diff --git a/CHANGELOG.md b/CHANGELOG.md index cbc0c92..3e3cdbe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Changed +- **Breaking:** the pipeline config is validated against an explicit pydantic schema (`mxalign.pipeline.config.PipelineConfig`, loaded with `load_config`) instead of being read as a free-form dict. Unknown sections or keys, and missing required keys, raise a `ValidationError` when the `Runner` is created; `Runner.config` is now the validated model. Per-dataset `dates` entries override individual fields of the top-level `dates`. @leifdenby - **Breaking:** file path patterns (`datasets..files` with a `dates:` section, and `alignment.save.path`) now use Python `str.format` syntax instead of earthkit-data patterns: `{reference_time:%Y%m%d%H}` instead of `{reference_time:strftime(%Y%m%d%H)}`, `{year:02d}` instead of `{year:int(%02d)}`. `{lead_time}` (integer hours) and `{valid_time}` are now supported in `files` patterns. `earthkit-data` is no longer a dependency. @michielv - **Breaking:** temporal alignment always runs in the pipeline; `alignment.time` is optional and only accepts `lead_time` (`reference` | `intersection` | `union`, forecast reference only). Unknown keys such as `return_as` or `method` now raise an error. `align_time` takes `reference` and an explicit `lead_time` instead of `**kwargs`. @michielv - Remove dataset loading and dataset validation and outsource it to [mlwp-data-loaders](https://github.com/mlwp-tools/mlwp-data-loaders) and [mlwp-data-specs](https://github.com/mlwp-tools/mlwp-data-specs) @michielv diff --git a/README.md b/README.md index b5c57ff..d359155 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ For a more comprehensive interactive example, check out the [introductory notebo ### Configuration Contents -The configuration file is divided into several main sections: +The configuration file is divided into several main sections. It is validated on load against the schema in `mxalign.pipeline.config` (`PipelineConfig`): unknown sections or keys, and missing required ones such as `alignment.reference`, raise an error up front. Keys that are passed through to a function, such as loader, transformation, metric and save options, are accepted as-is. ```yaml datasets: diff --git a/examples/advanced.ipynb b/examples/advanced.ipynb index c577565..b234aa2 100644 --- a/examples/advanced.ipynb +++ b/examples/advanced.ipynb @@ -455,7 +455,7 @@ } ], "source": [ - "runner.config()" + "runner.config" ] }, { diff --git a/pyproject.toml b/pyproject.toml index f1a9cee..8a70481 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ dependencies = [ "mlwp-data-specs", "mlwp-data-loaders", "pandas>=2.2", + "pydantic>=2", ] [project.scripts] diff --git a/src/mxalign/pipeline/config.py b/src/mxalign/pipeline/config.py index a4e0682..39b4a6d 100644 --- a/src/mxalign/pipeline/config.py +++ b/src/mxalign/pipeline/config.py @@ -1,62 +1,136 @@ +"""Schema for the pipeline YAML config. + +Sections and keys not listed here are rejected, except where a model allows +extra keys (``extra="allow"``); those are passed on as keyword arguments to +the function the section configures (loader, transformation, metric, save). +""" + +from datetime import datetime +from typing import Literal + import yaml +from pydantic import BaseModel, ConfigDict, model_validator from .dates import Dates -def load_yaml(fn: str) -> dict: - """Load a YAML file and return its contents as a dict.""" - with open(fn, "r") as f: - return yaml.safe_load(f) +class _Strict(BaseModel): + model_config = ConfigDict(extra="forbid") + + +class _PassThrough(BaseModel): + """Model whose unknown keys are kept in ``model_extra`` as function kwargs.""" + model_config = ConfigDict(extra="allow") -class Config: - """Pipeline configuration loaded from a YAML file or a plain dict. + @property + def kwargs(self) -> dict: + return dict(self.model_extra or {}) - Top-level ``dates`` entries are merged into each dataset's loader config - so that