diff --git a/docs/conf.py b/docs/conf.py index 3060786..de06ff1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -4,16 +4,15 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html import os -import re -import sys from datetime import date from linkml_arrays import __version__ + # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = 'linkml-arrays' +project = "linkml-arrays" copyright = f"{date.today().year}, Ryan Ly " -author = 'Ryan Ly ' +author = "Ryan Ly " release = __version__ # -- General configuration --------------------------------------------------- @@ -25,7 +24,7 @@ "sphinx_rtd_theme", "sphinx_click", "sphinx_autodoc_typehints", - "myst_parser" + "myst_parser", ] # generate autosummary pages @@ -46,13 +45,13 @@ # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] -templates_path = ['_templates'] +templates_path = ["_templates"] # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -html_theme = 'sphinx_rtd_theme' -html_static_path = ['_static'] +html_theme = "sphinx_rtd_theme" +html_static_path = ["_static"] # The name of an image file (relative to this directory) to place at the top # of the sidebar. diff --git a/poetry.lock b/poetry.lock index 60c75c0..b870fe9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,15 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] [[package]] name = "asciitree" @@ -12,126 +23,142 @@ files = [ [[package]] name = "attrs" -version = "23.1.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, - {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, ] [package.extras] cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[docs,tests]", "pre-commit"] +dev = ["attrs[tests]", "pre-commit"] docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] tests = ["attrs[tests-no-zope]", "zope-interface"] -tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] +tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] [[package]] name = "certifi" -version = "2022.12.7" +version = "2024.2.2" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"}, - {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"}, + {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, + {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, ] [[package]] name = "charset-normalizer" -version = "3.1.0" +version = "3.3.2" description = "The Real First Universal Charset Detector. 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] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] docs = [] @@ -1032,4 +1323,4 @@ docs = [] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "b345306101c64964677ffccc014ab1cefada92d3ab8dc293446a23a2876110d6" +content-hash = 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-11,6 +13,7 @@ logger = logging.getLogger(__name__) + @click.group() @click.option("-v", "--verbose", count=True) @click.option("-q", "--quiet") @@ -30,11 +33,11 @@ def main(verbose: int, quiet: bool): if quiet: logger.setLevel(level=logging.ERROR) + @main.command() def run(): """Run the linkml-arrays's demo command.""" demo() - if __name__ == "__main__": diff --git a/src/linkml_arrays/dumpers/__init__.py b/src/linkml_arrays/dumpers/__init__.py index fc4252e..8a080d9 100644 --- a/src/linkml_arrays/dumpers/__init__.py +++ b/src/linkml_arrays/dumpers/__init__.py @@ -1,5 +1,13 @@ """Dumper classes for linkml-arrays.""" -from .yaml_numpy_dumper import YamlNumpyDumper -from .yaml_hdf5_dumper import YamlHdf5Dumper + from .hdf5_dumper import Hdf5Dumper -from .zarr_directory_store_dumper import ZarrDirectoryStoreDumper \ No newline at end of file +from .yaml_hdf5_dumper import YamlHdf5Dumper +from .yaml_numpy_dumper import YamlNumpyDumper +from .zarr_directory_store_dumper import ZarrDirectoryStoreDumper + +__all__ = [ + "Hdf5Dumper", + "YamlHdf5Dumper", + "YamlNumpyDumper", + "ZarrDirectoryStoreDumper", +] diff --git a/src/linkml_arrays/dumpers/hdf5_dumper.py b/src/linkml_arrays/dumpers/hdf5_dumper.py index 90c25ed..28e8bf0 100644 --- a/src/linkml_arrays/dumpers/hdf5_dumper.py +++ b/src/linkml_arrays/dumpers/hdf5_dumper.py @@ -1,18 +1,22 @@ +"""Class for dumping a LinkML model to an HDF5 file.""" + from typing import Union import h5py -from pydantic import BaseModel - +from linkml_runtime import SchemaView from linkml_runtime.dumpers.dumper_root import Dumper from linkml_runtime.utils.yamlutils import YAMLRoot -from linkml_runtime import SchemaView +from pydantic import BaseModel -def iterate_element( - element: Union[YAMLRoot, BaseModel], - schemaview: SchemaView, - group: h5py.Group = None +def _iterate_element( + element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, group: h5py.Group = None ): + """Recursively iterate through the elements of a LinkML model and save them. + + Writes Pydantic BaseModel objects as groups, slots that implement "linkml:elements" + as datasets, and other slots as attributes. + """ # get the type of the element element_type = type(element).