fix(examples): use runnable local data paths in zinc_protein example

[wanghan-iapcm]

Problem

examples/zinc_protein/zinc_se_a_mask.json referenced its training and validation data with repo-root-relative paths (examples/zinc_protein/train_data_dp_mask/ and examples/zinc_protein/val_data_dp_mask/), while the data actually lives next to the config. Every other example uses paths relative to its own directory. As a result this example only trained when launched from the repository root; run from examples/zinc_protein, the paths resolved to examples/zinc_protein/examples/zinc_protein/..., which does not exist.

Fix

Use local train_data_dp_mask/ and val_data_dp_mask/ paths, matching the config-relative convention of the other examples.

Test

source/tests/common/test_examples.py already loaded this config, but only ran argument-checking (normalize), so an unresolvable data path passed. This PR adds test_data_paths_exist, which asserts that every example's training_data/validation_data systems resolve relative to the config's own directory. Across all listed examples this fails only for the two zinc_protein paths on the current tree and passes for every other example; after the fix it passes. It permanently guards the config-relative-path convention.

Known limitation

The new check covers the single-task input_files list (where this example lives); multi-task configs use a different nested data schema and are out of scope for this fix.

Fix #5694

Summary by CodeRabbit

• Bug Fixes
  • Updated example data paths to use shorter, relative locations so they resolve correctly from the example directory.
  • Added a check that example input files reference existing system data paths, helping catch broken paths earlier.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: 8a6dca92-dec2-4f79-bb75-9d94aae4fb39

📥 Commits

Reviewing files that changed from the base of the PR and between 0e5c170 and 147c8bd.

📒 Files selected for processing (2)

• examples/zinc_protein/zinc_se_a_mask.json
• source/tests/common/test_examples.py

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📝 Walkthrough

Walkthrough

The zinc_protein example JSON's training_data and validation_data systems paths were updated to remove a redundant directory prefix so they resolve correctly when run from the example's own directory. A new test was added to verify system data paths exist for all examples.

Changes

Zinc Protein Example Path Fix

Layer / File(s)	Summary
Corrected example data paths examples/zinc_protein/zinc_se_a_mask.json	Removed the examples/zinc_protein/ prefix from training_data.systems and validation_data.systems paths so they resolve relative to the example directory.
Path-existence validation test source/tests/common/test_examples.py	Added test_data_paths_exist, which loads each example's input.json, reads training_data/validation_data systems, and asserts each referenced path exists relative to the example directory.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Related issues: #5694 (directly addresses the repo-root-relative path issue in the zinc_protein example).

Suggested labels: documentation, tests

Suggested reviewers: (none identified from provided context)

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: making the zinc_protein example use local, runnable data paths.
Linked Issues check	✅ Passed	The PR fixes the reported repo-root-relative paths by switching to local example-relative paths and adds a guard test.
Out of Scope Changes check	✅ Passed	The new test is directly related to the path-fix objective and no unrelated changes are evident.

✨ Finishing Touches

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.78%. Comparing base (0e5c170) to head (147c8bd).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5698      +/-   ##
==========================================
- Coverage   81.97%   81.78%   -0.20%     
==========================================
  Files         959      959              
  Lines      105748   105748              
  Branches     4102     4104       +2     
==========================================
- Hits        86684    86483     -201     
- Misses      17573    17771     +198     
- Partials     1491     1494       +3     

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