diff --git a/.github/workflows/on_release.yml b/.github/workflows/on_release.yml index 5efecad..e440ae0 100644 --- a/.github/workflows/on_release.yml +++ b/.github/workflows/on_release.yml @@ -38,7 +38,7 @@ jobs: url: https://pypi.org/p/${{ vars.PACKAGE_NAME }} steps: - - uses: actions/download-artifact@v3 + - uses: actions/download-artifact@v4 with: # unpacks default artifact into dist/ # if `name: artifact` is omitted, the action will create extra parent dir diff --git a/.github/workflows/on_test_release.yml b/.github/workflows/on_test_release.yml index 7472e6c..446324c 100644 --- a/.github/workflows/on_test_release.yml +++ b/.github/workflows/on_test_release.yml @@ -21,7 +21,7 @@ jobs: url: https://test.pypi.org/p/${{ vars.PACKAGE_NAME }} steps: - - uses: actions/download-artifact@v3 + - uses: actions/download-artifact@v4 with: # unpacks default artifact into dist/ # if `name: artifact` is omitted, the action will create extra parent dir diff --git a/deker/locks.py b/deker/locks.py index 1aeca16..c17e3b2 100644 --- a/deker/locks.py +++ b/deker/locks.py @@ -417,80 +417,6 @@ def _inner_method_logic( return super()._inner_method_logic(lock, args, kwargs, func) -class CreateArrayLock(LockWithArrayMixin[Union["Array", "VArray", dict]], BaseLock): - """Lock that we set when we want to create an array.""" - - ALLOWED_TYPES = ["LocalArrayAdapter", "LocalVArrayAdapter"] - - path: Optional[Path] = None - - def get_path(self) -> Path: - """Return path to the file that should be locked.""" - # Get file directory path - dir_path = self.instance.collection_path - - # Create lock file - path = dir_path / _get_lock_filename(self.array.id, LocksExtensions.array_lock) - if not path.exists(): - path.open("w").close() - - self.path = path - self.logger.debug(f"got path for array.id {self.array.id} lock file: {path}") - return path - - def check_existing_lock(self, func_args: Sequence, func_kwargs: Dict) -> None: - """Check if there is currently lock for array creating. - - :param func_args: arguments for called method - :param func_kwargs: keyword arguments for called method - """ - from deker.arrays import Array, VArray - - array = self.array - # Check current read locks - if isinstance(array, dict): - adapter = array["adapter"].__class__.__name__ - if adapter not in self.ALLOWED_TYPES: - raise DekerLockError(f"Adapter {adapter} is not allowed to create locks for arrays") - - # TODO: figure out a way to avoid constructing Array object here - array_type = Array if adapter == self.ALLOWED_TYPES[0] else VArray - array = array_type(**array) - - dir_path = self.instance.collection_path - - # Pattern that has to find any create locks - glob_pattern = f"{array.id}:*{LocksExtensions.array_lock.value}" - for _ in dir_path.rglob(glob_pattern): - raise DekerLockError(f"Array {array.id} is locked for creating") - - func_kwargs["array"] = array - - def get_result(self, func: Callable, args: Any, kwargs: Any) -> Any: - """Call func, and get its result. - - :param func: decorated function - :param args: arguments of decorated function - :param kwargs: keyword arguments of decorated function - """ - if kw_array := kwargs.pop("array"): - args = list(args) - # First elem is self, so for functions with array, set array as next arg. - args[1] = kw_array - result = func(*tuple(args), **kwargs) - else: - result = func(*args, **kwargs) - return result - - def release(self, e: Optional[Exception] = None) -> None: - """Release Flock. - - :param e: exception that might have been raised - """ - self.path.unlink(missing_ok=True) - super().release(e) - - class UpdateMetaAttributeLock(LockWithArrayMixin[Union["Array", "VArray"]], BaseLock): """Lock for updating meta.""" diff --git a/deker/managers.py b/deker/managers.py index 32c8cf4..15559e2 100644 --- a/deker/managers.py +++ b/deker/managers.py @@ -132,9 +132,11 @@ def _create( # type: ignore "array_adapter": self.__array_adapter, # type: ignore[dict-item] } ) + array = VArray(**arr_params) # type: ignore[arg-type] else: arr_params.update({"adapter": self.__array_adapter}) # type: ignore[dict-item] - array = self._adapter.create(arr_params) + array = Array(**arr_params) # type: ignore[arg-type] + self._adapter.create(array) return array def create( diff --git a/deker/subset.py b/deker/subset.py index 850ff72..1bd2ba4 100644 --- a/deker/subset.py +++ b/deker/subset.py @@ -578,6 +578,7 @@ def update(self, data: Data) -> None: :param data: new data which shall match subset slicing """ + from deker.arrays import Array def _update(array_data: ArrayPositionedData) -> None: """If there is a need in the future to calculate Array's time dimension start value. # noqa: DAR101, D400 @@ -600,17 +601,17 @@ def _update(array_data: ArrayPositionedData) -> None: pos = array_data.vposition[n] custom_attributes[attr_name] = dim.start_value + dim.step * pos # type: ignore[operator] - array = self.