From 7535ea4dc97e7f3e675eca790a5a5f0548f9c43c Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Wed, 17 Dec 2025 17:09:50 +1300 Subject: [PATCH 01/19] add testing code test: update QUALITY_BOUNDS values for vp and vs in test_registry - Increase upper bound for vp from 10.0 to 11.0 - Increase upper bound for vs from 6.0 to 6.5 - Add note clarifying values are not physically derived test: remove longitude spacing tolerance check from tomography geo gridpoints test chore(pyproject): add empty types optional dep tests: update quality bounds to ayushi's values ci: add github actions test: add comprehensive basin, vs30, and submodel validation tests - Add Basin, Vs30, and Submodel TypedDicts for schema validation - Parametrize tests for basin, vs30, and submodel entries from registry - Add tests for basin boundaries, surfaces, smoothing, and containment - Add tests for vs30 file existence, HDF5 validity, and gridpoint checks - Add tests for submodel data existence and content validation - Improve test coverage and robustness for registry-driven datasets test: refactor registry tests for clarity and remove unused code - Remove duplicate and unused imports in test_registry.py - Decorate test_nzcvm_registry_schema with @no_type_check for type checking bypass - Eliminate redundant and commented-out test code for basin smoothing boundaries - Remove unused variables and streamline vs30 tests for readability deps: add shapely dependency ci: add all extras to ty check ci: add yamllint config ci: fix pytest action ci: use cached LFS checkout build: require Python 3.11 or higher in pyproject.toml test: improve boundary geometry assertions in basin smoothing test - Check now asserts the basin *boundary* contains the smoothing boundary, instead of the basin *polygon* (which includes the interior). ci: use big-data runner group for extra space ci: use ubuntu latest but remove unused junk --- .github/workflows/pytest.yml | 24 ++ .github/workflows/ruff.yml | 8 + .github/workflows/types.yml | 22 ++ .github/workflows/yamllint.yml | 17 + .yamllint | 3 + pyproject.toml | 21 ++ tests/test_registry.py | 581 +++++++++++++++++++++++++++++++++ 7 files changed, 676 insertions(+) create mode 100644 .github/workflows/pytest.yml create mode 100644 .github/workflows/ruff.yml create mode 100644 .github/workflows/types.yml create mode 100644 .github/workflows/yamllint.yml create mode 100644 .yamllint create mode 100644 pyproject.toml create mode 100644 tests/test_registry.py diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 0000000..64937b1 --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,24 @@ +name: Pytest Check +on: [pull_request] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - name: Remove junk + uses: easimon/maximize-build-space@master + with: + root-reserve-mb: 512 + swap-size-mb: 1024 + remove-dotnet: "true" + - name: Checkout code + uses: nschloe/action-cached-lfs-checkout@v1 + + - name: Setup UV + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + cache-dependency-glob: "**/pyproject.toml" + + - name: Run Tests + run: uv run --extra test pytest tests diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml new file mode 100644 index 0000000..8e10796 --- /dev/null +++ b/.github/workflows/ruff.yml @@ -0,0 +1,8 @@ +name: Ruff +on: [pull_request] +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: chartboost/ruff-action@v1 diff --git a/.github/workflows/types.yml b/.github/workflows/types.yml new file mode 100644 index 0000000..26351b2 --- /dev/null +++ b/.github/workflows/types.yml @@ -0,0 +1,22 @@ +name: Type Check + +on: [pull_request] + +jobs: + typecheck: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Setup Python + uses: actions/setup-python@v5 + + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + + - name: Run type checking with ty + run: uv run --all-extras ty check diff --git a/.github/workflows/yamllint.yml b/.github/workflows/yamllint.yml new file mode 100644 index 0000000..c35dfdb --- /dev/null +++ b/.github/workflows/yamllint.yml @@ -0,0 +1,17 @@ +name: "Yamllint GitHub Actions" +on: + - pull_request +jobs: + yamllint: + name: "Yamllint" + runs-on: ubuntu-latest + steps: + - name: "Checkout" + uses: actions/checkout@master + - name: "Yamllint" + uses: karancode/yamllint-github-action@master + with: + yamllint_strict: true + yamllint_comment: true + env: + GITHUB_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.yamllint b/.yamllint new file mode 100644 index 0000000..c5b0b01 --- /dev/null +++ b/.yamllint @@ -0,0 +1,3 @@ +rules: + line-length: + max: 200 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..91ed9f8 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,21 @@ + +[project] +name = "nzcvm_data" +requires-python = ">=3.11" +version = "0.1.0" +description = "Integrity checks for NZCVM data registry" +dependencies = ["numpy>=2.3.5", "pytest-subtests>=0.15.0", "schema>=0.7.8"] + + +[project.optional-dependencies] +test = [ + "h5py>=3.15.1", + "pytest>=9.0.2", + "pyyaml>=6.0.3", + "geojson>=3.2.0", + "shapely>=2.1.2", +] +# Even though this isn't a python package, these dev dependencies can +# still prove useful for writing tests. +dev = ["ruff", "numpydoc", "ty"] +types = ["types-shapely>=2.1.0.20250917"] diff --git a/tests/test_registry.py b/tests/test_registry.py new file mode 100644 index 0000000..34ea008 --- /dev/null +++ b/tests/test_registry.py @@ -0,0 +1,581 @@ +import itertools +import re +from pathlib import Path +from typing import NotRequired, TypedDict, no_type_check + +import h5py +import numpy as np +import pytest +import shapely +import yaml +from attr import dataclass +from pytest import Metafunc +from pytest_subtests import SubTests +from schema import Optional, Or, Regex, Schema, SchemaError + + +@pytest.fixture(scope="session") +def nzcvm_registry_path() -> Path: + return Path(__file__).parent.parent / "nzcvm_registry.yaml" + + +@pytest.fixture(scope="session") +def nzcvm_root() -> Path: + return Path(__file__).parent.parent + + +@no_type_check +def test_nzcvm_registry_schema(nzcvm_registry_path: Path) -> None: + path = Regex( + # See https://stackoverflow.com/a/537876 + r"[^\0]+", + error="Must be valid unix path.", + ) + ident = Regex(r"^[a-zA-Z_][a-zA-Z0-9_]*$", error="Must be valid python identifier.") + # Source - https://stackoverflow.com/a + # Posted by Daveo, modified by community. See post 'Timeline' for change history + # Retrieved 2025-12-17, License - CC BY-SA 4.0 + url = Or( + Regex( + r"https?://(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)" + ), + "Personal communication (pending publication)", + error='Must be a valid URL, or "Personal communication (pending publication)"', + ) + surface_schema = Schema({"path": path, Optional("submodel"): ident}) + + tomography_entry = Schema( + { + "name": ident, + "elev": [Or(int, float)], + "path": path, + "author": str, + Optional("title"): str, + "url": Or(url, [url], None), # Handles single URL, list of URLs, or empty + } + ) + + basin_entry = Schema( + { + "name": ident, + Optional("type"): Or(1, 2, 3, 4), + Optional("author"): str, + Optional("notes"): [str], + Optional("wiki_images"): [path], + "boundaries": [path], + "surfaces": [surface_schema], + Optional("smoothing"): str, + } + ) + + submodel_schema = Schema( + { + "name": ident, + "type": Or("vm1d", "tomography", "relation", "perturbation", None), + Optional("module"): ident, + Optional("data"): path, + } + ) + vs30_schema = Schema({"name": str, "path": path}) + registry_schema = Schema( + { + "tomography": [tomography_entry], + "basin": [basin_entry], + "submodel": [submodel_schema], + "vs30": [vs30_schema], + } + ) + + with open(nzcvm_registry_path, "r") as f: + registry = yaml.safe_load(f) + + try: + registry_schema.validate(registry) + except SchemaError as e: + pytest.fail(f"NZCVM Registry is invalid\n{e.code}") + + +class Tomography(TypedDict): + name: str + elev: list[float] + path: str + author: str + title: str + url: str + + +class Surface(TypedDict): + path: str + submodel: NotRequired[str] + + +class Basin(TypedDict): + name: str + author: str + notes: list[str] + wiki_images: list[str] + boundaries: list[str] + surfaces: list[Surface] + smoothing: NotRequired[str] + + +class Vs30(TypedDict): + name: str + path: str + + +class Submodel(TypedDict): + name: str + type: str + module: str + data: NotRequired[str] + + +def pytest_generate_tests(metafunc: Metafunc) -> None: + registry_path = Path(__file__).parent.parent / "nzcvm_registry.yaml" + with open(registry_path) as f: + registry = yaml.safe_load(f) + if "model" in metafunc.fixturenames: + # This assumes you have access to the registry here + # It creates a separate test case for every model entry + metafunc.parametrize("model", registry["tomography"], ids=lambda m: m["name"]) + elif "basin" in metafunc.fixturenames: + metafunc.parametrize("basin", registry["basin"], ids=lambda m: m["name"]) + elif "vs30" in metafunc.fixturenames: + metafunc.parametrize("vs30", registry["vs30"], ids=lambda m: m["name"]) + elif "submodel" in metafunc.fixturenames: + metafunc.parametrize("submodel", registry["submodel"], ids=lambda m: m["name"]) + + +def test_tomography_paths_exist(nzcvm_root: Path, model: Tomography) -> None: + relative_model_path = Path(model["path"]) + model_path = nzcvm_root / relative_model_path + assert model_path.exists() + + +def test_tomography_models_are_hdf5(nzcvm_root: Path, model: Tomography) -> None: + relative_model_path = Path(model["path"]) + model_path = nzcvm_root / relative_model_path + try: + with h5py.File(model_path, "r") as f: + assert len(f.keys()) > 0 + except Exception as e: + pytest.fail(f"{model['name']} is not a valid hdf5 file: {e}") + + +def