diff --git a/.github/release.yml b/.github/release.yml index aaad370..4ba92c1 100644 --- a/.github/release.yml +++ b/.github/release.yml @@ -20,4 +20,4 @@ changelog: - ci - title: 🤷🏻 Other changes labels: - - '*' + - "*" diff --git a/.github/scripts/read_version.sh b/.github/scripts/read_version.sh index 97a6446..d2397ae 100755 --- a/.github/scripts/read_version.sh +++ b/.github/scripts/read_version.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash -# first get line with version_info, then extract thing in parantheses, then replace ", " with "." +# first get line with version_info, then extract thing in parentheses, then replace ", " with "." grep "version_info =" | sed "s/^.*(\([^()]*\)).*$/\1/" | sed "s/, /./g" diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index fd52437..eb8a6c0 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -23,13 +23,13 @@ jobs: cache-name: benchmark-model-cache with: path: examples/benchmark_models - key: models-${{ hashFiles('benchmark.py', '.github/workflows/benchmark.yml') }} + key: models-${{ hashFiles('examples/benchmark.py', '.github/workflows/benchmark.yml') }} - name: Run benchmark run: | - python benchmark.py + python examples/benchmark.py echo "_(benchmark **${{ github.run_id }}** / attempt **${{ github.run_attempt }}**)_" >> result.md cat benchmark.md >> result.md - shell: pixi run bash {0} + shell: pixi run bash -e {0} - name: Comment on PR uses: actions/github-script@v7 if: github.event_name == 'pull_request' diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1ffa632..19eb617 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -53,19 +53,8 @@ jobs: steps: - name: Checkout branch uses: actions/checkout@v4 + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.6.0 - uses: quantco/pre-commit-conda@v1 with: - python-version: '3.8' - - lint-workflow-files: - name: "Lint workflow files" - runs-on: ubuntu-latest - steps: - - name: Checkout branch - uses: actions/checkout@v4 - # https://github.com/rhysd/actionlint/blob/main/docs/usage.md#use-actionlint-on-github-actions - - name: Download actionlint - id: get_actionlint - run: bash <(curl https://raw.githubusercontent.com/rhysd/actionlint/main/scripts/download-actionlint.bash) - - name: Check workflow files - run: ${{ steps.get_actionlint.outputs.executable }} -color + python-version: "3.8" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e676059..0e4830e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,17 +1,42 @@ +exclude: ^\.copier-answers\.yml$ repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + - repo: local hooks: - - id: check-yaml + # ruff + - id: ruff + name: ruff + entry: pixi run -e lint ruff check --fix --exit-non-zero-on-fix --force-exclude + language: system + types_or: [python, pyi] + require_serial: true + - id: ruff-format + name: ruff-format + entry: pixi run -e lint ruff format --force-exclude + language: system + types_or: [python, pyi] + require_serial: true + # mypy + - id: mypy + name: mypy + entry: pixi run -e default mypy + language: system + types: [python] + require_serial: true + # pre-commit-hooks + - id: trailing-whitespace-fixer + name: trailing-whitespace-fixer + entry: pixi run -e lint trailing-whitespace-fixer + language: system + types: [text] - id: end-of-file-fixer - - id: trailing-whitespace - - id: check-toml - - repo: https://github.com/quantco/pre-commit-mirrors-ruff - rev: 0.4.3 - hooks: - - id: ruff-conda - - id: ruff-format-conda - - repo: https://github.com/quantco/pre-commit-mirrors-mypy - rev: 1.10.0 - hooks: - - id: mypy-conda + name: end-of-file-fixer + entry: pixi run -e lint end-of-file-fixer + language: system + types: [text] + # typos + - id: typos + name: typos + entry: pixi run -e lint typos --force-exclude + language: system + types: [text] + require_serial: true diff --git a/benchmark.py b/examples/benchmark.py similarity index 98% rename from benchmark.py rename to examples/benchmark.py index 8aed120..210dd2b 100644 --- a/benchmark.py +++ b/examples/benchmark.py @@ -12,11 +12,11 @@ from slim_trees import dumps_lgbm_compressed, dumps_sklearn_compressed from slim_trees.pickling import