__array_adapter.create( - { - "collection": self.__collection, - "adapter": self.__array_adapter, - "primary_attributes": { - "vid": self.__array.id, - "v_position": array_data.vposition, - }, - "custom_attributes": custom_attributes, - } - ) + kwargs = { + "collection": self.__collection, + "adapter": self.__array_adapter, + "primary_attributes": { + "vid": self.__array.id, + "v_position": array_data.vposition, + }, + "custom_attributes": custom_attributes, + } + array = Array(**kwargs) # type: ignore[arg-type] + self.__array_adapter.create(array) subset = array[array_data.bounds] subset.update(array_data.data) diff --git a/poetry.lock b/poetry.lock index 2ae9f50..47dc925 100644 --- a/poetry.lock +++ b/poetry.lock @@ -115,13 +115,13 @@ Sphinx = ">=2.2,<8.0" [[package]] name = "babel" -version = "2.14.0" +version = "2.15.0" description = "Internationalization utilities" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, - {file = 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[[package]] name = "typing-extensions" -version = "4.10.0" +version = "4.11.0" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"}, - {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"}, + {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, + {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, ] [[package]] @@ -2620,13 +2616,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.25.1" +version = "20.26.1" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"}, - {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"}, + {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"}, + {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"}, ] [package.dependencies] @@ -2635,7 +2631,7 @@ filelock = ">=3.12.2,<4" platformdirs = ">=3.9.1,<5" [package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] @@ -2707,4 +2703,4 @@ xarray = ["xarray"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "d5be6ceef0a2525bbc779fe5809b7f395ee33a4628abb5e43e8564fba7b7c651" +content-hash = "a94291f635fab7ce16a9164c854bd3150468072cc9c9d400da90b204bc05595d" diff --git a/pyproject.toml b/pyproject.toml index de50866..761d030 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ attrs = "^23.1.0" typing-extensions = "^4.4.0" tqdm = "^4.64.1" psutil = "^5.9.5" -deker-local-adapters = "^1.0.1" +deker-local-adapters = "^1.1.1" deker-server-adapters = {version = "^1.0.0", optional = true} deker-shell = { version = "^1.0.0", optional = true } xarray = {version = "^2023.5.0", optional = true} diff --git a/tests/test_cases/test_arrays/test_array_methods.py b/tests/test_cases/test_arrays/test_array_methods.py index 080b8d2..b4370d2 100644 --- a/tests/test_cases/test_arrays/test_array_methods.py +++ b/tests/test_cases/test_arrays/test_array_methods.py @@ -1,6 +1,5 @@ import os import string -from copy import deepcopy from datetime import datetime, timedelta, timezone from pathlib import Path @@ -14,7 +13,6 @@ from deker_local_adapters.factory import AdaptersFactory from numpy import ndarray -from deker.types import ArrayMeta from tests.parameters.array_params import attributes_validation_params from tests.parameters.index_exp_params import invalid_index_params, valid_index_exp_params from tests.parameters.uri import embedded_uri @@ -26,6 +24,7 @@ from deker.errors import DekerCollectionAlreadyExistsError, DekerMemoryError, DekerValidationError from deker.schemas import ArraySchema, AttributeSchema, DimensionSchema from deker.tools import get_paths +from deker.types import ArrayMeta from deker.types.private.typings import FancySlice, NumericDtypes, Slice diff --git a/tests/test_cases/test_arrays/test_varray_methods.py b/tests/test_cases/test_arrays/test_varray_methods.py index 7fc6807..4c3d7e3 100644 --- a/tests/test_cases/test_arrays/test_varray_methods.py +++ b/tests/test_cases/test_arrays/test_varray_methods.py @@ -14,7 +14,6 @@ from deker_tools.path import is_empty from numpy import ndarray -from deker.types import ArrayMeta from tests.parameters.array_params import attributes_validation_params from tests.parameters.index_exp_params import invalid_index_params, valid_index_exp_params from tests.parameters.uri import embedded_uri @@ -26,6 +25,7 @@ from deker.errors import DekerMemoryError, DekerValidationError from deker.schemas import DimensionSchema, VArraySchema from deker.tools import get_paths +from deker.types import ArrayMeta from deker.types.private.typings import FancySlice, Slice diff --git a/tests/test_cases/test_concurrency/test_in_processes.py b/tests/test_cases/test_concurrency/test_in_processes.py index d83379a..50032a8 100644 --- a/tests/test_cases/test_concurrency/test_in_processes.py +++ b/tests/test_cases/test_concurrency/test_in_processes.py @@ -14,7 +14,6 @@ from typing import Callable, Dict, Literal from unittest.mock import patch -import h5py import numpy as np import pytest @@ -28,7 +27,6 @@ from deker.errors import DekerLockError from deker.locks import ( CollectionLock, - CreateArrayLock, Flock, ReadArrayLock, UpdateMetaAttributeLock, @@ -36,7 +34,6 @@ WriteVarrayLock, ) from deker.schemas import ArraySchema, DimensionSchema, VArraySchema -from deker.tools import get_paths from deker.types import LocksExtensions, Numeric @@ -100,21 +97,6 @@ def call_array_method( subset_slice = slice_converter[subset_slice] # Get Array object - if method == "create": - with patch.object( - CreateArrayLock, - "release", - wait_unlock(CreateArrayLock.release, lock_set, funcs_finished, wait), - ): - with patch("deker.ABC.base_array.get_id", lambda *a: id_): - try: - array = collection.create(primary_attributes, custom_attributes) - except DekerLockError: - return DekerLockError - except Exception: - traceback.print_exc() - return None - return try: array = collection.filter({"id": id_}).last() except DekerLockError: @@ -551,60 +533,6 @@ def test_varray_update_meta_lock( finally: proc.kill() - def test_varray_with_attributes_create_lock( - self, - client: Client, - array_schema_with_attributes: ArraySchema, - root_path, - varray_with_attributes: VArray, - ): - """Test create lock.""" - manager = Manager() - lock_set = manager.Event() - func_finished = manager.Event() - proc = Process( - target=call_array_method, - args=( - varray_with_attributes.collection, - str(embedded_uri(root_path)), - varray_with_attributes.id, - "create", - lock_set, - func_finished, - True, - True, - varray_with_attributes.primary_attributes, - varray_with_attributes.custom_attributes, - ), - ) - proc.start() - lock_set.wait() - try: - methods = ["create"] * 3 - with Pool(WORKERS) as pool: - result = pool.starmap( - call_array_method, - [ - ( - varray_with_attributes.collection, - str(embedded_uri(root_path)), - varray_with_attributes.id, - method, - lock_set, - func_finished, - False, - True, - varray_with_attributes.primary_attributes, - varray_with_attributes.custom_attributes, - ) - for method in methods - ], - ) - assert result.count(DekerLockError) == len(methods) - func_finished.set() - finally: - proc.kill() - def test_collection_create(self, client: Client, root_path): """Test if collection is locked on creation.""" manager = Manager() @@ -640,78 +568,5 @@ def test_collection_create(self, client: Client, root_path): proc.kill() -class TestMethods: - """Test if methods work correctly with multiple processes.""" - - def test_array_with_attributes_create_multiple_processes( - self, - client: Client, - array_schema_with_attributes: ArraySchema, - root_path, - array_with_attributes: Array, - array_data: np.ndarray, - storage_adapter, - ctx, - ): - manager = Manager() - lock_set = manager.Event() - func_finished = manager.Event() - proc = Process( - target=call_array_method, - args=( - array_with_attributes.collection, - str(embedded_uri(root_path)), - array_with_attributes.id, - "create", - lock_set, - func_finished, - True, - False, - array_with_attributes.primary_attributes, - array_with_attributes.custom_attributes, - ), - ) - proc.start() - lock_set.wait() - - methods = ["create"] * 3 - with Pool(WORKERS - 1) as pool: - result = pool.starmap( - call_array_method, - [ - ( - array_with_attributes.collection, - str(embedded_uri(root_path)), - array_with_attributes.id, - method, - lock_set, - func_finished, - False, - False, - array_with_attributes.primary_attributes, - array_with_attributes.custom_attributes, - ) - for method in methods - ], - ) - lock_set.wait() - assert result.count(DekerLockError) == len(methods) - func_finished.set() - - paths = get_paths( - array_with_attributes, - root_path / ctx.config.collections_directory / array_with_attributes.collection, - ) - filename = str(array_with_attributes.id) + storage_adapter.file_ext - file_path = paths.main / filename - symlink = paths.symlink / filename - assert file_path.exists() - assert symlink.exists() - array_with_attributes[:].update(array_data) - - with h5py.File(file_path) as f: - assert np.allclose(f["data"][:], np.asarray(array_data), equal_nan=True) - - if __name__ == "__main__": pytest.main() diff --git a/tests/test_cases/test_schemas/test_attributes_schema.py b/tests/test_cases/test_schemas/test_attributes_schema.py index 1a4e981..247ea53 100644 --- a/tests/test_cases/test_schemas/test_attributes_schema.py +++ b/tests/test_cases/test_schemas/test_attributes_schema.py @@ -4,7 +4,6 @@ from datetime import datetime from typing import FrozenSet -import numpy as np import pytest from deker_local_adapters import LocalArrayAdapter