Add testing workflow and dependencies

[lispandfound]

Adds a testing workflow to the data repository and properly specifies dependencies. Also:

1. Fixes the Dunedin smoothing boundary to make the tests pass. Probably should have a more elegant fix.
2. Style fixes the registry file.
3. Removes missing paths in the registry to "grisborne_basement.png".
4. Deletes the registry entry to the broken Chow model.

The Tests

Summary of NZCVM Registry Validation Tests

This test suite ensures the integrity of the New Zealand Community Velocity Model (NZCVM) by validating both the metadata registry and the underlying geophysical data files.

---

Registry Metadata Validation

• Schema Enforcement: Uses the schema library to verify nzcvm_registry.yaml structure, ensuring valid Unix paths, python identifiers for submodels, and correctly formatted URLs.
• Dynamic Test Generation: Uses pytest_generate_tests to automatically create individual test cases for every entry defined in the registry.

---

Tomography Model Tests

Verifies the high-resolution 3D velocity models stored in HDF5 format:

• File Integrity: Ensures paths exist and files are valid, non-empty HDF5 containers.
• Metadata Alignment: Cross-references elevation levels in the YAML registry against the actual datasets inside the HDF5 file.
• Structural Consistency: Validates that the dimensions of data arrays ($V_p$, $V_s$, and $\rho$) match the (Latitude $\times$ Longitude) grid dimensions.
• Geospatial Logic: * Latitudes must be between $-90$ and $90$.
  • Longitudes must be between $0$ and $185$.
  • Coordinates must be strictly monotonic (ascending or descending).
• Physical Constraints: Ensures no NaN values exist and data falls within predefined bounds:
  • $V_p$: $0$ to $11.0$ km/s
  • $V_s$: $0$ to $7.0$ km/s
  • $\rho$ (Density): $0$ to $5.0$ g/cm³

---

Basin & Surface Validation

Checks the geometry and depth surfaces of sedimentary basins:

• Boundary Geometry: Uses shapely to verify that basin boundaries (GeoJSON) are valid, non-empty, and composed of closed Polygons.
• Surface Coverage: Verifies that the HDF5 elevation surfaces spatially contain the entire basin boundary.
• Smoothing Transitions: Ensures that "smoothing boundaries" are correctly nested within the primary basin boundaries.
• Surface Data Quality: Validates that surface elevations are realistic (between $\pm10,000$m) and contain no missing data.

---

Vs30 & Submodel Tests

• Vs30 Verification: Validates near-surface velocity data, ensuring values are within $0$ to $2000$ m/s.
• 1D Velocity Models (vm1d): Parses 1D text-based model files (DEF HST format) to verify:
  • Correct header identification.
  • Positive layer thicknesses.
  • Valid seismic quality factors ($Q_p$, $Q_s$).

[gemini-code-assist]

Summary of Changes

Hello @lispandfound, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the robustness of the NZCVM data repository by integrating a new testing framework and formalizing dependency management. The changes ensure that the geophysical data and its metadata registry adhere to defined standards and are free from common errors, improving overall data reliability and maintainability. It also includes several targeted fixes and stylistic improvements to the registry file itself.

Highlights

• Testing Workflow: A comprehensive testing workflow has been added to the data repository to ensure the integrity and consistency of the New Zealand Community Velocity Model (NZCVM) data.
• Dependency Management: Project dependencies are now properly specified using a new 'pyproject.toml' file, including dedicated optional dependencies for testing and development.
• Registry Cleanup and Style Fixes: The 'nzcvm_registry.yaml' file has undergone significant cleanup, including reformatting, removal of outdated entries, correction of file paths, and general style improvements for readability.
• Dunedin Smoothing Boundary Fix: The Dunedin smoothing boundary definition has been adjusted to resolve issues, likely to ensure tests pass as mentioned in the PR description.

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Ignored Files

• Ignored by pattern: .github/workflows/** (4)
  • .github/workflows/pytest.yml
  • .github/workflows/ruff.yml
  • .github/workflows/types.yml
  • .github/workflows/yamllint.yml

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[gemini-code-assist]

Code Review

This pull request introduces a new pyproject.toml file to manage project dependencies and metadata, and a .yamllint configuration file to enforce a 200-character line length. The nzcvm_registry.yaml file has been updated by reformatting elev arrays for readability, removing two tomography entries (CHOW2020_EP2020_MIX, EP2025), standardizing basement file naming to lowercase 'basement' across multiple basin entries, removing an image from Gisborne_v21p7, and correcting various indentation and spacing issues throughout the basin and submodel sections. Additionally, a block of coordinate data was removed from regional/Dunedin/Dunedin_smoothing.txt. The review comments highlight several issues in tests/test_registry.py: the attrs library needs to be added as a test dependency in pyproject.toml, the wiki_images path validation logic was incorrect and needed to be relative to the repository root, and the test_submodel_data_is_valid test was improved to include rho validation and use pytest-subtests for better error reporting. Further suggestions included making latitude and longitude checks in test_surface_geo_gridpoints more robust by allowing both strictly ascending or descending order, and using line.strip().split() for parsing in read_smoothing_boundary and parse_submodel_data for improved robustness.

[lispandfound]

@sungeunbae type checking does work but fails in the installation step because of version resolution issues with numba.