anemoi-utils 0.4.4__py3-none-any.whl → 0.4.5__py3-none-any.whl

anemoi/utils/s3.py

@@ -7,554 +7,57 @@
 # granted to it by virtue of its status as an intergovernmental organisation
 # nor does it submit to any jurisdiction.
 
+import warnings
 
-"""This module provides functions to upload, download, list and delete files and folders on S3.
-The functions of this package expect that the AWS credentials are set up in the environment
-typicaly by setting the `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables or
-by creating a `~/.aws/credentials` file. It is also possible to set the `endpoint_url` in the same file
-to use a different S3 compatible service::
+from .remote import transfer
+from .remote.s3 import delete as delete_
+from .remote.s3 import s3_client as s3_client_
 
-    [default]
-    endpoint_url = https://some-storage.somewhere.world
-    aws_access_key_id = xxxxxxxxxxxxxxxxxxxxxxxx
-    aws_secret_access_key = xxxxxxxxxxxxxxxxxxxxxxxx
+warnings.warn(
+    "The anemoi.utils.s3 module is deprecated and will be removed in a future release. "
+    "Please use the 'anemoi.utils.remote' or 'anemoi.utils.remote.s3' module instead.",
+    DeprecationWarning,
+    stacklevel=2,
+)
 
-Alternatively, the `endpoint_url`, and keys can be set in one of
-the `~/.config/anemoi/settings.toml`
-or `~/.config/anemoi/settings-secrets.toml` files.
 
