anemoi-datasets 0.3.6__py3-none-any.whl → 0.3.8__py3-none-any.whl

anemoi/datasets/__init__.py

@@ -9,11 +9,14 @@ from ._version import __version__
 from .data import MissingDateError
 from .data import add_dataset_path
 from .data import add_named_dataset
+from .data import list_dataset_names
 from .data import open_dataset
 
 __all__ = [
-    "open_dataset",
-    "MissingDateError",
+    "__version__",
     "add_dataset_path",
     "add_named_dataset",
+    "list_dataset_names",
+    "MissingDateError",
+    "open_dataset",
 ]

anemoi/datasets/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.3.6'
-__version_tuple__ = version_tuple = (0, 3, 6)
+__version__ = version = '0.3.8'
+__version_tuple__ = version_tuple = (0, 3, 8)

anemoi/datasets/commands/copy.py

@@ -7,11 +7,14 @@
 
 import logging
 import os
+import shutil
 import sys
 from concurrent.futures import ThreadPoolExecutor
 from concurrent.futures import as_completed
 
 import tqdm
+from anemoi.utils.s3 import download
+from anemoi.utils.s3 import upload
 
 from . import Command
 
@@ -22,34 +25,63 @@ try:
 except AttributeError:
     isatty = False
 
-"""
 
-~/.aws/credentials
+class S3Downloader:
+    def __init__(self, source, target, transfers, overwrite, resume, verbosity, **kwargs):
+        self.source = source
+        self.target = target
+        self.transfers = transfers
+        self.overwrite = overwrite
+        self.resume = resume
+        self.verbosity = verbosity
 
-[default]
-endpoint_url = https://object-store.os-api.cci1.ecmwf.int
-aws_access_key_id=xxx
-aws_secret_access_key=xxxx
+    def run(self):
+        if self.target == ".":
+            self.target = os.path.basename(self.source)
+
+        if self.overwrite and os.path.exists(self.target):
+            LOG.info(f"Deleting {self.target}")
+            shutil.rmtree(self.target)
+
+        download(
+            self.source + "/" if not self.source.endswith("/") else self.source,
+            self.target,
+            overwrite=self.overwrite,
+            resume=self.resume,
+            verbosity=self.verbosity,
+            threads=self.transfers,
+        )
 
-Then:
 
-anemoi-datasets copy aifs-ea-an-oper-0001-mars-o96-1979-2022-1h-v3.zarr/
-    s3://ml-datasets/stable/aifs-ea-an-oper-0001-mars-o96-1979-2022-1h-v3.zarr
+class S3Uploader:
+    def __init__(self, source, target, transfers, overwrite, resume, verbosity, **kwargs):
+        self.source = source
+        self.target = target
+        self.transfers = transfers
+        self.overwrite = overwrite
+        self.resume = resume
+        self.verbosity = verbosity
 
-zinfo https://object-store.os-api.cci1.ecmwf.int/
-    ml-datasets/stable/aifs-ea-an-oper-0001-mars-o96-1979-2022-1h-v3.zarr
-"""
+    def run(self):
+        upload(
+            self.source,
+            self.target,
+            overwrite=self.overwrite,
+            resume=self.resume,
+            verbosity=self.verbosity,
+            threads=self.transfers,
+        )
 
 
-class Copier:
-    def __init__(self, source, target, transfers, block_size, overwrite, resume, progress, nested, rechunk, **kwargs):
+class DefaultCopier:
+    def __init__(self, source, target, transfers, block_size, overwrite, resume, verbosity, nested, rechunk, **kwargs):
         self.source = source
         self.target = target
         self.transfers = transfers
         self.block_size = block_size
         self.overwrite = overwrite
         self.resume = resume
-        self.progress = progress
+        self.verbosity = verbosity
         self.nested = nested
         self.rechunk = rechunk
 
@@ -62,7 +94,7 @@ class Copier:
             return zarr.storage.NestedDirectoryStore(path)
         return path
 
-    def copy_chunk(self, n, m, source, target, _copy, progress):
+    def copy_chunk(self, n, m, source, target, _copy, verbosity):
         if _copy[n:m].all():
             LOG.info(f"Skipping {n} to {m}")
             return None
@@ -82,7 +114,7 @@ class Copier:
                 range(n, m),
                 desc=f"Copying {n} to {m}",
                 leave=False,
-                disable=not isatty and not progress,
+                disable=not isatty and not verbosity,
             ):
                 target[i] = source[i]
 
@@ -107,7 +139,7 @@ class Copier:
             #    raise NotImplementedError("Rechunking with multiple transfers is not implemented")
         return chunks
 
-    def copy_data(self, source, target, _copy, progress):
+    def copy_data(self, source, target, _copy, verbosity):
         LOG.info("Copying data")
         source_data = source["data"]
 
@@ -121,6 +153,7 @@ class Copier:
                 shape=source_data.shape,
                 chunks=self.data_chunks,
                 dtype=source_data.dtype,
+                fill_value=source_data.fill_value,
             )
         )
 
@@ -136,7 +169,7 @@ class Copier:
                     source_data,
                     target_data,
                     _copy,
-                    progress,
+                    verbosity,
                 )
             )
             n += self.block_size
@@ -151,7 +184,7 @@ class Copier:
 
         LOG.info("Copied data")
 
-    def copy_array(self, name, source, target, _copy, progress):
+    def copy_array(self, name, source, target, _copy, verbosity):
         for k, v in source.attrs.items():
             target.attrs[k] = v
 
@@ -159,14 +192,14 @@ class Copier:
             return
 
         if name == "data":
-            self.copy_data(source, target, _copy, progress)
+            self.copy_data(source, target, _copy, verbosity)
             return
 
         LOG.info(f"Copying {name}")
         target[name] = source[name]
         LOG.info(f"Copied {name}")
 
-    def copy_group(self, source, target, _copy, progress):
+    def copy_group(self, source, target, _copy, verbosity):
         import zarr
 
         for k, v in source.attrs.items():
@@ -179,7 +212,7 @@ class Copier:
                     source[name],
                     group,
                     _copy,
-                    progress,
+                    verbosity,
                 )
             else:
                 self.copy_array(
@@ -187,10 +220,10 @@ class Copier:
                     source,
                     target,
                     _copy,
-                    progress,
+                    verbosity,
                 )
 