file-path patterns can be expanded to concrete paths. + +class DatesConfig(_Strict): + """Date range used to expand ``{reference_time}``/``{lead_time}``/``{valid_time}`` in ``files``. + + Every field is optional so a dataset can override part of the top-level + ``dates`` section; after merging, all five must be set. """ - def __init__(self, config: str | dict) -> None: - self.config = load_yaml(config) if isinstance(config, str) else config - if not isinstance(self.config, dict): - raise TypeError("config should be a dictionary.") - self.dates = self.config.pop("dates", None) - self._init_datasets() - print("Config initialized") - - def __getitem__(self, key: str) -> dict | None: - config = self.config.get(key, None) - if config: - return config.copy() - else: - return config - - def __call__(self) -> dict: - return self.config - - def _init_datasets(self) -> None: - for key, loader in self.config["datasets"].items(): - dates_loader = loader.pop("dates", None) - if self.dates: - if dates_loader: - keys_all = list(set(self.dates.keys()).union(dates_loader.keys())) - dates = { - key: ( - dates_loader[key] - if key in dates_loader.keys() - else self.dates[key] - ) - for key in keys_all - } - else: - dates = self.dates.copy() - else: - if dates_loader: - dates = dates_loader.copy() - else: - dates = None - - if dates: - dates = Dates(**dates) - loader["files"] = dates.substitute(loader["files"]) - self.config["datasets"][key] = loader + start: datetime | str | None = None + end: datetime | str | None = None + period: str | None = None + range: str | None = None + step: str | None = None + + +class DatasetConfig(_PassThrough): + """One entry of ``datasets``; extra keys go to ``load_and_validate_dataset``.""" + + loader: str + files: str | list[str] + variables: str | list[str] | None = None + grid_mapping: str | dict | None = None + dates: DatesConfig | None = None + + +class TransformationConfig(_PassThrough): + """One entry of ``transformations`` (keyed by transformation name); extra keys go to the transformation.""" + + datasets: list[str] | None = None + + +class TimeAlignmentConfig(_Strict): + lead_time: str | list[str] | None = None + + +class SpaceAlignmentConfig(_Strict): + """Interpolator/regridder kwargs, chosen by the kind of space alignment needed.""" + + interpolation: dict | None = None + regrid: dict | None = None + + +class SaveConfig(_PassThrough): + """Output for ``ds.(path, **kwargs)``; extra keys go to the save method.""" + + method: str + path: str + + +class AlignmentSaveConfig(SaveConfig): + datasets: Literal["all", "merge"] = "all" + + +class AlignmentConfig(_Strict): + reference: str + broadcast_nans: bool = True + time: TimeAlignmentConfig | None = None + space: SpaceAlignmentConfig | None = None + save: AlignmentSaveConfig | None = None + + +class MetricConfig(_PassThrough): + """One entry of ``verification.metrics``; extra keys go to the metric function.""" + + function: str + inputs: dict[str, Literal["forecast", "reference"]] + + +class VerificationConfig(_Strict): + reference: str + metrics: dict[str, MetricConfig] | None = None + save: SaveConfig | None = None + + +class PipelineConfig(_Strict): + dates: DatesConfig | None = None + datasets: dict[str, DatasetConfig] + transformations: dict[str, TransformationConfig] | None = None + alignment: AlignmentConfig + verification: VerificationConfig | None = None + + @model_validator(mode="after") + def _expand_files(self) -> "PipelineConfig": + """Expand each dataset's ``files`` pattern(s) over its (merged) ``dates``.""" + top = self.dates.model_dump(exclude_none=True) if self.dates else {} + for name, ds in self.datasets.items(): + own = ds.dates.model_dump(exclude_none=True) if ds.dates else {} + dates = {**top, **own} + if not dates: + continue + missing = set(DatesConfig.model_fields) - dates.keys() + if missing: + raise ValueError( + f"datasets.