-"""
-
-import concurrent.futures
-import logging
-import os
-import threading
-from copy import deepcopy
-
-import tqdm
-
-from .config import load_config
-from .humanize import bytes_to_human
-
-LOGGER = logging.getLogger(__name__)
-
-
-# s3_clients are not thread-safe, so we need to create a new client for each thread
-
-thread_local = threading.local()
-
-
-def s3_client(bucket, region=None):
-    import boto3
-    from botocore import UNSIGNED
-    from botocore.client import Config
-
-    if not hasattr(thread_local, "s3_clients"):
-        thread_local.s3_clients = {}
-
-    key = f"{bucket}-{region}"
-
-    boto3_config = dict(max_pool_connections=25)
-
-    if key in thread_local.s3_clients:
-        return thread_local.s3_clients[key]
-
-    boto3_config = dict(max_pool_connections=25)
-
-    if region:
-        # This is using AWS
-
-        options = {"region_name": region}
-
-        # Anonymous access
-        if not (
-            os.path.exists(os.path.expanduser("~/.aws/credentials"))
-            or ("AWS_ACCESS_KEY_ID" in os.environ and "AWS_SECRET_ACCESS_KEY" in os.environ)
-        ):
-            boto3_config["signature_version"] = UNSIGNED
-
-    else:
-
-        # We may be accessing a different S3 compatible service
-        # Use anemoi.config to get the configuration
-
-        options = {}
-        config = load_config(secrets=["aws_access_key_id", "aws_secret_access_key"])
-
-        cfg = config.get("object-storage", {})
-        for k, v in cfg.items():
-            if isinstance(v, (str, int, float, bool)):
-                options[k] = v
-
-        for k, v in cfg.get(bucket, {}).items():
-            if isinstance(v, (str, int, float, bool)):
-                options[k] = v
-
-        type = options.pop("type", "s3")
-        if type != "s3":
-            raise ValueError(f"Unsupported object storage type {type}")
-
-        if "config" in options:
-            boto3_config.update(options["config"])
-            del options["config"]
-            from botocore.client import Config
-
-    options["config"] = Config(**boto3_config)
-
-    thread_local.s3_clients[key] = boto3.client("s3", **options)
-
-    return thread_local.s3_clients[key]
-
-
-def _ignore(number_of_files, total_size, total_transferred, transfering):
-    pass
-
-
-class Transfer:
-
-    def transfer_folder(self, *, source, target, overwrite=False, resume=False, verbosity=1, threads=1, progress=None):
-        assert verbosity == 1, verbosity
-
-        if progress is None:
-            progress = _ignore
-
-        # from boto3.s3.transfer import TransferConfig
-        # config = TransferConfig(use_threads=False)
-        config = None
-        with concurrent.futures.ThreadPoolExecutor(max_workers=threads) as executor:
-            try:
-                if verbosity > 0:
-                    LOGGER.info(f"{self.action} {source} to {target}")
-
-                total_size = 0
-                total_transferred = 0
-
-                futures = []
-                for name in self.list_source(source):
-
-                    futures.append(
-                        executor.submit(
-                            self.transfer_file,
-                            source=self.source_path(name, source),
-                            target=self.target_path(name, source, target),
-                            overwrite=overwrite,
-                            resume=resume,
-                            verbosity=verbosity - 1,
-                            config=config,
-                        )
-                    )
-                    total_size += self.source_size(name)
-
-                    if len(futures) % 10000 == 0:
-
-                        progress(len(futures), total_size, 0, False)
-
-                        if verbosity > 0:
-                            LOGGER.info(f"Preparing transfer, {len(futures):,} files... ({bytes_to_human(total_size)})")
-                        done, _ = concurrent.futures.wait(
-                            futures,
-                            timeout=0.001,
-                            return_when=concurrent.futures.FIRST_EXCEPTION,
-                        )
-                        # Trigger exceptions if any
-                        for future in done:
-                            future.result()
-
-                number_of_files = len(futures)
-                progress(number_of_files, total_size, 0, True)
-
-                if verbosity > 0:
-                    LOGGER.info(f"{self.action} {number_of_files:,} files ({bytes_to_human(total_size)})")
-                    with tqdm.tqdm(total=total_size, unit="B", unit_scale=True, unit_divisor=1024) as pbar:
-                        for future in concurrent.futures.as_completed(futures):
-                            size = future.result()
-                            pbar.update(size)
-                            total_transferred += size
-                            progress(number_of_files, total_size, total_transferred, True)
-                else:
-                    for future in concurrent.futures.as_completed(futures):
-                        size = future.result()
-                        total_transferred += size
-                        progress(number_of_files, total_size, total_transferred, True)
-
-            except Exception:
-                executor.shutdown(wait=False, cancel_futures=True)
-                raise
-
-
-class Upload(Transfer):
-    action = "Uploading"
-
-    def list_source(self, source):
-        for root, _, files in os.walk(source):