-    def copy(self, source, target, progress):
+    def copy(self, source, target, verbosity):
         import zarr
 
         if "_copy" not in target:
@@ -201,7 +234,7 @@ class Copier:
         _copy = target["_copy"]
         _copy_np = _copy[:]
 
-        self.copy_group(source, target, _copy_np, progress)
+        self.copy_group(source, target, _copy_np, verbosity)
         del target["_copy"]
 
     def run(self):
@@ -260,7 +293,7 @@ class Copier:
         assert target is not None, target
 
         source = zarr.open(self._store(self.source), mode="r")
-        self.copy(source, target, self.progress)
+        self.copy(source, target, self.verbosity)
 
 
 class CopyMixin:
@@ -279,7 +312,10 @@ class CopyMixin:
         )
         command_parser.add_argument("--transfers", type=int, default=8, help="Number of parallel transfers.")
         command_parser.add_argument(
-            "--progress", action="store_true", help="Force show progress bar, even if not in an interactive shell."
+            "--verbosity",
+            type=int,
+            help="Verbosity level. 0 is silent, 1 is normal, 2 is verbose.",
+            default=1,
         )
         command_parser.add_argument("--nested", action="store_true", help="Use ZARR's nested directpry backend.")
         command_parser.add_argument(
@@ -295,7 +331,29 @@ class CopyMixin:
         command_parser.add_argument("target", help="Target location.")
 
     def run(self, args):
-        Copier(**vars(args)).run()
+        if args.source == args.target:
+            raise ValueError("Source and target are the same.")
+
+        kwargs = vars(args)
+
+        if args.overwrite and args.resume:
+            raise ValueError("Cannot use --overwrite and --resume together.")
+
+        source_in_s3 = args.source.startswith("s3://")
+        target_in_s3 = args.target.startswith("s3://")
+
+        copier = None
+
+        if args.rechunk or (source_in_s3 and target_in_s3):
+            copier = DefaultCopier(**kwargs)
+        else:
+            if source_in_s3:
+                copier = S3Downloader(**kwargs)
+
+            if target_in_s3:
+                copier = S3Uploader(**kwargs)
+
+        copier.run()
 
 
 class Copy(CopyMixin, Command):

anemoi/datasets/create/__init__.py

@@ -97,13 +97,14 @@ class Creator:
 
         apply_patch(self.path, **kwargs)
 
-    def init_additions(self, delta=[1, 3, 6, 12, 24]):
+    def init_additions(self, delta=[1, 3, 6, 12, 24], statistics=True):
         from .loaders import StatisticsAddition
         from .loaders import TendenciesStatisticsAddition
         from .loaders import TendenciesStatisticsDeltaNotMultipleOfFrequency
 
-        a = StatisticsAddition.from_dataset(path=self.path, print=self.print)
-        a.initialise()
+        if statistics:
+            a = StatisticsAddition.from_dataset(path=self.path, print=self.print)
+            a.initialise()
 
         for d in delta:
             try:
@@ -112,13 +113,14 @@ class Creator:
             except TendenciesStatisticsDeltaNotMultipleOfFrequency:
                 self.print(f"Skipping delta={d} as it is not a multiple of the frequency.")
 
-    def run_additions(self, parts=None, delta=[1, 3, 6, 12, 24]):
+    def run_additions(self, parts=None, delta=[1, 3, 6, 12, 24], statistics=True):
         from .loaders import StatisticsAddition
         from .loaders import TendenciesStatisticsAddition
         from .loaders import TendenciesStatisticsDeltaNotMultipleOfFrequency
 
-        a = StatisticsAddition.from_dataset(path=self.path, print=self.print)
-        a.run(parts)
+        if statistics:
+            a = StatisticsAddition.from_dataset(path=self.path, print=self.print)
+            a.run(parts)
 
         for d in delta:
             try:
@@ -127,13 +129,14 @@ class Creator:
             except TendenciesStatisticsDeltaNotMultipleOfFrequency:
                 self.print(f"Skipping delta={d} as it is not a multiple of the frequency.")
 
-    def finalise_additions(self, delta=[1, 3, 6, 12, 24]):
+    def finalise_additions(self, delta=[1, 3, 6, 12, 24], statistics=True):
         from .loaders import StatisticsAddition
         from .loaders import TendenciesStatisticsAddition
         from .loaders import TendenciesStatisticsDeltaNotMultipleOfFrequency
 
-        a = StatisticsAddition.from_dataset(path=self.path, print=self.print)
-        a.finalise()
+        if statistics:
+            a = StatisticsAddition.from_dataset(path=self.path, print=self.print)
+            a.finalise()
 
         for d in delta:
             try:

anemoi/datasets/create/functions/sources/accumulations.py

@@ -19,6 +19,8 @@ from climetlab.utils.availability import Availability
 
 from anemoi.datasets.create.utils import to_datetime_list
 
+from .mars import use_grib_paramid
+
 LOG = logging.getLogger(__name__)
 
 
@@ -85,6 +87,7 @@ class Accumulation:
             stepType="accum",
             startStep=self.startStep,
             endStep=self.endStep,
+            check_nans=True,
         )
         self.values = None
         self.done = True
@@ -230,6 +233,7 @@ def identity(x):
 
 
 def compute_accumulations(
+    context,
     dates,
     request,
     user_accumulation_period=6,
@@ -306,7 +310,10 @@ def compute_accumulations(
     ds = cml.load_source("empty")
     for r in compressed.iterate():
         request.update(r)
+        if context.use_grib_paramid and "param" in request:
+            request = use_grib_paramid(request)
         print("🌧️", request)
+
         ds = ds + cml.load_source("mars", **request)
 
     accumulations = {}
@@ -395,7 +402,7 @@ def accumulations(context, dates, **request):
     class_ = request.get("class", "od")
     stream = request.get("stream", "oper")
 
-    user_accumulation_period = request.get("accumulation_period", 6)
+    user_accumulation_period = request.pop("accumulation_period", 6)
 