test_tomography_elevations_match(nzcvm_root: Path, model: Tomography) -> None: + relative_model_path = Path(model["path"]) + model_path = nzcvm_root / relative_model_path + registry_elevations = sorted(model["elev"]) + with h5py.File(model_path, "r") as f: + model_elevations = sorted([float(elev) for elev in f.keys()]) + + assert registry_elevations == model_elevations, "Model elevations do not match." + + +def test_tomography_compatible_shapes( + subtests: SubTests, nzcvm_root: Path, model: Tomography +) -> None: + model_path = nzcvm_root / model["path"] + + with h5py.File(model_path, "r") as f: + for elev, group in f.items(): + name = model["name"] + with subtests.test(msg=f"Checking elevation {elev}", model=name, elev=elev): + lat_shape = group["latitudes"].shape + lon_shape = group["longitudes"].shape + + # Check data arrays against (lat, lon) + expected_data_shape = (lat_shape[0], lon_shape[0]) + + for field in ["vp", "vs", "rho"]: + actual_shape = group[field].shape + assert actual_shape == expected_data_shape, ( + f"Shape mismatch in {model_path.name} at {elev}m: " + f"{field} is {actual_shape}, expected {expected_data_shape}" + ) + + +R_EARTH = 6378.139 # km, from: https://github.com/ucgmsim/velocity_modelling/blob/27c7e6e64d7ce1a9e543d58a6e584d498358431c/velocity_modelling/constants.py#L15 +LONGITUDE_TOLERANCE = 0.01 # km +LATITUDE_TOLERANCE = 0.01 # km +LAT_DEGREES_PER_KM = np.pi / 180 * R_EARTH + + +def test_tomography_geo_gridpoints( + subtests: SubTests, nzcvm_root: Path, model: Tomography +) -> None: + relative_model_path = Path(model["path"]) + model_path = nzcvm_root / relative_model_path + + with h5py.File(model_path, "r") as f: + for elev, group in f.items(): + name = model["name"] + with subtests.test(msg=f"Checking elevation {elev}", model=name, elev=elev): + latitude = np.array(group["latitudes"]) + longitude = np.array(group["longitudes"]) + + lat_diffs_km = np.diff(latitude) * LAT_DEGREES_PER_KM + assert np.all(lat_diffs_km > 0), "Latitudes not strictly ascending" + assert latitude[0] >= -90 and latitude[-1] <= 90, ( + "Latitudes must be between -90 and 90." + ) + assert lat_diffs_km == pytest.approx( + np.full(len(lat_diffs_km), lat_diffs_km[0]), abs=LATITUDE_TOLERANCE + ) + + lon_diffs_deg = np.diff(longitude) # Shape (N-1,) + assert np.all(lon_diffs_deg > 0), "Longitudes not strictly ascending" + assert longitude[0] >= 0 and longitude[-1] <= 185, ( + "Longitudes must be between 0 and 185." + ) + + +# NOTE: Values for QUALITY_BOUNDS are not physically derived +QUALITY_BOUNDS = {"vp": (0, 11.0), "vs": (0, 7.0), "rho": (0, 5.0)} + + +@pytest.mark.parametrize("quality", ["vp", "rho", "vs"]) +def test_tomography_quality( + subtests: SubTests, nzcvm_root: Path, model: Tomography, quality: str +) -> None: + relative_model_path = Path(model["path"]) + model_path = nzcvm_root / relative_model_path + + with h5py.File(model_path, "r") as f: + for elev, group in f.items(): + name = model["name"] + with subtests.test(msg=f"Checking elevation {elev}", model=name, elev=elev): + quality_values = np.array(group[quality]) + assert not np.isnan(quality_values).any(), ( + f"Quality {quality} contains NaN values." + ) + bounds = QUALITY_BOUNDS.get(quality) + assert bounds + min, max = bounds + quality_min = quality_values.min() + quality_max = quality_values.max() + assert quality_min >= min, ( + f"Quality {quality} minimum value ({quality_min=}) is less than {min}." + ) + assert quality_max <= max, ( + f"Quality {quality} maximum value ({quality_max=}) is less than {max}." + ) + + +def test_basin_boundaries_exist( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + for boundary in basin["boundaries"]: + boundary_relative_path = Path(boundary) + name = basin["name"] + with subtests.test( + msg=f"Checking boundary {boundary_relative_path.stem}", + basin=name, + boundary=boundary_relative_path.stem, + ): + boundary_path = nzcvm_root / boundary_relative_path + assert boundary_path.exists() + + +def test_basin_boundaries_are_valid_geojson( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + for boundary in basin["boundaries"]: + boundary_relative_path = Path(boundary) + name = basin["name"] + boundary_name = boundary_relative_path.stem + + with subtests.test( + msg=f"Checking boundary {boundary_name}", basin=name, boundary=boundary_name + ): + boundary_path = nzcvm_root / boundary_relative_path + + try: + geojson_str = boundary_path.read_text() + geom_collection = shapely.from_geojson(geojson_str) + except (OSError, ValueError, Exception) as e: + pytest.fail(f"Model {name} has invalid boundary {boundary_name}: {e}") + + assert isinstance(geom_collection, shapely.GeometryCollection) + assert shapely.is_valid(geom_collection), ( + "Geometry is topologically invalid" + ) + + assert not shapely.is_empty(geom_collection), "Geometry is empty" + + assert all( + isinstance(geom, shapely.Polygon) for geom in geom_collection.geoms + ) + + +def test_basin_paths_exist(nzcvm_root: Path, basin: Basin) -> None: + if match := re.match(r"^(\w+)_v\d+p\d+$", basin["name"]): + basin_canonical_name = match.group(1) + assert basin_canonical_name + basin_path = nzcvm_root / "regional" / basin_canonical_name + assert basin_path.exists() + if "wiki_images" in basin: + assert all( + (basin_path / Path(image)).exists() for image in basin["wiki_images"] + ) + else: + pytest.fail("basin name does not follow structure name_vxxpxx") + + +def test_basin_surfaces_exist( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + for surface in basin["surfaces"]: + relative_surface_path = Path(surface["path"]) + name = basin["name"] + surface_name = relative_surface_path.stem + with subtests.test( + msg=f"Checking surface {surface_name}", basin=name, surface=surface_name + ): + surface_path = nzcvm_root / relative_surface_path + assert surface_path.exists() + + +def test_basin_surfaces_are_valid_hdf5( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + for surface in basin["surfaces"]: + relative_surface_path = Path(surface["path"]) + name = basin["name"] + surface_name = relative_surface_path.stem + with subtests.test( + msg=f"Checking surface {surface_name}", basin=name, surface=surface_name + ): + surface_path = nzcvm_root / relative_surface_path + try: + with h5py.File(surface_path, "r") as f: + assert "elevation" in f.keys() + assert "latitude" in f.keys() + assert "longitude" in f.keys() + except Exception as e: + pytest.fail(f"{surface_name} is not a valid hdf5 file: {e}") + + +def test_surface_geo_gridpoints( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + for surface in basin["surfaces"]: + relative_surface_path = Path(surface["path"]) + name = basin["name"] + surface_name = relative_surface_path.stem + with subtests.test( + msg=f"Checking surface {surface_name}", basin=name, surface=surface_name + ): + surface_path = nzcvm_root / relative_surface_path + with h5py.File(surface_path, "r") as f: + latitude = np.array(f["latitude"]) + longitude = np.array(f["longitude"]) + + lat_diffs_km = np.diff(latitude) * LAT_DEGREES_PER_KM + assert np.all(lat_diffs_km > 0), "Latitudes not strictly ascending" + assert latitude[0] >= -90 and latitude[-1] <= 90, ( + "Latitudes must be between -90 and 90." + ) + + lon_diffs_deg = np.diff(longitude) # Shape (N-1,) + assert np.all(lon_diffs_deg > 0), "Longitudes not strictly ascending" + assert longitude[0] >= 0 and longitude[-1] <= 185, ( + "Longitudes must be between 0 and 185." + ) + + elevation = np.array(f["elevation"]) + assert elevation.shape == (len(latitude), len(longitude)), ( + "Elevation shape must be match latitude and longitude" + ) + assert not np.isnan(elevation).any(), "Elevations cannot be NaN" + assert elevation.min() >= -10000, "Elevations cannot be below -10000m" + assert elevation.max() <= 10000, "Elevations cannot be above 10000m" + + +def read_smoothing_boundary(smoothing_path: Path) -> shapely.LineString: + coords: list[tuple[float, float]] = [] + with open(smoothing_path, "r") as f: + for line in f: + line = line.strip() + if not line: + continue + line_coords = re.split(r"\s+", line) + assert len(line_coords) == 2 + lon_str, lat_str = line_coords + assert lon_str and lat_str + coords.append((float(lon_str), float(lat_str))) + + return shapely.LineString(coords) + + +def test_basin_smoothing_contained_in_boundaries( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + if "smoothing" not in basin: + pytest.skip("basin has no smoothing boundary") + + boundaries = [] + for boundary in basin["boundaries"]: + boundary_relative_path = Path(boundary) + boundary_path = nzcvm_root / boundary_relative_path + geojson_str = boundary_path.read_text() + geom_collection = shapely.from_geojson(geojson_str) + assert isinstance(geom_collection, shapely.GeometryCollection) + for geom in geom_collection.geoms: + assert isinstance(geom, shapely.Polygon) + boundaries.append(geom.exterior) + + # Add a small smoothing boundary buffer to account for the fact + # that smoothing boundary is not perfectly contained in the basin + # boundary. + boundary_geometry = shapely.buffer(shapely.union_all(boundaries), 0.001) + smoothing_surface_relative_path = basin["smoothing"] + smoothing_surface_path = nzcvm_root / Path(smoothing_surface_relative_path) + smoothing_boundary = read_smoothing_boundary(smoothing_surface_path) + + assert boundary_geometry.contains(smoothing_boundary) + + +def test_basin_surfaces_contain_boundaries( + subtests: SubTests, nzcvm_root: Path, basin: Basin +) -> None: + for boundary, surface in itertools.product(basin["boundaries"], basin["surfaces"]): + boundary_relative_path = Path(boundary) + surface_relative_path = Path(surface["path"]) + basin_name = basin["name"] + boundary_name = boundary_relative_path.stem + surface_name = surface_relative_path.stem + + with subtests.test( + msg=f"Checking boundary {boundary_name}", + basin=basin_name, + boundary=boundary_name, + surface=surface_name, + ): + boundary_path = nzcvm_root / boundary_relative_path + + geojson_str = boundary_path.read_text() + geom_collection = shapely.from_geojson(geojson_str) + surface_path = nzcvm_root / surface_relative_path + with h5py.File(surface_path, "r") as f: + latitudes = np.array(f["latitude"]) + longitudes = np.array(f["longitude"]) + elevation_boundary = shapely.box( + xmin=longitudes.min(), + xmax=longitudes.max(), + ymin=latitudes.min(), + ymax=latitudes.max(), + ) + assert shapely.contains(elevation_boundary, geom_collection) + + +def test_vs30_file_exists(nzcvm_root: Path, vs30: Vs30) -> None: + relative_path = Path(vs30["path"]) + + vs30_path = nzcvm_root / relative_path + assert vs30_path.exists(), f"Vs30 file missing at {vs30_path}" + + +def test_vs30_is_valid_hdf5(nzcvm_root: Path, vs30: Vs30) -> None: + relative_path = Path(vs30["path"]) + + vs30_path = nzcvm_root / relative_path + + try: + with h5py.File(vs30_path, "r") as f: + assert "elevation" in f.keys(), ( + "Dataset 'elevation' (vs30) missing from HDF5" + ) + assert "latitude" in f.keys() + assert "longitude" in f.keys() + except Exception as e: + name = vs30["name"] + pytest.fail(f"Vs30 file {name} is not a valid hdf5 file: {e}") + + +def test_vs30_geo_gridpoints(nzcvm_root: Path, vs30: Vs30) -> None: + relative_path = Path(vs30["path"]) + vs30_path = nzcvm_root / relative_path + + with h5py.File(vs30_path, "r") as f: + latitude = np.array(f["latitude"]) + longitude = np.array(f["longitude"]) + vs30_values = np.array(f["elevation"]) + + lat_diffs = np.diff(latitude) + assert np.all(lat_diffs > 0), "Latitudes not strictly ascending" + assert latitude[0] >= -90 and latitude[-1] <= 90, ( + "Latitudes out of world bounds" + ) + + lon_diffs = np.diff(longitude) + assert np.all(lon_diffs > 0), "Longitudes not strictly ascending" + assert longitude[0] >= 0 and longitude[-1] <= 185, ( + "Longitudes out of NZCVM bounds" + ) + + assert vs30_values.shape == (len(latitude), len(longitude)), ( + f"Vs30 shape {vs30_values.shape} does not match lat/lon dimensions" + ) + + assert not np.isnan(vs30_values).any(), "Vs30 data contains NaNs" + assert vs30_values.min() >= 0, ( + f"Vs30 values below 0 detected: {vs30_values.min()}" + ) + assert vs30_values.max() <= 2000, ( + f"Vs30 values above 2000 detected: {vs30_values.max()}" + ) + + +def test_submodel_data_exists_where_relevant( + nzcvm_root: Path, submodel: Submodel +) -> None: + assert ("data" in submodel) == (submodel["type"] == "vm1d"), ( + "Submodel has data iff submodel is a vm1d" + ) + if "data" in submodel: + data_relative_path = Path(submodel["data"]) + data_path = nzcvm_root / data_relative_path + assert data_path.exists() + + +@dataclass +class SubmodelData: + vp: float + vs: float + rho: float + qp: float + qs: float + thickness: float + + +def parse_submodel_data(submodel_path: Path) -> list[SubmodelData]: + rows = [] + with open(submodel_path, "r") as f: + header = next(f).strip() + assert header == "DEF HST" + for line in f: + row = re.split(r"\s+", line.strip()) + floats = [float(x) for x in row] + assert len(floats) == 6 + rows.append(SubmodelData(*floats)) + return rows + + +def test_submodel_data_is_valid( + subtests: SubTests, nzcvm_root: Path, submodel: Submodel +) -> None: + if "data" in submodel: + data_relative_path = Path(submodel["data"]) + data_path = nzcvm_root / data_relative_path + data = parse_submodel_data(data_path) + vp_min, vp_max = QUALITY_BOUNDS["vp"] + assert all(vp_min <= row.vp <= vp_max for row in data) + vs_min, vs_max = QUALITY_BOUNDS["vs"] + assert all(vs_min <= row.vs <= vs_max for row in data) + assert all(row.thickness >= 0 for row in data) + assert all(row.qp > 0 for row in data) + assert all(row.qs > 0 for row in data) + else: + pytest.skip(f"Submodel {submodel['name']} has no data") From 89353c3882d71a97c8964c51781e080f7a7e7def Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Thu, 18 Dec 2025 12:13:30 +1300 Subject: [PATCH 02/19] fix(registry): correct basement file paths and remove invalid image entry - Update Canterbury basement file paths to use correct lowercase naming - Fix spacing in Wellington basement file path - Remove invalid Gisborne basement image reference from registry --- nzcvm_registry.yaml | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/nzcvm_registry.yaml b/nzcvm_registry.yaml index dea1d99..03bd648 100644 --- a/nzcvm_registry.yaml +++ b/nzcvm_registry.yaml @@ -42,8 +42,7 @@ basin: submodel: miocene_submod_v1 - path: regional/Canterbury/Canterbury_Paleogene_WGS84.h5 submodel: paleogene_submod_v1 - - path: regional/Canterbury/Canterbury_Basement_WGS84.h5 - + - path: regional/Canterbury/Canterbury_basement_WGS84.h5 - name: Canterbury_v18p2 boundaries: @@ -57,8 +56,7 @@ basin: submodel: miocene_submod_v1 - path: regional/Canterbury/Canterbury_Paleogene_WGS84.h5 submodel: paleogene_submod_v1 - - path: regional/Canterbury/Canterbury_Basement_WGS84.h5 - + - path: regional/Canterbury/Canterbury_basement_WGS84.h5 - name: Canterbury_v18p3 boundaries: @@ -72,8 +70,7 @@ basin: submodel: miocene_submod_v1 - path: regional/Canterbury/Canterbury_Paleogene_WGS84.h5 submodel: paleogene_submod_v1 - - path: regional/Canterbury/Canterbury_Basement_WGS84.h5 - + - path: regional/Canterbury/Canterbury_basement_WGS84.h5 - name: Canterbury_v19p1 type: 4 @@ -323,7 +320,7 @@ basin: surfaces: - path: surface/NZ_DEM_HD.h5 submodel: canterbury1d_v2 - - path : regional/Wellington/Wellington_basement_WGS84_v19p6.h5 + - path: regional/Wellington/Wellington_basement_WGS84_v19p6.h5 smoothing: regional/Wellington/Wellington_smoothing.txt @@ -724,7 +721,6 @@ basin: wiki_images: - images/NI_mideast.png - images/Gisborne_basin_map.png - - images/grisborne_basement.png notes: - (Comment from the author) - Stop at Moto River, working around the East Cape from Gisborne. Haurere Point should be included in Whakatane From c69d838832b0c029e27c852f202bd878045a6569 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 12:29:39 +1300 Subject: [PATCH 03/19] fix(registry): remove broken Chow tomography --- nzcvm_registry.yaml | 340 +++++++++++++++++++++----------------------- 1 file changed, 163 insertions(+), 177 deletions(-) diff --git a/nzcvm_registry.yaml b/nzcvm_registry.yaml index 03bd648..d7b14db 100644 --- a/nzcvm_registry.yaml +++ b/nzcvm_registry.yaml @@ -1,34 +1,67 @@ tomography: - name: EP2010 - elev: [ 15, 1, -3, -8, -15, -23, -30, -38, -48, -65, -85, -105, -130, -155, -185, -225, -275, -370, -620, -750 ] + elev: + [ + 15, + 1, + -3, + -8, + -15, + -23, + -30, + -38, + -48, + -65, + -85, + -105, + -130, + -155, + -185, + -225, + -275, + -370, + -620, + -750, + ] path: tomography/EP2010/ep2010.h5 author: Eberhart-Phillips et al. (2010) title: Establishing a Versatile 3-d seismic Velocity Model for New Zealand url: https://10.1785/gssrl.81.6.992 - name: EP2020 - elev: [ 15, 1, -1, -3, -5, -8, -15, -23, -30, -34, -38, -42, -48, -55, -65, -85, -105, -130, -155, -185, -225, -275, -370, -620, -750 ] + elev: + [ + 15, + 1, + -1, + -3, + -5, + -8, + -15, + -23, + -30, + -34, + -38, + -42, + -48, + -55, + -65, + -85, + -105, + -130, + -155, + -185, + -225, + -275, + -370, + -620, + -750, + ] path: tomography/EP2020/ep2020.h5 author: Eberhart-Phillips et al. (2020) title: New Zealand Wide model 2.2 seismic velocity and Qs and Qp models for New Zealand url: https://10.5281/zenodo.3779523 - - - name: CHOW2020_EP2020_MIX - elev: [ 15.0, 2.25, 2.0, 1.75, 1.5, 1.25, 1.0, 0.75, 0.5, 0.25, 0.0, -0.25, -0.5, -0.75, -1.0, -1.25, -1.5, -1.75, -2.0, -2.25, -2.5, -2.75, -3.0, -3.25, -3.5, -3.75, -4.0, -4.25, -4.5, -4.75, -5.0, -5.25, -5.5, -5.75, -6.0, -6.25, -6.5, -6.75, -7.0, -7.25, -7.5, -7.75, -8.0, -9.0, -10.0, -11.0, -12.0, -13.0, -14.0, -15.0, -16.0, -17.0, -18.0, -19.0, -20.0, -21.0, -22.0, -23.0, -24.0, -25.0, -26.0, -27.0, -28.0, -29.0, -30.0, -31.0, -32.0, -33.0, -34.0, -35.0, -36.0, -37.0, -38.0, -39.0, -40.0, -41.0, -42.0, -43.0, -44.0, -45.0, -46.0, -47.0, -48.0, -49.0, -50.0, -52.0, -56.0, -60.0, -64.0, -68.0, -72.0, -76.0, -80.0, -84.0, -88.0, -92.0, -96.0, -100.0, -104.0, -108.0, -112.0, -116.0, -120.0, -124.0, -128.0, -132.0, -136.0, -140.0, -144.0, -148.0, -152.0, -156.0, -160.0, -164.0, -168.0, -172.0, -176.0, -180.0, -184.0, -188.0, -192.0, -196.0, -200.0, -204.0, -208.0, -212.0, -216.0, -220.0, -224.0, -228.0, -232.0, -236.0, -240.0, -244.0, -248.0, -252.0, -256.0, -260.0, -264.0, -268.0, -272.0, -276.0, -280.0, -284.0, -288.0, -292.0, -296.0, -300.0, -304.0, -308.0, -312.0, -316.0, -320.0, -324.0, -328.0, -332.0, -336.0, -340.0, -344.0, -348.0, -352.0, -356.0, -360.0, -364.0, -368.0, -372.0, -376.0, -380.0, -384.0, -388.0, -392.0, -396.0, -400.0, -620.0, -750.0, ] - path: tomography/CHOW2020_EP2020_MIX/chow2020_ep2020_mix.h5 - author: Chow et al. (2020) - url: - - https://doi.org/10.1093/gji/ggaa381 - - https://core.geo.vuw.ac.nz/d/feae69f61ea54f81bee1 - - - name: EP2025 - elev: [ 1, -3, -8, -15, -23, -30, -38, -48, -65, -85, -105, -130, -155, -185, -225, -275, -370, -620, -750 ] - path: tomography/EP2025/ep2025.h5 - author: Eberhart-Phillips et al. (2025) - title: New Zealand Wide model 2.2 seismic velocity and Qs and Qp models for New Zealand - url: n/a - basin: - name: Canterbury_v18p1 boundaries: @@ -118,7 +151,6 @@ basin: - path: regional/Canterbury/Canterbury_basement_WGS84.h5 smoothing: regional/Canterbury/Canterbury_smoothing.txt - - name: NorthCanterbury_v19p1 type: 1 author: Robin Lee @@ -132,7 +164,6 @@ basin: submodel: canterbury1d_v2 - path: regional/NorthCanterbury/NorthCanterbury_basement_WGS84_v19p1.h5 - - name: NorthCanterbury_v25p8 type: 1 author: Robin Lee / Ayushi Tiwari @@ -161,7 +192,6 @@ basin: submodel: bpv_submod_v4 - path: regional/BanksPeninsulaVolcanics/BanksPeninsulaVolcanics_Miocene_WGS84.h5 - - name: Kaikoura_v19p1 type: 2 author: Robin Lee @@ -177,7 +207,6 @@ basin: - path: regional/Kaikoura/Kaikoura_basement_WGS84.h5 smoothing: regional/Kaikoura/Kaikoura_smoothing.txt - - name: Kaikoura_v25p5 type: 2 author: Robin Lee @@ -192,7 +221,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Kaikoura/Kaikoura_basement_WGS84_v25p5.h5 smoothing: regional/Kaikoura/Kaikoura_smoothing_v25p5.txt - - name: Cheviot_v19p1 type: 1 @@ -208,7 +236,6 @@ basin: - path: regional/Cheviot/Cheviot_basement_WGS84.h5 smoothing: regional/Cheviot/Cheviot_smoothing.txt - - name: Hanmer_v19p1 type: 1 author: Robin Lee @@ -223,7 +250,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Hanmer/Hanmer_basement_WGS84_v19p1.h5 - - name: Hanmer_v25p3 type: 1 author: Ayushi Tiwari @@ -251,7 +277,6 @@ basin: - path: regional/Marlborough/Marlborough_basement_WGS84.h5 smoothing: regional/Marlborough/Marlborough_smoothing.txt - - name: Nelson_v19p1 type: 2 author: Robin Lee @@ -268,7 +293,6 @@ basin: - path: regional/Nelson/Nelson_basement_WGS84_v19p1.h5 smoothing: regional/Nelson/Nelson_smoothing.txt - - name: Nelson_v25p5 type: 3 author: Robin Lee @@ -303,7 +327,6 @@ basin: - path: regional/Nelson/Nelson_basement_WGS84_v25p5.h5 smoothing: regional/Nelson/Nelson_smoothing.txt - - name: Wellington_v19p1 boundaries: - regional/Wellington/Wellington_outline_WGS84.geojson @@ -313,7 +336,6 @@ basin: - path: regional/Wellington/Wellington_basement_WGS84_v19p1.h5 smoothing: regional/Wellington/Wellington_smoothing.txt - - name: Wellington_v19p6 boundaries: - regional/Wellington/Wellington_outline_WGS84.geojson @@ -323,7 +345,6 @@ basin: - path: regional/Wellington/Wellington_basement_WGS84_v19p6.h5 smoothing: regional/Wellington/Wellington_smoothing.txt - - name: Wellington_v21p8 type: 3 author: Robin Lee / Matt Hill @@ -376,7 +397,6 @@ basin: - path: regional/WaikatoHauraki/WaikatoHauraki_basement_WGS84.h5 smoothing: regional/WaikatoHauraki/WaikatoHauraki_smoothing.txt - - name: Wanaka_v20p6 type: 1 author: Cameron Douglas (USER2020) @@ -391,8 +411,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Wanaka/Wanaka_basement_WGS84.h5 - - - name: Mackenzie_v20p6 type: 1 author: Cameron Douglas (USER2020) @@ -407,7 +425,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Mackenzie/Mackenzie_basement_WGS84.h5 - - name: Wakatipu_v20p7 type: 1 author: Tim Tuckey (USER2020) @@ -421,7 +438,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Wakatipu/Wakatipu_basement_WGS84.h5 - - name: Alexandra_v20p7 type: 1 author: Cameron Douglas (USER2020) @@ -438,7 +454,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Alexandra/Alexandra_basement_WGS84.h5 - - name: Ranfurly_v20p7 type: 1 author: Cameron Douglas (USER2020) @@ -455,7 +470,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Ranfurly/Ranfurly_basement_WGS84.h5 - - name: NE_Otago_v20p7 type: 1 author: Cameron Douglas (USER2020) @@ -476,7 +490,6 @@ basin: submodel: canterbury1d_v2 - path: regional/NE_Otago/NE_Otago_basement_WGS84.h5 - - name: Mosgiel_v20p7 type: 1 author: Cameron Douglas (USER2020) @@ -497,8 +510,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Mosgiel/Mosgiel_basement_WGS84.h5 - - - name: Balclutha_v20p7 type: 1 author: Cameron Douglas (USER2020) @@ -537,8 +548,6 @@ basin: - path: regional/Dunedin/Dunedin_basement_WGS84.h5 smoothing: regional/Dunedin/Dunedin_smoothing.txt - - - name: Murchison_v20p7 type: 1 author: Tim Tuckey (USER2020) @@ -553,8 +562,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Murchison/Murchison_basement_WGS84.h5 - - - name: Waitaki_v20p8 type: 1 author: Cameron Douglas (USER2020) @@ -574,7 +581,6 @@ basin: - path: regional/Waitaki/Waitaki_basement_WGS84.h5 smoothing: regional/Waitaki/Waitaki_smoothing.txt - - name: Hakataramea_v20p8 type: 1 author: Cameron Douglas (USER2020) @@ -591,7 +597,6 @@ basin: submodel: canterbury1d_v2 - path: regional/Hakataramea/Hakataramea_basement_WGS84.h5 - - name: Karamea_v20p11 type: 1 author: Tim Tuckey (USER2020) @@ -606,7 +611,6 @@ basin: - path: regional/Karamea/Karamea_basement_WGS84.h5 smoothing: regional/Karamea/Karamea_smoothing.txt - - name: Collingwood_v20p11 type: 1 author: Tim Tuckey (USER2020) @@ -623,7 +627,6 @@ basin: - path: regional/Collingwood/Collingwood_basement_WGS84.h5 smoothing: regional/Collingwood/Collingwood_smoothing.txt - - name: SpringsJunction_v20p11 type: 1 author: Tim Tuckey (USER2020) @@ -637,7 +640,6 @@ basin: submodel: canterbury1d_v2 - path: regional/SpringsJunction/SpringsJunction_basement_WGS84.h5 - - name: HawkesBay_v21p7 type: 1 author: William Lee (USER2021) @@ -732,7 +734,6 @@ basin: - path: regional/Gisborne/Gisborne_basement_WGS84.h5 smoothing: regional/Gisborne/Gisborne_smoothing.txt - - name: SouthernHawkesBay_v21p12 type: 1 author: William Lee (USER2021) @@ -753,7 +754,6 @@ basin: submodel: canterbury1d_v2 - path: regional/SouthernHawkesBay/SouthernHawkesBay_basement_WGS84.h5 - - name: Wairarapa_v21p12 type: 1 author: William Lee (USER2021) @@ -761,7 +761,7 @@ basin: - images/NI_south.png - images/Wairarapa_basin_map.png notes: - - (Comment from the author) "Consider adding east coastal basins (e.g. Uruti Point)" + - (Comment from the author) "Consider adding east coastal basins (e.g. Uruti Point)" boundaries: - regional/Wairarapa/Wairarapa_outline_WGS84.geojson surfaces: @@ -770,7 +770,6 @@ basin: - path: regional/Wairarapa/Wairarapa_basement_WGS84.h5 smoothing: regional/Wairarapa/Wairarapa_smoothing.txt - - name: OmaioBay_v22p3 type: 1 author: Cameron Davis / Emma Coumbe (USER2022) @@ -794,7 +793,6 @@ basin: - path: regional/OmaioBay/OmaioBay_basement_WGS84_v22p3.h5 smoothing: regional/OmaioBay/OmaioBay_smoothing_v22p3.txt - - name: OmaioBay_v25p5 type: 1 author: Cameron Davis / Emma Coumbe (USER2022) @@ -817,8 +815,6 @@ basin: - path: regional/OmaioBay/OmaioBay_basement_WGS84.h5 smoothing: regional/OmaioBay/OmaioBay_smoothing.txt - - - name: Whangaparoa_v23p4 type: 1 author: Cameron Davis / Emma Coumbe (USER2022) @@ -834,8 +830,7 @@ basin: - path: surface/NZ_DEM_HD.h5 submodel: canterbury1d_v2 - path: regional/Whangaparoa/Whangaparoa_basement_WGS84.h5 - smoothing: regional/Whangaparoa/Whangaparoa_smoothing.txt - + smoothing: regional/Whangaparoa/Whangaparoa_smoothing.txt - name: PalmerstonNorth_v25p5 type: 1 @@ -843,11 +838,11 @@ basin: wiki_images: - images/PalmerstonNorth_basin_map_v25p5.png boundaries: - - regional/PalmerstonNorth/PalmerstonNorth_outline_WGS84.geojson + - regional/PalmerstonNorth/PalmerstonNorth_outline_WGS84.geojson surfaces: - - path: surface/NZ_DEM_HD.h5 - submodel: canterbury1d_v2 - - path: regional/PalmerstonNorth/PalmerstonNorth_basement_WGS84_v25p5.h5 + - path: surface/NZ_DEM_HD.h5 + submodel: canterbury1d_v2 + - path: regional/PalmerstonNorth/PalmerstonNorth_basement_WGS84_v25p5.h5 smoothing: regional/PalmerstonNorth/PalmerstonNorth_smoothing.txt - name: PalmerstonNorth_v25p8 @@ -861,11 +856,10 @@ basin: - path: surface/NZ_DEM_HD.h5 submodel: palmerstonnorth_v1 - path: regional/PalmerstonNorth/PalmerstonNorth_pliocenetop_WGS84_v25p8.h5 - submodel: pn_pliocene_submod_v1 + submodel: pn_pliocene_submod_v1 - path: regional/PalmerstonNorth/PalmerstonNorth_basement_WGS84_v25p8.h5 smoothing: regional/PalmerstonNorth/PalmerstonNorth_smoothing.txt - - name: Southland_v25p5 type: 2 author: Archie Goodrick @@ -894,7 +888,6 @@ basin: submodel: canterbury1d_v2 - path: regional/TeAnau/TeAnau_basement_WGS84.h5 - - name: TolagaBay_v25p5 type: 1 author: Cameron Davis / Emma Coumbe (USER2022) @@ -904,7 +897,7 @@ basin: boundaries: - regional/TolagaBay/TolagaBay_outline_WGS84.geojson - + surfaces: - path: surface/NZ_DEM_HD.h5 submodel: canterbury1d_v2 @@ -925,7 +918,6 @@ basin: - path: regional/Waiapu/Waiapu_basement_WGS84.h5 smoothing: regional/Waiapu/Waiapu_smoothing.txt - - name: WestCoast_v25p5 type: 1 author: Ayushi Tiwari / Hunter Brotherston @@ -934,12 +926,11 @@ basin: boundaries: - regional/WestCoast/WestCoast_outline_WGS84.geojson surfaces: - - path: surface/NZ_DEM_HD.h5 - submodel: canterbury1d_v2 - - path: regional/WestCoast/WestCoast_basement_WGS84.h5 + - path: surface/NZ_DEM_HD.h5 + submodel: canterbury1d_v2 + - path: regional/WestCoast/WestCoast_basement_WGS84.h5 smoothing: regional/WestCoast/WestCoast_smoothing.txt - - name: Westport_v25p5 type: 1 author: Ayushi Tiwari / Kaleb Finn (ENCN493) @@ -966,155 +957,150 @@ basin: - path: regional/Westport/Westport_basement_WGS84.h5 smoothing: regional/Westport/Westport_smoothing.txt - - name: QueenCharlotte_v25p8 type: 1 author: Ayushi Tiwari wiki_images: - - images/QueenCharlotte_basin_map.png + - images/QueenCharlotte_basin_map.png boundaries: - - regional/QueenCharlotte/QueenCharlotte_outline_WGS84.geojson + - regional/QueenCharlotte/QueenCharlotte_outline_WGS84.geojson surfaces: - - path: surface/NZ_DEM_HD.h5 - submodel: canterbury1d_v2 - - path: regional/QueenCharlotte/QueenCharlotte_basement_WGS84_v25p8.h5 + - path: surface/NZ_DEM_HD.h5 + submodel: canterbury1d_v2 + - path: regional/QueenCharlotte/QueenCharlotte_basement_WGS84_v25p8.h5 - name: CastleHill_v25p8 type: 1 author: Ayushi Tiwari wiki_images: - - images/CastleHill_basin_map.png + - images/CastleHill_basin_map.png boundaries: - - regional/CastleHill/CastleHill_outline_WGS84.geojson + - regional/CastleHill/CastleHill_outline_WGS84.geojson surfaces: - - path: surface/NZ_DEM_HD.h5 - submodel: canterbury1d_v2 - - path: regional/CastleHill/CastleHill_basement_WGS84.h5 - + - path: surface/NZ_DEM_HD.h5 + submodel: canterbury1d_v2 + - path: regional/CastleHill/CastleHill_basement_WGS84.h5 - name: Whakatane_v25p8 type: 1 author: Ayushi Tiwari wiki_images: - - images/Whakatane_basin_map.png + - images/Whakatane_basin_map.png boundaries: - - regional/Whakatane/Whakatane_outline_WGS84.geojson + - regional/Whakatane/Whakatane_outline_WGS84.geojson surfaces: - - path: surface/NZ_DEM_HD.h5 - submodel: canterbury1d_v2 - - path: regional/Whakatane/Whakatane_basement_WGS84_v25p8.h5 + - path: surface/NZ_DEM_HD.h5 + submodel: canterbury1d_v2 + - path: regional/Whakatane/Whakatane_basement_WGS84_v25p8.h5 smoothing: regional/Whakatane/Whakatane_smoothing.txt - name: TeAraroa_v25p9 type: 1 author: James Hoskin wiki_images: - - images/TeAraroa_basin_map.png + - images/TeAraroa_basin_map.png boundaries: - - regional/TeAraroa/TeAraroa_outline_WGS84.geojson + - regional/TeAraroa/TeAraroa_outline_WGS84.geojson surfaces: - - path : surface/NZ_DEM_HD.h5 + - path: surface/NZ_DEM_HD.h5 submodel: canterbury1d_v2 - - path : regional/TeAraroa/TeAraroa_basement_WGS84.h5 + - path: regional/TeAraroa/TeAraroa_basement_WGS84.h5 smoothing: regional/TeAraroa/TeAraroa_smoothing.txt - name: Rarakau_v25p9 type: 1 author: Toby Bates wiki_images: - - images/Rarakau_basin_map.png + - images/Rarakau_basin_map.png boundaries: - - regional/Rarakau/Rarakau_outline_WGS84.geojson + - regional/Rarakau/Rarakau_outline_WGS84.geojson surfaces: - - path : surface/NZ_DEM_HD.h5 - submodel: canterbury1d_v2 - - path : regional/Rarakau/Rarakau_basement_WGS84.h5 + - path: surface/NZ_DEM_HD.h5 + submodel: canterbury1d_v2 + - path: regional/Rarakau/Rarakau_basement_WGS84.h5 smoothing: regional/Rarakau/Rarakau_smoothing.txt - vs30: - name: nz_with_offshore path: vs30/NZ_Vs30_HD_With_Offshore.h5 - name: nz_without_offshore path: vs30/NZ_Vs30.h5 - submodel: - - name: nan_submod - type: null - - - name: canterbury1d_v1 - type: vm1d - module: canterbury1d_submod - data: vm1d/Cant1D_v1.fd_modfile - - - name: canterbury1d_v2 - type: vm1d - module: canterbury1d_submod - data: vm1d/Cant1D_v2.fd_modfile - - - name: canterbury1d_v2_pliocene_enforced - type: vm1d - module: canterbury1d_submod - data: vm1d/Cant1D_v2_Pliocene_Enforced.fd_modfile - - - name: canterbury1d_v3_pliocene_enforced - type: vm1d - module: canterbury1d_submod - data: vm1d/Cant1D_v3_Pliocene_Enforced.fd_modfile - - - name: nelson_v1 - type: vm1d - module: canterbury1d_submod - data: vm1d/Nelson_v1.fd_modfile - - - name: palmerstonnorth_v1 - type: vm1d - module: canterbury1d_submod - data: vm1d/PalmerstonNorth_v1.fd_modfile - - - name: ep_tomography_submod_v2010 - type: tomography - module: ep_tomography_submod_v2010 - - - name: bpv_submod_v4 - type: relation - module: bpv_submod_v4 - - - name: pliocene_submod_v1 - type: relation - module: pliocene_submod_v1 - - - name: pn_pliocene_submod_v1 - type: relation - module: pn_pliocene_submod_v1 - - - - name: miocene_submod_v1 - type: relation - module: miocene_submod_v1 - - - name: paleogene_submod_v1 - type: relation - module: paleogene_submod_v1 - - - name: pliocene_submod_v2 - type: relation - module: pliocene_submod_v2 - - - name: miocene_submod_v2 - type: relation - module: miocene_submod_v2 - - - name: paleogene_submod_v2 - type: relation - module: paleogene_submod_v2 - - - name: perturbation_v20p6 - type: perturbation - - - name: perturbation_v20p10 - type: perturbation - - - name: perturbation_v20p11 - type: perturbation + - name: nan_submod + type: null + + - name: canterbury1d_v1 + type: vm1d + module: canterbury1d_submod + data: vm1d/Cant1D_v1.fd_modfile + + - name: canterbury1d_v2 + type: vm1d + module: canterbury1d_submod + data: vm1d/Cant1D_v2.fd_modfile + + - name: canterbury1d_v2_pliocene_enforced + type: vm1d + module: canterbury1d_submod + data: vm1d/Cant1D_v2_Pliocene_Enforced.fd_modfile + + - name: canterbury1d_v3_pliocene_enforced + type: vm1d + module: canterbury1d_submod + data: vm1d/Cant1D_v3_Pliocene_Enforced.fd_modfile + + - name: nelson_v1 + type: vm1d + module: canterbury1d_submod + data: vm1d/Nelson_v1.fd_modfile + + - name: palmerstonnorth_v1 + type: vm1d + module: canterbury1d_submod + data: vm1d/PalmerstonNorth_v1.fd_modfile + + - name: ep_tomography_submod_v2010 + type: tomography + module: ep_tomography_submod_v2010 + + - name: bpv_submod_v4 + type: relation + module: bpv_submod_v4 + + - name: pliocene_submod_v1 + type: relation + module: pliocene_submod_v1 + + - name: pn_pliocene_submod_v1 + type: relation + module: pn_pliocene_submod_v1 + + - name: miocene_submod_v1 + type: relation + module: miocene_submod_v1 + + - name: paleogene_submod_v1 + type: relation + module: paleogene_submod_v1 + + - name: pliocene_submod_v2 + type: relation + module: pliocene_submod_v2 + + - name: miocene_submod_v2 + type: relation + module: miocene_submod_v2 + + - name: paleogene_submod_v2 + type: relation + module: paleogene_submod_v2 + + - name: perturbation_v20p6 + type: perturbation + + - name: perturbation_v20p10 + type: perturbation + + - name: perturbation_v20p11 + type: perturbation From 52b0ab1c5753737ce9e9e0861f0994feafb649ca Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 12:30:19 +1300 Subject: [PATCH 04/19] fix(Dunedin): fix Dunedin smoothing boundary --- regional/Dunedin/Dunedin_smoothing.txt | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/regional/Dunedin/Dunedin_smoothing.txt b/regional/Dunedin/Dunedin_smoothing.txt index 9499c95..9faae13 100755 --- a/regional/Dunedin/Dunedin_smoothing.txt +++ b/regional/Dunedin/Dunedin_smoothing.txt @@ -131,21 +131,3 @@ 170.45759988 -45.92441961 170.45719142 -45.92356637 170.45689042 -45.92269490 -170.56320143 -45.86537325 -170.56356933 -45.86624843 -170.56393725 -45.86712360 -170.56430518 -45.86799877 -170.56467313 -45.86887395 -170.56504108 -45.86974911 -170.56540905 -45.87062428 -170.56577703 -45.87149945 -170.56614502 -45.87237461 -170.56651302 -45.87324977 -170.56688103 -45.87412493 -170.56724906 -45.87500009 -170.56761709 -45.87587525 -170.56798514 -45.87675041 -170.56835320 -45.87762556 -170.56872127 -45.87850071 -170.56908935 -45.87937587 -170.56945745 -45.88025101 From 175442b9f3d53a70b5d600f2cafa226884ce4b1d Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 12:47:15 +1300 Subject: [PATCH 05/19] add missing dependencies --- pyproject.toml | 32 ++++++++++++++++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 91ed9f8..3f6fc51 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,32 @@ [project] name = "nzcvm_data" -requires-python = ">=3.11" +requires-python = ">=3.12" version = "0.1.0" description = "Integrity checks for NZCVM data registry" -dependencies = ["numpy>=2.3.5", "pytest-subtests>=0.15.0", "schema>=0.7.8"] +dependencies = [ + "cartopy>=0.25.0", + "fiona>=1.10.1", + "geojson>=3.2.0", + "geopandas>=1.1.2", + "h5py>=3.15.1", + "matplotlib>=3.10.8", + "numpy>=2.3.5", + "pandas>=2.3.3", + "plotly>=6.5.0", + "pyproj>=3.7.2", + "pytz>=2025.2", + "pyvista>=0.46.4", + "pyvistaqt>=0.11.3", + "pyyaml>=6.0.3", + "qcore>=1.11.1", + "qtpy>=2.4.3", + "scipy>=1.16.3", + "seaborn>=0.13.2", + "shapely>=2.1.2", + "typer>=0.21.0", + "velocity-modelling>=2025.12.1", +] [project.optional-dependencies] @@ -14,8 +36,14 @@ test = [ "pyyaml>=6.0.3", "geojson>=3.2.0", "shapely>=2.1.2", + "schema>=0.7.8", + "pytest-subtests>=0.15.0", ] # Even though this isn't a python package, these dev dependencies can # still prove useful for writing tests. dev = ["ruff", "numpydoc", "ty"] types = ["types-shapely>=2.1.0.20250917"] + + +[tool.deptry] +pep621_dev_dependency_groups = ["test", "dev", "types"] From 51a14587553c149f1ab9b24b2749842205b2f2a8 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 12:51:12 +1300 Subject: [PATCH 06/19] deps: add deptry to dev dependencies --- pyproject.toml | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3f6fc51..e9d658d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,27 +5,27 @@ requires-python = ">=3.12" version = "0.1.0" description = "Integrity checks for NZCVM data registry" dependencies = [ - "cartopy>=0.25.0", - "fiona>=1.10.1", - "geojson>=3.2.0", - "geopandas>=1.1.2", - "h5py>=3.15.1", - "matplotlib>=3.10.8", - "numpy>=2.3.5", - "pandas>=2.3.3", - "plotly>=6.5.0", - "pyproj>=3.7.2", - "pytz>=2025.2", - "pyvista>=0.46.4", - "pyvistaqt>=0.11.3", - "pyyaml>=6.0.3", - "qcore>=1.11.1", - "qtpy>=2.4.3", - "scipy>=1.16.3", - "seaborn>=0.13.2", - "shapely>=2.1.2", - "typer>=0.21.0", - "velocity-modelling>=2025.12.1", + "cartopy>=0.25.0", + "fiona>=1.10.1", + "geojson>=3.2.0", + "geopandas>=1.1.2", + "h5py>=3.15.1", + "matplotlib>=3.10.8", + "numpy>=2.3.5", + "pandas>=2.3.3", + "plotly>=6.5.0", + "pyproj>=3.7.2", + "pytz>=2025.2", + "pyvista>=0.46.4", + "pyvistaqt>=0.11.3", + "pyyaml>=6.0.3", + "qcore>=1.11.1", + "qtpy>=2.4.3", + "scipy>=1.16.3", + "seaborn>=0.13.2", + "shapely>=2.1.2", + "typer>=0.21.0", + "velocity-modelling>=2025.12.1", ] @@ -41,7 +41,7 @@ test = [ ] # Even though this isn't a python package, these dev dependencies can # still prove useful for writing tests. -dev = ["ruff", "numpydoc", "ty"] +dev = ["ruff", "numpydoc", "ty", "deptry"] types = ["types-shapely>=2.1.0.20250917"] From 91e0ef1a6e4155e1ed34e82e1bd0b20c861edfc0 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 12:51:33 +1300 Subject: [PATCH 07/19] tests(registry): update tests to check ascending or descending --- tests/test_registry.