__name__ @@ -25,23 +29,26 @@ def iterate_element( if isinstance(v, BaseModel): # create a subgroup and recurse subgroup = group.create_group(k) - iterate_element(v, schemaview, subgroup) + _iterate_element(v, schemaview, subgroup) else: # create an attribute on the group group.attrs[k] = v class Hdf5Dumper(Dumper): + """Dumper class for LinkML models to HDF5 files.""" + + # TODO is this the right method to overwrite? it does not dump a string + def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **kwargs): + """Dump the element to an HDF5 file. - def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **kwargs) -> str: - """ Return element formatted as a YAML string with paths to HDF5 files containing the arrays as datasets""" + Raises: + ValueError: If the class requires an identifier and it is not provided. + """ id_slot = schemaview.get_identifier_slot(element.__class__.__name__) if id_slot is None: raise ValueError("The class requires an identifier.") id_value = getattr(element, id_slot.name) output_file_path = f"{id_value}.h5" with h5py.File(output_file_path, "w") as f: - iterate_element(element, schemaview, f) - - - + _iterate_element(element, schemaview, f) diff --git a/src/linkml_arrays/dumpers/yaml_hdf5_dumper.py b/src/linkml_arrays/dumpers/yaml_hdf5_dumper.py index 493599f..0d95fe8 100644 --- a/src/linkml_arrays/dumpers/yaml_hdf5_dumper.py +++ b/src/linkml_arrays/dumpers/yaml_hdf5_dumper.py @@ -1,15 +1,28 @@ +"""Class for dumping a LinkML model to a YAML file with paths to HDF5 files.""" + from typing import Union import h5py -from pydantic import BaseModel import yaml - +from linkml_runtime import SchemaView from linkml_runtime.dumpers.dumper_root import Dumper from linkml_runtime.utils.yamlutils import YAMLRoot -from linkml_runtime import SchemaView +from pydantic import BaseModel + + +def _iterate_element( + element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, parent_identifier=None +): + """Recursively iterate through the elements of a LinkML model and save them. + Returns a dictionary with the same structure as the input element, but with the slots + that implement "linkml:elements" (arrays) are written to HDF5 files and the paths to these + files are returned in the dictionary. Each array is written to an HDF5 dataset at path + "/data" in a new HDF5 file. -def iterate_element(element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, parent_identifier = None): + Raises: + ValueError: If the class requires an identifier and it is not provided. + """ # get the type of the element element_type = type(element).__name__ @@ -33,12 +46,14 @@ def iterate_element(element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, output_file_path = f"{parent_identifier}.{found_class.name}.{found_slot.name}.h5" else: output_file_path = f"{found_class.name}.{found_slot.name}.h5" - with h5py.File(output_file_path, "w") as f: # TODO do not assume that there is only one by this name + with h5py.File( + output_file_path, "w" + ) as f: # TODO do not assume that there is only one by this name f.create_dataset("data", data=v) ret_dict[k] = f"file:./{output_file_path}" # TODO make this nicer else: if isinstance(v, BaseModel): - v2 = iterate_element(v, schemaview, id_value) + v2 = _iterate_element(v, schemaview, id_value) ret_dict[k] = v2 else: ret_dict[k] = v @@ -46,11 +61,10 @@ def iterate_element(element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, class YamlHdf5Dumper(Dumper): + """Class for dumping a LinkML model to a YAML file with paths to HDF5 files.""" def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **kwargs) -> str: - """ Return element formatted as a YAML string with paths to HDF5 files containing the arrays as datasets""" - input = iterate_element(element, schemaview) + """Return element formatted as a YAML string.""" + input = _iterate_element(element, schemaview) return yaml.dump(input) - - diff --git a/src/linkml_arrays/dumpers/yaml_numpy_dumper.py b/src/linkml_arrays/dumpers/yaml_numpy_dumper.py index 9a13fe1..71433be 100644 --- a/src/linkml_arrays/dumpers/yaml_numpy_dumper.py +++ b/src/linkml_arrays/dumpers/yaml_numpy_dumper.py @@ -1,15 +1,28 @@ +"""Class for dumpling a LinkML model to a YAML file with paths to NumPy files.""" + from typing import Union import numpy as np -from pydantic import BaseModel import yaml - +from linkml_runtime import SchemaView from linkml_runtime.dumpers.dumper_root import Dumper from linkml_runtime.utils.yamlutils import YAMLRoot -from linkml_runtime import SchemaView +from pydantic import BaseModel + + +def _iterate_element( + element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, parent_identifier=None +): + """Recursively iterate through the elements of a LinkML model and save them. + Returns a dictionary with the same structure as the input element, but with the slots + that implement "linkml:elements" (arrays) are written to HDF5 files and the paths to these + files are returned in the dictionary. Each array is written to an HDF5 dataset at path + "/data" in a new HDF5 file. -def iterate_element(element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, parent_identifier = None): + Raises: + ValueError: If the class requires an identifier and it is not provided. + """ # get the type of the element element_type = type(element).