diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d3a6bdcd..6e5e79f1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,25 +23,9 @@ jobs: steps: - uses: actions/checkout@v4 - - name: install poetry - run: | - pipx install poetry - poetry config virtualenvs.create true --local - poetry config virtualenvs.in-project true --local - - - uses: actions/setup-python@v5 + - uses: scientific-python/repo-review@v0.11.2 with: - python-version: "3.11" - cache: poetry - - - name: poetry check - run: poetry check - - - name: poetry install - run: poetry install --without debug,docs --all-extras - - - name: repo-review - run: poetry run repo-review . + plugins: sp-repo-review - name: markdownlint uses: DavidAnson/markdownlint-cli2-action@v17 @@ -49,21 +33,34 @@ jobs: config: ".markdownlint.yaml" globs: "*.md" + - name: Install uv + uses: astral-sh/setup-uv@v3 + with: + enable-cache: true + + - name: uv sync + run: > + uv sync + --frozen + --python 3.11 + --no-group debug + --no-group docs + - name: blacken-docs - run: git ls-files -z -- '*.md' | xargs -0 poetry run blacken-docs + run: git ls-files -z -- '*.md' | xargs -0 uv run blacken-docs - name: codespell - run: poetry run codespell . + run: uv run codespell . - name: ruff check run: | - poetry run ruff check --output-format=github - poetry run ruff format --check + uv run ruff check --output-format=github + uv run ruff format --check - name: basedpyright run: | - poetry run basedpyright - poetry run basedpyright --ignoreexternal --verifytypes lmo + uv run basedpyright + uv run basedpyright --ignoreexternal --verifytypes lmo test: timeout-minutes: 20 @@ -73,7 +70,7 @@ jobs: matrix: os: [ubuntu-latest, windows-latest] python-version: ["3.11", "3.13"] - pandas: ["without", "with"] + pandas: ["--no-group pandas", ""] exclude: - python-version: "3.13" pandas: "with" @@ -83,20 +80,20 @@ jobs: steps: - uses: actions/checkout@v4 - - name: install poetry - run: pipx install poetry - - - uses: actions/setup-python@v5 + - name: setup uv + uses: astral-sh/setup-uv@v3 with: - python-version: ${{ matrix.python-version }} - cache: poetry + enable-cache: true + + - name: setup python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} - - name: poetry install + - name: uv sync run: > - poetry install - --without debug,docs - --with github - --${{ matrix.pandas }} pandas + uv sync + --no-group debug + --no-group docs + ${{ matrix.pandas }} - name: pytest - run: poetry run pytest + run: uv run pytest diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 26ec78af..7b49e9de 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,6 @@ ci: autoupdate_commit_msg: "update pre-commit hooks" skip: - markdownlint - - poetry-check - codespell - ruff - ruff-format @@ -67,18 +66,13 @@ repos: - id: blacken-docs additional_dependencies: [black==24.*] - - repo: https://github.com/python-poetry/poetry - rev: 1.8.4 - hooks: - - id: poetry-check - - repo: https://github.com/codespell-project/codespell rev: v2.3.0 hooks: - id: codespell - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.2 + rev: v0.7.3 hooks: - id: ruff args: [--fix, --show-fixes] @@ -88,13 +82,13 @@ repos: hooks: - id: basedpyright name: basedpyright - entry: poetry run basedpyright + entry: uv run basedpyright language: system types_or: [python, pyi] - id: basedpyright-verifytypes name: basedpyright --verifytypes - entry: poetry run basedpyright --ignoreexternal --verifytypes lmo + entry: uv run basedpyright --ignoreexternal --verifytypes