     KWARGS = {
         ("od", "oper"): dict(patch=scda),
@@ -409,6 +416,7 @@ def accumulations(context, dates, **request):
     context.trace("🌧️", f"accumulations {request} {user_accumulation_period} {kwargs}")
 
     return compute_accumulations(
+        context,
         dates,
         request,
         user_accumulation_period=user_accumulation_period,

anemoi/datasets/create/functions/sources/mars.py

@@ -9,6 +9,7 @@
 import datetime
 from copy import deepcopy
 
+from anemoi.utils.humanize import did_you_mean
 from climetlab import load_source
 from climetlab.utils.availability import Availability
 
@@ -102,6 +103,74 @@ def use_grib_paramid(r):
     return r
 
 
+MARS_KEYS = [
+    "accuracy",
+    "activity",
+    "anoffset",
+    "area",
+    "bitmap",
+    "channel",
+    "class",
+    "database",
+    "dataset",
+    "date",
+    "diagnostic",
+    "direction",
+    "domain",
+    "expect",
+    "experiment",
+    "expver",
+    "fcmonth",
+    "fcperiod",
+    "fieldset",
+    "filter",
+    "format",
+    "frame",
+    "frequency",
+    "gaussian",
+    "generation",
+    "grid",
+    "hdate",
+    "ident",
+    "instrument",
+    "interpolation",
+    "intgrid",
+    "iteration",
+    "level",
+    "levelist",
+    "levtype",
+    "method",
+    "model",
+    "month",
+    "number",
+    "obsgroup",
+    "obstype",
+    "offsetdate",
+    "offsettime",
+    "optimise",
+    "origin",
+    "packing",
+    "padding",
+    "param",
+    "quantile",
+    "realization",
+    "reference",
+    "reportype",
+    "repres",
+    "resol",
+    "resolution",
+    "rotation",
+    "step",
+    "stream",
+    "system",
+    "target",
+    "time",
+    "truncation",
+    "type",
+    "year",
+]
+
+
 def mars(context, dates, *requests, date_key="date", **kwargs):
     if not requests:
         requests = [kwargs]
@@ -117,6 +186,11 @@ def mars(context, dates, *requests, date_key="date", **kwargs):
         if DEBUG:
             context.trace("✅", f"load_source(mars, {r}")
 
+        for k, v in r.items():
+            if k not in MARS_KEYS:
+                raise ValueError(
+                    f"⚠️ Unknown key {k}={v} in MARS request. Did you mean '{did_you_mean(k, MARS_KEYS)}' ?"
+                )
         ds = ds + load_source("mars", **r)
     return ds
 

anemoi/datasets/create/loaders.py

@@ -46,8 +46,44 @@ LOG = logging.getLogger(__name__)
 VERSION = "0.20"
 
 
+def set_to_test_mode(cfg):
+    NUMBER_OF_DATES = 4
+
+    dates = cfg.dates
+    LOG.warn(f"Running in test mode. Changing the list of dates to use only {NUMBER_OF_DATES}.")
+    groups = Groups(**cfg.dates)
+    dates = groups.dates
+    cfg.dates = dict(
+        start=dates[0],
+        end=dates[NUMBER_OF_DATES - 1],
+        frequency=dates.frequency,
+        group_by=NUMBER_OF_DATES,
+    )
+
+    def set_element_to_test(obj):
+        if isinstance(obj, (list, tuple)):
+            for v in obj:
+                set_element_to_test(v)
+            return
+        if isinstance(obj, (dict, DictObj)):
+            if "grid" in obj:
+                previous = obj["grid"]
+                obj["grid"] = "20./20."
+                LOG.warn(f"Running in test mode. Setting grid to {obj['grid']} instead of {previous}")
+            if "number" in obj:
+                if isinstance(obj["number"], (list, tuple)):
+                    previous = obj["number"]
+                    obj["number"] = previous[0:3]
+                    LOG.warn(f"Running in test mode. Setting number to {obj['number']} instead of {previous}")
+            for k, v in obj.items():
+                set_element_to_test(v)
+
+    set_element_to_test(cfg)
+
+
 class GenericDatasetHandler:
     def __init__(self, *, path, print=print, **kwargs):
+
         # Catch all floating point errors, including overflow, sqrt(<0), etc
         np.seterr(all="raise", under="warn")
 
@@ -61,12 +97,15 @@ class GenericDatasetHandler:
 
     @classmethod
     def from_config(cls, *, config, path, print=print, **kwargs):
-        # config is the path to the config file or a dict with the config
+        """Config is the path to the config file or a dict with the config"""
+
         assert isinstance(config, dict) or isinstance(config, str), config
         return cls(config=config, path=path, print=print, **kwargs)
 
     @classmethod
     def from_dataset_config(cls, *, path, print=print, **kwargs):
+        """Read the config saved inside the zarr dataset and instantiate the class for this config."""
+
         assert os.path.exists(path), f"Path {path} does not exist."
         z = zarr.open(path, mode="r")
         config = z.attrs["_create_yaml_config"]
@@ -75,6 +114,8 @@ class GenericDatasetHandler:
 
     @classmethod
     def from_dataset(cls, *, path, **kwargs):
+        """Instanciate the class from the path to the zarr dataset, without config."""
+
         assert os.path.exists(path), f"Path {path} does not exist."
         return cls(path=path, **kwargs)
 
@@ -156,68 +197,50 @@ class Loader(DatasetHandlerWithStatistics):
 class InitialiserLoader(Loader):
     def __init__(self, config, **kwargs):
         super().__init__(**kwargs)
-        self.main_config = loader_config(config)
-
-        self.tmp_statistics.delete()
 