__name__ @@ -37,7 +50,7 @@ def iterate_element(element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, ret_dict[k] = f"file:./{output_file_path}" # TODO make this nicer else: if isinstance(v, BaseModel): - v2 = iterate_element(v, schemaview, id_value) + v2 = _iterate_element(v, schemaview, id_value) ret_dict[k] = v2 else: ret_dict[k] = v @@ -45,11 +58,10 @@ def iterate_element(element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, class YamlNumpyDumper(Dumper): + """Dumper class for LinkML models to YAML files with paths to NumPy files.""" def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **kwargs) -> str: - """ Return element formatted as a YAML string with paths to numpy files containing the ndarrays""" - input = iterate_element(element, schemaview) + """Return element formatted as a YAML string.""" + input = _iterate_element(element, schemaview) return yaml.dump(input) - - diff --git a/src/linkml_arrays/dumpers/zarr_directory_store_dumper.py b/src/linkml_arrays/dumpers/zarr_directory_store_dumper.py index ae98747..2c899ec 100644 --- a/src/linkml_arrays/dumpers/zarr_directory_store_dumper.py +++ b/src/linkml_arrays/dumpers/zarr_directory_store_dumper.py @@ -1,18 +1,22 @@ +"""Class for dumping a LinkML model to a Zarr directory store.""" + from typing import Union import zarr -from pydantic import BaseModel - +from linkml_runtime import SchemaView from linkml_runtime.dumpers.dumper_root import Dumper from linkml_runtime.utils.yamlutils import YAMLRoot -from linkml_runtime import SchemaView +from pydantic import BaseModel -def iterate_element( - element: Union[YAMLRoot, BaseModel], - schemaview: SchemaView, - group: zarr.hierarchy.Group = None +def _iterate_element( + element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, group: zarr.hierarchy.Group = None ): + """Recursively iterate through the elements of a LinkML model and save them. + + Writes Pydantic BaseModel objects as groups, slots that implement "linkml:elements" + as datasets, and other slots as attributes. + """ # get the type of the element element_type = type(element).__name__ @@ -25,16 +29,22 @@ def iterate_element( if isinstance(v, BaseModel): # create a subgroup and recurse subgroup = group.create_group(k) - iterate_element(v, schemaview, subgroup) + _iterate_element(v, schemaview, subgroup) else: # create an attribute on the group group.attrs[k] = v class ZarrDirectoryStoreDumper(Dumper): + """Dumper class for LinkML models to Zarr directory stores.""" + + # TODO is this the right method to overwrite? it does not dump a string + def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **kwargs): + """Dump the element to a Zarr directory store. - def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **kwargs) -> str: - """ Return element formatted as a YAML string with paths to HDF5 files containing the arrays as datasets""" + Raises: + ValueError: If the class requires an identifier and it is not provided. + """ id_slot = schemaview.get_identifier_slot(element.__class__.__name__) if id_slot is None: raise ValueError("The class requires an identifier.") @@ -42,7 +52,4 @@ def dumps(self, element: Union[YAMLRoot, BaseModel], schemaview: SchemaView, **k output_file_path = f"{id_value}.zarr" store = zarr.DirectoryStore(output_file_path) root = zarr.group(store=store, overwrite=True) - iterate_element(element, schemaview, root) - - - + _iterate_element(element, schemaview, root) diff --git a/src/linkml_arrays/loaders/__init__.py b/src/linkml_arrays/loaders/__init__.py index f21765b..44a9c5b 100644 --- a/src/linkml_arrays/loaders/__init__.py +++ b/src/linkml_arrays/loaders/__init__.py @@ -1,5 +1,13 @@ """Dumper classes for linkml-arrays.""" -from .yaml_numpy_loader import YamlNumpyLoader -from .yaml_hdf5_loader import YamlHdf5Loader + from .hdf5_loader import Hdf5Loader -from .zarr_directory_store_loader import ZarrDirectoryStoreLoader \ No newline at end of file +from .yaml_hdf5_loader import YamlHdf5Loader +from .yaml_numpy_loader import YamlNumpyLoader +from .zarr_directory_store_loader import ZarrDirectoryStoreLoader + +__all__ = [ + "Hdf5Loader", + "YamlHdf5Loader", + "YamlNumpyLoader", + "ZarrDirectoryStoreLoader", +] diff --git a/src/linkml_arrays/loaders/hdf5_loader.py b/src/linkml_arrays/loaders/hdf5_loader.py index 30bbd4c..92e6bff 100644 --- a/src/linkml_arrays/loaders/hdf5_loader.py +++ b/src/linkml_arrays/loaders/hdf5_loader.py @@ -1,27 +1,36 @@ +"""Class for loading a LinkML model from an HDF5 file.""" + from typing import Type, Union import h5py -from pydantic import BaseModel - -from linkml_runtime.loaders.loader_root