{name}: dates is missing {', '.join(sorted(missing))}" + ) + patterns = [ds.files] if isinstance(ds.files, str) else ds.files + dates = Dates(**dates) + ds.files = [path for p in patterns for path in dates.substitute(p)] + return self + + +def load_config(config: str | dict) -> PipelineConfig: + """Validate a pipeline config given as a YAML file path or a dict.""" + if isinstance(config, str): + with open(config, "r") as f: + config = yaml.safe_load(f) + return PipelineConfig.model_validate(config) diff --git a/src/mxalign/pipeline/runner.py b/src/mxalign/pipeline/runner.py index 57014b2..080201d 100644 --- a/src/mxalign/pipeline/runner.py +++ b/src/mxalign/pipeline/runner.py @@ -3,7 +3,12 @@ from mlwp_data_loaders import load_and_validate_dataset -from .config import Config +from .config import ( + PipelineConfig, + SpaceAlignmentConfig, + TimeAlignmentConfig, + load_config, +) from .transformations.transform import transform from ..alignment.time import align_time from ..alignment.nans import broadcast_nans @@ -13,7 +18,7 @@ class Runner: def __init__(self, config: str | dict): - self.config = Config(config) + self.config: PipelineConfig = load_config(config) self.datasets = {} def run(self): @@ -26,16 +31,11 @@ def run(self): self.verify() def load_datasets(self): - config = self.config["datasets"] - if config is None: - raise ValueError("No datasets section in the config.") - for name, config_ds in config.items(): - config_ds = config_ds.copy() - loader = config_ds.pop("loader") - variables = config_ds.pop("variables", None) - grid_mapping = config_ds.pop("grid_mapping", None) - - raw_files = config_ds.pop("files") + for name, config_ds in self.config.datasets.items(): + variables = config_ds.variables + grid_mapping = config_ds.grid_mapping + + raw_files = config_ds.files if isinstance(raw_files, str): raw_files = [raw_files] files = [] @@ -48,8 +48,8 @@ def load_datasets(self): ds = load_and_validate_dataset( dataset_path, - loader=loader, - **config_ds, + loader=config_ds.loader, + **config_ds.kwargs, ) if variables is not None: @@ -61,85 +61,74 @@ def load_datasets(self): self.datasets[name] = ds def transform_datasets(self): - config = self.config["transformations"] - if config is None: + if self.config.transformations is None: return - for transformation, config_trans in config.items(): - config_trans = config_trans.copy() + for transformation, config_trans in self.config.transformations.items(): # if no datasets specified, apply to all datasets - names_ds = config_trans.pop("datasets", self.datasets.keys()) + names_ds = config_trans.datasets + if names_ds is None: + names_ds = self.datasets.keys() for name in names_ds: ds = self.datasets[name] self.datasets[name] = transform( - name=transformation, datasets=ds, **config_trans + name=transformation, datasets=ds, **config_trans.kwargs ) def align(self): - config = self.config["alignment"] - reference = config.pop("reference") - brdcst_nans = config.pop("broadcast_nans", True) - config_align_time = config.get("time", None) - config_align_space = config.get("space", None) - config_align_save = config.get("save", None) + config = self.config.alignment + reference = config.reference # align in time (always; the time section only holds options) - self.align_time(config_align_time, reference_name=reference) + self.align_time(config.time, reference_name=reference) # align in space - if config_align_space: - self.align_space(reference=reference, config=config_align_space) + if config.space is not None: + self.align_space(reference=reference, config=config.space) else: print("Skipping spatial alignment") # broadcast NaNs - if brdcst_nans: + if config.broadcast_nans: self.datasets = broadcast_nans(self.datasets) # Save aligned datasets - if config_align_save: - config = config_align_save.copy() - method = config.pop("method") - datasets = config.pop("datasets", "all") - if datasets == "all": + if config.save is not None: + save = config.save + kwargs = {"path": save.path, **save.kwargs} + if save.datasets == "all": for name, ds in