+        self.main_config = loader_config(config)
         if self.test:
-
-            def test_dates(cfg, n=4):
-                LOG.warn("Running in test mode. Changing the list of dates to use only 4.")
-                groups = Groups(**cfg)
-                dates = groups.dates
-                return dict(start=dates[0], end=dates[n - 1], frequency=dates.frequency, group_by=n)
-
-            self.main_config.dates = test_dates(self.main_config.dates)
-
-            def set_to_test_mode(obj):
-                if isinstance(obj, (list, tuple)):
-                    for v in obj:
-                        set_to_test_mode(v)
-                    return
-                if isinstance(obj, (dict, DictObj)):
-                    if "grid" in obj:
-                        previous = obj["grid"]
-                        obj["grid"] = "20./20."
-                        LOG.warn(f"Running in test mode. Setting grid to {obj['grid']} instead of {previous}")
-                    if "number" in obj:
-                        if isinstance(obj["number"], (list, tuple)):
-                            previous = obj["number"]
-                            obj["number"] = previous[0:3]
-                            LOG.warn(f"Running in test mode. Setting number to {obj['number']} instead of {previous}")
-                    for k, v in obj.items():
-                        set_to_test_mode(v)
-
             set_to_test_mode(self.main_config)
 
         LOG.info(self.main_config.dates)
 
+        self.tmp_statistics.delete()
+
         self.groups = Groups(**self.main_config.dates)
+        LOG.info(self.groups)
 
         self.output = build_output(self.main_config.output, parent=self)
         self.input = self.build_input()
-
         LOG.info(self.input)
-        all_dates = self.groups.dates
-        self.minimal_input = self.input.select([all_dates[0]])
 
-        LOG.info(self.groups)
-        LOG.info("MINIMAL INPUT :")
+        first_date = self.groups.dates[0]
+        self.minimal_input = self.input.select([first_date])
+        LOG.info("Minimal input (using only the first date) :")
         LOG.info(self.minimal_input)
 
     def build_statistics_dates(self, start, end):
+        """Compute the start and end dates for the statistics, based on :
+        - The start and end dates in the config
+        - The default statistics dates convention
+
+        Then adapt according to the actual dates in the dataset.
+        """
+
         ds = open_dataset(self.path)
         dates = ds.dates
 
+        # if not specified, use the default statistics dates
         default_start, default_end = default_statistics_dates(dates)
         if start is None:
             start = default_start
         if end is None:
             end = default_end
 
+        # in any case, adapt to the actual dates in the dataset
         start = as_first_date(start, dates)
         end = as_last_date(end, dates)
 
+        # and convert to datetime to isoformat
         start = start.astype(datetime.datetime)
         end = end.astype(datetime.datetime)
         return (start.isoformat(), end.isoformat())
@@ -227,7 +250,10 @@ class InitialiserLoader(Loader):
         z.create_group("_build")
 
     def initialise(self, check_name=True):
-        """Create empty dataset."""
+        """Create an empty dataset of the right final shape
+
+        Read a small part of the data to get the shape of the data and the resolution and more metadata.
+        """
 
         self.print("Config loaded ok:")
         LOG.info(self.main_config)
@@ -276,11 +302,10 @@ class InitialiserLoader(Loader):
         metadata["_create_yaml_config"] = self.main_config.get_serialisable_dict()
 
         metadata["description"] = self.main_config.description
-        metadata["version"] = VERSION
+        metadata["licence"] = self.main_config["licence"]
+        metadata["attribution"] = self.main_config["attribution"]
 
-        metadata["data_request"] = self.minimal_input.data_request
         metadata["remapping"] = self.output.remapping
-
         metadata["order_by"] = self.output.order_by_as_list
         metadata["flatten_grid"] = self.output.flatten_grid
 
@@ -288,26 +313,21 @@ class InitialiserLoader(Loader):
         metadata["variables"] = variables
         metadata["variables_with_nans"] = variables_with_nans
         metadata["resolution"] = resolution
+
+        metadata["data_request"] = self.minimal_input.data_request
         metadata["field_shape"] = self.minimal_input.field_shape
         metadata["proj_string"] = self.minimal_input.proj_string
 
-        metadata["licence"] = self.main_config["licence"]
-        metadata["attribution"] = self.main_config["attribution"]
-
-        metadata["frequency"] = frequency
         metadata["start_date"] = dates[0].isoformat()
         metadata["end_date"] = dates[-1].isoformat()
+        metadata["frequency"] = frequency
         metadata["missing_dates"] = [_.isoformat() for _ in dates.missing]
 
+        metadata["version"] = VERSION
+
         if check_name:
             basename, ext = os.path.splitext(os.path.basename(self.path))  # noqa: F841
-            ds_name = DatasetName(
-                basename,
-                resolution,
-                dates[0],
-                dates[-1],
-                frequency,
-            )
+            ds_name = DatasetName(basename, resolution, dates[0], dates[-1], frequency)
             ds_name.raise_if_not_valid(print=self.print)
 
         if len(dates) != total_shape[0]:
@@ -316,17 +336,12 @@ class InitialiserLoader(Loader):
                 f"does not match data shape {total_shape[0]}. {total_shape=}"
             )
 
-        dates = normalize_and_check_dates(
-            dates,
-            metadata["start_date"],
-            metadata["end_date"],
-            metadata["frequency"],
-        )
+        dates = normalize_and_check_dates(dates, metadata["start_date"], metadata["end_date"], metadata["frequency"])
 
         metadata.update(self.main_config.get("force_metadata", {}))
 
         ###############################################################
-        # write data
+        # write metadata
         ###############################################################
 
         self.initialise_dataset_backend()
@@ -346,10 +361,7 @@ class InitialiserLoader(Loader):
             self.main_config.statistics.get("start"),
             self.main_config.statistics.get("end"),
         )
-        self.update_metadata(
-            statistics_start_date=statistics_start,
-            statistics_end_date=statistics_end,
-        )
+        self.update_metadata(statistics_start_date=statistics_start, statistics_end_date=statistics_end)
         LOG.info(f"Will compute statistics from {statistics_start} to {statistics_end}")
 
         self.registry.add_to_history("init finished")
@@ -586,37 +598,22 @@ class GenericAdditions(GenericDatasetHandler):
 
     @property
     def tmp_storage_path(self):
-        raise NotImplementedError
+        """This should be implemented in the subclass."""
+        raise NotImplementedError()
 
     @property
     def final_storage_path(self):
-        raise NotImplementedError
+        """This should be implemented in the subclass."""
+        raise NotImplementedError()
 
     def initialise(self):
         self.tmp_storage.delete()
         self.tmp_storage.create()
         LOG.info(f"Dataset {self.path} additions initialized.")
 
