diff --git a/mkdocs/docs/configuration.md b/mkdocs/docs/configuration.md index 1269e34a83..2ed58091bb 100644 --- a/mkdocs/docs/configuration.md +++ b/mkdocs/docs/configuration.md @@ -340,8 +340,8 @@ catalog: -!!! warning "Deprecated Properties" - `profile_name`, `region_name`, `botocore_session`, `aws_access_key_id`, `aws_secret_access_key`, `aws_session_token` are deprecated and will be removed in 0.8.0: +!!! warning "Removed Properties" + The properties `profile_name`, `region_name`, `botocore_session`, `aws_access_key_id`, `aws_secret_access_key`, and `aws_session_token` were deprecated and removed in 0.8.0 @@ -396,8 +396,8 @@ catalog: -!!! warning "Deprecated Properties" - `profile_name`, `region_name`, `botocore_session`, `aws_access_key_id`, `aws_secret_access_key`, `aws_session_token` are deprecated and will be removed in 0.8.0: +!!! warning "Removed Properties" + The properties `profile_name`, `region_name`, `botocore_session`, `aws_access_key_id`, `aws_secret_access_key`, and `aws_session_token` were deprecated and removed in 0.8.0 diff --git a/mkdocs/requirements.txt b/mkdocs/requirements.txt index 936a5455f0..290bc27ad9 100644 --- a/mkdocs/requirements.txt +++ b/mkdocs/requirements.txt @@ -23,6 +23,6 @@ mkdocstrings-python==1.11.1 mkdocs-literate-nav==0.6.1 mkdocs-autorefs==1.2.0 mkdocs-gen-files==0.5.0 -mkdocs-material==9.5.36 +mkdocs-material==9.5.42 mkdocs-material-extensions==1.3.1 mkdocs-section-index==0.3.9 diff --git a/poetry.lock b/poetry.lock index 0a82824b63..e5c6b288cc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -25,24 +25,24 @@ tests = ["arrow", "dask[dataframe]", "docker", "pytest", "pytest-mock"] [[package]] name = "aiobotocore" -version = "2.15.0" +version = "2.15.2" description = "Async client for aws services using botocore and aiohttp" optional = true python-versions = ">=3.8" files = [ - {file = "aiobotocore-2.15.0-py3-none-any.whl", hash = "sha256:6d0b4a51d70bc33b1b4eba411076b0cc979aecbdad8e084bab202202423c0725"}, - {file = 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comprehensive WSGI web application library." optional = false python-versions = ">=3.8" files = [ - {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"}, - {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"}, + {file = "werkzeug-3.0.6-py3-none-any.whl", hash = "sha256:1bc0c2310d2fbb07b1dd1105eba2f7af72f322e1e455f2f93c993bee8c8a5f17"}, + {file = "werkzeug-3.0.6.tar.gz", hash = "sha256:a8dd59d4de28ca70471a34cba79bed5f7ef2e036a76b3ab0835474246eb41f8d"}, ] [package.dependencies] @@ -4501,14 +4519,14 @@ cffi = ["cffi (>=1.11)"] [extras] adlfs = ["adlfs"] daft = ["getdaft"] -duckdb = ["duckdb", "numpy", "pyarrow"] +duckdb = ["duckdb", "pyarrow"] dynamodb = ["boto3"] gcsfs = ["gcsfs"] glue = ["boto3", "mypy-boto3-glue"] hive = ["thrift"] -pandas = ["numpy", "pandas", "pyarrow"] -pyarrow = ["numpy", "pyarrow"] -ray = ["numpy", "pandas", "pyarrow", "ray", "ray"] +pandas = ["pandas", "pyarrow"] +pyarrow = ["pyarrow"] +ray = ["pandas", "pyarrow", "ray", "ray"] s3fs = ["s3fs"] snappy = ["python-snappy"] sql-postgres = ["psycopg2-binary", "sqlalchemy"] @@ -4518,4 +4536,4 @@ zstandard = ["zstandard"] [metadata] lock-version = "2.0" python-versions = "^3.9, <3.13, !=3.9.7" -content-hash = "5cdebb3402937b7a82cc7688a322b8e3ebd8cdd574feef50e813ac26571057c5" +content-hash = "e256d722105033e816531d539c1e110c6779bffbbbb91c44bfea99d1cb7fa0a8" diff --git a/pyiceberg/__init__.py b/pyiceberg/__init__.py index 6a71a4d567..42c6e12f1b 100644 --- a/pyiceberg/__init__.py +++ b/pyiceberg/__init__.py @@ -15,4 +15,4 @@ # specific language governing permissions and limitations # under the License. -__version__ = "0.7.1" +__version__ = "0.8.0" diff --git a/pyiceberg/catalog/__init__.py b/pyiceberg/catalog/__init__.py index 7eb8b02d40..2104fcab7a 100644 --- a/pyiceberg/catalog/__init__.py +++ b/pyiceberg/catalog/__init__.py @@ -106,21 +106,6 @@ re.X, ) -DEPRECATED_PROFILE_NAME = "profile_name" -DEPRECATED_REGION = "region_name" -DEPRECATED_BOTOCORE_SESSION = "botocore_session" -DEPRECATED_ACCESS_KEY_ID = "aws_access_key_id" -DEPRECATED_SECRET_ACCESS_KEY = "aws_secret_access_key" -DEPRECATED_SESSION_TOKEN = "aws_session_token" -DEPRECATED_PROPERTY_NAMES = { - DEPRECATED_PROFILE_NAME, - DEPRECATED_REGION, - DEPRECATED_BOTOCORE_SESSION, - DEPRECATED_ACCESS_KEY_ID, - DEPRECATED_SECRET_ACCESS_KEY, - DEPRECATED_SESSION_TOKEN, -} - class CatalogType(Enum): REST = "rest" @@ -794,14 +779,6 @@ class MetastoreCatalog(Catalog, ABC): def __init__(self, name: str, **properties: str): super().__init__(name, **properties) - for property_name in DEPRECATED_PROPERTY_NAMES: - if self.properties.get(property_name): - deprecation_message( - deprecated_in="0.7.0", - removed_in="0.8.0", - help_message=f"The property {property_name} is deprecated. Please use properties that start with client., glue., and dynamo. instead", - ) - def create_table_transaction( self, identifier: Union[str, Identifier], @@ -1011,4 +988,4 @@ def _empty_table_metadata() -> TableMetadata: Returns: TableMetadata: An empty TableMetadata instance. """ - return TableMetadataV1(location="", last_column_id=-1, schema=Schema()) + return TableMetadataV1.model_construct(last_column_id=-1, schema=Schema()) diff --git a/pyiceberg/catalog/dynamodb.py b/pyiceberg/catalog/dynamodb.py index 59cbe8ce28..b999df218a 100644 --- a/pyiceberg/catalog/dynamodb.py +++ b/pyiceberg/catalog/dynamodb.py @@ -30,12 +30,6 @@ import boto3 from pyiceberg.catalog import ( - DEPRECATED_ACCESS_KEY_ID, - DEPRECATED_BOTOCORE_SESSION, - DEPRECATED_PROFILE_NAME, - DEPRECATED_REGION, - DEPRECATED_SECRET_ACCESS_KEY, - DEPRECATED_SESSION_TOKEN, ICEBERG, METADATA_LOCATION, PREVIOUS_METADATA_LOCATION, @@ -102,18 +96,11 @@ def __init__(self, name: str, **properties: str): super().