import Loader -from linkml_runtime.utils.yamlutils import YAMLRoot from linkml_runtime import SchemaView from linkml_runtime.linkml_model import ClassDefinition +from linkml_runtime.loaders.loader_root import Loader +from linkml_runtime.utils.yamlutils import YAMLRoot +from pydantic import BaseModel + +def _iterate_element( + group: h5py.Group, element_type: ClassDefinition, schemaview: SchemaView +) -> dict: + """Recursively iterate through the elements of a LinkML model and load them into a dict. -def iterate_element(group: h5py.Group, element_type: ClassDefinition, schemaview: SchemaView) -> dict: + Datasets are read into memory. + """ ret_dict = dict() for k, v in group.attrs.items(): ret_dict[k] = v for k, v in group.items(): - found_slot = schemaview.induced_slot(k, element_type.name) # assumes the slot name has been written as the name which is OK for now. + found_slot = schemaview.induced_slot( + k, element_type.name + ) # assumes the slot name has been written as the name which is OK for now. if "linkml:elements" in found_slot.implements: assert isinstance(v, h5py.Dataset) - v = v[()] # read all the values into memory + v = v[()] # read all the values into memory TODO: support lazy loading elif isinstance(v, h5py.Group): # it's a subgroup found_slot_range = schemaview.get_class(found_slot.range) - v = iterate_element(v, found_slot_range, schemaview) + v = _iterate_element(v, found_slot_range, schemaview) # else: do not transform v ret_dict[k] = v @@ -29,22 +38,27 @@ def iterate_element(group: h5py.Group, element_type: ClassDefinition, schemaview class Hdf5Loader(Loader): + """Class for loading a LinkML model from an HDF5 file.""" def load_any(self, source: str, **kwargs): - """ Return element formatted as a YAML string with the path to an HDF5 file""" + """Create an instance of the target class from an HDF5 file.""" return self.load(source, **kwargs) def loads(self, source: str, **kwargs): - """ Return element formatted as a YAML string with the path to an HDF5 file""" + """Create an instance of the target class from an HDF5 file.""" return self.load(source, **kwargs) - def load(self, source: str, target_class: Type[Union[YAMLRoot, BaseModel]], schemaview: SchemaView, **kwargs): - """ Return element formatted as a YAML string with the path to an HDF5 file""" + def load( + self, + source: str, + target_class: Type[Union[YAMLRoot, BaseModel]], + schemaview: SchemaView, + **kwargs, + ): + """Create an instance of the target class from an HDF5 file.""" element_type = schemaview.get_class(target_class.__name__) with h5py.File(source, "r") as f: - element = iterate_element(f, element_type, schemaview) + element = _iterate_element(f, element_type, schemaview) obj = target_class(**element) return obj - - diff --git a/src/linkml_arrays/loaders/yaml_hdf5_loader.py b/src/linkml_arrays/loaders/yaml_hdf5_loader.py index f203e0c..771600f 100644 --- a/src/linkml_arrays/loaders/yaml_hdf5_loader.py +++ b/src/linkml_arrays/loaders/yaml_hdf5_loader.py @@ -1,26 +1,33 @@ +"""Class for loading a LinkML model from a YAML file with HDF5 file paths.""" + from typing import Type, Union import h5py -from pydantic import BaseModel import yaml - -from linkml_runtime.loaders.loader_root import Loader -from linkml_runtime.utils.yamlutils import YAMLRoot from linkml_runtime import SchemaView from linkml_runtime.linkml_model import ClassDefinition +from linkml_runtime.loaders.loader_root import Loader +from linkml_runtime.utils.yamlutils import YAMLRoot +from pydantic import BaseModel + +def _iterate_element( + input_dict: dict, element_type: ClassDefinition, schemaview: SchemaView +) -> dict: + """Recursively iterate through the elements of a LinkML model and load them into a dict. -def iterate_element(input_dict: dict, element_type: ClassDefinition, schemaview: SchemaView) -> dict: + Datasets are read into memory. + """ ret_dict = dict() for k, v in input_dict.items(): found_slot = schemaview.induced_slot(k, element_type.name) if "linkml:elements" in found_slot.implements: array_file_path = v.replace("file:./", "") with h5py.File(array_file_path, "r") as f: - v = f["data"][()] # read all the values into memory + v = f["data"][()] # read all the values into memory TODO: support lazy loading elif isinstance(v, dict): found_slot_range = schemaview.get_class(found_slot.range) - v = iterate_element(v, found_slot_range, schemaview) + v = _iterate_element(v, found_slot_range, schemaview) # else: do not transform v ret_dict[k] = v @@ -28,23 +35,28 @@ def iterate_element(input_dict: dict, element_type: ClassDefinition, schemaview: class YamlHdf5Loader(Loader): + """Class for loading a LinkML model from a YAML file with HDF5 file paths.""" def load_any(self, source: str, **kwargs): - """ Return element formatted as a YAML string with paths to HDF5 files containing the arrays as datasets""" + """Create an instance of the target class from a YAML file with HDF5 file