-    @cached_property
-    def _variables_with_nans(self):
-        z = zarr.open(self.path, mode="r")
-        if "variables_with_nans" in z.attrs:
-            return z.attrs["variables_with_nans"]
-        return None
-
-    def allow_nan(self, name):
-        if self._variables_with_nans is not None:
-            return name in self._variables_with_nans
-        warnings.warn(f"❗Cannot find 'variables_with_nans' in {self.path}, Assuming nans allowed for {name}.")
-        return True
-
-    @classmethod
-    def _check_type_equal(cls, a, b):
-        a = list(a)
-        b = list(b)
-        a = a[0] if a else None
-        b = b[0] if b else None
-        assert type(a) is type(b), (type(a), type(b))
+    def run(self, parts):
+        """This should be implemented in the subclass."""
+        raise NotImplementedError()
 
     def finalise(self):
         shape = (len(self.dates), len(self.variables))
@@ -696,7 +693,7 @@ class GenericAdditions(GenericDatasetHandler):
             variables_names=self.variables,
             has_nans=has_nans,
         )
-        LOG.info(f"Dataset {self.path} additions finalized.")
+        LOG.info(f"Dataset {self.path} additions finalised.")
         self.check_statistics()
         self._write(self.summary)
         self.tmp_storage.delete()
@@ -711,6 +708,19 @@ class GenericAdditions(GenericDatasetHandler):
     def check_statistics(self):
         pass
 
+    @cached_property
+    def _variables_with_nans(self):
+        z = zarr.open(self.path, mode="r")
+        if "variables_with_nans" in z.attrs:
+            return z.attrs["variables_with_nans"]
+        return None
+
+    def allow_nan(self, name):
+        if self._variables_with_nans is not None:
+            return name in self._variables_with_nans
+        warnings.warn(f"❗Cannot find 'variables_with_nans' in {self.path}, Assuming nans allowed for {name}.")
+        return True
+
 
 class StatisticsAddition(GenericAdditions):
     def __init__(self, **kwargs):
@@ -798,7 +808,7 @@ class TendenciesStatisticsAddition(GenericAdditions):
         start = z.attrs["statistics_start_date"]
         end = z.attrs["statistics_end_date"]
         start = datetime.datetime.fromisoformat(start)
-        ds = open_dataset(self.path, start=start + datetime.timedelta(hours=delta), end=end)
+        ds = open_dataset(self.path, start=start, end=end)
         self.dates = ds.dates
         self.total = len(self.dates)
 

anemoi/datasets/create/statistics/__init__.py

@@ -98,6 +98,8 @@ def check_variance(x, variables_names, minimum, maximum, mean, count, sums, squa
 
 
 def compute_statistics(array, check_variables_names=None, allow_nan=False):
+    """Compute statistics for a given array, provides minimum, maximum, sum, squares, count and has_nans as a dictionary."""
+
     nvars = array.shape[1]
 
     LOG.info(f"Stats {nvars}, {array.shape}, {check_variables_names}")
@@ -242,10 +244,7 @@ class StatAggregator:
         offset = 0
         for _, _dates, stats in self.owner._gather_data():
             assert isinstance(stats, dict), stats
-            assert stats["minimum"].shape[0] == len(_dates), (
-                stats["minimum"].shape,
-                len(_dates),
-            )
+            assert stats["minimum"].shape[0] == len(_dates), (stats["minimum"].shape, len(_dates))
             assert stats["minimum"].shape[1] == len(self.variables_names), (
                 stats["minimum"].shape,
                 len(self.variables_names),
@@ -270,19 +269,13 @@ class StatAggregator:
             for k in self.NAMES:
                 stats[k] = stats[k][bitmap]
 
-            assert stats["minimum"].shape[0] == len(dates), (
-                stats["minimum"].shape,
-                len(dates),
-            )
+            assert stats["minimum"].shape[0] == len(dates), (stats["minimum"].shape, len(dates))
 
             # store data in self
             found |= set(dates)
             for name in self.NAMES:
                 array = getattr(self, name)
-                assert stats[name].shape[0] == len(dates), (
-                    stats[name].shape,
-                    len(dates),
-                )
+                assert stats[name].shape[0] == len(dates), (stats[name].shape, len(dates))
                 array[offset : offset + len(dates)] = stats[name]
             offset += len(dates)
 
@@ -310,133 +303,7 @@ class StatAggregator:
         stdev = np.sqrt(x)
 