-            for file in files:
-                yield os.path.join(root, file)
-
-    def source_path(self, local_path, source):
-        return local_path
-
-    def target_path(self, source_path, source, target):
-        relative_path = os.path.relpath(source_path, source)
-        s3_path = os.path.join(target, relative_path)
-        return s3_path
-
-    def source_size(self, local_path):
-        return os.path.getsize(local_path)
-
-    def transfer_file(self, source, target, overwrite, resume, verbosity, progress=None, config=None):
-        try:
-            return self._transfer_file(source, target, overwrite, resume, verbosity, config=config)
-        except Exception as e:
-            LOGGER.exception(f"Error transferring {source} to {target}")
-            LOGGER.error(e)
-            raise
-
-    def _transfer_file(self, source, target, overwrite, resume, verbosity, config=None):
-
-        from botocore.exceptions import ClientError
-
-        assert target.startswith("s3://")
-
-        _, _, bucket, key = target.split("/", 3)
-        s3 = s3_client(bucket)
-
-        size = os.path.getsize(source)
-
-        if verbosity > 0:
-            LOGGER.info(f"{self.action} {source} to {target} ({bytes_to_human(size)})")
-
-        try:
-            results = s3.head_object(Bucket=bucket, Key=key)
-            remote_size = int(results["ContentLength"])
-        except ClientError as e:
-            if e.response["Error"]["Code"] != "404":
-                raise
-            remote_size = None
-
-        if remote_size is not None:
-            if remote_size != size:
-                LOGGER.warning(
-                    f"{target} already exists, but with different size, re-uploading (remote={remote_size}, local={size})"
-                )
-            elif resume:
-                # LOGGER.info(f"{target} already exists, skipping")
-                return size
-
-        if remote_size is not None and not overwrite and not resume:
-            raise ValueError(f"{target} already exists, use 'overwrite' to replace or 'resume' to skip")
-
-        if verbosity > 0:
-            with tqdm.tqdm(total=size, unit="B", unit_scale=True, unit_divisor=1024, leave=False) as pbar:
-                s3.upload_file(source, bucket, key, Callback=lambda x: pbar.update(x), Config=config)
-        else:
-            s3.upload_file(source, bucket, key, Config=config)
-
-        return size
-
-
-class Download(Transfer):
-    action = "Downloading"
-
-    def list_source(self, source):
-        yield from _list_objects(source)
-
-    def source_path(self, s3_object, source):
-        _, _, bucket, _ = source.split("/", 3)
-        return f"s3://{bucket}/{s3_object['Key']}"
-
-    def target_path(self, s3_object, source, target):
-        _, _, _, folder = source.split("/", 3)
-        local_path = os.path.join(target, os.path.relpath(s3_object["Key"], folder))
-        os.makedirs(os.path.dirname(local_path), exist_ok=True)
-        return local_path
-
-    def source_size(self, s3_object):
-        return s3_object["Size"]
-
-    def transfer_file(self, source, target, overwrite, resume, verbosity, progress=None, config=None):
-        try:
-            return self._transfer_file(source, target, overwrite, resume, verbosity, config=config)
-        except Exception as e:
-            LOGGER.exception(f"Error transferring {source} to {target}")
-            LOGGER.error(e)
-            raise
-
-    def _transfer_file(self, source, target, overwrite, resume, verbosity, config=None):
-        # from boto3.s3.transfer import TransferConfig
-
-        _, _, bucket, key = source.split("/", 3)
-        s3 = s3_client(bucket)
-
-        try:
-            response = s3.head_object(Bucket=bucket, Key=key)
-        except s3.exceptions.ClientError as e:
-            if e.response["Error"]["Code"] == "404":
-                raise ValueError(f"{source} does not exist ({bucket}, {key})")
-            raise
-
-        size = int(response["ContentLength"])
-
-        if verbosity > 0:
-            LOGGER.info(f"Downloading {source} to {target} ({bytes_to_human(size)})")
-
-        if overwrite:
-            resume = False
-
-        if resume:
-            if os.path.exists(target):
-                local_size = os.path.getsize(target)
-                if local_size != size:
-                    LOGGER.warning(
-                        f"{target} already with different size, re-downloading (remote={size}, local={size})"
-                    )
-                else:
-                    # if verbosity > 0:
-                    #     LOGGER.info(f"{target} already exists, skipping")
-                    return size
-
-        if os.path.exists(target) and not overwrite:
-            raise ValueError(f"{target} already exists, use 'overwrite' to replace or 'resume' to skip")
-
-        if verbosity > 0:
-            with tqdm.tqdm(total=size, unit="B", unit_scale=True, unit_divisor=1024, leave=False) as pbar:
-                s3.download_file(bucket, key, target, Callback=lambda x: pbar.update(x), Config=config)
-        else:
-            s3.download_file(bucket, key, target, Config=config)
-
-        return size
+def s3_client(*args, **kwargs):
+    warnings.warn(
+        "The 's3_client' function (from anemoi.utils.s3 import s3_client) function is deprecated and will be removed in a future release. "
+        "Please use the 's3_client' function (from anemoi.utils.remote.s3 import s3_client) instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return s3_client_(*args, **kwargs)
 