paths.""" return self.load(source, **kwargs) def loads(self, source: str, **kwargs): - """ Return element formatted as a YAML string with paths to HDF5 files containing the arrays as datasets""" + """Create an instance of the target class from a YAML file with HDF5 file paths.""" return self.load(source, **kwargs) - def load(self, source: str, target_class: Type[Union[YAMLRoot, BaseModel]], schemaview: SchemaView, **kwargs): - """ Return element formatted as a YAML string with paths to HDF5 files containing the arrays as datasets""" + def load( + self, + source: str, + target_class: Type[Union[YAMLRoot, BaseModel]], + schemaview: SchemaView, + **kwargs, + ): + """Create an instance of the target class from a YAML file with HDF5 file paths.""" input_dict = yaml.safe_load(source) element_type = schemaview.get_class(target_class.__name__) - element = iterate_element(input_dict, element_type, schemaview) + element = _iterate_element(input_dict, element_type, schemaview) obj = target_class(**element) return obj - - diff --git a/src/linkml_arrays/loaders/yaml_numpy_loader.py b/src/linkml_arrays/loaders/yaml_numpy_loader.py index 5fab4e1..5b2bd63 100644 --- a/src/linkml_arrays/loaders/yaml_numpy_loader.py +++ b/src/linkml_arrays/loaders/yaml_numpy_loader.py @@ -1,25 +1,32 @@ +"""Class for loading a LinkML model from a YAML file with NumPy file paths.""" + from typing import Type, Union import numpy as np -from pydantic import BaseModel import yaml - -from linkml_runtime.loaders.loader_root import Loader -from linkml_runtime.utils.yamlutils import YAMLRoot from linkml_runtime import SchemaView from linkml_runtime.linkml_model import ClassDefinition +from linkml_runtime.loaders.loader_root import Loader +from linkml_runtime.utils.yamlutils import YAMLRoot +from pydantic import BaseModel + +def _iterate_element( + input_dict: dict, element_type: ClassDefinition, schemaview: SchemaView +) -> dict: + """Recursively iterate through the elements of a LinkML model and load them into a dict. -def iterate_element(input_dict: dict, element_type: ClassDefinition, schemaview: SchemaView) -> dict: + Datasets are read into memory. + """ ret_dict = dict() for k, v in input_dict.items(): found_slot = schemaview.induced_slot(k, element_type.name) if "linkml:elements" in found_slot.implements: array_file_path = v.replace("file:./", "") - v = np.load(array_file_path) + v = np.load(array_file_path) # TODO: support lazy loading elif isinstance(v, dict): found_slot_range = schemaview.get_class(found_slot.range) - v = iterate_element(v, found_slot_range, schemaview) + v = _iterate_element(v, found_slot_range, schemaview) # else: do not transform v ret_dict[k] = v @@ -27,23 +34,28 @@ def iterate_element(input_dict: dict, element_type: ClassDefinition, schemaview: class YamlNumpyLoader(Loader): + """Class for loading a LinkML model from a YAML file with NumPy file paths.""" def load_any(self, source: str, **kwargs): - """ Return element formatted as a YAML string with paths to numpy files containing the ndarrays""" + """Create an instance of the target class from a YAML file with NumPy file paths.""" return self.load(source, **kwargs) def loads(self, source: str, **kwargs): - """ Return element formatted as a YAML string with paths to numpy files containing the ndarrays""" + """Create an instance of the target class from a YAML file with NumPy file paths.""" return self.load(source, **kwargs) - def load(self, source: str, target_class: Type[Union[YAMLRoot, BaseModel]], schemaview: SchemaView, **kwargs): - """ Return element formatted as a YAML string with paths to numpy files containing the ndarrays""" + def load( + self, + source: str, + target_class: Type[Union[YAMLRoot, BaseModel]], + schemaview: SchemaView, + **kwargs, + ): + """Create an instance of the target class from a YAML file with NumPy file paths.""" input_dict = yaml.safe_load(source) element_type = schemaview.get_class(target_class.__name__) - element = iterate_element(input_dict, element_type, schemaview) + element = _iterate_element(input_dict, element_type, schemaview) obj = target_class(**element) return obj - - diff --git a/src/linkml_arrays/loaders/zarr_directory_store_loader.py b/src/linkml_arrays/loaders/zarr_directory_store_loader.py index b3e76cc..29707d5 100644 --- a/src/linkml_arrays/loaders/zarr_directory_store_loader.py +++ b/src/linkml_arrays/loaders/zarr_directory_store_loader.py @@ -1,27 +1,36 @@ +"""Class for loading a LinkML model from a Zarr directory store.""" + from typing import Type, Union import zarr -from pydantic import BaseModel - -from linkml_runtime.loaders.loader_root import Loader -from linkml_runtime.utils.yamlutils import YAMLRoot from linkml_runtime import SchemaView from linkml_runtime.linkml_model import ClassDefinition +from linkml_runtime.loaders.loader_root import Loader +from linkml_runtime.utils.yamlutils import YAMLRoot +from pydantic import BaseModel + +def _iterate_element( + group: zarr.hierarchy.Group, element_type: ClassDefinition, schemaview: SchemaView +) -> dict: + """Recursively iterate through the elements of a LinkML model and load them into a dict. -def iterate_element(group: zarr.hierarchy.Group, element_type: ClassDefinition, schemaview: SchemaView) -> dict: + Datasets are read into memory. + """ ret_dict = dict() for k, v in group.attrs.items(): ret_dict[k] = v for k, v in group.items(): - found_slot = schemaview.induced_slot(k, element_type.name) # assumes the slot name has been written as the name which is OK for now. + found_slot = schemaview.induced_slot( + k, element_type.name + ) # assumes the slot name has been written as the name which is OK for now. if "linkml:elements" in found_slot.implements: assert isinstance(v, zarr.Array) - v = v[()] # read all the values into memory + v = v[()] # read all the values into memory # TODO support lazy loading elif isinstance(v, zarr.hierarchy.Group): # it's a subgroup found_slot_range = schemaview.get_class(found_slot.range) - v = iterate_element(v, found_slot_range, schemaview) + v = _iterate_element(v, found_slot_range, schemaview) # else: do not transform v ret_dict[k] = v @@ -29,22 +38,27 @@ def iterate_element(group: zarr.hierarchy.Group, element_type: ClassDefinition, class ZarrDirectoryStoreLoader(Loader): + """Class for loading a LinkML model from a Zarr directory store.""" def load_any(self, source: str, **kwargs): - """ Return element formatted as a YAML string with the path to a Zarr directory store""" + """Create an instance of the target class from a Zarr directory store.""" return self.load(source, **kwargs) def loads(self, source: str, **kwargs): - """ Return element formatted as a YAML string with the path to a Zarr directory store""" + """Create an instance of the target class from a Zarr directory store.""" return self.load(source, **kwargs) - def load(self, source: str, target_class: Type[Union[YAMLRoot, BaseModel]], schemaview: SchemaView, **kwargs): - """ Return element formatted as a YAML string with the path to a Zarr directory store""" + def load( + self, + source: str, + target_class: Type[Union[YAMLRoot, BaseModel]], + schemaview: SchemaView, + **kwargs, + ): + """Create an instance of the target class from a Zarr directory store.""" element_type = schemaview.get_class(target_class.__name__) z = zarr.open(source, mode="r") - element = iterate_element(z, element_type, schemaview) + element = _iterate_element(z, element_type, schemaview) obj = target_class(**element) return obj - - diff --git a/src/linkml_arrays/main.py b/src/linkml_arrays/main.py index ac70b87..5a05fe2 100644 --- a/src/linkml_arrays/main.py +++ b/src/linkml_arrays/main.py @@ -1,9 +1,10 @@ """Main python file.""" + def demo(): """Define API.""" print("Hello, World!") -if __name__ == '__main__': +if __name__ == "__main__": demo() diff --git a/tests/__init__.py b/tests/__init__.py index 0ce79f8..4060715 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1 +1 @@ -"""Tests for linkml-arrays.""" \ No newline at end of file +"""Tests for linkml-arrays.""" diff --git a/tests/demo_test.py b/tests/demo_test.py index f6e448d..1eaf64b 100644 --- a/tests/demo_test.py +++ b/tests/demo_test.py @@ -10,4 +10,4 @@ class TestVersion(unittest.TestCase): def test_version_type(self): """Demo test.""" - self.assertIsInstance(__version__, str) \ No newline at end of file + self.assertIsInstance(__version__, str) diff --git a/tests/test_dumpers/__init__.py b/tests/test_dumpers/__init__.py index 169c228..a176c6a 100644 --- a/tests/test_dumpers/__init__.py +++ b/tests/test_dumpers/__init__.py @@ -1 +1 @@ -"""Tests for dumpers of linkml-arrays.""" \ No newline at end of file +"""Tests for dumpers of linkml-arrays.""" diff --git a/tests/test_dumpers/array_classes.py b/tests/test_dumpers/array_classes.py index 5b94a5c..1656a5c 100644 --- a/tests/test_dumpers/array_classes.py +++ b/tests/test_dumpers/array_classes.py @@ -1,81 +1,68 @@ from __future__ import annotations -from datetime import datetime, date -from enum import Enum import numpy as np -from typing import List, Dict, Optional, Any, Union -from pydantic import BaseModel as BaseModel, Field, validator -import re -import sys -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal +from pydantic import BaseModel as BaseModel, ConfigDict, Field metamodel_version = "None" version = "None" -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = 'forbid', - arbitrary_types_allowed = True, - use_enum_values = True): +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment=True, + validate_default=True, + extra="forbid", + arbitrary_types_allowed=True, + use_enum_values=True, + ) pass class TemperatureDataset(ConfiguredBaseModel): - + name: str = Field(...) latitude_in_deg: LatitudeSeries = Field(...) longitude_in_deg: LongitudeSeries = Field(...) time_in_d: DaySeries = Field(...) temperatures_in_K: TemperatureMatrix = Field(...) - - + class