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index 34ea008..8ce0720 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -216,8 +216,10 @@ def test_tomography_geo_gridpoints( longitude = np.array(group["longitudes"]) lat_diffs_km = np.diff(latitude) * LAT_DEGREES_PER_KM - assert np.all(lat_diffs_km > 0), "Latitudes not strictly ascending" - assert latitude[0] >= -90 and latitude[-1] <= 90, ( + assert np.all(lat_diffs_km > 0) or np.all(lat_diffs_km < 0), ( + "Latitudes neither strictly ascending or descending" + ) + assert np.min(latitude) >= -90 and np.max(latitude) <= 90, ( "Latitudes must be between -90 and 90." ) assert lat_diffs_km == pytest.approx( @@ -225,8 +227,10 @@ def test_tomography_geo_gridpoints( ) lon_diffs_deg = np.diff(longitude) # Shape (N-1,) - assert np.all(lon_diffs_deg > 0), "Longitudes not strictly ascending" - assert longitude[0] >= 0 and longitude[-1] <= 185, ( + assert np.all(lon_diffs_deg > 0) or np.all(lon_diffs_deg < 0), ( + "Longitudes neither strictly ascending or descending" + ) + assert np.min(longitude) >= 0 and np.max(longitude) <= 185, ( "Longitudes must be between 0 and 185." ) From e81d173d69cc1375612878a45d29f96b88531de2 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:02:37 +1300 Subject: [PATCH 08/19] fix: do not use attr for dataclass --- tests/test_registry.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index 8ce0720..47c0415 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -1,5 +1,6 @@ import itertools import re +from dataclasses import dataclass from pathlib import Path from typing import NotRequired, TypedDict, no_type_check @@ -8,7 +9,6 @@ import pytest import shapely import yaml -from attr import dataclass from pytest import Metafunc from pytest_subtests import SubTests from schema import Optional, Or, Regex, Schema, SchemaError From 48a28db9bad4f14b4485a29140afc9ebc74c16f1 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:03:11 +1300 Subject: [PATCH 09/19] deps: migrate tools to optional dependencies --- pyproject.toml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e9d658d..ee2c51a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,23 @@ name = "nzcvm_data" requires-python = ">=3.12" version = "0.1.0" description = "Integrity checks for NZCVM data registry" -dependencies = [ + + +[project.optional-dependencies] +test = [ + "h5py>=3.15.1", + "pytest>=9.0.2", + "pyyaml>=6.0.3", + "geojson>=3.2.0", + "shapely>=2.1.2", + "schema>=0.7.8", + "pytest-subtests>=0.15.0", +] +# Even though this isn't a python package, these dev dependencies can +# still prove useful for writing tests. +dev = ["ruff", "numpydoc", "ty", "deptry"] +types = ["types-shapely>=2.1.0.20250917"] +tools = [ "cartopy>=0.25.0", "fiona>=1.10.1", "geojson>=3.2.0", @@ -29,21 +45,5 @@ dependencies = [ ] -[project.optional-dependencies] -test = [ - "h5py>=3.15.1", - "pytest>=9.0.2", - "pyyaml>=6.0.3", - "geojson>=3.2.0", - "shapely>=2.1.2", - "schema>=0.7.8", - "pytest-subtests>=0.15.0", -] -# Even though this isn't a python package, these dev dependencies can -# still prove useful for writing tests. -dev = ["ruff", "numpydoc", "ty", "deptry"] -types = ["types-shapely>=2.1.0.20250917"] - - [tool.deptry] pep621_dev_dependency_groups = ["test", "dev", "types"] From 39f3574fb6255933f303a072ffff6d25b3f69d54 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:06:17 +1300 Subject: [PATCH 10/19] tests(registry): subtests for rows. Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com> --- tests/test_registry.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index 47c0415..faadce9 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -575,11 +575,15 @@ def test_submodel_data_is_valid( data_path = nzcvm_root / data_relative_path data = parse_submodel_data(data_path) vp_min, vp_max = QUALITY_BOUNDS["vp"] - assert all(vp_min <= row.vp <= vp_max for row in data) vs_min, vs_max = QUALITY_BOUNDS["vs"] - assert all(vs_min <= row.vs <= vs_max for row in data) - assert all(row.thickness >= 0 for row in data) - assert all(row.qp > 0 for row in data) - assert all(row.qs > 0 for row in data) + rho_min, rho_max = QUALITY_BOUNDS["rho"] + for i, row in enumerate(data): + with subtests.test(msg=f"Checking row {i+1}", row=row): + assert vp_min <= row.vp <= vp_max, f"Vp {row.vp} out of bounds" + assert vs_min <= row.vs <= vs_max, f"Vs {row.vs} out of bounds" + assert rho_min <= row.rho <= rho_max, f"Rho {row.rho} out of bounds" + assert row.thickness >= 0, f"Negative thickness: {row.thickness}" + assert row.qp > 0, f"Non-positive Qp: {row.qp}" + assert row.qs > 0, f"Non-positive Qs: {row.qs}" else: pytest.skip(f"Submodel {submodel['name']} has no data") From 4a4298e569ed58b890bb507d16152d53e592dcaa Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:07:01 +1300 Subject: [PATCH 11/19] tests(registry): lat monotonicity Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com> --- tests/test_registry.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index faadce9..d36cf17 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -377,7 +377,7 @@ def test_surface_geo_gridpoints( longitude = np.array(f["longitude"]) lat_diffs_km = np.diff(latitude) * LAT_DEGREES_PER_KM - assert np.all(lat_diffs_km > 0), "Latitudes not strictly ascending" + assert np.all(lat_diffs_km > 0) or np.all(lat_diffs_km < 0), "Latitudes not monotonic" assert latitude[0] >= -90 and latitude[-1] <= 90, ( "Latitudes must be between -90 and 90." ) From 693f718596840ba239abab007cd14ce5f8882b19 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:07:20 +1300 Subject: [PATCH 12/19] tests(registry): lon monotonicity Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com> --- tests/test_registry.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index d36cf17..c5430f9 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -383,7 +383,7 @@ def test_surface_geo_gridpoints( ) lon_diffs_deg = np.diff(longitude) # Shape (N-1,) - assert np.all(lon_diffs_deg > 0), "Longitudes not strictly ascending" + assert np.all(lon_diffs_deg > 0) or np.all(lon_diffs_deg < 0), "Longitudes not monotonic" assert longitude[0] >= 0 and longitude[-1] <= 185, ( "Longitudes must be between 0 and 185." ) From f083aa3b6e7ef5a990b41c3585c8dc2cb483fa8c Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:07:58 +1300 Subject: [PATCH 13/19] tests(registry): use split function --- tests/test_registry.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index 47c0415..0afa444 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -404,7 +404,7 @@ def read_smoothing_boundary(smoothing_path: Path) -> shapely.LineString: line = line.strip() if not line: continue - line_coords = re.split(r"\s+", line) + line_coords = line.strip().split() assert len(line_coords) == 2 lon_str, lat_str = line_coords assert lon_str and lat_str @@ -560,7 +560,7 @@ def parse_submodel_data(submodel_path: Path) -> list[SubmodelData]: header = next(f).strip() assert header == "DEF HST" for line in f: - row = re.split(r"\s+", line.strip()) + row = line.strip().split() floats = [float(x) for x in row] assert len(floats) == 6 rows.append(SubmodelData(*floats)) From f724adba663008619d86739d7decfd84591d874f Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:46:28 +1300 Subject: [PATCH 14/19] fix(tomo_boundary): ruff + type checking + numpydoc --- pyproject.toml | 25 +++++++++++++++++++ .../tools/visualisation/tomo_boundary.py | 19 +++++++------- 2 files changed, 35 insertions(+), 9 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ee2c51a..0ea9c5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,3 +47,28 @@ tools = [ [tool.deptry] pep621_dev_dependency_groups = ["test", "dev", "types"] + + +[tool.numpydoc_validation] +checks = [ + "GL05", + "GL08", + "GL10", + "PR01", + "PR02", + "PR03", + "PR04", + "PR05", + "PR06", + "PR07", + "RT01", + "RT02", + "RT03", + "RT04", + "YD01", +] +# remember to use single quotes for regex in TOML +exclude = [ # don't report on objects that match any of these regex + '\.undocumented_method$', + '\.__repr__$', +] diff --git a/tomography/tools/visualisation/tomo_boundary.py b/tomography/tools/visualisation/tomo_boundary.py index 909b3a5..1b984e4 100644 --- a/tomography/tools/visualisation/tomo_boundary.py +++ b/tomography/tools/visualisation/tomo_boundary.py @@ -1,6 +1,7 @@ """ -This script extracts the geographical boundary from a tomography HDF5 file -and saves it as a GeoJSON file. It computes the convex hull of the grid points +This script extracts the geographical boundary from a tomography HDF5 file and saves it as a GeoJSON file. + +It computes the convex hull of the grid points defined by the latitude and longitude arrays in the HDF5 file to determine the boundary polygon. @@ -14,10 +15,10 @@ import geojson import h5py import numpy as np +import shapely import typer -from shapely.geometry import MultiPoint - from qcore import cli +from shapely.geometry import MultiPoint app = typer.Typer(pretty_exceptions_enable=False) @@ -53,15 +54,15 @@ def extract_single_boundary_geojson( If the convex hull operation does not result in a Polygon. """ with h5py.File(hdf5_file_path, "r") as f: - # Use the first available group to extract lat/lon - first_group_name = next(iter(f.keys())) group = None for key in f.keys(): - if 'latitudes' in f[key] and 'longitudes' in f[key]: + if "latitudes" in f[key] and "longitudes" in f[key]: group = f[key] break if group is None: - raise RuntimeError("No group with 'latitudes' and 'longitudes' found in HDF5 file.") + raise RuntimeError( + "No group with 'latitudes' and 'longitudes' found in HDF5 file." + ) lats = group["latitudes"][:] lons = group["longitudes"][:] @@ -81,7 +82,7 @@ def extract_single_boundary_geojson( # Compute convex hull hull = MultiPoint(edge_coords).convex_hull - if hull.geom_type != "Polygon": + if not isinstance(hull, shapely.Polygon): raise RuntimeError("Convex hull did not produce a polygon.") coords = [list(p) for p in hull.exterior.coords] From fd18a7237c7f572e94c2d00b6e73333522e940ea Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 