__init__(name, **properties) session = boto3.Session( - profile_name=get_first_property_value(properties, DYNAMODB_PROFILE_NAME, DEPRECATED_PROFILE_NAME), - region_name=get_first_property_value(properties, DYNAMODB_REGION, AWS_REGION, DEPRECATED_REGION), - botocore_session=properties.get(DEPRECATED_BOTOCORE_SESSION), - aws_access_key_id=get_first_property_value( - properties, DYNAMODB_ACCESS_KEY_ID, AWS_ACCESS_KEY_ID, DEPRECATED_ACCESS_KEY_ID - ), - aws_secret_access_key=get_first_property_value( - properties, DYNAMODB_SECRET_ACCESS_KEY, AWS_SECRET_ACCESS_KEY, DEPRECATED_SECRET_ACCESS_KEY - ), - aws_session_token=get_first_property_value( - properties, DYNAMODB_SESSION_TOKEN, AWS_SESSION_TOKEN, DEPRECATED_SESSION_TOKEN - ), + profile_name=properties.get(DYNAMODB_PROFILE_NAME), + region_name=get_first_property_value(properties, DYNAMODB_REGION, AWS_REGION), + aws_access_key_id=get_first_property_value(properties, DYNAMODB_ACCESS_KEY_ID, AWS_ACCESS_KEY_ID), + aws_secret_access_key=get_first_property_value(properties, DYNAMODB_SECRET_ACCESS_KEY, AWS_SECRET_ACCESS_KEY), + aws_session_token=get_first_property_value(properties, DYNAMODB_SESSION_TOKEN, AWS_SESSION_TOKEN), ) self.dynamodb = session.client(DYNAMODB_CLIENT) self.dynamodb_table_name = self.properties.get(DYNAMODB_TABLE_NAME, DYNAMODB_TABLE_NAME_DEFAULT) diff --git a/pyiceberg/catalog/glue.py b/pyiceberg/catalog/glue.py index 5c7b1ddcbd..385873c45b 100644 --- a/pyiceberg/catalog/glue.py +++ b/pyiceberg/catalog/glue.py @@ -40,12 +40,6 @@ ) from pyiceberg.catalog import ( - DEPRECATED_ACCESS_KEY_ID, - DEPRECATED_BOTOCORE_SESSION, - DEPRECATED_PROFILE_NAME, - DEPRECATED_REGION, - DEPRECATED_SECRET_ACCESS_KEY, - DEPRECATED_SESSION_TOKEN, EXTERNAL_TABLE, ICEBERG, LOCATION, @@ -303,18 +297,11 @@ def __init__(self, name: str, **properties: Any): super().__init__(name, **properties) session = boto3.Session( - profile_name=get_first_property_value(properties, GLUE_PROFILE_NAME, DEPRECATED_PROFILE_NAME), - region_name=get_first_property_value(properties, GLUE_REGION, AWS_REGION, DEPRECATED_REGION), - botocore_session=properties.get(DEPRECATED_BOTOCORE_SESSION), - aws_access_key_id=get_first_property_value( - properties, GLUE_ACCESS_KEY_ID, AWS_ACCESS_KEY_ID, DEPRECATED_ACCESS_KEY_ID - ), - aws_secret_access_key=get_first_property_value( - properties, GLUE_SECRET_ACCESS_KEY, AWS_SECRET_ACCESS_KEY, DEPRECATED_SECRET_ACCESS_KEY - ), - aws_session_token=get_first_property_value( - properties, GLUE_SESSION_TOKEN, AWS_SESSION_TOKEN, DEPRECATED_SESSION_TOKEN - ), + profile_name=properties.get(GLUE_PROFILE_NAME), + region_name=get_first_property_value(properties, GLUE_REGION, AWS_REGION), + aws_access_key_id=get_first_property_value(properties, GLUE_ACCESS_KEY_ID, AWS_ACCESS_KEY_ID), + aws_secret_access_key=get_first_property_value(properties, GLUE_SECRET_ACCESS_KEY, AWS_SECRET_ACCESS_KEY), + aws_session_token=get_first_property_value(properties, GLUE_SESSION_TOKEN, AWS_SESSION_TOKEN), ) self.glue: GlueClient = session.client("glue", endpoint_url=properties.get(GLUE_CATALOG_ENDPOINT)) @@ -784,4 +771,4 @@ def drop_view(self, identifier: Union[str, Identifier]) -> None: @staticmethod def __is_iceberg_table(table: TableTypeDef) -> bool: - return table["Parameters"] is not None and table["Parameters"][TABLE_TYPE].lower() == ICEBERG + return table.get("Parameters", {}).get("table_type", "").lower() == ICEBERG diff --git a/pyiceberg/io/pyarrow.py b/pyiceberg/io/pyarrow.py index aa27796081..ab4de5185b 100644 --- a/pyiceberg/io/pyarrow.py +++ b/pyiceberg/io/pyarrow.py @@ -57,7 +57,6 @@ ) from urllib.parse import urlparse -import numpy as np import pyarrow as pa import pyarrow.compute as pc import pyarrow.dataset as ds @@ -812,7 +811,17 @@ def _combine_positional_deletes(positional_deletes: List[pa.ChunkedArray], start all_chunks = positional_deletes[0] else: all_chunks = pa.chunked_array(itertools.chain(*[arr.chunks for arr in positional_deletes])) - return np.subtract(np.setdiff1d(np.arange(start_index, end_index), all_chunks, assume_unique=False), start_index) + + # Create the full range array with pyarrow + full_range = pa.array(range(start_index, end_index)) + # When available, replace with Arrow generator to improve performance + # See https://github.com/apache/iceberg-python/issues/1271 for details + + # Filter out values in all_chunks from full_range + result = pc.filter(full_range, pc.invert(pc.is_in(full_range, value_set=all_chunks))) + + # Subtract the start_index from each element in the result + return pc.subtract(result, pa.scalar(start_index)) def pyarrow_to_schema( @@ -1679,23 +1688,6 @@ def project_batches( total_row_count += len(batch) -@deprecated( - deprecated_in="0.7.0", - removed_in="0.8.0", - help_message="The