lmo language: system always_run: true pass_filenames: false diff --git a/docs/contributing.md b/docs/contributing.md index 4f36bd42..797ef25b 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -12,19 +12,12 @@ the bug. ## Environment setup -Ensure you have [poetry](https://python-poetry.org/docs/#installation) +Ensure you have [uv](https://docs.astral.sh/uv/getting-started/installation/) installed. -It can help to use Lmo's lowest-supported Python version, so that you don't -accidentally use those bleeding-edge Python features that you shouldn't, e.g. +You can install the dev dependencies using ```bash -poetry env use python3.10 -``` - -Now you can install the dev dependencies using - -```bash -poetry install --sync +uv sync ``` ### pre-commit @@ -33,13 +26,13 @@ Lmo uses [pre-commit](https://pre-commit.com/) to ensure that the code is formatted and typed correctly when committing the changes. ```bash -poetry run pre-commit install +uv run pre-commit install ``` It can also be manually run: ```bash -poetry run pre-commit --all-files +uv run pre-commit --all-files ``` ### Testing @@ -51,7 +44,7 @@ framework. The tests can be run using ```bash -poetry run pytest +uv run pytest ``` ## Documentation @@ -60,7 +53,7 @@ If your change involves documentation updates, you can conjure up a live preview: ```bash -poetry run mkdocs serve +uv run mkdocs serve ``` This will require `pandoc` and `pandoc-citeproc` to be installed on your diff --git a/lmo/contrib/scipy_stats.py b/lmo/contrib/scipy_stats.py index e638323b..2bdaedcb 100644 --- a/lmo/contrib/scipy_stats.py +++ b/lmo/contrib/scipy_stats.py @@ -573,7 +573,7 @@ def l_moments_cov( /, *args: Any, trim: lmt.AnyTrim = 0, - quad_opts: lspt.NQuadOptions | None = None, + quad_opts: lspt.QuadOptions | None = None, **kwds: Any, ) -> _ArrF8: r""" @@ -1419,7 +1419,7 @@ def l_moments_cov( # noqa: D102 r_max: int, /, trim: lmt.AnyTrim = 0, - quad_opts: lspt.NQuadOptions | None = None, + quad_opts: lspt.QuadOptions | None = None, ) -> _ArrF8: return self.dist.l_moments_cov( r_max, diff --git a/lmo/inference/_l_gmm.py b/lmo/inference/_l_gmm.py index 44ca0bc3..6b67afe5 100644 --- a/lmo/inference/_l_gmm.py +++ b/lmo/inference/_l_gmm.py @@ -440,7 +440,7 @@ def fit( # noqa: C901 args=(_l_moment_fn, _r, l_r, _trim, w_rr), **kwds, ) - i += cast(int, res.nfev) + i += res.nfev fun = res.fun theta = res.x diff --git a/lmo/theoretical/_f_to_lcm.py b/lmo/theoretical/_f_to_lcm.py index 2b49730f..2c558442 100644 --- a/lmo/theoretical/_f_to_lcm.py +++ b/lmo/theoretical/_f_to_lcm.py @@ -3,7 +3,7 @@ from __future__ import annotations from functools import partial -from typing import TYPE_CHECKING, Protocol, TypeAlias, TypeVar, cast +from typing import TYPE_CHECKING, Protocol, TypeAlias, TypeVar import numpy as np import numpy.typing as npt @@ -241,10 +241,7 @@ def integrand(*xs: float, i: int, j: int) -> float: ) elif _r: fn = partial(integrand, i=i, j=j) - # TODO(jorenham): remove this casting with the next scipy-stubs release - # https://github.com/jorenham/scipy-stubs/issues/155 - nquad_opts = cast("lspt.NQuadOptions", quad_opts) if quad_opts else None - l_r[i, j] = nquad(fn, limits, opts=nquad_opts)[0] + l_r[i, j] = nquad(fn, limits, opts=quad_opts)[0] return round0(l_r) diff --git a/lmo/theoretical/_f_to_lm_cov.py b/lmo/theoretical/_f_to_lm_cov.py index 45368780..8daf2e58 100644 --- a/lmo/theoretical/_f_to_lm_cov.py +++ b/lmo/theoretical/_f_to_lm_cov.py @@ -38,7 +38,7 @@ def l_moment_cov_from_cdf( trim: lmt.AnyTrim = 0, *, support: _Pair[float] | None = None, - quad_opts: lspt.NQuadOptions | None = None, + quad_opts: lspt.QuadOptions | None = None, ) -> _ArrF8: r""" L-moments that are estimated from $n$ samples of a distribution with CDF @@ -295,15 +295,7 @@ def l_stats_cov_from_cdf( """ rs = clean_order(num, "num", 0) - ll_kr = l_moment_cov_from_cdf( - cdf, - rs, - trim, - support=support, - # TODO(jorenham): remove this casting with the next scipy-stubs release - # https://github.com/jorenham/scipy-stubs/issues/155 - quad_opts=cast("lspt.NQuadOptions", quad_opts) if quad_opts else None, - ) + ll_kr = l_moment_cov_from_cdf(cdf, rs, trim, support=support, quad_opts=quad_opts) if rs <= 2: return ll_kr diff --git a/lmo/theoretical/_utils.py b/lmo/theoretical/_utils.py index 03f13033..b7a8de4a 100644 --- a/lmo/theoretical/_utils.py +++ b/lmo/theoretical/_utils.py @@ -106,7 +106,7 @@ def tighten_cdf_support( def nquad( integrand: Callable[Concatenate[float, float, _Tss], float], domains: Sequence[tuple[float, float] | Callable[..., tuple[float, float]],], - opts: lspt.NQuadOptions | None = None, + opts: lspt.QuadOptions | None = None, *args: _Tss.args, **kwds: _Tss.kwargs, ) -> float: diff --git a/lmo/typing/scipy.py b/lmo/typing/scipy.py index a14a2d15..e576313f 100644 --- a/lmo/typing/scipy.py +++ b/lmo/typing/scipy.py @@ -17,6 +17,9 @@ import numpy as np import numpy.typing as npt +from numpy._typing import ( + _ArrayLikeFloat_co, # noqa: TCH002 # pyright: ignore[reportPrivateUsage] +) from scipy.stats._distn_infrastructure import ( rv_continuous, rv_continuous_frozen, @@ -32,9 +35,8 @@ from typing_extensions import ParamSpec, Protocol, TypeVar, runtime_checkable if TYPE_CHECKING: - from collections.abc import ItemsView, Iterator, KeysView, Sequence, ValuesView + from collections.abc import ItemsView, Iterator, KeysView, ValuesView - import optype as op import optype.numpy as onpt import lmo.typing.np as lnpt @@ -43,7 +45,6 @@ __all__ = ( "RV", "FitResult", - "NQuadOptions", "OptimizeResult", "QuadOptions", "QuadWeights", @@ -69,8 +70,8 @@ "cauchy", ] -_IntLike: TypeAlias = int | np.int64 | np.int32 | np.int16 -_FloatLike: TypeAlias = float | np.float64 | np.float32 +_IntLike: TypeAlias = int | np.integer[Any] +_FloatLike: TypeAlias = float | np.floating[Any] class QuadOptions(TypedDict, total=False): @@ -82,24 +83,10 @@ class QuadOptions(TypedDict, total=False): epsabs: _FloatLike epsrel: _FloatLike limit: _IntLike - points: Sequence[float] | onpt.CanArray[Any, np.dtype[np.float64 | np.float32]] + points: _ArrayLikeFloat_co weight: QuadWeights wvar: _FloatLike | tuple[_FloatLike, _FloatLike] - wopts: tuple[int, npt.NDArray[np.float64 | np.float32]] - maxp1: _IntLike - limlst: _IntLike - - -class NQuadOptions(TypedDict, total=False): # noqa: D101 - # TODO(jorenham): Replace this with `QuadOptions` after the next scipy-stubs - # https://github.com/jorenham/scipy-stubs/issues/155 - epsabs: float - epsrel: float - limit: int - points: op.CanGetitem[int, float | np.floating[Any] | np.integer[Any] | np.bool_] - weight: QuadWeights - wvar: float | tuple[float, float] - wopts: tuple[int, npt.NDArray[np.float32 | np.float64]] + wopts: tuple[_IntLike, npt.NDArray[np.float32 | np.float64]] # scipy.optimize diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 5f484c6d..00000000 --- a/poetry.lock +++ /dev/null @@ -1,3600 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. - 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