         for j, name in enumerate(self.variables_names):
-            check_data_values(
-                np.array(
-                    [
-                        mean[j],
-                    ]
-                ),
-                name=name,
-                allow_nan=False,
-            )
-
-        return Summary(
-            minimum=minimum,
-            maximum=maximum,
-            mean=mean,
-            count=count,
-            sums=sums,
-            squares=squares,
-            stdev=stdev,
-            variables_names=self.variables_names,
-            has_nans=has_nans,
-        )
-
-
-class SummaryAggregator:
-    NAMES = ["minimum", "maximum", "sums", "squares", "count", "has_nans"]
-
-    def __init__(self, owner, dates, variables_names, allow_nan):
-        dates = sorted(dates)
-        dates = to_datetimes(dates)
-        assert dates, "No dates selected"
-        self.owner = owner
-        self.dates = dates
-        self.variables_names = variables_names
-        self.allow_nan = allow_nan
-
-        self.shape = (len(self.dates), len(self.variables_names))
-        LOG.info(f"Aggregating statistics on shape={self.shape}. Variables : {self.variables_names}")
-
-        self.minimum = np.full(self.shape, np.nan, dtype=np.float64)
-        self.maximum = np.full(self.shape, np.nan, dtype=np.float64)
-        self.sums = np.full(self.shape, np.nan, dtype=np.float64)
-        self.squares = np.full(self.shape, np.nan, dtype=np.float64)
-        self.count = np.full(self.shape, -1, dtype=np.int64)
-        self.has_nans = np.full(self.shape, False, dtype=np.bool_)
-
-        self._read()
-
-    def _read(self):
-        def check_type(a, b):
-            a = list(a)
-            b = list(b)
-            a = a[0] if a else None
-            b = b[0] if b else None
-            assert type(a) is type(b), (type(a), type(b))
-
-        found = set()
-        offset = 0
-        for _, _dates, stats in self.owner._gather_data():
-            for n in self.NAMES:
-                assert n in stats, (n, list(stats.keys()))
-            _dates = to_datetimes(_dates)
-            check_type(_dates, self.dates)
-            if found:
-                check_type(found, self.dates)
-                assert found.isdisjoint(_dates), "Duplicate dates found in precomputed statistics"
-
-            # filter dates
-            dates = set(_dates) & set(self.dates)
-
-            if not dates:
-                # dates have been completely filtered for this chunk
-                continue
-
-            # filter data
-            bitmap = np.isin(_dates, self.dates)
-            for k in self.NAMES:
-                stats[k] = stats[k][bitmap]
-
-            assert stats["minimum"].shape[0] == len(dates), (
-                stats["minimum"].shape,
-                len(dates),
-            )
-
-            # store data in self
-            found |= set(dates)
-            for name in self.NAMES:
-                array = getattr(self, name)
-                assert stats[name].shape[0] == len(dates), (
-                    stats[name].shape,
-                    len(dates),
-                )
-                array[offset : offset + len(dates)] = stats[name]
-            offset += len(dates)
-
-        for d in self.dates:
-            assert d in found, f"Statistics for date {d} not precomputed."
-        assert len(self.dates) == len(found), "Not all dates found in precomputed statistics"
-        assert len(self.dates) == offset, "Not all dates found in precomputed statistics."
-        LOG.info(f"Statistics for {len(found)} dates found.")
-
-    def aggregate(self):
-        minimum = np.nanmin(self.minimum, axis=0)
-        maximum = np.nanmax(self.maximum, axis=0)
-        sums = np.nansum(self.sums, axis=0)
-        squares = np.nansum(self.squares, axis=0)
-        count = np.nansum(self.count, axis=0)
-        has_nans = np.any(self.has_nans, axis=0)
-        mean = sums / count
-
-        assert sums.shape == count.shape == squares.shape == mean.shape == minimum.shape == maximum.shape
-
-        x = squares / count - mean * mean
-        # remove negative variance due to numerical errors
-        # x[- 1e-15 < (x / (np.sqrt(squares / count) + np.abs(mean))) < 0] = 0
-        check_variance(x, self.variables_names, minimum, maximum, mean, count, sums, squares)
-        stdev = np.sqrt(x)
-
-        for j, name in enumerate(self.variables_names):
-            check_data_values(
-                np.array(
-                    [
-                        mean[j],
-                    ]
-                ),
-                name=name,
-                allow_nan=False,
-            )
+            check_data_values(np.array([mean[j]]), name=name, allow_nan=False)
 
         return Summary(
             minimum=minimum,

anemoi/datasets/data/__init__.py

@@ -30,3 +30,10 @@ def open_dataset(*args, **kwargs):
     ds.arguments = {"args": args, "kwargs": kwargs}
     ds._check()
     return ds
+
+
+def list_dataset_names(*args, **kwargs):
+    ds = _open_dataset(*args, **kwargs)
+    names = set()
+    ds.get_dataset_names(names)
+    return sorted(names)

anemoi/datasets/data/dataset.py

@@ -226,3 +226,6 @@ class Dataset:
     @property
     def label(self):
         return self.__class__.__name__.lower()
+
+    def get_dataset_names(self, names):
+        raise NotImplementedError(self)

anemoi/datasets/data/forwards.py

@@ -103,6 +103,9 @@ class Forwards(Dataset):
             f"subclass_metadata_specific() must be implemented in derived class {self.__class__.__name__}"
         )
 
+    def get_dataset_names(self, names):
+        self.forward.get_dataset_names(names)
+
 
 class Combined(Forwards):
     def __init__(self, datasets):
@@ -193,6 +196,10 @@ class Combined(Forwards):
             offset += len(d)
         return result
 
+    def get_dataset_names(self, names):
+        for d in self.datasets:
+            d.get_dataset_names(names)
+
 
 class GivenAxis(Combined):
     """Given a given axis, combine the datasets along that axis."""

anemoi/datasets/data/masked.py

@@ -70,8 +70,12 @@ class Thinning(Masked):
         self.thinning = thinning
         self.method = method
 
-        latitudes = forward.latitudes.reshape(forward.field_shape)
-        longitudes = forward.longitudes.reshape(forward.field_shape)
+        shape = forward.field_shape
+        if len(shape) != 2:
+            raise ValueError("Thinning only works latitude/longitude fields")
+
+        latitudes = forward.latitudes.reshape(shape)
+        longitudes = forward.longitudes.reshape(shape)
         latitudes = latitudes[::thinning, ::thinning].flatten()
         longitudes = longitudes[::thinning, ::thinning].flatten()
 

anemoi/datasets/data/misc.py

@@ -49,7 +49,9 @@ def load_config():
     if CONFIG is not None:
         return CONFIG
 
-    conf = os.path.expanduser("~/.anemoi.toml")
+    conf = os.path.expanduser("~/.config/anemoi/settings.toml")
+    if not os.path.exists(conf):
+        conf = os.path.expanduser("~/.anemoi.toml")
 
     if os.path.exists(conf):
 

anemoi/datasets/data/select.py

@@ -23,15 +23,19 @@ LOG = logging.getLogger(__name__)
 class Select(Forwards):
     """Select a subset of the variables."""
 
