From 72ae234f410b8146de037b7cf4afaf378055a287 Mon Sep 17 00:00:00 2001 From: Zach Kurtz Date: Thu, 28 Nov 2024 10:02:12 -0500 Subject: [PATCH] add onnx --- README.md | 1 + dummio/__init__.py | 9 +- dummio/constants.py | 20 +++- dummio/onnx.py | 28 +++++ dummio/pandas/__init__.py | 7 -- pyproject.toml | 3 + tests/test_assert_module_protocol.py | 20 ++++ tests/test_onnx.py | 28 +++++ tests/test_pandas.py | 2 - uv.lock | 173 ++++++++++++++++++++++++++- 10 files changed, 279 insertions(+), 12 deletions(-) create mode 100644 dummio/onnx.py create mode 100644 tests/test_assert_module_protocol.py create mode 100644 tests/test_onnx.py diff --git a/README.md b/README.md index c15fa5f..ee07a63 100644 --- a/README.md +++ b/README.md @@ -28,6 +28,7 @@ So far we support: - pandas dataframes: - csv - parquet +- onnx.ModelProto instances ## Dependencies diff --git a/dummio/__init__.py b/dummio/__init__.py index a872e0d..1e2db21 100644 --- a/dummio/__init__.py +++ b/dummio/__init__.py @@ -5,9 +5,16 @@ from dummio import json as json from dummio import text as text +from dummio.constants import ModuleProtocol as ModuleProtocol try: from dummio import yaml as yaml except ImportError: - # yaml is an optional dependency + # this would require an optional yaml dependency such as pyyaml + pass + +try: + from dummio import onnx as onnx +except ImportError: + # this would require the optional dependency onnx pass diff --git a/dummio/constants.py b/dummio/constants.py index 1323831..2ebfd74 100644 --- a/dummio/constants.py +++ b/dummio/constants.py @@ -1,10 +1,28 @@ """Constants for dummio.""" +import typing from pathlib import Path -from typing import Any, TypeAlias +from typing import Any, Protocol, TypeAlias PathType: TypeAlias = str | Path AnyDict: TypeAlias = dict[Any, Any] +# pyright expect a type var to be used at least twice within a single method. It's having +# trouble respecting how it's use *accross* methods of a class. +T = typing.TypeVar("T") # pyright: ignore + DEFAULT_ENCODING = "utf-8" DEFAULT_WRITE_MODE = "w" + + +@typing.runtime_checkable +class ModuleProtocol(Protocol): + """Protocol for dummio's IO modules.""" + + def save(self, data: T, *, filepath: PathType) -> None: # pyright: ignore[reportInvalidTypeVarUse] + """Declares the signature of an IO module save method.""" + ... + + def load(self, filepath: PathType) -> T: # pyright: ignore[reportInvalidTypeVarUse] + """Declares the signature of an IO module load method.""" + ... diff --git a/dummio/onnx.py b/dummio/onnx.py new file mode 100644 index 0000000..ad9f61c --- /dev/null +++ b/dummio/onnx.py @@ -0,0 +1,28 @@ +"""IO methods for sklearn models using ONNX serialization.""" + +import onnx + +from dummio.constants import PathType + + +def save(data: onnx.ModelProto, *, filepath: PathType) -> None: + """Saves a sklearn model to a file using ONNX serialization. + + Args: + data: Data to save. This needs to be an sklearn model. + filepath: Path to save the data. + """ + byte_str = data.SerializeToString() + with open(filepath, "wb") as file: + file.write(byte_str) + + +def load(filepath: PathType) -> onnx.ModelProto: + """Loads a sklearn model from a file using ONNX serialization. + + Args: + filepath: Path to read the data. + """ + with open(filepath, "rb") as file: + byte_str = file.read() + return onnx.load_model_from_string(byte_str) diff --git a/dummio/pandas/__init__.py b/dummio/pandas/__init__.py index b176500..f939c86 100644 --- a/dummio/pandas/__init__.py +++ b/dummio/pandas/__init__.py @@ -1,9 +1,2 @@ -try: - import pandas - - del pandas -except ImportError: - raise ImportError("Please install pandas to use dummio.pandas") - from dummio.pandas import df_csv as df_csv from dummio.pandas import df_parquet as df_parquet diff --git a/pyproject.toml b/pyproject.toml index 51f2885..9b426ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,11 +12,14 @@ dev = [ "pyright >=1.1.378", "ruff >=0.7.4", "pytest >=8.3.2", + "scikit-learn >=1.0.2", + "skl2onnx >=1.10.1", ] extras = [ "fastparquet>=2024.11.0", "pandas>=1.5.0", "pyyaml>=6.0.2", + "onnx>=1.10.1", ] [project.urls] diff --git a/tests/test_assert_module_protocol.py b/tests/test_assert_module_protocol.py new file mode 100644 index 0000000..c54c6e7 --- /dev/null +++ b/tests/test_assert_module_protocol.py @@ -0,0 +1,20 @@ +"""Assert that every IO module implements the ModuleProtocol.""" + +import importlib + +from dummio import ModuleProtocol + +IO_MODULES = [ + "dummio.json", + "dummio.onnx", + "dummio.text", + "dummio.yaml", + "dummio.pandas.df_csv", + "dummio.pandas.df_parquet", +] + + +def test_assert_module_protocol() -> None: + for module_name in IO_MODULES: + module = importlib.import_module(module_name) + assert isinstance(module, ModuleProtocol) diff --git a/tests/test_onnx.py b/tests/test_onnx.py new file mode 100644 index 0000000..6f920c2 --- /dev/null +++ b/tests/test_onnx.py @@ -0,0 +1,28 @@ +import onnx +from skl2onnx import convert_sklearn +from skl2onnx.common.data_types import FloatTensorType +from sklearn.datasets import load_iris +from sklearn.linear_model import LogisticRegression + +from dummio import onnx as onnx_io + + +def test_onnx_io_cycle(tmp_path) -> None: + # Empty model: + model = onnx.ModelProto() + filepath = tmp_path / "model.onnx" + onnx_io.save(model, filepath=filepath) + loaded_model = onnx_io.load(filepath=filepath) + assert model.SerializeToString() == loaded_model.SerializeToString() + + # Minimal sklearn model: + iris = load_iris() + clr = LogisticRegression(solver="saga", max_iter=10000) + clr.fit(iris.data, iris.target) # pyright: ignore[reportAttributeAccessIssue] + initial_type = [("float_input", FloatTensorType([None, 4]))] + onx = convert_sklearn(clr, initial_types=initial_type) + assert isinstance(onx, onnx.ModelProto) # pyright wasn't sure + filepath = tmp_path / "model.onnx" + onnx_io.save(onx, filepath=filepath) + loaded_onx = onnx_io.load(filepath=filepath) + assert onx.SerializeToString() == loaded_onx.SerializeToString() diff --git a/tests/test_pandas.py b/tests/test_pandas.py index e86fd82..b5e901a 100644 --- a/tests/test_pandas.py +++ b/tests/test_pandas.py @@ -1,5 +1,3 @@ -"""Test IO methods for tabulare data types.""" - from pathlib import Path from types import ModuleType diff --git a/uv.lock b/uv.lock index 3ccd6b3..fc02084 100644 --- a/uv.lock +++ b/uv.lock @@ -104,7 +104,7 @@ wheels = [ [[package]] name = "dummio" -version = "0.2.0" +version = "1.0.0" source = { editable = "." } [package.dev-dependencies] @@ -113,9 +113,12 @@ dev = [ { name = "pyright" }, { name = "pytest" }, { name = "ruff" }, + { name = "scikit-learn" }, + { name = "skl2onnx" }, ] extras = [ { name = "fastparquet" }, + { name = "onnx" }, { name = "pandas" }, { name = "pyyaml" }, ] @@ -128,9 +131,12 @@ dev = [ { name = "pyright", specifier = ">=1.1.378" }, { name = "pytest", specifier = ">=8.3.2" }, { name = "ruff", 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