 
 def upload(source, target, *, overwrite=False, resume=False, verbosity=1, progress=None, threads=1) -> None:
-    """Upload a file or a folder to S3.
-
-    Parameters
-    ----------
-    source : str
-        A path to a file or a folder to upload.
-    target : str
-        A URL to a file or a folder on S3. The url should start with 's3://'.
-    overwrite : bool, optional
-        If the data is alreay on S3 it will be overwritten, by default False
-    resume : bool, optional
-        If the data is alreay on S3 it will not be uploaded, unless the remote file
-        has a different size, by default False
-    verbosity : int, optional
-        The level of verbosity, by default 1
-    progress: callable, optional
-        A callable that will be called with the number of files, the total size of the files, the total size
-        transferred and a boolean indicating if the transfer has started. By default None
-    threads : int, optional
-        The number of threads to use when uploading a directory, by default 1
-    """
-
-    uploader = Upload()
-
-    if os.path.isdir(source):
-        uploader.transfer_folder(
-            source=source,
-            target=target,
-            overwrite=overwrite,
-            resume=resume,
-            verbosity=verbosity,
-            progress=progress,
-            threads=threads,
-        )
-    else:
-        uploader.transfer_file(
-            source=source,
-            target=target,
-            overwrite=overwrite,
-            resume=resume,
-            verbosity=verbosity,
-            progress=progress,
-        )
-
-
-def download(source, target, *, overwrite=False, resume=False, verbosity=1, progress=None, threads=1) -> None:
-    """Download a file or a folder from S3.
-
-    Parameters
-    ----------
-    source : str
-        The URL of a file or a folder on S3. The url should start with 's3://'. If the URL ends with a '/' it is
-        assumed to be a folder, otherwise it is assumed to be a file.
-    target : str
-        The local path where the file or folder will be downloaded.
-    overwrite : bool, optional
-        If false, files which have already been download will be skipped, unless their size
-        does not match their size on S3 , by default False
-    resume : bool, optional
-        If the data is alreay on local it will not be downloaded, unless the remote file
-        has a different size, by default False
-    verbosity : int, optional
-        The level of verbosity, by default 1
-    progress: callable, optional
-        A callable that will be called with the number of files, the total size of the files, the total size
-        transferred and a boolean indicating if the transfer has started. By default None
-    threads : int, optional
-        The number of threads to use when downloading a directory, by default 1
-    """
-    assert source.startswith("s3://")
-
-    downloader = Download()
-
-    if source.endswith("/"):
-        downloader.transfer_folder(
-            source=source,
-            target=target,
-            overwrite=overwrite,
-            resume=resume,
-            verbosity=verbosity,
-            progress=progress,
-            threads=threads,
-        )
-    else:
-        downloader.transfer_file(
-            source=source,
-            target=target,
-            overwrite=overwrite,
-            resume=resume,
-            verbosity=verbosity,
-            progress=progress,
-        )
-
-
-def _list_objects(target, batch=False):
-    _, _, bucket, prefix = target.split("/", 3)
-    s3 = s3_client(bucket)
-
-    paginator = s3.get_paginator("list_objects_v2")
-
-    for page in paginator.paginate(Bucket=bucket, Prefix=prefix):
-        if "Contents" in page:
-            objects = deepcopy(page["Contents"])
-            if batch:
-                yield objects
-            else:
-                yield from objects
-
-
-def _delete_folder(target) -> None:
-    _, _, bucket, _ = target.split("/", 3)
-    s3 = s3_client(bucket)
-
-    total = 0
-    for batch in _list_objects(target, batch=True):
-        LOGGER.info(f"Deleting {len(batch):,} objects from {target}")
-        s3.delete_objects(Bucket=bucket, Delete={"Objects": [{"Key": o["Key"]} for o in batch]})
-        total += len(batch)
-        LOGGER.info(f"Deleted {len(batch):,} objects (total={total:,})")
-
-
-def _delete_file(target) -> None:
-    from botocore.exceptions import ClientError
-
-    _, _, bucket, key = target.split("/", 3)
-    s3 = s3_client(bucket)
-
-    try:
-        s3.head_object(Bucket=bucket, Key=key)
-        exits = True
-    except ClientError as e:
-        if e.response["Error"]["Code"] != "404":
-            raise
-        exits = False
-
-    if not exits:
-        LOGGER.warning(f"{target} does not exist. Did you mean to delete a folder? Then add a trailing '/'")
-        return
-
-    LOGGER.info(f"Deleting {target}")
-    s3.delete_object(Bucket=bucket, Key=key)
-    LOGGER.info(f"{target} is deleted")
-
-
-def delete(target) -> None:
-    """Delete a file or a folder from S3.
-
-    Parameters
-    ----------
-    target : str
-        The URL of a file or a folder on S3. The url should start with 's3://'. If the URL ends with a '/' it is
-        assumed to be a folder, otherwise it is assumed to be a file.
-    """
-
-    assert target.startswith("s3://")
-
-    if target.endswith("/"):
-        _delete_folder(target)
-    else:
-        _delete_file(target)
-
-
-def list_folder(folder) -> list:
-    """List the sub folders in a folder on S3.
-
-    Parameters
-    ----------
-    folder : str
-        The URL of a folder on S3. The url should start with 's3://'.
-
-    Returns
-    -------
-    list
-        A list of the subfolders names in the folder.
-    """
-
-    assert folder.startswith("s3://")
-    if not folder.endswith("/"):
-        folder += "/"
-
-    _, _, bucket, prefix = folder.split("/", 3)
-
-    s3 = s3_client(bucket)
-    paginator = s3.get_paginator("list_objects_v2")
-
-    for page in paginator.paginate(Bucket=bucket, Prefix=prefix, Delimiter="/"):
-        if "CommonPrefixes" in page:
-            yield from [folder + _["Prefix"] for _ in page.get("CommonPrefixes")]
-
-
-def object_info(target) -> dict:
-    """Get information about an object on S3.
-
-    Parameters
-    ----------
-    target : str
-        The URL of a file or a folder on S3. The url should start with 's3://'.
-
-    Returns
-    -------
-    dict
-        A dictionary with information about the object.
-    """
-
-    _, _, bucket, key = target.split("/", 3)
-    s3 = s3_client(bucket)
-
-    try:
-        return s3.head_object(Bucket=bucket, Key=key)
-    except s3.exceptions.ClientError as e:
-        if e.response["Error"]["Code"] == "404":
-            raise ValueError(f"{target} does not exist")
-        raise
-
-
-def object_acl(target) -> dict:
-    """Get information about an object's ACL on S3.
-
-    Parameters
-    ----------
-    target : str
-        The URL of a file or a folder on S3. The url should start with 's3://'.
-
-    Returns
-    -------
-    dict
-        A dictionary with information about the object's ACL.
-    """
-
-    _, _, bucket, key = target.split("/", 3)
-    s3 = s3_client()
-
-    return s3.get_object_acl(Bucket=bucket, Key=key)
+    warnings.warn(
+        "The 'upload' function (from anemoi.utils.s3 import upload) function is deprecated and will be removed in a future release. "
+        "Please use the 'transfer' function (from anemoi.utils.remote import transfer) instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return transfer(
+        source, target, overwrite=overwrite, resume=resume, verbosity=verbosity, progress=progress, threads=threads
+    )
+
+
+def download(*args, **kwargs):
+    warnings.warn(
+        "The 'download' function (from anemoi.utils.s3 import download) function is deprecated and will be removed in a future release. "
+        "Please use the 'transfer' function (from anemoi.utils.remote import transfer) instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return transfer(*args, **kwargs)
+
+
+def delete(*args, **kwargs):
+    warnings.warn(
+        "The 'delete' function (from anemoi.utils.s3 import delete) function is deprecated and will be removed in a future release. "
+        "Please use the 'transfer' function (from anemoi.utils.remote.s3 import delete) instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return delete_(*args, **kwargs)