-    def __init__(self, dataset, indices, title):
+    def __init__(self, dataset, indices, reason):
+
+        reason = reason.copy()
+
         while isinstance(dataset, Select):
             indices = [dataset.indices[i] for i in indices]
+            reason.update(dataset.reason)
             dataset = dataset.dataset
 
         self.dataset = dataset
         self.indices = list(indices)
         assert len(self.indices) > 0
-        self.title = title or {"indices": self.indices}
+        self.reason = reason or {"indices": self.indices}
 
         # Forward other properties to the main dataset
         super().__init__(dataset)
@@ -86,11 +90,11 @@ class Select(Forwards):
         return Source(self, index, self.dataset.source(self.indices[index]))
 
     def tree(self):
-        return Node(self, [self.dataset.tree()], **self.title)
+        return Node(self, [self.dataset.tree()], **self.reason)
 
     def subclass_metadata_specific(self):
         # return dict(indices=self.indices)
-        return {}
+        return self.reason
 
 
 class Rename(Forwards):

anemoi/datasets/data/statistics.py

@@ -39,3 +39,7 @@ class Statistics(Forwards):
 
     def tree(self):
         return Node(self, [self.forward.tree()])
+
+    def get_dataset_names(self, names):
+        super().get_dataset_names(names)
+        self._statistic.get_dataset_names(names)

anemoi/datasets/data/stores.py

@@ -6,6 +6,7 @@
 # nor does it submit to any jurisdiction.
 
 import logging
+import os
 import warnings
 from functools import cached_property
 
@@ -235,7 +236,11 @@ class Zarr(Dataset):
 
     @property
     def field_shape(self):
-        return tuple(self.z.attrs["field_shape"])
+        try:
+            return tuple(self.z.attrs["field_shape"])
+        except KeyError:
+            LOG.warning("No 'field_shape' in %r, assuming 1D fields", self)
+            return (self.shape[-1],)
 
     @property
     def frequency(self):
@@ -288,6 +293,10 @@ class Zarr(Dataset):
     def tree(self):
         return Node(self, [], path=self.path)
 
+    def get_dataset_names(self, names):
+        name, _ = os.path.splitext(os.path.basename(self.path))
+        names.add(name)
+
 
 class ZarrWithMissingDates(Zarr):
     def __init__(self, path):

{anemoi_datasets-0.3.6.dist-info → anemoi_datasets-0.3.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: anemoi-datasets
-Version: 0.3.6
+Version: 0.3.8
 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
@@ -223,7 +223,7 @@ Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Python: >=3.9
 License-File: LICENSE
-Requires-Dist: anemoi-utils[provenance] >=0.3
+Requires-Dist: anemoi-utils[provenance] >=0.3.4
 Requires-Dist: numpy
 Requires-Dist: pyyaml
 Requires-Dist: semantic-version

