From b76a576009f92f588e4de9e7e666b0aadc86bd67 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 11 Aug 2026 23:48:23 +0000 Subject: [PATCH] chore(deps): bump the python-dependencies group with 9 updates Updates the requirements on [numpy](https://github.com/numpy/numpy), [pandas](https://github.com/pandas-dev/pandas), [argcomplete](https://github.com/kislyuk/argcomplete), [pyarrow](https://github.com/apache/arrow), [pytest](https://github.com/pytest-dev/pytest), [mypy](https://github.com/python/mypy), [ruff](https://github.com/astral-sh/ruff), [pandas-stubs](https://github.com/pandas-dev/pandas-stubs) and [hatchling](https://github.com/pypa/hatch) to permit the latest version. Updates `numpy` from 2.4.4 to 2.5.1 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.4.4...v2.5.1) Updates `pandas` from 3.0.2 to 3.0.5 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v3.0.2...v3.0.5) Updates `argcomplete` from 3.6.3 to 3.7.2 - [Release notes](https://github.com/kislyuk/argcomplete/releases) - [Changelog](https://github.com/kislyuk/argcomplete/blob/main/Changes.rst) - [Commits](https://github.com/kislyuk/argcomplete/compare/v3.6.3...v3.7.2) Updates `pyarrow` from 24.0.0 to 25.0.0 - [Release notes](https://github.com/apache/arrow/releases) - [Commits](https://github.com/apache/arrow/compare/apache-arrow-24.0.0...apache-arrow-25.0.0) Updates `pytest` from 9.0.2 to 9.1.1 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/9.0.2...9.1.1) Updates `mypy` from 1.20.0 to 2.3.0 - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](https://github.com/python/mypy/compare/v1.20.0...v2.3.0) Updates `ruff` from 0.15.8 to 0.16.2 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.15.8...0.16.2) Updates `pandas-stubs` from 3.0.0.260204 to 3.0.5.260730 - [Changelog](https://github.com/pandas-dev/pandas-stubs/blob/main/docs/release_procedure.md) - [Commits](https://github.com/pandas-dev/pandas-stubs/compare/v3.0.0.260204...v3.0.5.260730) Updates `hatchling` to 1.31.0 - [Release notes](https://github.com/pypa/hatch/releases) - [Commits](https://github.com/pypa/hatch/compare/hatchling-v1.25.0...hatchling-v1.31.0) --- updated-dependencies: - dependency-name: numpy dependency-version: 2.5.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pandas dependency-version: 3.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: argcomplete dependency-version: 3.7.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pyarrow dependency-version: 25.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: python-dependencies - dependency-name: pytest dependency-version: 9.1.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: mypy dependency-version: 2.3.0 dependency-type: direct:development update-type: version-update:semver-major dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.16.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pandas-stubs dependency-version: 3.0.5.260730 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: hatchling dependency-version: 1.31.0 dependency-type: direct:development dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] --- pyproject.toml | 18 +- uv.lock | 601 ++++++++++++++++++++++++++++--------------------- 2 files changed, 353 insertions(+), 266 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3b232c4..db8258e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,8 +19,8 @@ classifiers = [ "Topic :: Scientific/Engineering :: Bio-Informatics", ] dependencies = [ - "numpy>=1.24", - "pandas>=2.0", + "numpy>=2.5.1", + "pandas>=3.0.5", ] [project.optional-dependencies] @@ -29,10 +29,10 @@ config = [ "pyyaml>=6.0", ] # pip install harmonizepy[completion] → enables shell tab-completion via argcomplete -completion = ["argcomplete>=3.0"] +completion = ["argcomplete>=3.7.2"] # pip install harmonizepy[io] → pyarrow for faster IO and parquet output io = [ - "pyarrow>=14.0", + "pyarrow>=25.0.0", ] # pip install harmonizepy[all] → everything all = [ @@ -48,15 +48,15 @@ Issues = "https://github.com/LangeLab/HarmonizePy/issues" [dependency-groups] dev = [ - 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