public API for 'to_requested_schema' is deprecated and is replaced by '_to_requested_schema'", -) -def to_requested_schema(requested_schema: Schema, file_schema: Schema, table: pa.Table) -> pa.Table: - struct_array = visit_with_partner(requested_schema, table, ArrowProjectionVisitor(file_schema), ArrowAccessor(file_schema)) - - arrays = [] - fields = [] - for pos, field in enumerate(requested_schema.fields): - array = struct_array.field(pos) - arrays.append(array) - fields.append(pa.field(field.name, array.type, field.optional)) - return pa.Table.from_arrays(arrays, schema=pa.schema(fields)) - - def _to_requested_schema( requested_schema: Schema, file_schema: Schema, @@ -1807,7 +1799,11 @@ def struct( else: raise ResolveError(f"Field is required, and could not be found in the file: {field}") - return pa.StructArray.from_arrays(arrays=field_arrays, fields=pa.struct(fields)) + return pa.StructArray.from_arrays( + arrays=field_arrays, + fields=pa.struct(fields), + mask=struct_array.is_null() if isinstance(struct_array, pa.StructArray) else None, + ) def field(self, field: NestedField, _: Optional[pa.Array], field_array: Optional[pa.Array]) -> Optional[pa.Array]: return field_array diff --git a/pyiceberg/table/__init__.py b/pyiceberg/table/__init__.py index f94d9c8a14..e431101ba9 100644 --- a/pyiceberg/table/__init__.py +++ b/pyiceberg/table/__init__.py @@ -23,6 +23,7 @@ from dataclasses import dataclass from functools import cached_property from itertools import chain +from types import TracebackType from typing import ( TYPE_CHECKING, Any, @@ -33,6 +34,7 @@ Optional, Set, Tuple, + Type, TypeVar, Union, ) @@ -87,7 +89,6 @@ from pyiceberg.table.update import ( AddPartitionSpecUpdate, AddSchemaUpdate, - AddSnapshotUpdate, AddSortOrderUpdate, AssertCreate, AssertRefSnapshotId, @@ -237,9 +238,12 @@ def __enter__(self) -> Transaction: """Start a transaction to update the table.""" return self - def __exit__(self, _: Any, value: Any, traceback: Any) -> None: - """Close and commit the transaction.""" - self.commit_transaction() + def __exit__( + self, exctype: Optional[Type[BaseException]], excinst: Optional[BaseException], exctb: Optional[TracebackType] + ) -> None: + """Close and commit the transaction if no exceptions have been raised.""" + if exctype is None and excinst is None and exctb is None: + self.commit_transaction() def _apply(self, updates: Tuple[TableUpdate, ...], requirements: Tuple[TableRequirement, ...] = ()) -> Transaction: """Check if the requirements are met, and applies the updates to the metadata.""" @@ -309,55 +313,6 @@ def set_properties(self, properties: Properties = EMPTY_DICT, **kwargs: Any) -> updates = properties or kwargs return self._apply((SetPropertiesUpdate(updates=updates),)) - @deprecated( - deprecated_in="0.7.0", - removed_in="0.8.0", - help_message="Please use one of the functions in ManageSnapshots instead", - ) - def add_snapshot(self, snapshot: Snapshot) -> Transaction: - """Add a new snapshot to the table. - - Returns: - The transaction with the add-snapshot staged. - """ - updates = (AddSnapshotUpdate(snapshot=snapshot),) - - return self._apply(updates, ()) - - @deprecated( - deprecated_in="0.7.0", - removed_in="0.8.0", - help_message="Please use one of the functions in ManageSnapshots instead", - ) - def set_ref_snapshot( - self, - snapshot_id: int, - parent_snapshot_id: Optional[int], - ref_name: str, - type: str, - max_ref_age_ms: Optional[int] = None, - max_snapshot_age_ms: Optional[int] = None, - min_snapshots_to_keep: Optional[int] = None, - ) -> Transaction: - """Update a ref to a snapshot. - - Returns: - The transaction with the set-snapshot-ref staged - """ - updates = ( - SetSnapshotRefUpdate( - snapshot_id=snapshot_id, - ref_name=ref_name, - type=type, - max_ref_age_ms=max_ref_age_ms, - max_snapshot_age_ms=max_snapshot_age_ms, - min_snapshots_to_keep=min_snapshots_to_keep, - ), - ) - - requirements = (AssertRefSnapshotId(snapshot_id=parent_snapshot_id, ref="main"),) - return self._apply(updates, requirements) - def _set_ref_snapshot( self, snapshot_id: int, @@ -698,22 +653,22 @@ def _initial_changes(self, table_metadata: TableMetadata) -> None: schema: Schema = table_metadata.schema() self._updates += ( - AddSchemaUpdate(schema_=schema, last_column_id=schema.highest_field_id, initial_change=True), + AddSchemaUpdate(schema_=schema, last_column_id=schema.highest_field_id), SetCurrentSchemaUpdate(schema_id=-1), ) spec: PartitionSpec = table_metadata.spec() if spec.is_unpartitioned(): - self._updates += (AddPartitionSpecUpdate(spec=UNPARTITIONED_PARTITION_SPEC, initial_change=True),) + self._updates += (AddPartitionSpecUpdate(spec=UNPARTITIONED_PARTITION_SPEC),) else: - self._updates += (AddPartitionSpecUpdate(spec=spec, initial_change=True),) + self._updates += (AddPartitionSpecUpdate(spec=spec),) self._updates += (SetDefaultSpecUpdate(spec_id=-1),) sort_order: Optional[SortOrder] = table_metadata.sort_order_by_id(table_metadata.default_sort_order_id) if sort_order is None or sort_order.is_unsorted: - self._updates += (AddSortOrderUpdate(sort_order=UNSORTED_SORT_ORDER, initial_change=True),) + self._updates += (AddSortOrderUpdate(sort_order=UNSORTED_SORT_ORDER),) else: - self._updates += (AddSortOrderUpdate(sort_order=sort_order, initial_change=True),) + self._updates += (AddSortOrderUpdate(sort_order=sort_order),) self._updates += (SetDefaultSortOrderUpdate(sort_order_id=-1),) self._updates += ( diff --git a/pyiceberg/table/metadata.py b/pyiceberg/table/metadata.py index 1fea33010c..8173bb2c03 100644 --- a/pyiceberg/table/metadata.py +++ b/pyiceberg/table/metadata.py @@ -587,5 +587,21 @@ def parse_obj(data: Dict[str, Any]) -> TableMetadata: else: raise ValidationError(f"Unknown format version: {format_version}") + @staticmethod + def _construct_without_validation(table_metadata: TableMetadata) -> TableMetadata: + """Construct table metadata from an existing table without performing validation. + + This method is useful during a sequence of table updates when the model needs to be re-constructed but is not yet ready for validation. + """ + if table_metadata.format_version is None: + raise ValidationError(f"Missing format-version in TableMetadata: {table_metadata}") + + if table_metadata.format_version == 1: + return TableMetadataV1.model_construct(**dict(table_metadata)) + elif table_metadata.format_version == 2: + return TableMetadataV2.model_construct(**dict(table_metadata)) + else: + raise ValidationError(f"Unknown format version: {table_metadata.format_version}") + TableMetadata = Annotated[Union[TableMetadataV1, TableMetadataV2], Field(discriminator="format_version")] # type: ignore diff --git a/pyiceberg/table/snapshots.py b/pyiceberg/table/snapshots.py index 829bd60290..c5cb57e691 100644 --- a/pyiceberg/table/snapshots.py +++ b/pyiceberg/table/snapshots.py @@ -17,6 +17,7 @@ from __future__ import annotations import time +import warnings from collections import defaultdict from enum import Enum from typing import TYPE_CHECKING, Any, DefaultDict, Dict, Iterable, List, Mapping, Optional @@ -182,7 +183,10 @@ class Summary(IcebergBaseModel, Mapping[str, str]): operation: Operation = Field() _additional_properties: Dict[str, str] = PrivateAttr() - def __init__(self, operation: Operation, **data: Any) -> None: + def __init__(self, operation: Optional[Operation] = None, **data: Any) -> None: + if operation is None: + warnings.warn("Encountered invalid snapshot summary: operation is missing, defaulting to overwrite") + operation = Operation.OVERWRITE super().__init__(operation=operation, **data) self._additional_properties = data diff --git a/pyiceberg/table/update/__init__.py b/pyiceberg/table/update/__init__.py index 6e14046f9a..b81a2bf7f4 100644 --- a/pyiceberg/table/update/__init__.py +++ b/pyiceberg/table/update/__init__.py @@ -18,7 +18,6 @@ import uuid from abc import ABC, abstractmethod -from copy import copy from datetime import datetime from functools import singledispatch from typing import TYPE_CHECKING, Any, Dict, Generic, List, Literal, Optional, Tuple, TypeVar, Union @@ -45,6 +44,7 @@ transform_dict_value_to_str, ) from pyiceberg.utils.datetime import datetime_to_millis +from pyiceberg.utils.deprecated import deprecation_notice from pyiceberg.utils.properties import property_as_int if TYPE_CHECKING: @@ -90,7 +90,13 @@ class AddSchemaUpdate(IcebergBaseModel): # This field is required: https://github.com/apache/iceberg/pull/7445 last_column_id: int = Field(alias="last-column-id") - initial_change: bool = Field(default=False, exclude=True) + initial_change: bool = Field( + default=False, + exclude=True, + deprecated=deprecation_notice( + deprecated_in="0.8.0", removed_in="0.9.0", help_message="CreateTableTransaction can work without this field" + ), + ) class SetCurrentSchemaUpdate(IcebergBaseModel): @@ -104,7 +110,13 @@ class AddPartitionSpecUpdate(IcebergBaseModel): action: Literal["add-spec"] = Field(default="add-spec") spec: PartitionSpec - initial_change: bool = Field(default=False, exclude=True) + initial_change: bool = Field( + default=False, + exclude=True, + deprecated=deprecation_notice( + deprecated_in="0.8.0", removed_in="0.9.0", help_message="CreateTableTransaction can work without this field" + ), + ) class SetDefaultSpecUpdate(IcebergBaseModel): @@ -118,7 +130,13 @@ class AddSortOrderUpdate(IcebergBaseModel): action: Literal["add-sort-order"] = Field(default="add-sort-order") sort_order: SortOrder = Field(alias="sort-order") - initial_change: bool = Field(default=False, exclude=True) + initial_change: bool = Field( + default=False, + exclude=True, + deprecated=deprecation_notice( + deprecated_in="0.8.0", removed_in="0.9.0", help_message="CreateTableTransaction can work without this field" + ), + ) class SetDefaultSortOrderUpdate(IcebergBaseModel): @@ -267,11 +285,10 @@ def _( elif update.format_version == base_metadata.format_version: return base_metadata - updated_metadata_data = copy(base_metadata.model_dump()) - updated_metadata_data["format-version"] = update.format_version + updated_metadata = base_metadata.model_copy(update={"format_version": update.format_version}) context.add_update(update) - return TableMetadataUtil.parse_obj(updated_metadata_data) + return TableMetadataUtil._construct_without_validation(updated_metadata) @_apply_table_update.register(SetPropertiesUpdate) @@ -306,7 +323,7 @@ def _(update: AddSchemaUpdate, base_metadata: TableMetadata, context: _TableMeta metadata_updates: