From 7dad9b0b2467adce9df44be7d8955c32602b5cba Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 30 Oct 2026 20:24:53 +0000 Subject: [PATCH] build(deps): bump the production group with 17 updates Bumps the production group with 17 updates: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.4.2` | `2.5.4` | | [pydantic](https://github.com/pydantic/pydantic) | `2.12.5` | `2.14.1` | | [scikit-fingerprints](https://github.com/scikit-fingerprints/scikit-fingerprints) | `1.18.0` | `2.1.0` | | [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.8.0` | `1.9.1` | | [scipy](https://github.com/scipy/scipy) | `1.17.1` | `1.18.1` | | [umap-learn](https://github.com/lmcinnes/umap) | `0.5.11` | `0.5.12` | | [mlflow-skinny](https://github.com/mlflow/mlflow) | `3.10.0` | `3.17.2` | | [plotly](https://github.com/plotly/plotly.py) | `6.5.2` | `7.1.0` | | [mlflow](https://github.com/mlflow/mlflow) | `3.10.0` | `3.17.2` | | [fastparquet](https://github.com/dask/fastparquet) | `2026.3.0` | `2026.9.0` | | [torch-geometric](https://github.com/pyg-team/pytorch_geometric) | `2.7.0` | `2.8.1` | | [optuna](https://github.com/optuna/optuna) | `4.7.0` | `5.0.0` | | [optuna-integration](https://github.com/optuna/optuna-integration) | `4.7.0` | `5.0.0` | | [transformers](https://github.com/huggingface/transformers) | `4.57.6` | `5.21.0` | | [chemprop](https://github.com/chemprop/chemprop) | `2.2.2` | `2.3.1` | | [myst-parser](https://github.com/executablebooks/MyST-Parser) | `4.0.1` | `5.1.0` | | [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) | `3.8.0` | `3.8.1` | Updates `numpy` from 2.4.2 to 2.5.4 - [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/v2.4.2...v2.5.4) Updates `pydantic` from 2.12.5 to 2.14.1 - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](https://github.com/pydantic/pydantic/compare/v2.12.5...v2.14.1) Updates `scikit-fingerprints` from 1.18.0 to 2.1.0 - [Release notes](https://github.com/scikit-fingerprints/scikit-fingerprints/releases) - [Commits](https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.18.0...v2.1.0) Updates `scikit-learn` from 1.8.0 to 1.9.1 - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.8.0...1.9.1) Updates `scipy` from 1.17.1 to 1.18.1 - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.17.1...v1.18.1) Updates `umap-learn` from 0.5.11 to 0.5.12 - [Release notes](https://github.com/lmcinnes/umap/releases) - [Changelog](https://github.com/lmcinnes/umap/blob/master/doc/release_notes.rst) - [Commits](https://github.com/lmcinnes/umap/compare/release-0.5.11...release-0.5.12) Updates `mlflow-skinny` from 3.10.0 to 3.17.2 - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/mlflow/mlflow/compare/v3.10.0...v3.17.2) Updates `plotly` from 6.5.2 to 7.1.0 - [Release notes](https://github.com/plotly/plotly.py/releases) - [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md) - [Commits](https://github.com/plotly/plotly.py/compare/v6.5.2...v7.1.0) Updates `mlflow` from 3.10.0 to 3.17.2 - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/mlflow/mlflow/compare/v3.10.0...v3.17.2) Updates `fastparquet` from 2026.3.0 to 2026.9.0 - [Commits](https://github.com/dask/fastparquet/compare/2026.3.0...2026.9.0) Updates `torch-geometric` from 2.7.0 to 2.8.1 - [Release notes](https://github.com/pyg-team/pytorch_geometric/releases) - [Changelog](https://github.com/pyg-team/pytorch_geometric/blob/master/CHANGELOG.md) - [Commits](https://github.com/pyg-team/pytorch_geometric/compare/2.7.0...2.8.1) Updates `optuna` from 4.7.0 to 5.0.0 - [Release notes](https://github.com/optuna/optuna/releases) - [Commits](https://github.com/optuna/optuna/compare/v4.7.0...v5.0.0) Updates `optuna-integration` from 4.7.0 to 5.0.0 - [Release notes](https://github.com/optuna/optuna-integration/releases) - [Commits](https://github.com/optuna/optuna-integration/compare/v4.7.0...v5.0.0) Updates `transformers` from 4.57.6 to 5.21.0 - [Release notes](https://github.com/huggingface/transformers/releases) - [Commits](https://github.com/huggingface/transformers/compare/v4.57.6...v5.21) Updates `chemprop` from 2.2.2 to 2.3.1 - [Release notes](https://github.com/chemprop/chemprop/releases) - [Commits](https://github.com/chemprop/chemprop/compare/v2.2.2...v2.3.1) Updates `myst-parser` from 4.0.1 to 5.1.0 - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/MyST-Parser/compare/v4.0.1...v5.1.0) Updates `sphinx-autoapi` from 3.8.0 to 3.8.1 - [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases) - [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst) - [Commits](https://github.com/readthedocs/sphinx-autoapi/compare/v3.8.0...v3.8.1) --- updated-dependencies: - dependency-name: numpy dependency-version: 2.5.4 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: pydantic dependency-version: 2.14.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: scikit-fingerprints dependency-version: 2.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: scikit-learn dependency-version: 1.9.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: scipy dependency-version: 1.18.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: umap-learn dependency-version: 0.5.12 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: production - dependency-name: mlflow-skinny dependency-version: 3.17.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: plotly dependency-version: 7.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: mlflow dependency-version: 3.17.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: fastparquet dependency-version: 2026.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: torch-geometric dependency-version: 2.8.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: optuna dependency-version: 5.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: optuna-integration dependency-version: 5.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: transformers dependency-version: 5.21.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: chemprop dependency-version: 2.3.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: myst-parser dependency-version: 5.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: sphinx-autoapi dependency-version: 3.8.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: production ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- pyproject.toml | 18 +- uv.lock | 708 +++++++++++++++++++++++------------------- 3 files changed, 396 insertions(+), 332 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index d038048..b25d2f1 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -7,7 +7,7 @@ # Keep the version bounds below in sync with pyproject.toml. sphinx>=8.1.0,<9.0.0 sphinx-rtd-theme>=3.0.2,<4.0.0 -myst-parser>=4.0.0,<5.0.0 +myst-parser>=4.0.0,<6.0.0 sphinx-autoapi>=3.6.0,<4.0.0 nbsphinx>=0.9.5,<0.10.0 jupyter-sphinx>=0.5.3,<0.6.0 diff --git a/pyproject.toml b/pyproject.toml index 4f1cf7a..8ed78fb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,12 +10,12 @@ dependencies = [ 'pandas>=2.3.3,<3.0.0', 'pydantic>=2.12.5,<3.0.0', 'rdkit>=2025.3.6', - 'scikit-fingerprints>=1.18.0,<2.0.0', + 'scikit-fingerprints>=1.18.0,<3.0.0', 'scikit-learn>=1.8.0,<2.0.0', 'scipy>=1.17.0,<2.0.0', 'umap-learn>=0.5.11,<0.6.0', 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