anemoi-datasets 0.5.26__py3-none-any.whl → 0.5.28__py3-none-any.whl

anemoi/datasets/validate.py

@@ -0,0 +1,598 @@
+# (C) Copyright 2025- Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+
+
+import logging
+import math
+from collections import defaultdict
+
+import numpy as np
+
+from anemoi.datasets.data.dataset import Dataset
+from anemoi.datasets.testing import default_test_indexing
+
+LOG = logging.getLogger(__name__)
+# List of methods called during training. To update the list, run training with ANEMOI_DATASETS_TRACE=1
+
+TRAINING_METHODS = [
+    "__getitem__",
+    "__len__",
+    "latitudes",
+    "longitudes",
+    "metadata",  # Accessed when checkpointing
+    "missing",
+    "name_to_index",
+    "shape",
+    "statistics",
+    "supporting_arrays",  # Accessed when checkpointing
+    "variables",
+]
+
+EXTRA_TRAINING_METHODS = [
+    "statistics_tendencies",
+]
+
+DEBUGGING_METHODS = [
+    "plot",
+    "to_index",
+    "tree",
+    "source",
+]
+
+PUBLIC_METADATA_METHODS = [
+    "arguments",
+    "dtype",
+    "end_date",
+    "resolution",
+    "start_date",
+    "field_shape",
+    "frequency",
+    "dates",
+    "typed_variables",
+    "variables_metadata",
+]
+
+PRIVATE_METADATA_METHODS = [
+    "computed_constant_fields",
+    "constant_fields",
+    "dataset_metadata",
+    "label",
+    "metadata_specific",
+    "provenance",
+]
+
+INTERNAL_METHODS = [
+    "mutate",
+    "swap_with_parent",
+    "dates_interval_to_indices",
+]
+
+EXPERIMENTAL_METHODS = [
+    "get_dataset_names",
+    "name",
+    "grids",
+]
+
+OTHER_METHODS = [
+    "collect_input_sources",
+    "collect_supporting_arrays",
+    "sub_shape",
+]
+
+
+METHODS_CATEGORIES = {k: v for k, v in list(globals().items()) if k.endswith("_METHODS")}
+
+
+METHODS = set(sum(METHODS_CATEGORIES.values(), []))
+
+
+KWARGS = {
+    "__len__": {},
+    "__getitem__": {"index": 0},
+    "get_dataset_names": {"names": set()},
+    "metadata": {},
+    "metadata_specific": {},
+    "mutate": {},
+    "plot": {"date": 0, "variable": 0},
+    "provenance": {},
+    "source": {"index": 0},
+    "statistics_tendencies": {},
+    "sub_shape": {},
+    "supporting_arrays": {},
+    "swap_with_parent": {},
+    "to_index": {"date": 0, "variable": 0},
+    "tree": {},
+}
+
+
+class Unknown:
+    emoji = "❓"
+
+
+class Success:
+    emoji = "✅"
+    success = True
+
+    def __repr__(self):
+        return "Success"
+
+
+class Error:
+    success = False
+
+    def __init__(self, message):
+        self.message = message
+
+    def __repr__(self):
+        return str(self.message) or repr(self.message) or "Error"
+
+
+class Failure(Error):
+    emoji = "💥"
+
+
+class Internal(Error):
+    emoji = "💣"
+
+
+class Invalid(Error):
+    emoji = "❌"
+
+
+class Report:
+
+    def __init__(self):
+        self.report = {}
+        self.methods = {}
+        self.warnings = defaultdict(list)
+
+    def method(self, name, method):
+        self.methods[name] = method
+
+    def success(self, name):
+        self.report[name] = Success()
+
+    def failure(self, name, message):
+        self.report[name] = Failure(message)
+
+    def internal(self, name, message):
+        self.report[name] = Internal(message)
+
+    def invalid(self, name, exception):
+        self.report[name] = Invalid(exception)
+
+    def warning(self, name, message):
+        self.warnings[name].append(message)
+
+    def summary(self, detailed=False):
+
+        maxlen = max(len(name) for name in self.report.keys())
+
+        for name, methods in METHODS_CATEGORIES.items():
+            print()
+            print(f"{name.title().replace('_', ' ')}:")
+            print("-" * (len(name) + 1))
+            print()
+
+            for method in methods:
+                r = self.report.get(method, Unknown())
+                msg = repr(r)
+                if not msg.endswith("."):
+                    msg += "."