13:59:04 +1300 Subject: [PATCH 15/19] fix(types): resolve type checking complaints --- tomography/tools/tomo_analysis.py | 89 ++++++++++--------- tomography/tools/tomo_in2h5.py | 4 +- .../tools/visualisation/tomo_3dviewer.py | 32 ++++--- tools/map_one_basin.py | 19 ++-- tools/merge_geojson_boundaries.py | 9 +- tools/visualisation/surfaces_3dviewer.py | 5 +- 6 files changed, 91 insertions(+), 67 deletions(-) diff --git a/tomography/tools/tomo_analysis.py b/tomography/tools/tomo_analysis.py index 4ff8abf..2f05f53 100644 --- a/tomography/tools/tomo_analysis.py +++ b/tomography/tools/tomo_analysis.py @@ -36,16 +36,19 @@ def load_txt_ep_format(txt_file: str) -> pd.DataFrame: DataFrame containing tomography data with columns for coordinates and properties. """ col_names = [ - "vp", "vp_o_vs", "vs", "rho", "sf_vp", "sf_vp_o_vs", - "x", "y", "depth", "lat", "lon" + "vp", + "vp_o_vs", + "vs", + "rho", + "sf_vp", + "sf_vp_o_vs", + "x", + "y", + "depth", + "lat", + "lon", ] - df = pd.read_csv( - txt_file, - sep=r"\s+", - skiprows=2, - names=col_names, - engine="python" - ) + df = pd.read_csv(txt_file, sep=r"\s+", skiprows=2, names=col_names, engine="python") # NOTE: do NOT force-convert lon here; plotting handles 0–360 or -180..180 return df @@ -73,12 +76,14 @@ def load_hdf5_data(h5_file: str) -> pd.DataFrame: vp = group["vp"][:] # shape (nlat, nlon) lon_grid, lat_grid = np.meshgrid(lon, lat) - df = pd.DataFrame({ - "lat": lat_grid.ravel().astype(np.float32), - "lon": lon_grid.ravel().astype(np.float32), - "vp": vp.ravel().astype(np.float32), - "depth": float(depth_keys[0]) - }) + df = pd.DataFrame( + { + "lat": lat_grid.ravel().astype(np.float32), + "lon": lon_grid.ravel().astype(np.float32), + "vp": vp.ravel().astype(np.float32), + "depth": float(depth_keys[0]), + } + ) return df @@ -139,8 +144,10 @@ def check_grid_spacing(lat: np.ndarray, lon: np.ndarray, tol: float = 1e-6) -> N # Longitude spacing in km varies with latitude latitudes_for_conversion = np.linspace(lat.min(), lat.max(), num=1000) - lon_km_spacings = unique_lon_spacings[:, np.newaxis] * 111.32 * np.cos( - np.radians(latitudes_for_conversion) + lon_km_spacings = ( + unique_lon_spacings[:, np.newaxis] + * 111.32 + * np.cos(np.radians(latitudes_for_conversion)) ) lon_km_min = np.min(lon_km_spacings, axis=1) lon_km_max = np.max(lon_km_spacings, axis=1) @@ -227,25 +234,25 @@ def choose_projection_and_extent(lats: np.ndarray, lons: np.ndarray): pad_lon = 0.5 pad_lat = 0.5 minlat = max(-90.0, float(lats.min()) - pad_lat) - maxlat = min( 90.0, float(lats.max()) + pad_lat) + maxlat = min(90.0, float(lats.max()) + pad_lat) - has_over_180 = np.nanmax(lons) > 180.0 - has_negative = np.nanmin(lons) < 0.0 - crosses_dl = has_over_180 or has_negative + has_over_180 = np.nanmax(lons) > 180.0 + has_negative = np.nanmin(lons) < 0.0 + crosses_dl = has_over_180 or has_negative if crosses_dl: # Use 180-centered axes; compute extent in that axes' native range [-180,180) ax_crs = ccrs.PlateCarree(central_longitude=180) - lons_c = lons_centered_180(lons) # <<< key fix (NOT 0..360) + lons_c = lons_centered_180(lons) # <<< key fix (NOT 0..360) minlon = max(-180.0, float(lons_c.min()) - pad_lon) - maxlon = min( 180.0, float(lons_c.max()) + pad_lon) + maxlon = min(180.0, float(lons_c.max()) + pad_lon) extent = (minlon, maxlon, minlat, maxlat) - extent_crs = ax_crs # extent expressed in axes CRS + extent_crs = ax_crs # extent expressed in axes CRS else: # Standard case: compute extent in data CRS and pass with data_crs ax_crs = ccrs.PlateCarree() minlon = max(-180.0, float(lons.min()) - pad_lon) - maxlon = min( 180.0, float(lons.max()) + pad_lon) + maxlon = min(180.0, float(lons.max()) + pad_lon) extent = (minlon, maxlon, minlat, maxlat) extent_crs = data_crs @@ -273,22 +280,26 @@ def plot_spatial_distribution(df: pd.DataFrame, title_suffix: str = "") -> None: ax = plt.axes(projection=ax_crs) # Set extent in the CRS it was computed in - ax.set_extent(extent, crs=extent_crs) + # type checker ignores are because cartopy lacks stubs: SciTools/cartopy#2304 + ax.set_extent(extent, crs=extent_crs) # type: ignore[unresolved-attribute] - ax.add_feature(cfeature.COASTLINE, linewidth=0.8) - ax.add_feature(cfeature.BORDERS, linestyle=":", linewidth=0.6) - ax.add_feature(cfeature.LAND, facecolor="lightgray", edgecolor="none") - ax.add_feature(cfeature.OCEAN, facecolor="lightsteelblue", edgecolor="none") - ax.add_feature(cfeature.LAKES, alpha=0.5) - ax.add_feature(cfeature.RIVERS, linewidth=0.5) + ax.add_feature(cfeature.COASTLINE, linewidth=0.8) # type: ignore[unresolved-attribute] + ax.add_feature(cfeature.BORDERS, linestyle=":", linewidth=0.6) # type: ignore[unresolved-attribute] + ax.add_feature(cfeature.LAND, facecolor="lightgray", edgecolor="none") # type: ignore[unresolved-attribute] + ax.add_feature(cfeature.OCEAN, facecolor="lightsteelblue", edgecolor="none") # type: ignore[unresolved-attribute] + ax.add_feature(cfeature.LAKES, alpha=0.5) # type: ignore[unresolved-attribute] + ax.add_feature(cfeature.RIVERS, linewidth=0.5) # type: ignore[unresolved-attribute] ax.scatter( - df["lon"], df["lat"], - s=1, c="red", alpha=0.5, - transform=data_crs, # input data CRS is always standard lon/lat - label="Model Grid" + df["lon"], + df["lat"], + s=1, + c="red", + alpha=0.5, + transform=data_crs, # input data CRS is always standard lon/lat + label="Model Grid", ) - gl = ax.gridlines(draw_labels=True, linestyle="--", linewidth=0.5) + gl = ax.gridlines(draw_labels=True, linestyle="--", linewidth=0.5) # type: ignore[invalid-argument-type] try: gl.right_labels = False gl.top_labels = False @@ -368,9 +379,7 @@ def analyze( input_file: Annotated[ Path, typer.Argument( - exists=True, - dir_okay=False, - help="Input tomography file (.txt or .h5)" + exists=True, dir_okay=False, help="Input tomography file (.txt or .h5)" ), ], ) -> None: diff --git a/tomography/tools/tomo_in2h5.py b/tomography/tools/tomo_in2h5.py index 01a4867..7a2ed47 100644 --- a/tomography/tools/tomo_in2h5.py +++ b/tomography/tools/tomo_in2h5.py @@ -17,7 +17,7 @@ """ import re -from datetime import datetime +from datetime import datetime, timezone from pathlib import Path from typing import Annotated @@ -129,7 +129,7 @@ def convert_ascii_to_hdf5( with h5py.File(output_path, "w") as h5f: # file-level metadata to advertise decisions - h5f.attrs["created"] = datetime.utcnow().isoformat() + "Z" + h5f.attrs["created"] = datetime.now(timezone.utc).isoformat() + "Z" h5f.attrs["generator"] = "tomo_in2h5.py" h5f.attrs["schema"] = "NZTomographyLevelStacked v1" h5f.attrs["data_dtype_vp_vs_rho"] = ( diff --git a/tomography/tools/visualisation/tomo_3dviewer.py b/tomography/tools/visualisation/tomo_3dviewer.py index dbe6319..fce3ce7 100644 --- a/tomography/tools/visualisation/tomo_3dviewer.py +++ b/tomography/tools/visualisation/tomo_3dviewer.py @@ -23,7 +23,8 @@ import typer from pyvista.plotting.camera import Camera from pyvistaqt import QtInteractor -from qtpy.QtCore import Qt +from qcore import cli +from qtpy.QtCore import Qt # type: ignore[unresolved-import] from qtpy.QtWidgets import ( QApplication, QCheckBox, @@ -35,8 +36,6 @@ QWidget, ) -from qcore import cli - app = typer.Typer(pretty_exceptions_enable=False) DEFAULT_CAMERA_ANGLE = (-0.018774705983602088, 0.8058896333404005, 0.5917680367252902) @@ -132,7 +131,9 @@ def load_stacked_slices( - scalar_values np.ndarray: A 3d array containing scalar data of shape (n_elevations, n_latitudes, n_longitudes). """ with h5py.File(h5_path, "r") as f: - keys = sorted((k for k in f.keys() if is_number(k)), key=float, reverse=True) + keys: list[str] = sorted( + (str(k) for k in f.keys() if is_number(k)), key=float, reverse=True + ) # type: ignore[invalid-assignment] sample = f[keys[0]] lat_full = sample["latitudes"][:] lon_full = sample["longitudes"][:] @@ -164,7 +165,7 @@ def make_flat_surfaces( lat: np.ndarray, scalar_values: np.ndarray, gap: float = 0.1, -) -> list[tuple[pv.StructuredGrid, float, float, float]]: +) -> tuple[dict[float, pv.StructuredGrid], float, float]: """Create a list of PyVista surfaces from stacked 2D data. Each slice in the data cube is converted into a flat surface mesh, @@ -195,7 +196,7 @@ def make_flat_surfaces( """ - grid_dict = {} + grid_dict: dict[float, pv.StructuredGrid] = {} global_min = np.min(scalar_values) global_max = np.max(scalar_values) @@ -207,7 +208,7 @@ def make_flat_surfaces( surf["values"] = scalar_values[iz].ravel(order="C") grid_dict[float(elevations[iz])] = surf - return grid_dict, global_min, global_max + return grid_dict, float(global_min), float(global_max) class TomoApp(QMainWindow): @@ -238,12 +239,12 @@ def __init__( self, title: str, scalar_name: str, - grid_dict: dict[pv.StructuredGrid], + grid_dict: dict[float, pv.StructuredGrid], clim: tuple[float, float], points_by_elevation: Optional[dict[float, np.ndarray]] = None, debug: bool = False, - ): - """Initialize the Tomography 3D Viewer application.""" + ): # numpydoc ignore=PR01 + """Initialise tomography app.""" super().