[mwyau]

Why

The existing SPDX pre-commit hook runs reuse annotate, which may rewrite files when committing. Header validation should be read-only and behave the same locally and in CI.

What changed

• Replace the local annotation hook with SPDX Header Check v0.1.0. Developers run it through prek; CI uses the published GitHub Action.
• Add missing SPDX headers to the benchmark runner, Sphinx configuration, and TrackJSON schema generator.
• Restore 12 test-package __init__.py files to zero bytes rather than leaving header-only files.
• Run the remaining pre-commit checks in CI: JSON/TOML/YAML validation, merge-conflict detection, whitespace/line-ending/EOF/BOM checks, and mdformat. Ruff, ty, mypy, and TrackJSON validation retain their dedicated steps.
• Add uv lock --check and update ty to 0.0.91 consistently in the pre-commit hook, project dependencies, CI command, and regenerated uv.lock.

The SPDX checker validates headers without adding metadata, changing license identifiers, or updating copyright years. There are no changes to scientific code or algorithms.

Local checks

uvx prek run --all-files
uv lock --check

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.16%. Comparing base (569f5b2) to head (b4d75a7).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #271   +/-   ##
=======================================
  Coverage   78.16%   78.16%           
=======================================
  Files          59       59           
  Lines        9664     9664           
  Branches     1884     1884           
=======================================
  Hits         7554     7554           
  Misses       1374     1374           
  Partials      736      736           

Flag	Coverage Δ
integration	51.33% <ø> (ø)
parity	17.06% <ø> (ø)
unit	57.00% <ø> (ø)
unit-jit-coverage	72.36% <ø> (ø)
unit-jit-disabled	73.69% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

[Copilot]

🟢 Approval recommended

No unresolved issues were identified, and all review assessments indicate approval readiness.

No open issues 🎉

What changed in this PR

This pull request replaces mutating SPDX annotation with read-only header validation, aligns local and CI checks, updates ty, and adds or removes SPDX headers as appropriate without changing scientific code.

Changes:

• Replaces reuse annotate with spdx-header-check locally and in CI.
• Adds housekeeping, lockfile, Markdown, type-checking, schema, and SPDX validation steps.
• Updates ty to 0.0.91 and refreshes uv.lock.
• Adds headers to uncovered source files while keeping empty test package initializers empty.

File	Description
uv.lock	Updates the lock revision and pins ty 0.0.91.
tests/​unit/​simple/​__init__.py	Keeps the empty package initializer empty.
tests/​unit/​preprocessing/​__init__.py	Keeps the empty package initializer empty.
tests/​unit/​models/​__init__.py	Keeps the empty package initializer empty.
tests/​unit/​io/​__init__.py	Keeps the empty package initializer empty.
tests/​unit/​hodges/​__init__.py	Keeps the empty package initializer empty.
tests/​unit/​healpix/​__init__.py	Keeps the empty package initializer empty.
tests/​unit/​__init__.py	Keeps the empty package initializer empty.
tests/​parity/​ncl_spherepack/​__init__.py	Keeps the empty package initializer empty.
tests/​parity/​legacy/​__init__.py	Keeps the empty package initializer empty.
tests/​parity/​__init__.py	Keeps the empty package initializer empty.
tests/​integration/​__init__.py	Keeps the empty package initializer empty.
tests/​__init__.py	Keeps the empty package initializer empty.
scripts/​generate_trackjson_schema.py	Adds the required SPDX header.
pyproject.toml	Updates the development ty dependency to 0.0.91.
docs/​conf.py	Adds the required SPDX header.
benchmarks/​run_benchmark_detailed.py	Adds the required SPDX header.
.pre-commit-config.yaml	Replaces the mutating SPDX hook with the read-only checker and updates ty.
.github/​workflows/​ci.yml	Adds housekeeping, lockfile, type-checking, and SPDX validation steps.

_{Review effort: Lite}