dumps_compressed, get_pickled_size, loads_compressed -MODELS_PATH = "examples/benchmark_models" +MODELS_PATH = Path("examples/benchmark_models") def load_model(model_name: str, generate: Callable) -> Any: - model_path = Path(f"{MODELS_PATH}/{model_name}.pkl") + model_path = Path(MODELS_PATH / f"{model_name}.pkl") if model_path.exists(): print(f"Loading model `{model_name}.pkl` from disk...") diff --git a/examples/pickle_lgbm.py b/examples/pickle_lgbm.py index b6cc375..031b30b 100644 --- a/examples/pickle_lgbm.py +++ b/examples/pickle_lgbm.py @@ -4,12 +4,12 @@ import lightgbm as lgb from lightgbm import Booster -from utils import ( + +from examples.utils import ( evaluate_compression_performance, evaluate_prediction_difference, generate_dataset, ) - from slim_trees import dump_lgbm_compressed from slim_trees.lgbm_booster import dump from slim_trees.pickling import load_compressed diff --git a/examples/pickle_sklearn.py b/examples/pickle_sklearn.py index 91a8f85..eec4439 100644 --- a/examples/pickle_sklearn.py +++ b/examples/pickle_sklearn.py @@ -2,12 +2,12 @@ import tempfile from sklearn.ensemble import RandomForestRegressor -from utils import ( + +from examples.utils import ( evaluate_compression_performance, evaluate_prediction_difference, generate_dataset, ) - from slim_trees import dump_sklearn_compressed from slim_trees.pickling import load_compressed from slim_trees.sklearn_tree import dump diff --git a/examples/utils.py b/examples/utils/__init__.py similarity index 100% rename from examples/utils.py rename to examples/utils/__init__.py diff --git a/pixi.lock b/pixi.lock index b4ab843..67a652c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 4 +version: 5 environments: default: channels: @@ -19,7 +19,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-19_linux64_openblas.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-19_linux64_openblas.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2 - 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__osx >=10.12 + constrains: + - __osx >=10.12 + license: MIT + license_family: MIT + size: 3341025 + timestamp: 1714549800380 - kind: conda name: tzdata version: 2023d @@ -19069,26 +18247,6 @@ packages: license_family: MIT size: 17235 timestamp: 1695549871621 -- kind: conda - name: ukkonen - version: 1.0.1 - build: py312h1e303ce_4 - build_number: 4 - subdir: linux-ppc64le - url: https://conda.anaconda.org/conda-forge/linux-ppc64le/ukkonen-1.0.1-py312h1e303ce_4.conda - sha256: 74cc077845106fd1c451893ddfad9c5384afb13781a029cffe988b40dda093ef - md5: 40a69656eb37ffebb4abe1295a6b4dbb - depends: - - cffi - - libgcc-ng >=12 - - libstdcxx-ng >=12 - - python >=3.12.0rc3,<3.13.0a0 - - python >=3.12.0rc3,<3.13.0a0 *_cpython - - python_abi 3.12.* *_cp312 - license: MIT - license_family: MIT - size: 15113 - timestamp: 1695549684438 - kind: conda name: ukkonen version: 1.0.1 @@ -19430,19 +18588,6 @@ packages: license: LGPL-2.1 and GPL-2.0 size: 440555 timestamp: 1660348056328 -- kind: conda - name: xz - version: 5.2.6 - build: hb283c62_0 - subdir: linux-ppc64le - url: https://conda.anaconda.org/conda-forge/linux-ppc64le/xz-5.2.6-hb283c62_0.tar.bz2 - sha256: d03eb2b53dc61ac97c88b3ca023cf19c2b83b97520725b3c2ec0bff2c47f4a98 - md5: a411645e44054e333573ee5280fdb89b - depends: - - libgcc-ng >=12 - license: LGPL-2.1 and GPL-2.0 - size: 443552 - timestamp: 1660348160401 - kind: conda name: yaml version: 0.2.5 @@ -19469,21 +18614,6 @@ packages: license_family: MIT size: 88016 timestamp: 1641347076660 -- kind: conda - name: yaml - version: 0.2.5 - build: h4e0d66e_2 - build_number: 2 - subdir: linux-ppc64le - url: https://conda.anaconda.org/conda-forge/linux-ppc64le/yaml-0.2.5-h4e0d66e_2.tar.bz2 - sha256: 1fdf204ef2126b10b1e783e862c49a1fdadfb440c7c51cd49df792000450b1d1 - md5: e480df649632a5f96b7a24dfc213fd3d - depends: - - libgcc-ng >=9.4.0 - license: MIT - license_family: MIT - size: 109261 - timestamp: 1641348050084 - kind: conda name: yaml version: 0.2.5 @@ -19530,21 +18660,6 @@ packages: license_family: MIT size: 92927 timestamp: 1641347626613 -- kind: conda - name: zipp - version: 3.17.0 - build: pyhd8ed1ab_0 - subdir: noarch - noarch: python - url: https://conda.anaconda.org/conda-forge/noarch/zipp-3.17.0-pyhd8ed1ab_0.conda - sha256: bced1423fdbf77bca0a735187d05d9b9812d2163f60ab426fc10f11f92ecbe26 - md5: 2e4d6bc0b14e10f895fc6791a7d9b26a - depends: - - python >=3.8 - license: MIT - license_family: MIT - size: 18954 - timestamp: 1695255262261 - kind: conda name: zipp version: 3.17.0 diff --git a/pixi.toml b/pixi.toml index 0a03216..1db6e82 100644 --- a/pixi.toml +++ b/pixi.toml @@ -1,9 +1,8 @@ [project] # TODO: move to pyproject.toml once pixi supports it name = "slim-trees" description = "A python package for efficient pickling of ML models." -authors = ["Pavel Zwerschke "] channels = ["conda-forge"] -platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64", "linux-ppc64le", "win-64"] +platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64", "win-64"] [tasks] postinstall = "pip install --no-build-isolation --no-deps --disable-pip-version-check -e ." @@ -23,6 +22,8 @@ pytest = ">=7.0" pytest-md = "*" pytest-emoji = "*" pandas = "*" +mypy = "*" +pandas-stubs = "*" [feature.test.tasks] test = "pytest" @@ -59,8 +60,12 @@ python = ">=3.12,<3.13" [feature.lint.dependencies] pre-commit = "*" +ruff = "*" +pre-commit-hooks = "*" +typos = "*" [feature.lint.tasks] -lint = "pre-commit run -a" +pre-commit-install = "pre-commit install" +pre-commit-run = "pre-commit run -a" [environments] default = ["test"] @@ -79,4 +84,4 @@ py39 = ["py39", "test"] py310 = ["py310", "test"] py311 = ["py311", "test"] py312 = ["py312", "test"] -lint = ["lint"] +lint = { features = ["lint"], no-default-feature = true } diff --git a/pyproject.toml b/pyproject.toml index d1d8b12..a78ae87 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "hatchling.build" [project] name = "slim-trees" description = "A python package for efficient pickling of ML models." -version = "0.2.8" +version = "0.2.9" readme = "README.md" license = {file = "LICENSE"} requires-python = ">=3.8" @@ -85,6 +85,10 @@ indent-style = "space" [tool.mypy] python_version = "3.8" -ignore_missing_imports = true no_implicit_optional = true check_untyped_defs = true + +[[tool.mypy.overrides]] +# https://github.com/scikit-learn/scikit-learn/issues/16705 +module = ["sklearn.*"] +ignore_missing_imports = true diff --git a/slim_trees/compression_utils.py b/slim_trees/compression_utils.py index 8499760..b26f924 100644 --- a/slim_trees/compression_utils.py +++ b/slim_trees/compression_utils.py @@ -1,13 +1,16 @@ +from typing import Dict + import numpy as np +from numpy.typing import DTypeLike, NDArray -def safe_cast(arr: np.array, dtype): +def safe_cast(arr: NDArray, dtype: DTypeLike) -> NDArray: if np.can_cast(arr.max(), dtype) and np.can_cast(arr.min(), dtype): return arr.astype(dtype) raise ValueError(f"Cannot cast array to {dtype}.") -def _is_in_neighborhood_of_int(arr, iinfo, eps=1e-12): +def _is_in_neighborhood_of_int(arr: NDArray, iinfo: np.iinfo, eps: float = 1e-12): """ Checks if the numbers are around an integer. np.abs(arr % 1 - 1) < eps checks if the number is in an epsilon neighborhood on the right side @@ -21,7 +24,9 @@ def _is_in_neighborhood_of_int(arr, iinfo, eps=1e-12): ) -def compress_half_int_float_array(a, compression_dtype="int8"): +def compress_half_int_float_array( + a: NDArray, compression_dtype: DTypeLike = "int8" +) -> Dict: """Compress small integer and half-integer floats in a lossless fashion Idea: @@ -48,7 +53,7 @@ def compress_half_int_float_array(a, compression_dtype="int8"): return state -def decompress_half_int_float_array(state): +def decompress_half_int_float_array(state: Dict) -> NDArray: n_thresholds = len(state["a2_compressible"]) + len(state["a_incompressible"]) is_compressible = np.unpackbits( state["is_compressible"], count=n_thresholds diff --git a/slim_trees/lgbm_booster.py b/slim_trees/lgbm_booster.py index 33001a2..9a16b1f 100644 --- a/slim_trees/lgbm_booster.py +++ b/slim_trees/lgbm_booster.py @@ -4,9 +4,10 @@ import pickle import re import sys -from typing import Any, BinaryIO, List, Tuple +from typing import Any, BinaryIO, Dict, List, Optional, Tuple, Union import numpy as np +from numpy.typing import DTypeLike, NDArray from packaging.version import Version from slim_trees import __version__ as slim_trees_version @@ -42,7 +43,7 @@ def dumps(model: Any) -> bytes: def _booster_pickle(booster: Booster): assert isinstance(booster, Booster) - reconstructor, args, state = booster.