+                print(f"{r.emoji} {method.ljust(maxlen)}: {msg}")
+
+                for w in self.warnings.get(method, []):
+                    print(" " * (maxlen + 4), "⚠️", w)
+
+                if r.success:
+                    continue
+
+                if not detailed:
+                    continue
+
+                if method not in self.methods:
+                    continue
+
+                proc = self.methods[method]
+
+                doc = proc.__doc__
+                if doc:
+                    width = 80
+                    indent = maxlen + 4
+                    doc = "\n".join(["=" * width, "", doc, "=" * width])
+                    indented_doc = "\n".join(" " * indent + line for line in doc.splitlines())
+                    print()
+                    print(indented_doc)
+                    print()
+                    print()
+
+        print()
+
+
+def _no_validate(report, dataset, name, result):
+    report.warning(name, f"Validation for {name} not implemented. Result: {type(result)}")
+
+
+def validate_variables(report, dataset, name, result):
+    """Validate the variables of the dataset."""
+
+    if not isinstance(result, (list, tuple)):
+        raise ValueError(f"Result is not a list or tuple {type(result)}")
+
+    if len(result) != dataset.shape[1]:
+        raise ValueError(f"Result has wrong length: {len(result)} != {dataset.shape[1]}")
+
+    for value in result:
+        if not isinstance(value, str):
+            raise ValueError(f"`{value}` is not a string")
+
+
+def validate_latitudes(report, dataset, name, result):
+    """Validate the latitudes of the dataset."""
+
+    if not isinstance(result, np.ndarray):
+        raise ValueError(f"Result is not a np.ndarray {type(result)}")
+
+    if len(result) != dataset.shape[3]:
+        raise ValueError(f"Result has wrong length: {len(result)} != {dataset.shape[3]}")
+
+    if not np.all(np.isfinite(result)):
+        raise ValueError("Result contains non-finite values")
+
+    if np.isnan(result).any():
+        report.invalid(name, ValueError("Result contains NaN values"))
+        return
+
+    if not np.all((result >= -90) & (result <= 90)):
+        raise ValueError("Result contains values outside the range [-90, 90]")
+
+    if np.all((result >= -np.pi) & (result <= np.pi)):
+        report.warning(name, "All latitudes are in the range [-π, π]. Are they in radians?")
+
+
+def validate_longitudes(report, dataset, name, result):
+    """Validate the longitudes of the dataset."""
+
+    if not isinstance(result, np.ndarray):
+        raise ValueError(f"Result is not a np.ndarray {type(result)}")
+
+    if len(result) != dataset.shape[3]:
+        raise ValueError(f"Result has wrong length: {len(result)} != {dataset.shape[2]}")
+
+    if not np.all(np.isfinite(result)):
+        raise ValueError("Result contains non-finite values")
+
+    if np.isnan(result).any():
+        report.invalid(name, ValueError("Result contains NaN values"))
+        return
+
+    if not np.all((result >= -180) & (result <= 360)):
+        raise ValueError("Result contains values outside the range [-180, 360]")
+
+    if np.all((result >= -np.pi) & (result <= 2 * np.pi)):
+        report.warning(name, "All longitudes are in the range [-π, 2π]. Are they in radians?")
+
+
+def validate_statistics(report, dataset, name, result):
+    """Validate the statistics of the dataset."""