Dict[str, Any] = { "last_column_id": update.last_column_id, - "schemas": [update.schema_] if update.initial_change else base_metadata.schemas + [update.schema_], + "schemas": base_metadata.schemas + [update.schema_], } context.add_update(update) @@ -336,11 +353,11 @@ def _(update: SetCurrentSchemaUpdate, base_metadata: TableMetadata, context: _Ta @_apply_table_update.register(AddPartitionSpecUpdate) def _(update: AddPartitionSpecUpdate, base_metadata: TableMetadata, context: _TableMetadataUpdateContext) -> TableMetadata: for spec in base_metadata.partition_specs: - if spec.spec_id == update.spec.spec_id and not update.initial_change: + if spec.spec_id == update.spec.spec_id: raise ValueError(f"Partition spec with id {spec.spec_id} already exists: {spec}") metadata_updates: Dict[str, Any] = { - "partition_specs": [update.spec] if update.initial_change else base_metadata.partition_specs + [update.spec], + "partition_specs": base_metadata.partition_specs + [update.spec], "last_partition_id": max( max([field.field_id for field in update.spec.fields], default=0), base_metadata.last_partition_id or PARTITION_FIELD_ID_START - 1, @@ -448,7 +465,7 @@ def _(update: AddSortOrderUpdate, base_metadata: TableMetadata, context: _TableM context.add_update(update) return base_metadata.model_copy( update={ - "sort_orders": [update.sort_order] if update.initial_change else base_metadata.sort_orders + [update.sort_order], + "sort_orders": base_metadata.sort_orders + [update.sort_order], } ) diff --git a/pyiceberg/utils/deprecated.py b/pyiceberg/utils/deprecated.py index 92051b4fe6..188d0ce68b 100644 --- a/pyiceberg/utils/deprecated.py +++ b/pyiceberg/utils/deprecated.py @@ -41,14 +41,17 @@ def new_func(*args: Any, **kwargs: Any) -> Any: return decorator +def deprecation_notice(deprecated_in: str, removed_in: str, help_message: Optional[str]) -> str: + """Return a deprecation notice.""" + return f"Deprecated in {deprecated_in}, will be removed in {removed_in}. {help_message}" + + def deprecation_message(deprecated_in: str, removed_in: str, help_message: Optional[str]) -> None: """Mark properties or behaviors as deprecated. Adding this will result in a warning being emitted. """ - message = f"Deprecated in {deprecated_in}, will be removed in {removed_in}. {help_message}" - - _deprecation_warning(message) + _deprecation_warning(deprecation_notice(deprecated_in, removed_in, help_message)) def _deprecation_warning(message: str) -> None: diff --git a/pyproject.toml b/pyproject.toml index 12fec1a82a..b4c5717327 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ # under the License. [tool.poetry] name = "pyiceberg" -version = "0.7.1" +version = "0.8.0" readme = "README.md" homepage = "https://py.iceberg.apache.org/" repository = "https://github.com/apache/iceberg-python" @@ -50,7 +50,7 @@ include = [ [tool.poetry.dependencies] python = "^3.9, <3.13, !=3.9.7" -mmh3 = ">=4.0.0,<5.0.0" +mmh3 = ">=4.0.0,<6.0.0" requests = ">=2.20.0,<3.0.0" click = ">=7.1.1,<9.0.0" rich = ">=10.11.0,<14.0.0" @@ -61,7 +61,7 @@ fsspec = ">=2023.1.0,<2025.1.0" pyparsing = ">=3.1.0,<4.0.0" zstandard = ">=0.13.0,<1.0.0" tenacity = ">=8.2.3,<10.0.0" -pyarrow = { version = ">=14.0.0,<18.0.0", optional = true } +pyarrow = { version = ">=14.0.0,<19.0.0", optional = true } pandas = { version = ">=1.0.0,<3.0.0", optional = true } duckdb = { version = ">=0.5.0,<2.0.0", optional = true } ray = [ @@ -78,23 +78,20 @@ gcsfs = { version = ">=2023.1.0,<2024.1.0", optional = true } psycopg2-binary = { version = ">=2.9.6", optional = true } sqlalchemy = { version = "^2.0.18", optional = true } getdaft = { version = ">=0.2.12", optional = true } -numpy = [ - { version = "1.26.0", python = ">=3.9,<3.13", optional = true }, -] cachetools = "^5.5.0" [tool.poetry.group.dev.dependencies] pytest = "7.4.4" pytest-checkdocs = "2.10.1" pytest-lazy-fixture = "0.6.3" -pre-commit = "3.5.0" +pre-commit = "4.0.1" fastavro = "1.9.7" coverage = { version = "^7.4.2", extras = ["toml"] } requests-mock = "1.12.1" moto = { version = "^5.0.2", extras = ["server"] } typing-extensions = "4.12.2" pytest-mock = "3.14.0" -pyspark = "3.5.2" +pyspark = "3.5.3" cython = "3.0.11" deptry = ">=0.14,<0.21" docutils = "!=0.21.post1" # https://github.com/python-poetry/poetry/issues/9248#issuecomment-2026240520 @@ -238,10 +235,6 @@ ignore_missing_imports = true module = "sortedcontainers.*" ignore_missing_imports = true -[[tool.mypy.overrides]] -module = "numpy.*" -ignore_missing_imports = true - [[tool.mypy.overrides]] module = "sqlalchemy.*" ignore_missing_imports = true @@ -394,10 +387,6 @@ ignore_missing_imports = true module = "sortedcontainers.*" ignore_missing_imports = true -[[tool.mypy.overrides]] -module = "numpy.*" -ignore_missing_imports = true - [[tool.mypy.overrides]] module = "sqlalchemy.*" ignore_missing_imports = true @@ -550,10 +539,6 @@ ignore_missing_imports = true module = "sortedcontainers.*" ignore_missing_imports = true -[[tool.mypy.overrides]] -module = "numpy.*" -ignore_missing_imports = true - [[tool.mypy.overrides]] module = "sqlalchemy.*" ignore_missing_imports = true @@ -706,10 +691,6 @@ ignore_missing_imports = true module = "sortedcontainers.*" ignore_missing_imports = true -[[tool.mypy.overrides]] -module = "numpy.