__reduce__() + reconstructor, args, state = booster.__reduce__() # type: ignore compressed_state = _compress_booster_state(state) return _booster_unpickle, ( reconstructor, @@ -125,9 +126,9 @@ def _validate_feature_lengths(feats_map: dict): assert len(feats_map["leaf_value"]) == num_leaves -def parse(str_list, dtype): +def parse(str_list: Union[List[str], List[Optional[str]]], dtype: DTypeLike): if np.can_cast(dtype, np.int64): - int64_array = np.array(str_list, dtype=np.int64) + int64_array: NDArray = np.array(str_list, dtype=np.int64) return safe_cast(int64_array, dtype) assert np.can_cast(dtype, np.float64) return np.array(str_list, dtype=dtype) @@ -159,8 +160,8 @@ def _compress_booster_handle(model_string: str) -> Tuple[str, List[dict], str]: assert int(tree_idx) == i # extract features -- filter out empty ones - features = [f for f in features_list.split("\n") if "=" in f] - feats_map = dict(_extract_feature(fl) for fl in features) + features: List[str] = [f for f in features_list.split("\n") if "=" in f] + feats_map: Dict[str, List[str]] = dict(_extract_feature(fl) for fl in features) _validate_feature_lengths(feats_map) tree_values = { @@ -185,7 +186,7 @@ def _compress_booster_handle(model_string: str) -> Tuple[str, List[dict], str]: tree_values["num_features"] = parse(feats_map["num_features"], np.int32) tree_values["leaf_const"] = parse(feats_map["leaf_const"], LEAF_VALUE_DTYPE) tree_values["leaf_features"] = parse( - [s if s else -1 for s in feats_map["leaf_features"]], + [s if s else "-1" for s in feats_map["leaf_features"]], np.int16, ) tree_values["leaf_coeff"] = parse( diff --git a/slim_trees/py.typed b/slim_trees/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/slim_trees/sklearn_tree.py b/slim_trees/sklearn_tree.py index 3c643aa..71648a5 100644 --- a/slim_trees/sklearn_tree.py +++ b/slim_trees/sklearn_tree.py @@ -24,9 +24,10 @@ import copyreg import pickle -from typing import Any, BinaryIO +from typing import Any, BinaryIO, Dict import numpy as np +from numpy.typing import NDArray def dump(model: Any, file: BinaryIO): @@ -42,7 +43,7 @@ def dumps(model: Any) -> bytes: return bytes_io.getvalue() -def _tree_pickle(tree): +def _tree_pickle(tree: Tree): assert isinstance(tree, Tree) reconstructor, args, state = tree.__reduce__() compressed_state = _compress_tree_state(state) @@ -59,7 +60,7 @@ def _tree_unpickle(reconstructor, args, compressed_state): return tree -def _compress_tree_state(state: dict): +def _compress_tree_state(state: Dict) -> Dict: """ Compresses a Tree state. :param state: dictionary with 'max_depth', 'node_count', 'nodes', 'values' as keys. @@ -119,7 +120,7 @@ def _compress_tree_state(state: dict): } -def _decompress_tree_state(state: dict): +def _decompress_tree_state(state: Dict) -> Dict: """ Decompresses a Tree state. :param state: 'children_left', 'children_right', 'features', 'thresholds', 'values' as keys. @@ -148,13 +149,13 @@ def _decompress_tree_state(state: dict): ) n_nodes = state["node_count"] - children_left = np.zeros(n_nodes, dtype=np.int64) - children_right = np.zeros(n_nodes, dtype=np.int64) - features = np.zeros(n_nodes, dtype=np.int64) - thresholds = np.zeros(n_nodes, dtype=np.float64) + children_left: NDArray = np.zeros(n_nodes, dtype=np.int64) + children_right: NDArray = np.zeros(n_nodes, dtype=np.int64) + features: NDArray = np.zeros(n_nodes, dtype=np.int64) + thresholds: NDArray = np.zeros(n_nodes, dtype=np.float64) # same shape as values but with all nodes instead of only the leaves - values = np.zeros((n_nodes, *state["values"].shape[1:]), dtype=np.float64) - missing_go_to_left = np.zeros(n_nodes, dtype="uint8") + values: NDArray = np.zeros((n_nodes, *state["values"].shape[1:]), dtype=np.float64) + missing_go_to_left: NDArray = np.zeros(n_nodes, dtype="uint8") is_leaf = np.unpackbits(state["is_leaf"], count=n_nodes).astype("bool") children_left[~is_leaf] = state["children_left"]