TemperatureMatrix(ConfiguredBaseModel): """ A 3D array of temperatures """ + values: np.ndarray = Field(None) - - + class LatitudeSeries(ConfiguredBaseModel): """ A series whose values represent latitude """ + values: np.ndarray = Field(None) - - + class LongitudeSeries(ConfiguredBaseModel): """ A series whose values represent longitude """ + values: np.ndarray = Field(None) - - + class DaySeries(ConfiguredBaseModel): """ A series whose values represent the days since the start of the measurement period """ - values: np.ndarray = Field(None) - - + values: np.ndarray = Field(None) -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -TemperatureDataset.update_forward_refs() -TemperatureMatrix.update_forward_refs() -LatitudeSeries.update_forward_refs() -LongitudeSeries.update_forward_refs() -DaySeries.update_forward_refs() +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +TemperatureDataset.model_rebuild() +TemperatureMatrix.model_rebuild() +LatitudeSeries.model_rebuild() +LongitudeSeries.model_rebuild() +DaySeries.model_rebuild() diff --git a/tests/test_dumpers/test_dumpers.py b/tests/test_dumpers/test_dumpers.py index 3511484..2c65612 100644 --- a/tests/test_dumpers/test_dumpers.py +++ b/tests/test_dumpers/test_dumpers.py @@ -1,24 +1,32 @@ -import unittest +"""Test dumping LinkML models in pydantic-style classes to various file formats.""" -import h5py +import os +import unittest from pathlib import Path + import numpy as np -import os -from linkml_arrays.dumpers import YamlNumpyDumper, YamlHdf5Dumper, Hdf5Dumper, ZarrDirectoryStoreDumper from linkml_runtime import SchemaView +from linkml_arrays.dumpers import ( + Hdf5Dumper, + YamlHdf5Dumper, + YamlNumpyDumper, + ZarrDirectoryStoreDumper, +) from tests.test_dumpers.array_classes import ( - LatitudeSeries, LongitudeSeries, DaySeries, - TemperatureMatrix, TemperatureDataset - ) + DaySeries, + LatitudeSeries, + LongitudeSeries, + TemperatureDataset, + TemperatureMatrix, +) class YamlNumpyDumpersTestCase(unittest.TestCase): - """ - Test dumping of pydantic-style classes from LinkML schemas into YAML + Numpy arrays - """ + """Test dumping of pydantic-style classes from LinkML schemas into YAML + NumPy files.""" def test_dump_pydantic_arrays(self): + """Test dumping pydantic classes with numpy arrays to a YAML + NumPy files.""" latitude_in_deg = LatitudeSeries(values=np.array([1, 2, 3])) longitude_in_deg = LongitudeSeries(values=np.array([4, 5, 6])) time_in_d = DaySeries(values=np.array([7, 8, 9])) @@ -50,11 +58,10 @@ def test_dump_pydantic_arrays(self): class YamlHdf5DumpersTestCase(unittest.TestCase): - """ - Test dumping of pydantic-style classes from LinkML schemas into YAML + HDF5 datasets - """ + """Test dumping of pydantic-style classes from LinkML schemas into YAML + HDF5 datasets.""" def test_dump_pydantic_arrays(self): + """Test dumping pydantic classes with numpy arrays to a YAML + HDF5 datasets.""" latitude_in_deg = LatitudeSeries(values=np.array([1, 2, 3])) longitude_in_deg = LongitudeSeries(values=np.array([4, 5, 6])) time_in_d = DaySeries(values=np.array([7, 8, 9])) @@ -86,11 +93,10 @@ def test_dump_pydantic_arrays(self): class Hdf5DumpersTestCase(unittest.TestCase): - """ - Test dumping of pydantic-style classes from LinkML schemas into a single HDF5 file - """ + """Test dumping of pydantic-style classes from LinkML schemas into a single HDF5 file.""" def test_dump_pydantic_arrays(self): + """Test dumping pydantic classes with numpy arrays to a signle HDF5 file.""" latitude_in_deg = LatitudeSeries(values=np.array([1, 2, 3])) longitude_in_deg = LongitudeSeries(values=np.array([4, 5, 6])) time_in_d = DaySeries(values=np.array([7, 8, 9])) @@ -112,11 +118,10 @@ def test_dump_pydantic_arrays(self): class ZarrDirectoryStoreDumpersTestCase(unittest.TestCase): - """ - Test dumping of pydantic-style classes from LinkML schemas into a single Zarr directory store - """ + """Test dumping of pydantic-style classes from LinkML schemas into a Zarr directory store.""" def test_dump_pydantic_arrays(self): + """Test dumping pydantic classes with numpy arrays to a Zarr directory store.""" latitude_in_deg = LatitudeSeries(values=np.array([1, 2, 3])) longitude_in_deg = LongitudeSeries(values=np.array([4, 5, 6])) time_in_d = DaySeries(values=np.array([7, 8, 9])) @@ -135,5 +140,3 @@ def test_dump_pydantic_arrays(self): ZarrDirectoryStoreDumper().dumps(temperature, schemaview=schemaview) assert os.path.exists("my_temperature.zarr") - - diff --git a/tests/test_loaders/__init__.py b/tests/test_loaders/__init__.py index 2714cfc..b87c3be 100644 --- a/tests/test_loaders/__init__.py +++ b/tests/test_loaders/__init__.py @@ -1 +1 @@ -"""Tests for loaders of linkml-arrays.""" \ No newline at end of file +"""Tests for loaders of linkml-arrays.""" diff --git a/tests/test_loaders/test_loaders.py b/tests/test_loaders/test_loaders.py index 683c452..9fe9eca 100644 --- a/tests/test_loaders/test_loaders.py +++ b/tests/test_loaders/test_loaders.py @@ -1,26 +1,39 @@ -import unittest +"""Test loading data from various file formats into LinkML models.""" -from hbreader import hbread +import unittest from pathlib import Path + import numpy as np +from hbreader import hbread from linkml_runtime import SchemaView -from linkml_arrays.loaders import YamlNumpyLoader, YamlHdf5Loader, Hdf5Loader, ZarrDirectoryStoreLoader +from linkml_arrays.loaders import ( + Hdf5Loader, + YamlHdf5Loader, + YamlNumpyLoader, + ZarrDirectoryStoreLoader, +) from tests.test_dumpers.array_classes import ( - LatitudeSeries, LongitudeSeries, DaySeries, - TemperatureMatrix, TemperatureDataset + DaySeries, + LatitudeSeries, + LongitudeSeries, + TemperatureDataset, + TemperatureMatrix, ) class YamlNumpyLoadersTestCase(unittest.TestCase): - """ - Test loading of pydantic-style classes from YAML + Numpy arrays into LinkML schemas - """ + """Test loading of pydantic-style classes from YAML + Numpy arrays.""" def test_load_pydantic_arrays(self): - read_yaml = hbread("temperature_dataset_npy_dumped.yaml", base_path=str(Path(__file__) / "../../input")) + """Test loading of pydantic-style classes from YAML + Numpy arrays.""" + read_yaml = hbread( + "temperature_dataset_npy_dumped.yaml", base_path=str(Path(__file__) / "../../input") + ) schemaview = SchemaView(Path(__file__) / "../../input/temperature_dataset.yaml") - ret = YamlNumpyLoader().loads(read_yaml, target_class=TemperatureDataset, schemaview=schemaview) + ret = YamlNumpyLoader().loads( + read_yaml, target_class=TemperatureDataset, schemaview=schemaview + ) assert isinstance(ret, TemperatureDataset) assert ret.name == "my_temperature" @@ -39,14 +52,17 @@ def test_load_pydantic_arrays(self): class YamlHdf5LoadersTestCase(unittest.TestCase): - """ - Test loading of pydantic-style classes from YAML + HDF5 datasets into LinkML schemas - """ + """Test loading of pydantic-style classes from YAML + HDF5 datasets.""" def test_load_pydantic_arrays(self): - read_yaml = hbread("temperature_dataset_hdf5_dumped.yaml", base_path=str(Path(__file__) / "../../input")) + """Test loading of pydantic-style classes from YAML + HDF5 datasets.""" + read_yaml = hbread( + "temperature_dataset_hdf5_dumped.yaml", base_path=str(Path(__file__) / "../../input") + ) schemaview = SchemaView(Path(__file__) / "../../input/temperature_dataset.yaml") - ret = YamlHdf5Loader().loads(read_yaml, target_class=TemperatureDataset, schemaview=schemaview) + ret = YamlHdf5Loader().loads( + read_yaml, target_class=TemperatureDataset, schemaview=schemaview + ) assert isinstance(ret, TemperatureDataset) assert ret.name == "my_temperature" @@ -65,11 +81,10 @@ def test_load_pydantic_arrays(self): class Hdf5LoadersTestCase(unittest.TestCase): - """ - Test loading of pydantic-style classes from an HDF5 file into LinkML schemas - """ + """Test loading of pydantic-style classes from an HDF5 file.""" def test_load_pydantic_arrays(self): + """Test loading of pydantic-style classes from an HDF5 file.""" file_path = str(Path(__file__).parent.parent / "input" / "my_temperature.h5") schemaview = SchemaView(Path(__file__) / "../../input/temperature_dataset.yaml") ret = Hdf5Loader().loads(file_path, target_class=TemperatureDataset, schemaview=schemaview) @@ -91,14 +106,15 @@ def test_load_pydantic_arrays(self): class ZarrDirectoryStoreLoadersTestCase(unittest.TestCase): - """ - Test loading of pydantic-style classes from a Zarr directory store file into LinkML schemas - """ + """Test loading of pydantic-style classes from a Zarr directory store.""" def test_load_pydantic_arrays(self): + """Test loading of pydantic-style classes from a Zarr directory store.""" file_path = str(Path(__file__).parent.parent / "input" / "my_temperature.zarr") schemaview = SchemaView(Path(__file__) / "../../input/temperature_dataset.yaml") - ret = ZarrDirectoryStoreLoader().loads(file_path, target_class=TemperatureDataset, schemaview=schemaview) + ret = ZarrDirectoryStoreLoader().loads( + file_path, target_class=TemperatureDataset, schemaview=schemaview + ) assert isinstance(ret, TemperatureDataset) assert ret.name == "my_temperature" @@ -114,4 +130,3 @@ def test_load_pydantic_arrays(self): assert isinstance(ret.temperatures_in_K, TemperatureMatrix) np.testing.assert_array_equal(ret.temperatures_in_K.values, np.ones((3, 3, 3))) - diff --git a/tox.ini b/tox.ini index 51541be..19869bd 100644 --- a/tox.ini +++ b/tox.ini @@ -71,12 +71,16 @@ description = Run the flake8 tool with several plugins (bandit, docstrings, impo # (.flake8) # ######################### [flake8] +max-line-length = 100 ignore = DAR101 # Missing parameter(s) in Docstring: - with_git_hash DAR201 # Missing "Returns" in Docstring: - return DAR301 # Missing "Yields" in Docstring: - yield E111 # indentation is not a multiple of 4 T201 # print found. + S101 # Use of assert detected. +exclude = + tests/test_dumpers/array_classes.py [testenv:mypy] deps = mypy