*" -ignore_missing_imports = true - [[tool.mypy.overrides]] module = "sqlalchemy.*" ignore_missing_imports = true @@ -862,10 +843,6 @@ ignore_missing_imports = true module = "sortedcontainers.*" ignore_missing_imports = true -[[tool.mypy.overrides]] -module = "numpy.*" -ignore_missing_imports = true - [[tool.mypy.overrides]] module = "sqlalchemy.*" ignore_missing_imports = true @@ -894,10 +871,10 @@ generate-setup-file = false script = "build-module.py" [tool.poetry.extras] -pyarrow = ["pyarrow", "numpy"] -pandas = ["pandas", "pyarrow", "numpy"] -duckdb = ["duckdb", "pyarrow", "numpy"] -ray = ["ray", "pyarrow", "pandas", "numpy"] +pyarrow = ["pyarrow"] +pandas = ["pandas", "pyarrow"] +duckdb = ["duckdb", "pyarrow"] +ray = ["ray", "pyarrow", "pandas"] daft = ["getdaft"] snappy = ["python-snappy"] hive = ["thrift"] @@ -1084,10 +1061,6 @@ ignore_missing_imports = true module = "sortedcontainers.*" ignore_missing_imports = true -[[tool.mypy.overrides]] -module = "numpy.*" -ignore_missing_imports = true - [[tool.mypy.overrides]] module = "sqlalchemy.*" ignore_missing_imports = true diff --git a/tests/catalog/test_dynamodb.py b/tests/catalog/test_dynamodb.py index 0289c5d0bb..194caf46b7 100644 --- a/tests/catalog/test_dynamodb.py +++ b/tests/catalog/test_dynamodb.py @@ -45,7 +45,6 @@ from pyiceberg.typedef import Properties from tests.conftest import ( BUCKET_NAME, - DEPRECATED_AWS_SESSION_PROPERTIES, TABLE_METADATA_LOCATION_REGEX, UNIFIED_AWS_SESSION_PROPERTIES, ) @@ -563,28 +562,6 @@ def test_update_namespace_properties_overlap_update_removal(_bucket_initialize: assert test_catalog.load_namespace_properties(database_name) == test_properties -def test_passing_provided_profile() -> None: - catalog_name = "test_ddb_catalog" - session_props = { - "aws_access_key_id": "abc", - "aws_secret_access_key": "def", - "aws_session_token": "ghi", - "region_name": "eu-central-1", - "botocore_session": None, - "profile_name": None, - } - props = {"py-io-impl": "pyiceberg.io.fsspec.FsspecFileIO"} - props.update(session_props) # type: ignore - with mock.patch("boto3.Session", return_value=mock.Mock()) as mock_session: - mock_client = mock.Mock() - mock_session.return_value.client.return_value = mock_client - mock_client.describe_table.return_value = {"Table": {"TableStatus": "ACTIVE"}} - test_catalog = DynamoDbCatalog(catalog_name, **props) - assert test_catalog.dynamodb is mock_client - mock_session.assert_called_with(**session_props) - assert test_catalog.dynamodb is mock_session().client() - - @mock_aws def test_passing_glue_session_properties() -> None: session_properties: Properties = { @@ -594,7 +571,6 @@ def test_passing_glue_session_properties() -> None: "dynamodb.region": "dynamodb.region", "dynamodb.session-token": "dynamodb.session-token", **UNIFIED_AWS_SESSION_PROPERTIES, - **DEPRECATED_AWS_SESSION_PROPERTIES, } with mock.patch("boto3.Session") as mock_session: @@ -609,7 +585,6 @@ def test_passing_glue_session_properties() -> None: aws_session_token="dynamodb.session-token", region_name="dynamodb.region", profile_name="dynamodb.profile-name", - botocore_session=None, ) assert test_catalog.dynamodb is mock_session().client() @@ -619,7 +594,6 @@ def test_passing_unified_session_properties_to_dynamodb() -> None: session_properties: Properties = { "dynamodb.profile-name": "dynamodb.profile-name", **UNIFIED_AWS_SESSION_PROPERTIES, - **DEPRECATED_AWS_SESSION_PROPERTIES, } with mock.patch("boto3.Session") as mock_session: @@ -634,7 +608,6 @@ def test_passing_unified_session_properties_to_dynamodb() -> None: aws_session_token="client.session-token", region_name="client.region", profile_name="dynamodb.profile-name", - botocore_session=None, ) assert test_catalog.dynamodb is mock_session().client() diff --git a/tests/catalog/test_glue.py b/tests/catalog/test_glue.py index 53af750446..41b196facf 100644 --- a/tests/catalog/test_glue.py +++ b/tests/catalog/test_glue.py @@ -14,7 +14,7 @@ # KIND, either express or implied. See the License for the # specific language governing permissions and limitations # under the License. -from typing import Any, Dict, List +from typing import List from unittest import mock import boto3 @@ -40,7 +40,6 @@ from pyiceberg.types import IntegerType from tests.conftest import ( BUCKET_NAME, - DEPRECATED_AWS_SESSION_PROPERTIES, TABLE_METADATA_LOCATION_REGEX, UNIFIED_AWS_SESSION_PROPERTIES, ) @@ -638,26 +637,6 @@ def test_update_namespace_properties_overlap_update_removal( assert test_catalog.load_namespace_properties(database_name) == test_properties -@mock_aws -def test_passing_profile_name() -> None: - session_properties: Dict[str, Any] = { - "aws_access_key_id": "abc", - "aws_secret_access_key": "def", - "aws_session_token": "ghi", - "region_name": "eu-central-1", - "profile_name": "sandbox", - "botocore_session": None, - } - test_properties = {"type": "glue"} - test_properties.update(session_properties) - - with mock.patch("boto3.Session") as mock_session: - test_catalog = GlueCatalog("glue", **test_properties) - - mock_session.assert_called_with(**session_properties) - assert test_catalog.glue is mock_session().client() - - @mock_aws def test_passing_glue_session_properties() -> None: session_properties: Properties = { @@ -667,7 +646,6 @@ def