+
+    if not isinstance(result, dict):
+        raise ValueError(f"Result is not a dict {type(result)}")
+
+    for key in ["mean", "stdev", "minimum", "maximum"]:
+
+        if key not in result:
+            raise ValueError(f"Result does not contain `{key}`")
+
+        if not isinstance(result[key], np.ndarray):
+            raise ValueError(f"Result[{key}] is not a np.ndarray {type(result[key])}")
+
+        if len(result[key].shape) != 1:
+            raise ValueError(f"Result[{key}] has wrong shape: {len(result[key].shape)} != 1")
+
+        if result[key].shape[0] != len(dataset.variables):
+            raise ValueError(f"Result[{key}] has wrong length: {result[key].shape[0]} != {len(dataset.variables)}")
+
+        if not np.all(np.isfinite(result[key])):
+            raise ValueError(f"Result[{key}] contains non-finite values")
+
+        if np.isnan(result[key]).any():
+            report.invalid(name, ValueError(f"Result[{key}] contains NaN values"))
+
+
+def validate_shape(report, dataset, name, result):
+    """Validate the shape of the dataset."""
+
+    if not isinstance(result, tuple):
+        raise ValueError(f"Result is not a tuple {type(result)}")
+
+    if len(result) != 4:
+        raise ValueError(f"Result has wrong length: {len(result)} != {len(dataset.shape)}")
+
+    if result[0] != len(dataset):
+        raise ValueError(f"Result[0] has wrong length: {result[0]} != {len(dataset)}")
+
+    if result[1] != len(dataset.variables):
+        raise ValueError(f"Result[1] has wrong length: {result[1]} != {len(dataset.variables)}")
+
+    if result[2] != 1:  # We ignore ensemble dimension for now
+        pass
+
+    if result[3] != len(dataset.latitudes):
+        raise ValueError(f"Result[3] has wrong length: {result[3]} != {len(dataset.latitudes)}")
+
+
+def validate_supporting_arrays(report, dataset, name, result):
+    """Validate the supporting arrays of the dataset."""
+
+    if not isinstance(result, dict):
+        raise ValueError(f"Result is not a dict {type(result)}")
+
+    if "latitudes" not in result:
+        raise ValueError("Result does not contain `latitudes`")
+
+    if "longitudes" not in result:
+        raise ValueError("Result does not contain `longitudes`")
+
+    if not isinstance(result["latitudes"], np.ndarray):
+        raise ValueError(f"Result[latitudes] is not a np.ndarray {type(result['latitudes'])}")
+
+    if not isinstance(result["longitudes"], np.ndarray):
+        raise ValueError(f"Result[longitudes] is not a np.ndarray {type(result['longitudes'])}")
+
+    if np.any(result["latitudes"] != dataset.latitudes):
+        raise ValueError("Result[latitudes] does not match dataset.latitudes")
+
+    if np.any(result["longitudes"] != dataset.longitudes):
+        raise ValueError("Result[longitudes] does not match dataset.longitudes")
+
+
+def validate_dates(report, dataset, name, result):
+    """Validate the dates of the dataset."""
+
+    if not isinstance(result, np.ndarray):
+        raise ValueError(f"Result is not a np.ndarray {type(result)}")
+
+    if len(result.shape) != 1:
+        raise ValueError(f"Result has wrong shape: {len(result.shape)} != 1")
+
+    if result.shape[0] != len(dataset.dates):
+        raise ValueError(f"Result has wrong length: {result.shape[0]} != {len(dataset.dates)}")
+
+    if not np.issubdtype(result.dtype, np.datetime64):
+        raise ValueError(f"Result is not a datetime64 array {result.dtype}")
+
+    if len(result) != len(dataset.dates):
+        raise ValueError(f"Result has wrong length: {len(result)} != {len(dataset.dates)}")
+
+    if not np.all(np.isfinite(result)):
+        raise ValueError("Result contains non-finite values")
+
+    if np.isnan(result).any():
+        report.invalid(name, ValueError("Result contains NaN values"))
+        return
+
+    for d1, d2 in zip(result[:-1], result[1:]):
+        if d1 >= d2:
+            raise ValueError(f"Result contains non-increasing dates: {d1} >= {d2}")
+
+    frequency = np.diff(result)
+    if not np.all(frequency == frequency[0]):
+        raise ValueError("Result contains non-constant frequency")
+
+
+def validate_metadata(report, dataset, name, result):
+    """Validate the metadata of the dataset."""
+
+    if not isinstance(result, dict):
+        raise ValueError(f"Result is not a dict {type(result)}")
+
+
+def validate_missing(report, dataset, name, result):
+    """Validate the missing values of the dataset."""