{anemoi_utils-0.4.4.dist-info → anemoi_utils-0.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: anemoi-utils
-Version: 0.4.4
+Version: 0.4.5
 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
@@ -219,6 +219,7 @@ 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

anemoi_utils-0.4.5.dist-info/RECORD

@@ -0,0 +1,32 @@
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+anemoi/utils/__main__.py,sha256=5NW2A3OgTimB4ptwYThivIRSeCrvabMuvnr8mmnVx0E,715
+anemoi/utils/_version.py,sha256=XyejXnBNtqNdR37CiSnJ022K8vUHKAlzN9lbcpmmftA,411
+anemoi/utils/caching.py,sha256=0cznpvaaox14NSVi-Q3PqumfuGtXo0YNcEFwDPxvMZw,1948
+anemoi/utils/checkpoints.py,sha256=q8QqKlZ6qChjzEfq7KM1gVXuyqgsVRGIb4dJFtkGk58,7774
+anemoi/utils/cli.py,sha256=rmMP60VY3em99rQP6TCrKibMngWwVe5h_0GDcf16c5U,4117
+anemoi/utils/compatibility.py,sha256=0_nIcbdQbNMrS6AkqrBgJGJlSJXW8R23ncaZaDwdJ4c,2190
+anemoi/utils/config.py,sha256=Fpy4wzj3dahTwwO75Iet6zmQQFGmTvhXml6-EsTEvgk,9873
+anemoi/utils/dates.py,sha256=wwYD5_QI7EWY_jhpENNYtL5O7fjwYkzmqHkNoayvmrY,12452
+anemoi/utils/grib.py,sha256=zBICyOsYtR_9px1C5UDT6wL_D6kiIhUi_00kjFmas5c,3047
+anemoi/utils/hindcasts.py,sha256=OUOY2nDa3LBnzJ3ncgANzJDapouh82KgVyofDAu7K_Q,1426
+anemoi/utils/humanize.py,sha256=tSQkiUHiDj3VYk-DeruHp9P79sJO1b0whsPBphqy9qA,16627
+anemoi/utils/provenance.py,sha256=SqOiNoY1y36Zec83Pjt7OhihbwxMyknscfmogHCuriA,10894
+anemoi/utils/registry.py,sha256=I1r7grsIEsqAoJ9LPxfWMj10EoMazxRb4d8FPWdHsqk,3903
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