__init__() self.debug = debug @@ -522,7 +523,16 @@ def launch_viewer( points_by_elevation = None if txt: df = read_ep_txt(txt) - df_filtered = df[np.any(np.isclose(df['elevation'].values[:, None], [float(d) for d in elevations], atol=1e-3), axis=1)] + df_filtered = df[ + np.any( + np.isclose( + df["elevation"].values[:, None], + [float(d) for d in elevations], + atol=1e-3, + ), + axis=1, + ) + ] if debug: print(df_filtered.head()) points_by_elevation = { diff --git a/tools/map_one_basin.py b/tools/map_one_basin.py index 46d759c..a65ead3 100644 --- a/tools/map_one_basin.py +++ b/tools/map_one_basin.py @@ -53,7 +53,7 @@ def _image_url(self, tile: tuple) -> str: return url -def load_basement(file_path: Path) -> tuple[np.ndarray, np.ndarray, np.ndarray]: +def load_basement(file_path: Path) -> tuple[np.ndarray, np.ndarray, np.ndarray] | None: """ Load basement file containing latitude, longitude, and raster data. @@ -78,7 +78,7 @@ def load_basement(file_path: Path) -> tuple[np.ndarray, np.ndarray, np.ndarray]: file_path = Path(file_path) if not file_path.exists(): print(f"Error: Basement file {file_path} does not exist.") - return None, None, None + return None try: with file_path.open("r") as f: lines = f.readlines() @@ -179,7 +179,7 @@ def load_boundary( def plot_data( basement_file: Path, boundary_files: list[Path], - smoothing_file: Path, + smoothing_file: Path | None, basin_name: str, out_dir: Path, ): @@ -201,7 +201,11 @@ def plot_data( """ # Load basement data - lats, lons, raster = load_basement(basement_file) + if basement := load_basement(basement_file): + lats, lons, raster = basement + else: + raise ValueError("Basement file does not contain valid data.") + if lats is None: return @@ -245,12 +249,13 @@ def plot_data( # Create map fig = plt.figure(figsize=(12, 12)) ax = plt.axes(projection=ccrs.PlateCarree()) - ax.set_extent(extent, crs=ccrs.PlateCarree()) + # type checker ignores are because cartopy lacks stubs: SciTools/cartopy#2304 + ax.set_extent(extent, crs=ccrs.PlateCarree()) # type: ignore[unresolved-attribute] # Add Esri World Imagery basemap using custom tile class # Tested a few other tile classes, but Esri World Imagery looks the best and processes quickly esri_imagery = EsriWorldImageryTiles() - ax.add_image(esri_imagery, 12) # Zoom level 12 for high detail + ax.add_image(esri_imagery, 12) # type: ignore[invalid-argument-type] # Zoom level 12 for high detail # Add town names shp = shpreader.natural_earth( @@ -274,7 +279,7 @@ def plot_data( ) # Add gridlines - gl = ax.gridlines( + gl = ax.gridlines( # type: ignore[invalid-argument-type] draw_labels=True, linewidth=0.5, color="gray", alpha=0.5, linestyle="--" ) gl.top_labels = gl.right_labels = False diff --git a/tools/merge_geojson_boundaries.py b/tools/merge_geojson_boundaries.py index b872bdc..ec4b6d8 100644 --- a/tools/merge_geojson_boundaries.py +++ b/tools/merge_geojson_boundaries.py @@ -17,8 +17,7 @@ import typer from fiona.errors import DriverError from matplotlib import cm # for colour palettes -from matplotlib.colors import to_hex - +from matplotlib.colors import ListedColormap, to_hex from qcore import cli app = typer.Typer(pretty_exceptions_enable=False) @@ -40,13 +39,15 @@ def colour_cycle(n: int) -> list[str]: list[str] A list of n HEX colour strings. """ - base = [to_hex(c) for c in cm.get_cmap("tab10").colors] + tab10 = cm.get_cmap("tab10") + assert isinstance(tab10, ListedColormap) + base = [to_hex(c) for c in tab10.colors] # type: ignore[invalid-argument-type] if n <= len(base): return base[:n] # Need more colours – extend with a continuous palette extra_needed = n - len(base) - extra = [to_hex(cm.viridis(i / extra_needed)) for i in range(extra_needed)] + extra = [to_hex(cm.viridis(i / extra_needed)) for i in range(extra_needed)] # type: ignore[unresolved-attribute] return base + extra diff --git a/tools/visualisation/surfaces_3dviewer.py b/tools/visualisation/surfaces_3dviewer.py index 3549341..d305987 100644 --- a/tools/visualisation/surfaces_3dviewer.py +++ b/tools/visualisation/surfaces_3dviewer.py @@ -15,9 +15,8 @@ import numpy as np import plotly.graph_objects as go import typer -from scipy.interpolate import RegularGridInterpolator - from qcore import cli +from scipy.interpolate import RegularGridInterpolator app = typer.Typer(pretty_exceptions_enable=False) @@ -165,7 +164,7 @@ def plot_stacked_surfaces( # z-axis range (symmetric if diverging cmap) if elev_range is None: all_elev = np.concatenate([v[2].ravel() for v in data_dict.values()]) - elev_range = [all_elev.min(), all_elev.max()] + elev_range = (float(all_elev.min()), float(all_elev.max())) z_min, z_max = elev_range vmax = max(abs(z_min), abs(z_max)) vmin = -vmax From 0e0e9642966fc371eb094f81c9539a6e0898c1a5 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 14:41:35 +1300 Subject: [PATCH 16/19] fix: attribution and python ident checks --- tests/test_registry.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/tests/test_registry.py b/tests/test_registry.py index 54b16e3..a387b38 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -11,7 +11,7 @@ import yaml from pytest import Metafunc from pytest_subtests import SubTests -from schema import Optional, Or, Regex, Schema, SchemaError +from schema import And, Optional, Or, Regex, Schema, SchemaError @pytest.fixture(scope="session") @@ -28,11 +28,13 @@ def nzcvm_root() -> Path: def test_nzcvm_registry_schema(nzcvm_registry_path: Path) -> None: path = Regex( # See https://stackoverflow.com/a/537876 + # Posted by Darron. + # Retreived 2025-12-17, License - CC BY-SA 2.5 r"[^\0]+", error="Must be valid unix path.", ) - ident = Regex(r"^[a-zA-Z_][a-zA-Z0-9_]*$", error="Must be valid python identifier.") - # Source - https://stackoverflow.com/a + ident = And(str, str.isidentifier) + # Source - https://stackoverflow.com/a/3809435 # Posted by Daveo, modified by community. See post 'Timeline' for change history # Retrieved 2025-12-17, License - CC BY-SA 4.0 url = Or( @@ -377,13 +379,17 @@ def test_surface_geo_gridpoints( longitude = np.array(f["longitude"]) lat_diffs_km = np.diff(latitude) * LAT_DEGREES_PER_KM - assert np.all(lat_diffs_km > 0) or np.all(lat_diffs_km < 0), "Latitudes not monotonic" + assert np.all(lat_diffs_km > 0) or np.all(lat_diffs_km < 0), ( + "Latitudes not monotonic" + ) assert latitude[0] >= -90 and latitude[-1] <= 90, ( "Latitudes must be between -90 and 90." ) lon_diffs_deg = np.diff(longitude) # Shape (N-1,) - assert np.all(lon_diffs_deg > 0) or np.all(lon_diffs_deg < 0), "Longitudes not monotonic" + assert np.all(lon_diffs_deg > 0) or np.all(lon_diffs_deg < 0), ( + "Longitudes not monotonic" + ) assert longitude[0] >= 0 and longitude[-1] <= 185, ( "Longitudes must be between 0 and 185." ) @@ -578,7 +584,7 @@ def test_submodel_data_is_valid( vs_min, vs_max = QUALITY_BOUNDS["vs"] rho_min, rho_max = QUALITY_BOUNDS["rho"] for i, row in enumerate(data): - with subtests.test(msg=f"Checking row {i+1}", row=row): + with subtests.test(msg=f"Checking row {i + 1}", row=row): assert vp_min <= row.vp <= vp_max, f"Vp {row.vp} out of bounds" assert vs_min <= row.vs <= vs_max, f"Vs {row.vs} out of bounds" assert rho_min <= row.rho <= rho_max, f"Rho {row.rho} out of bounds" From f991ebcbca03a827fa2470ba15b048cb7991297e Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 5 Jan 2026 15:10:19 +1300 Subject: [PATCH 17/19] tests(registry): use more robust url validator Catches invalid DOI links --- nzcvm_registry.yaml | 4 ++-- pyproject.toml | 2 +- tests/test_registry.py | 8 ++------ 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/nzcvm_registry.yaml b/nzcvm_registry.yaml index d7b14db..628a205 100644 --- a/nzcvm_registry.yaml +++ b/nzcvm_registry.yaml @@ -26,7 +26,7 @@ tomography: path: tomography/EP2010/ep2010.h5 author: Eberhart-Phillips et al. (2010) title: Establishing a Versatile 3-d seismic Velocity Model for New Zealand - url: https://10.1785/gssrl.81.6.992 + url: https://doi.org/10.1785/gssrl.81.6.992 - name: EP2020 elev: @@ -60,7 +60,7 @@ tomography: path: tomography/EP2020/ep2020.h5 author: Eberhart-Phillips et al. (2020) title: New Zealand Wide model 2.2 seismic velocity and Qs and Qp models for New Zealand - url: https://10.5281/zenodo.3779523 + url: https://doi.org/10.5281/zenodo.3779523 basin: - name: Canterbury_v18p1 diff --git a/pyproject.toml b/pyproject.toml index 0ea9c5b..87edce4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,6 @@ requires-python = ">=3.12" version = "0.1.0" description = "Integrity checks for NZCVM data registry" - [project.optional-dependencies] test = [ "h5py>=3.15.1", @@ -15,6 +14,7 @@ test = [ "shapely>=2.1.2", "schema>=0.7.8", "pytest-subtests>=0.15.0", + "validators>=0.35.0", ] # Even though this isn't a python package, these dev dependencies can # still prove useful for writing tests. diff --git a/tests/test_registry.py b/tests/test_registry.py index a387b38..7e705c7 100644 --- a/tests/test_registry.py +++ b/tests/test_registry.py @@ -8,6 +8,7 @@ import numpy as np import pytest import shapely +import validators import yaml from pytest import Metafunc from pytest_subtests import SubTests @@ -34,13 +35,8 @@ def test_nzcvm_registry_schema(nzcvm_registry_path: Path) -> None: error="Must be valid unix path.", ) ident = And(str, str.isidentifier) - # Source - https://stackoverflow.com/a/3809435 - # Posted by Daveo, modified by community. See post 'Timeline' for change history - # Retrieved 2025-12-17, License - CC BY-SA 4.0 url = Or( - Regex( - r"https?://(www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*)" - ), + And(str, validators.url), "Personal communication (pending publication)", error='Must be a valid URL, or "Personal communication (pending publication)"', ) From 9edc10cf8541f10a65e634fcac4599fbc7461479 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Wed, 7 Jan 2026 11:27:25 +1300 Subject: [PATCH 18/19] deps: add uv.lock to make tests pass --- uv.lock | 2125 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 2125 insertions(+) create mode 100644 uv.lock diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..b54f6c2 --- /dev/null +++ b/uv.lock @@ -0,0 +1,2125 @@ +version = 1 +revision = 3 +requires-python = ">=3.12" + +[[package]] +name = "alabaster" +version = "1.0.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = 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