+
+    if not isinstance(result, set):
+        raise ValueError(f"Result is not a set {type(result)}")
+
+    if not all(isinstance(item, int) for item in result):
+        raise ValueError("Result contains non-integer values")
+
+    if len(result) > 0:
+        if min(result) < 0:
+            raise ValueError("Result contains negative values")
+
+        if max(result) >= len(dataset):
+            raise ValueError(f"Result contains values greater than {len(dataset)}")
+
+
+def validate_name_to_index(report, dataset, name, result):
+    """Validate the name to index mapping of the dataset."""
+
+    if not isinstance(result, dict):
+        raise ValueError(f"Result is not a dict {type(result)}")
+
+    for key in dataset.variables:
+        if key not in result:
+            raise ValueError(f"Result does not contain `{key}`")
+
+        if not isinstance(result[key], int):
+            raise ValueError(f"Result[{key}] is not an int {type(result[key])}")
+
+        if result[key] < 0 or result[key] >= len(dataset.variables):
+            raise ValueError(f"Result[{key}] is out of bounds: {result[key]}")
+
+    index_to_name = {v: k for k, v in result.items()}
+    for i in range(len(dataset.variables)):
+        if i not in index_to_name:
+            raise ValueError(f"Result does not contain index `{i}`")
+
+        if not isinstance(index_to_name[i], str):
+            raise ValueError(f"Result[{i}] is not a string {type(index_to_name[i])}")
+
+        if index_to_name[i] != dataset.variables[i]:
+            raise ValueError(
+                f"Result[{i}] does not match dataset.variables[{i}]: {index_to_name[i]} != {dataset.variables[i]}"
+            )
+
+
+def validate___getitem__(report, dataset, name, result):
+    """Validate the __getitem__ method of the dataset."""
+
+    if not isinstance(result, np.ndarray):
+        raise ValueError(f"Result is not a np.ndarray {type(result)}")
+
+    if result.shape != dataset.shape[1:]:
+        raise ValueError(f"Result has wrong shape: {result.shape} != {dataset.shape[1:]}")
+
+
+def validate___len__(report, dataset, name, result):
+    """Validate the __len__ method of the dataset."""
+
+    if not isinstance(result, int):
+        raise ValueError(f"Result is not an int {type(result)}")
+
+    if result != dataset.shape[0]:
+        raise ValueError(f"Result has wrong length: {result} != {len(dataset)}")
+
+    if result != len(dataset.dates):
+        raise ValueError(f"Result has wrong length: {result} != {len(dataset.dates)}")
+
+
+def validate_start_date(report, dataset, name, result):
+    """Validate the start date of the dataset."""
+
+    if not isinstance(result, np.datetime64):
+        raise ValueError(f"Result is not a datetime64 {type(result)}")
+
+    if result != dataset.dates[0]:
+        raise ValueError(f"Result has wrong start date: {result} != {dataset.dates[0]}")
+
+
+def validate_end_date(report, dataset, name, result):
+    """Validate the end date of the dataset."""
+
+    if not isinstance(result, np.datetime64):
+        raise ValueError(f"Result is not a datetime64 {type(result)}")
+
+    if result != dataset.dates[-1]:
+        raise ValueError(f"Result has wrong end date: {result} != {dataset.dates[-1]}")
+
+
+def validate_field_shape(report, dataset, name, result):
+    """Validate the field shape of the dataset."""
+
+    if not isinstance(result, tuple):
+        raise ValueError(f"Result is not a tuple {type(result)}")
+
+    if math.prod(result) != dataset.shape[-1]:
+        raise ValueError(f"Result has wrong shape: {result} != {dataset.shape[-1]}")
+
+
+def validate(report, dataset, name, kwargs=None):
+
+    try:
+
+        validate_fn = globals().get(f"validate_{name}", _no_validate)
+
+        # Check if the method is still in the Dataset class
+        try:
+            report.method(name, getattr(Dataset, name))
+        except AttributeError:
+            report.internal(name, "Attribute not found in Dataset class. Please update the list of methods.")
