Include linked assets in source distribution

[sergioald]

Summary

Includes the documentation and reproducibility assets referenced by files in the source distribution.

Why

PR #43 added MANIFEST.in so source distributions retain the repository documentation and example materials. However, the original patterns included only:

recursive-include docs *.md *.tex *.pdf
recursive-include examples *.md *.json *.csv

This omitted files that the included documentation depends on, including:

• images under docs/figures/, such as cover.png;
• YAML templates such as examples/run_manifest_template.yml;
• reproducibility scripts such as regenerate.py;
• supporting text files such as expected_tree.txt.

As a result, an unpacked source distribution could contain documentation with broken links or incomplete reproducibility instructions even though the files are present in the GitHub repository.

Changes

• expands the docs/ source-distribution pattern to include:
  • PNG;
  • JPG and JPEG;
  • SVG;
• expands the examples/ source-distribution pattern to include:
  • YAML and YML;
  • Python scripts;
  • text files;
• updates the metadata regression test so the expanded patterns remain required.

The resulting manifest patterns are:

recursive-include docs *.md *.tex *.pdf *.png *.jpg *.jpeg *.svg
recursive-include examples *.md *.json *.csv *.yml *.yaml *.py *.txt

Validation

python -m py_compile tests/test_project_metadata.py
python -m pytest tests/test_project_metadata.py
python -m pytest
python -m pre_commit run --all-files

rm -rf build dist
python -m build
python -m twine check dist/*

The source distribution should also be inspected to confirm that the linked assets are present, including:

docs/figures/cover.png
examples/run_manifest_template.yml

and any reproducibility example files such as:

regenerate.py
expected_tree.txt

Compatibility

• no solver mathematics are changed;
• no CLI or GUI behaviour is changed;
• package version remains 0.6.5;
• runtime dependencies are unchanged;
• input and output schemas are unchanged;
• wheel contents and installed runtime behaviour are unaffected except for the improved completeness of the source distribution.

Scope

This is a packaging-only correction following the review of PR #43. It does not create a release, publish to PyPI or Zenodo, or change numerical behaviour.