self.datasets.items(): - save_dataset(method, name, ds, **config) - elif datasets == "merge": + save_dataset(save.method, name, ds, **kwargs) + elif save.datasets == "merge": ds = xr.concat( self.datasets.values(), dim=xr.Variable("model", list(self.datasets.keys())), ) - save_dataset(method, "merged", ds, **config) - else: - raise ValueError("Unknown option for dataset saving.") + save_dataset(save.method, "merged", ds, **kwargs) def verify(self): - config = self.config["verification"] - reference = self.datasets[config["reference"]] - config_metrics = config.get("metrics", None) - config_save_metrics = config.get("save", None) + config = self.config.verification + if config is None: + return + reference = self.datasets[config.reference] common_vars = set(reference.data_vars) for ds in self.datasets.values(): common_vars.intersection_update(set(ds.data_vars)) common_vars = list(common_vars) - if config_metrics: + if config.metrics: metrics = {} - for metric_name, config_metric in config["metrics"].items(): - config_metric = config_metric.copy() - func_path = config_metric.pop("function") - inputs = config_metric.pop("inputs") - + for metric_name, config_metric in config.metrics.items(): metric = Metric( name=metric_name, - func_path=func_path, + func_path=config_metric.function, ds_ref=reference[common_vars], - inputs=inputs, - **config_metric, + inputs=config_metric.inputs, + **config_metric.kwargs, ) models = {} for ds_name, ds in self.datasets.items(): - if ds_name != config["reference"]: + if ds_name != config.reference: models[ds_name] = metric.compute(ds[common_vars]) models = xr.concat( models.values(), dim=xr.Variable("model", list(models.keys())) @@ -150,28 +139,24 @@ def verify(self): ) self.metrics = metrics.transpose("model", "metric", ...).compute() - if config_save_metrics: - config = config_save_metrics.copy() - method = config.pop("method") - save_metrics(method, self.metrics, **config) - - def align_time(self, config, reference_name=None): - config = dict(config or {}) - lead_time = config.pop("lead_time", None) - if config: - raise ValueError( - f"Unknown option(s) in alignment.time: {', '.join(config)}. " - "Only lead_time is supported." - ) + if config.save is not None: + save = config.save + save_metrics(save.method, self.metrics, path=save.path, **save.kwargs) + + def align_time( + self, config: TimeAlignmentConfig | None, reference_name: str | None = None + ): + lead_time = config.lead_time if config is not None else None self.datasets = align_time( self.datasets, reference=reference_name, lead_time=lead_time ) - def align_space(self, reference, config): + def align_space(self, reference: str, config: SpaceAlignmentConfig): ds_ref = self.datasets[reference] for name, ds in self.datasets.items(): if name != reference: - options = config.get(get_spatial_alignment(ds, ds_ref), {}) + kind = get_spatial_alignment(ds, ds_ref) + options = getattr(config, kind, None) or {} self.datasets[name] = ds.mx.align_space_with(ds_ref, **options) diff --git a/tests/test_config.py b/tests/test_config.py new file mode 100644 index 0000000..dd5fbda --- /dev/null +++ b/tests/test_config.py @@ -0,0 +1,75 @@ +from pathlib import Path + +import pytest +from pydantic import ValidationError + +from mxalign.pipeline.config import load_config + +EXAMPLE_CONFIG = Path(__file__).parent.parent / "examples" / "config.yaml" + +DATES = dict(start="2020-01-01", end="2020-01-02", period="1D", range="12h", step="12h") + + +def _config(**sections) -> dict: + return { + "datasets": {"fc": {"loader": "x", "files": "/d/fc.nc"}}, + "alignment": {"reference": "fc"}, + **sections, + } + + +def test_example_config_validates(): + config = load_config(str(EXAMPLE_CONFIG)) + assert config.alignment.reference == "cerra" + assert config.alignment.space.interpolation == {"method": "delaunay"} + assert config.verification.metrics["rmse"].kwargs == { + "dim": ["reference_time", "grid_index"], + "skipna": True, + } + # files patterns are expanded over the dates section + assert