+            return
+
+        # Check if the method is supported by the dataset instance
+        try:
+            result = getattr(dataset, name)
+        except AttributeError as e:
+            report.failure(name, e)
+            return
+
+        # Check if the method is callable
+        if callable(result):
+            if kwargs is None:
+                report.internal(
+                    name, f"`{name}` is a callable method, not an attribute. Please update KWARGS accordingly."
+                )
+                return
+        else:
+            if kwargs is not None:
+                report.internal(name, f"`{name}` is not callable. Please remove entry from KWARGS.")
+                return
+
+        if kwargs is not None:
+            result = result(**kwargs)
+
+        if isinstance(result, np.ndarray) and np.isnan(result).any():
+            report.invalid(name, ValueError("Result contains NaN values"))
+            return
+
+        try:
+            validate_fn(report, dataset, name, result)
+        except Exception as e:
+            report.invalid(name, e)
+            return
+
+        report.success(name)
+
+    except Exception as e:
+        report.failure(name, e)
+
+
+def validate_dtype(report, dataset, name, result):
+    """Validate the dtype of the dataset."""
+
+    if not isinstance(result, np.dtype):
+        raise ValueError(f"Result is not a np.dtype {type(result)}")
+
+
+def validate_dataset(dataset, costly_checks=False, detailed=False):
+    """Validate the dataset."""
+
+    report = Report()
+
+    if costly_checks:
+        # This check is expensive as it loads the entire dataset into memory
+        # so we make it optional
+        default_test_indexing(dataset)
+
+        for i, x in enumerate(dataset):
+            y = dataset[i]
+            assert (x == y).all(), f"Dataset indexing failed at index {i}: {x} != {y}"
+
+    for name in METHODS:
+        validate(report, dataset, name, kwargs=KWARGS.get(name))
+
+    report.summary(detailed=detailed)
+
+
+if __name__ == "__main__":
+    methods = METHODS_CATEGORIES.copy()
+    methods.pop("OTHER_METHODS")
+
+    o = set(OTHER_METHODS)
+    overlap = False
+    for m in methods:
+        if set(methods[m]).intersection(set(OTHER_METHODS)):
+            print(
+                f"WARNING: {m} contains methods from OTHER_METHODS: {set(methods[m]).intersection(set(OTHER_METHODS))}"
+            )
+            o = o - set(methods[m])
+            overlap = True
+
+    for m in methods:
+        for n in methods:
+            if n is not m:
+                if set(methods[m]).intersection(set(methods[n])):
+                    print(
+                        f"WARNING: {m} and {n} have methods in common: {set(methods[m]).intersection(set(methods[n]))}"
+                    )
+
+    if overlap:
+        print(sorted(o))

{anemoi_datasets-0.5.26.dist-info → anemoi_datasets-0.5.28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anemoi-datasets
-Version: 0.5.26
+Version: 0.5.28
 Summary: A package to hold various functions to support training of ML models on ECMWF data.
 Author-email: "European Centre for Medium-Range Weather Forecasts (ECMWF)" <software.support@ecmwf.int>
 License:                                  Apache License
@@ -216,21 +216,23 @@ Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 License-File: LICENSE
 Requires-Dist: anemoi-transform>=0.1.10
-Requires-Dist: anemoi-utils[provenance]>=0.4.26
+Requires-Dist: anemoi-utils[provenance]>=0.4.38
 Requires-Dist: cfunits
+Requires-Dist: glom
+Requires-Dist: jsonschema
 Requires-Dist: numcodecs<0.16
 Requires-Dist: numpy
 Requires-Dist: pyyaml
+Requires-Dist: ruamel-yaml
 Requires-Dist: semantic-version
 Requires-Dist: tqdm
 Requires-Dist: zarr<=2.18.4
@@ -262,6 +264,7 @@ Requires-Dist: requests; extra == "remote"
 Provides-Extra: tests
 Requires-Dist: anemoi-datasets[xarray]; extra == "tests"
 Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-skip-slow; extra == "tests"
 Requires-Dist: pytest-xdist; extra == "tests"
 Provides-Extra: xarray
 Requires-Dist: adlfs; extra == "xarray"