test_passing_glue_session_properties() -> None: "glue.region": "glue.region", "glue.session-token": "glue.session-token", **UNIFIED_AWS_SESSION_PROPERTIES, - **DEPRECATED_AWS_SESSION_PROPERTIES, } with mock.patch("boto3.Session") as mock_session: @@ -679,7 +657,6 @@ def test_passing_glue_session_properties() -> None: aws_session_token="glue.session-token", region_name="glue.region", profile_name="glue.profile-name", - botocore_session=None, ) assert test_catalog.glue is mock_session().client() @@ -689,7 +666,6 @@ def test_passing_unified_session_properties_to_glue() -> None: session_properties: Properties = { "glue.profile-name": "glue.profile-name", **UNIFIED_AWS_SESSION_PROPERTIES, - **DEPRECATED_AWS_SESSION_PROPERTIES, } with mock.patch("boto3.Session") as mock_session: @@ -701,7 +677,6 @@ def test_passing_unified_session_properties_to_glue() -> None: aws_session_token="client.session-token", region_name="client.region", profile_name="glue.profile-name", - botocore_session=None, ) assert test_catalog.glue is mock_session().client() diff --git a/tests/conftest.py b/tests/conftest.py index b05947ebe6..e7e73375d7 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2029,14 +2029,6 @@ def hierarchical_namespace_list(hierarchical_namespace_name: str) -> List[str]: re.X, ) -DEPRECATED_AWS_SESSION_PROPERTIES = { - "aws_access_key_id": "aws_access_key_id", - "aws_secret_access_key": "aws_secret_access_key", - "aws_session_token": "aws_session_token", - "region_name": "region_name", - "profile_name": "profile_name", -} - UNIFIED_AWS_SESSION_PROPERTIES = { "client.access-key-id": "client.access-key-id", "client.secret-access-key": "client.secret-access-key", diff --git a/tests/integration/test_writes/test_writes.py b/tests/integration/test_writes/test_writes.py index fc2746c614..e0b788e88c 100644 --- a/tests/integration/test_writes/test_writes.py +++ b/tests/integration/test_writes/test_writes.py @@ -17,13 +17,13 @@ # pylint:disable=redefined-outer-name import math import os +import random import time from datetime import date, datetime, timedelta from pathlib import Path from typing import Any, Dict from urllib.parse import urlparse -import numpy as np import pandas as pd import pyarrow as pa import pyarrow.compute as pc @@ -45,6 +45,7 @@ from pyiceberg.partitioning import PartitionField, PartitionSpec from pyiceberg.schema import Schema from pyiceberg.table import TableProperties +from pyiceberg.table.sorting import SortDirection, SortField, SortOrder from pyiceberg.transforms import DayTransform, HourTransform, IdentityTransform from pyiceberg.types import ( DateType, @@ -738,7 +739,7 @@ def test_write_and_evolve(session_catalog: Catalog, format_version: int) -> None def test_create_table_transaction(catalog: Catalog, format_version: int) -> None: if format_version == 1 and isinstance(catalog, RestCatalog): pytest.skip( - "There is a bug in the REST catalog (maybe server side) that prevents create and commit a staged version 1 table" + "There is a bug in the REST catalog image (https://github.com/apache/iceberg/issues/8756) that prevents create and commit a staged version 1 table" ) identifier = f"default.arrow_create_table_transaction_{catalog.name}_{format_version}" @@ -787,6 +788,62 @@ def test_create_table_transaction(catalog: Catalog, format_version: int) -> None assert len(tbl.scan().to_arrow()) == 6 +@pytest.mark.integration +@pytest.mark.parametrize("format_version", [1, 2]) +@pytest.mark.parametrize("catalog", [pytest.lazy_fixture("session_catalog_hive"), pytest.lazy_fixture("session_catalog")]) +def test_create_table_with_non_default_values(catalog: Catalog, table_schema_with_all_types: Schema, format_version: int) -> None: + if format_version == 1 and isinstance(catalog, RestCatalog): + pytest.skip( + "There is a bug in the REST catalog image (https://github.com/apache/iceberg/issues/8756) that prevents create and commit a staged version 1 table" + ) + + identifier = f"default.arrow_create_table_transaction_with_non_default_values_{catalog.name}_{format_version}" + identifier_ref = f"default.arrow_create_table_transaction_with_non_default_values_ref_{catalog.name}_{format_version}" + + try: + catalog.drop_table(identifier=identifier) + except NoSuchTableError: + pass + + try: + catalog.drop_table(identifier=identifier_ref) + except NoSuchTableError: + pass + + iceberg_spec = PartitionSpec(*[ + PartitionField(source_id=2, field_id=1001, transform=IdentityTransform(), name="integer_partition") + ]) + + sort_order = SortOrder(*[SortField(source_id=2, transform=IdentityTransform(), direction=SortDirection.ASC)]) + + txn = catalog.create_table_transaction( + identifier=identifier, + schema=table_schema_with_all_types, + partition_spec=iceberg_spec, + sort_order=sort_order, + properties={"format-version": format_version}, + ) + txn.commit_transaction() + + tbl = catalog.load_table(identifier) + + tbl_ref = catalog.create_table( + identifier=identifier_ref, + schema=table_schema_with_all_types, + partition_spec=iceberg_spec, + sort_order=sort_order, + properties={"format-version": format_version}, + ) + + assert tbl.format_version == tbl_ref.format_version + assert tbl.schema() == tbl_ref.schema() + assert tbl.schemas() == tbl_ref.schemas() + assert