{anemoi_datasets-0.3.6.dist-info → anemoi_datasets-0.3.8.dist-info}/RECORD

@@ -1,21 +1,21 @@
-anemoi/datasets/__init__.py,sha256=DC7ttKT--pmhBQALX_Cn7P28dngsJucKi5y-Ydm28QM,700
+anemoi/datasets/__init__.py,sha256=Z1gqZWhecLcT0RZQqYBLlz01MUlUZd0kWEj_RavbITM,782
 anemoi/datasets/__main__.py,sha256=cLA2PidDTOUHaDGzd0_E5iioKYNe-PSTv567Y2fuwQk,723
-anemoi/datasets/_version.py,sha256=IKAQ4gPrCQ2FWMXOFRqouULC2EQI1zCb4iXHsnfbmTQ,411
+anemoi/datasets/_version.py,sha256=FAr0t5Ub_Olk5Ke3Xi4Oeu5jcLPAvKpdk9naAtMuou8,411
 anemoi/datasets/grids.py,sha256=3YBMMJodgYhavarXPAlMZHaMtDT9v2IbTmAXZTqf8Qo,8481
 anemoi/datasets/commands/__init__.py,sha256=qAybFZPBBQs0dyx7dZ3X5JsLpE90pwrqt1vSV7cqEIw,706
 anemoi/datasets/commands/compare.py,sha256=p2jQOAC3JhScCLF0GjTCO8goYLWLN8p7vzy_gf5fFcI,1473
-anemoi/datasets/commands/copy.py,sha256=fba-zjD0iTHHXHhPEcm8VhDzsXQXDUxlbtTA1TovyT0,9991
+anemoi/datasets/commands/copy.py,sha256=SxAeN51owyN5gwtwpt30xhJSIJRlJb9YOUt_4K4m-D8,11780
 anemoi/datasets/commands/create.py,sha256=POdOsVDlvRrHFFkI3SNXNgNIbSxkVUUPMoo660x7Ma0,987
 anemoi/datasets/commands/inspect.py,sha256=G3fzcgiLaU8jln7GKvgamN7Y06-qC_JnFw2SbNn1_E4,18646
 anemoi/datasets/commands/scan.py,sha256=HxsLdCgBMSdEXjlJfPq5M_9LxXHHQIoZ1ZEHO_AoPgA,2881
 anemoi/datasets/compute/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 anemoi/datasets/compute/recentre.py,sha256=GRxI6rY_KyXJnZGPxU_UO9YDb-rY_raK70Fiwv1mjhs,4792
-anemoi/datasets/create/__init__.py,sha256=jji65Zni5aPTvS269fAMix4pN9ukmSoK0z5SVsbpr5E,5807
+anemoi/datasets/create/__init__.py,sha256=Q8uXUdbE-SRYYaZd5cPQ2RVbSoHnGX7-eKdOJHYVhDk,5951
 anemoi/datasets/create/check.py,sha256=DLjw-eyaCNxPhoKFsP4Yn_l3SIr57YHdyPR-tE5vx80,5791
 anemoi/datasets/create/chunks.py,sha256=YEDcr0K2KiiceSTiBuZzj0TbRbzZ9J546XO7rrrTFQw,2441
 anemoi/datasets/create/config.py,sha256=uLIp1WHg3hbqwwMV9EepMwJQsXJAGImkbo0okBeEVd4,7683
 anemoi/datasets/create/input.py,sha256=3G7sqdn7R1pLBeeswXwwi8VRAHrBnjq1PdRYHJBe594,27741
-anemoi/datasets/create/loaders.py,sha256=Y9HwH_yPDvnrOTpXVwZxB6VKqGYrHC4xMKhizUhR4lU,30081
+anemoi/datasets/create/loaders.py,sha256=-fJ9qKjsCd8Wvnobn34WsQpE9uAjon5M4REgCpW5q_w,30594
 anemoi/datasets/create/patch.py,sha256=xjCLhvIQKRqmypsKInRU1CvFh1uoaB3YGSQP1UVZZik,3682
 anemoi/datasets/create/persistent.py,sha256=nT8gvhVPdI1H3zW_F7uViGKIlQQ94jCDrMSWTmhQ2_A,4290
 anemoi/datasets/create/size.py,sha256=A1w6RkaL0L9IlwIdmYsCTJTecmY_QtvbkGf__jvQle0,1068
@@ -31,43 +31,43 @@ anemoi/datasets/create/functions/filters/rename.py,sha256=cGoHr-IS-PhYEtZvXDpH03
 anemoi/datasets/create/functions/filters/rotate_winds.py,sha256=fUdh8ILcMzMzckGlvwzdgG-c7w5R9NnWfaijp28Bf5M,4092
 anemoi/datasets/create/functions/filters/unrotate_winds.py,sha256=nsa3EHly8ppWd2WH4ROoMczM8WFu5qKaIhO_UFcL9TY,3502
 anemoi/datasets/create/functions/sources/__init__.py,sha256=Xe9G54CKvCI3ji-7k0R5l0WZZdhlydRgawsXuBcX_hg,379
-anemoi/datasets/create/functions/sources/accumulations.py,sha256=li1tpEew1XUv4sJzNCFYJHx1bve8LuXhEv-mgDoUqPE,12739
+anemoi/datasets/create/functions/sources/accumulations.py,sha256=klbp-akoZlOk9jByDFsgPfHRCdfLvpatTLMxDPZaNZc,12943
 anemoi/datasets/create/functions/sources/constants.py,sha256=aqquu6HDc8t-zsF9KRFLaj0eV4S0UPZ59BVna8E3bU8,785
 anemoi/datasets/create/functions/sources/empty.py,sha256=SBuAfC33imbfcRnFnnOR44y8Q3KSQcqx3juIcXfCa3c,481
 anemoi/datasets/create/functions/sources/forcings.py,sha256=EVcdu8puMSW451qj3LKCWWXaSf2LlmF8YXVs8hSMxkU,643
 anemoi/datasets/create/functions/sources/grib.py,sha256=YQNuGnlh2EYb2NIHYpzlipwUTmOhrmyQtP3zgk8MAUU,1661
 anemoi/datasets/create/functions/sources/hindcasts.py,sha256=0Psnsx2J0cRLMpJuNN-gESm1xJFC1gmQzI8sdnXCoYE,13042
-anemoi/datasets/create/functions/sources/mars.py,sha256=Jau-ceN_cI3Z2-uql92iS4-Emh9Pie7omdRkFB5oe1I,4025
+anemoi/datasets/create/functions/sources/mars.py,sha256=JWsbzyoXF95HPk2VWzmX53f_SJwXhKkaJvXtXJMGLig,5285
 anemoi/datasets/create/functions/sources/netcdf.py,sha256=kic6PH7SAK3gseXChD38IDXw6Zcg2zhF4SeDXB2LQ8Q,2084
 anemoi/datasets/create/functions/sources/opendap.py,sha256=T0CPinscfafrVLaye5ue-PbiCNbcNqf_3m6pphN9rCU,543
 anemoi/datasets/create/functions/sources/recentre.py,sha256=t07LIXG3Hp9gmPkPriILVt86TxubsHyS1EL1lzwgtXY,1810
 anemoi/datasets/create/functions/sources/source.py,sha256=hPQnV_6UIxFw97uRKcTA8TplcgG1kC8NlFHoEaaLet4,1418
 anemoi/datasets/create/functions/sources/tendencies.py,sha256=kwS_GZt8R9kpfs5RrvxPb0Gj-5nDP0sgJgfSRCAwwww,4057
-anemoi/datasets/create/statistics/__init__.py,sha256=X50drgE-ltuNe7bSIyvyeC4GeTqGTQGbglh2-2aVWKE,15445
+anemoi/datasets/create/statistics/__init__.py,sha256=eXyOdlgXBt6QdVWM7ZVyUWdFMv6iNsFefkjvOVvZAlQ,11010
 anemoi/datasets/create/statistics/summary.py,sha256=sgmhA24y3VRyjmDUgTnPIqcHSlWBbFA0qynx6gJ9Xw8,3370
-anemoi/datasets/data/__init__.py,sha256=tacn6K_VZ-pYhLmGePG5sze8kmqGpqscYb-bMyQnWtk,888
+anemoi/datasets/data/__init__.py,sha256=to9L_RZVQ4OgyHUpX6lcvt4GqJdZjBa5HCTaWx1aGKo,1046
 anemoi/datasets/data/concat.py,sha256=AkpyOs16OjW7X0cdyYFQfWSCV6dteXBp-x9WlokO-DI,3550
-anemoi/datasets/data/dataset.py,sha256=UDnidq2amyCT2COH05pGfDCJcmkdMj1ubtHk9cl-qcE,7384
+anemoi/datasets/data/dataset.py,sha256=LBUwWhwcAcovLv0FOLT-rA-yNZhcBFUMc03BfVh7UFc,7465
 anemoi/datasets/data/debug.css,sha256=z2X_ZDSnZ9C3pyZPWnQiEyAxuMxUaxJxET4oaCImTAQ,211
 anemoi/datasets/data/debug.py,sha256=PcyrjgxaLzeb_vf12pvUtPPVvBRHNm1SimythZvqsP4,6303
 anemoi/datasets/data/ensemble.py,sha256=AsP7Xx0ZHLoZs6a4EC0jtyGYIcOvZvvKXhgNsIvqIN8,1137
-anemoi/datasets/data/forwards.py,sha256=t9YQCN7j75VMInt0uP9JUJoh1klF1Z1xnwy5_kDMDQs,7700
+anemoi/datasets/data/forwards.py,sha256=UZOOMUblGS21aaPoFfQa0ONSUaxkqlZQF3KGRhlCr9I,7899
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{anemoi_datasets-0.3.6.dist-info → anemoi_datasets-0.3.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.1)
 Root-Is-Purelib: true
 Tag: py3-none-any