len(config.datasets["la-1024-ea-00"].files) > 1 + + +def test_unknown_top_level_key_is_rejected(): + with pytest.raises(ValidationError, match="not_a_section"): + load_config(_config(not_a_section={"reference": "fc"})) + + +def test_missing_alignment_reference_is_rejected(): + config = _config() + config["alignment"] = {"broadcast_nans": False} + with pytest.raises(ValidationError, match="alignment.reference"): + load_config(config) + + +def test_unknown_save_datasets_option_is_rejected(): + save = {"method": "to_netcdf", "path": "out.nc", "datasets": "some"} + with pytest.raises(ValidationError, match="alignment.save.datasets"): + load_config(_config(alignment={"reference": "fc", "save": save})) + + +def test_extra_dataset_keys_are_passed_to_loader(): + config = _config() + config["datasets"]["fc"]["chunks"] = {"time": 1} + assert load_config(config).datasets["fc"].kwargs == {"chunks": {"time": 1}} + + +def test_dataset_dates_override_top_level_dates(): + config = _config(dates=DATES) + config["datasets"]["fc"] = { + "loader": "x", + "files": "/d/{reference_time:%Y%m%d}.nc", + "dates": {"end": "2020-01-03"}, + } + assert load_config(config).datasets["fc"].files == [ + "/d/20200101.nc", + "/d/20200102.nc", + "/d/20200103.nc", + ] + + +def test_incomplete_dates_are_rejected(): + config = _config() + config["datasets"]["fc"]["dates"] = {"start": "2020-01-01"} + with pytest.raises(ValidationError, match="dates is missing end, period"): + load_config(config) diff --git a/tests/test_dates.py b/tests/test_dates.py index c37a6bb..441eac5 100644 --- a/tests/test_dates.py +++ b/tests/test_dates.py @@ -2,7 +2,7 @@ import pytest -from mxalign.pipeline.config import Config +from mxalign.pipeline.config import load_config from mxalign.pipeline.dates import Dates from mxalign.pipeline.save import DatasetPath @@ -45,15 +45,16 @@ def test_substitute_lead_time_requires_whole_hours(): def test_config_expands_files_from_dates_section(): # YAML parses unquoted timestamps to datetime objects - config = Config( + config = load_config( { "dates": {**DATES, "start": datetime.datetime(2020, 1, 1)}, "datasets": { "fc": {"loader": "x", "files": "/d/{reference_time:%Y%m%d}.nc"} }, + "alignment": {"reference": "fc"}, } ) - assert config["datasets"]["fc"]["files"] == [ + assert config.datasets["fc"].files == [ "/d/20200101.nc", "/d/20200102.nc", "/d/20200103.nc", diff --git a/tests/test_runner.py b/tests/test_runner.py index b3aa11d..d84eded 100644 --- a/tests/test_runner.py +++ b/tests/test_runner.py @@ -1,4 +1,5 @@ import pytest +from pydantic import ValidationError from mxalign.pipeline.runner import Runner @@ -19,10 +20,14 @@ def test_align_runs_time_alignment_without_time_section(ds_fcst, ds_obs): assert runner.datasets["obs"].mx.is_forecast() -def test_align_time_rejects_unknown_options(ds_fcst, ds_obs): - runner = _runner({"fcst": ds_fcst, "obs": ds_obs}, {"reference": "obs"}) - with pytest.raises(ValueError, match="Unknown option.*return_as"): - runner.align_time({"return_as": "forecast"}, reference_name="obs") +def test_align_time_rejects_unknown_options(): + with pytest.raises(ValidationError, match="alignment.time.return_as"): + Runner( + { + "datasets": {}, + "alignment": {"reference": "obs", "time": {"return_as": "forecast"}}, + } + ) def test_transform_datasets_without_transformations_section(ds_obs): diff --git a/uv.lock b/uv.lock index 6ce6399..1e99d4f 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,5 @@ version = 1 -revision = 5 +revision = 3 requires-python = ">=3.12" resolution-markers = [ "python_full_version >= '3.14' and sys_platform == 'win32'", @@ -204,6 +204,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl", hash = "sha256:053243f8b92b990551949e63930a839ff0cf0b0ebbe0597b0f3fb19e1a0fe82e", size = 7490, upload-time = "2025-07-03T22:54:42.156Z" }, ] +[[package]] +name = "annotated-types" +version = "0.8.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = 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