tbl.spec() == tbl_ref.spec() + assert tbl.specs() == tbl_ref.specs() + assert tbl.sort_order() == tbl_ref.sort_order() + assert tbl.sort_orders() == tbl_ref.sort_orders() + + @pytest.mark.integration @pytest.mark.parametrize("format_version", [1, 2]) def test_table_properties_int_value( @@ -1373,14 +1430,14 @@ def test_delete_threshold(session_catalog: Catalog) -> None: date_start, date_end = date(2024, 1, 1), date(2024, 2, 1) # Generate the 'id' column - id_column = np.random.randint(id_min, id_max, num_rows) + id_column = [random.randint(id_min, id_max) for _ in range(num_rows)] # Generate the 'created_at' column as dates only - date_range = pd.date_range(start=date_start, end=date_end, freq="D") # Daily frequency for dates - created_at_column = np.random.choice(date_range, num_rows) # Convert to string (YYYY-MM-DD format) + date_range = pd.date_range(start=date_start, end=date_end, freq="D").to_list() # Daily frequency for dates + created_at_column = [random.choice(date_range) for _ in range(num_rows)] # Convert to string (YYYY-MM-DD format) # Generate the 'relevancy_score' column with a peak around 0.1 - relevancy_score_column = np.random.beta(a=2, b=20, size=num_rows) # Adjusting parameters to peak around 0.1 + relevancy_score_column = [random.betavariate(2, 20) for _ in range(num_rows)] # Adjusting parameters to peak around 0.1 # Create the dataframe df = pd.DataFrame({"id": id_column, "created_at": created_at_column, "relevancy_score": relevancy_score_column}) @@ -1403,12 +1460,12 @@ def test_delete_threshold(session_catalog: Catalog) -> None: @pytest.mark.integration def test_rewrite_manifest_after_partition_evolution(session_catalog: Catalog) -> None: - np.random.seed(876) + random.seed(876) N = 1440 d = { "timestamp": pa.array([datetime(2023, 1, 1, 0, 0, 0) + timedelta(minutes=i) for i in range(N)]), - "category": pa.array([np.random.choice(["A", "B", "C"]) for _ in range(N)]), - "value": pa.array(np.random.normal(size=N)), + "category": pa.array([random.choice(["A", "B", "C"]) for _ in range(N)]), + "value": pa.array([random.gauss(0, 1) for _ in range(N)]), } data = pa.Table.from_pydict(d) @@ -1448,3 +1505,68 @@ def test_rewrite_manifest_after_partition_evolution(session_catalog: Catalog) -> EqualTo("category", "A"), ), ) + + +@pytest.mark.integration +def test_writing_null_structs(session_catalog: Catalog) -> None: + import pyarrow as pa + + schema = pa.schema([ + pa.field( + "struct_field_1", + pa.struct([ + pa.field("string_nested_1", pa.string()), + pa.field("int_item_2", pa.int32()), + pa.field("float_item_2", pa.float32()), + ]), + ), + ]) + + records = [ + { + "struct_field_1": { + "string_nested_1": "nest_1", + "int_item_2": 1234, + "float_item_2": 1.234, + }, + }, + {}, + ] + + try: + session_catalog.drop_table( + identifier="default.test_writing_null_structs", + ) + except NoSuchTableError: + pass + + table = session_catalog.create_table("default.test_writing_null_structs", schema) + + pyarrow_table: pa.Table = pa.Table.from_pylist(records, schema=schema) + table.append(pyarrow_table) + + assert pyarrow_table.to_pandas()["struct_field_1"].tolist() == table.scan().to_pandas()["struct_field_1"].tolist() + + +@pytest.mark.integration +@pytest.mark.parametrize("format_version", [1, 2]) +def test_abort_table_transaction_on_exception( + spark: SparkSession, session_catalog: Catalog, arrow_table_with_null: pa.Table, format_version: int +) -> None: + identifier = "default.table_test_abort_table_transaction_on_exception" + tbl = _create_table(session_catalog, identifier, properties={"format-version": format_version}) + + # Pre-populate some data + tbl.append(arrow_table_with_null) + table_size = len(arrow_table_with_null) + assert len(tbl.scan().to_pandas()) == table_size + + # try to commit a transaction that raises exception at the middle + with pytest.raises(ValueError): + with tbl.transaction() as txn: + txn.append(arrow_table_with_null) + raise ValueError + txn.append(arrow_table_with_null) # type: ignore + + # Validate the transaction is aborted and no partial update is applied + assert len(tbl.scan().to_pandas()) == table_size # type: ignore diff --git a/tests/table/test_snapshots.py b/tests/table/test_snapshots.py index ff9d92cea3..b4dde217d4 100644 --- a/tests/table/test_snapshots.py +++ b/tests/table/test_snapshots.py @@ -112,6 +112,13 @@ def test_deserialize_snapshot(snapshot: Snapshot) -> None: assert actual == snapshot +def test_deserialize_snapshot_without_operation(snapshot: Snapshot) -> None: + payload = """{"snapshot-id": 25, "parent-snapshot-id": 19, "sequence-number": 200, "timestamp-ms": 1602638573590, "manifest-list": "s3:/a/b/c.avro", "summary": {}, "schema-id": 3}""" + with pytest.warns(UserWarning, match="Encountered invalid snapshot summary: operation is missing, defaulting to overwrite"): + actual = Snapshot.model_validate_json(payload) + assert actual.summary.operation == Operation.OVERWRITE + + def test_deserialize_snapshot_with_properties(snapshot_with_properties: Snapshot) -> None: payload = """{"snapshot-id":25,"parent-snapshot-id":19,"sequence-number":200,"timestamp-ms":1602638573590,"manifest-list":"s3:/a/b/c.avro","summary":{"operation":"append","foo":"bar"},"schema-id":3}""" snapshot = Snapshot.model_validate_json(payload)