodpy/​utils/​tests/​test_write_to_datablock.py	Reviewed consolidated utility test coverage.
agrifoodpy/​utils/​tests/​test_print_datablock.py	Reviewed; nested tuple-path coverage remains needed.
agrifoodpy/​utils/​tests/​test_nodes.py	Consolidates utility node tests.
agrifoodpy/​utils/​tests/​test_load_dataset.py	Reviewed; nested output-path coverage remains needed.
agrifoodpy/​utils/​tests/​test_copy_datablock.py	Reviewed; nested key and output-path coverage remains needed.
agrifoodpy/​utils/​tests/​test_add_years.py	Reviewed consolidated utility test coverage.
agrifoodpy/​utils/​tests/​test_add_items.py	Reviewed consolidated utility test coverage.
agrifoodpy/​utils/​nodes.py	Adds tuple-path handling; standalone dataset loading has an unresolved tuple-path lookup issue.
agrifoodpy/​pipeline/​tests/​test_pipeline.py	Tests pipeline configuration APIs.
agrifoodpy/​pipeline/​pipeline.py	Adds skip and parameter controls; numbering, CLI name handling, and boolean validation require changes.
agrifoodpy/​land/​model.py	Clarifies a function docstring.

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