From c1f27f0ecafcaafb775c5d76ee05cdc7a282accb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Apr 2026 01:12:40 +0000 Subject: [PATCH] Build(deps): Bump the python-packages group with 12 updates Updates the requirements on [scyjava](https://github.com/scijava/scyjava), [pyimagej](https://github.com/imagej/pyimagej), [jpype1](https://github.com/jpype-project/jpype), [networkx](https://github.com/networkx/networkx), [pymupdf](https://github.com/pymupdf/pymupdf), [pyobjc-framework-cocoa](https://github.com/ronaldoussoren/pyobjc), [zarr](https://github.com/zarr-developers/zarr-python), [fsspec](https://github.com/fsspec/filesystem_spec), [pytest](https://github.com/pytest-dev/pytest), [sphinx](https://github.com/sphinx-doc/sphinx), [myst-nb](https://github.com/executablebooks/myst-nb) and [setuptools](https://github.com/pypa/setuptools) to permit the latest version. Updates `scyjava` to 1.12.4 - [Commits](https://github.com/scijava/scyjava/compare/1.12.1...1.12.4) Updates `pyimagej` to 1.8.0 - [Commits](https://github.com/imagej/pyimagej/compare/1.7.0...1.8.0) Updates `jpype1` to 1.7.0 - [Release notes](https://github.com/jpype-project/jpype/releases) - [Changelog](https://github.com/jpype-project/jpype/blob/master/doc/CHANGELOG.rst) - [Commits](https://github.com/jpype-project/jpype/compare/v1.5.0...v1.7.0) Updates `networkx` to 3.2.1 - [Release notes](https://github.com/networkx/networkx/releases) - [Commits](https://github.com/networkx/networkx/compare/networkx-3.0...networkx-3.2.1) Updates `pymupdf` to 1.26.5 - [Release notes](https://github.com/pymupdf/pymupdf/releases) - [Changelog](https://github.com/pymupdf/PyMuPDF/blob/main/changes.txt) - [Commits](https://github.com/pymupdf/pymupdf/compare/1.26.3...1.26.5) Updates `pyobjc-framework-cocoa` to 12.0 - [Release notes](https://github.com/ronaldoussoren/pyobjc/releases) - [Changelog](https://github.com/ronaldoussoren/pyobjc/blob/main/docs/changelog.rst) - [Commits](https://github.com/ronaldoussoren/pyobjc/compare/v11.1...v12.0) Updates `zarr` to 2.18.2 - [Release notes](https://github.com/zarr-developers/zarr-python/releases) - [Changelog](https://github.com/zarr-developers/zarr-python/blob/v2.18.2/docs/release.rst) - [Commits](https://github.com/zarr-developers/zarr-python/compare/v2.10.0...v2.18.2) Updates `fsspec` to 2025.10.0 - [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.1.0...2025.10.0) Updates `pytest` to 8.4.2 - [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/6.0.0...8.4.2) Updates `sphinx` to 7.4.7 - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/v7.4.7/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v5.0.0...v7.4.7) Updates `myst-nb` to 1.3.0 - [Release notes](https://github.com/executablebooks/myst-nb/releases) - [Changelog](https://github.com/executablebooks/MyST-NB/blob/main/CHANGELOG.md) - [Commits](https://github.com/executablebooks/myst-nb/compare/v0.15.0...v1.3.0) Updates `setuptools` to 82.0.1 - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](https://github.com/pypa/setuptools/compare/v61.0.0...v82.0.1) --- updated-dependencies: - dependency-name: scyjava dependency-version: 1.12.4 dependency-type: direct:production dependency-group: python-packages - dependency-name: pyimagej dependency-version: 1.8.0 dependency-type: direct:production dependency-group: python-packages - dependency-name: jpype1 dependency-version: 1.7.0 dependency-type: direct:production dependency-group: python-packages - dependency-name: networkx dependency-version: 3.2.1 dependency-type: direct:production dependency-group: python-packages - dependency-name: pymupdf dependency-version: 1.26.5 dependency-type: direct:production dependency-group: python-packages - dependency-name: pyobjc-framework-cocoa dependency-version: '12.0' dependency-type: direct:production dependency-group: python-packages - dependency-name: zarr dependency-version: 2.18.2 dependency-type: direct:production dependency-group: python-packages - dependency-name: fsspec dependency-version: 2025.10.0 dependency-type: direct:production dependency-group: python-packages - dependency-name: pytest dependency-version: 8.4.2 dependency-type: direct:development dependency-group: python-packages - dependency-name: sphinx dependency-version: 7.4.7 dependency-type: direct:production dependency-group: python-packages - dependency-name: myst-nb dependency-version: 1.3.0 dependency-type: direct:production dependency-group: python-packages - dependency-name: setuptools dependency-version: 82.0.1 dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] --- pyproject.toml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3324a35..39c2e78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=61.0", "wheel"] +requires = ["setuptools>=82.0.1", "wheel"] build-backend = "setuptools.build_meta" [project] @@ -25,9 +25,9 @@ classifiers = [ "Programming Language :: Python :: 3.12", ] dependencies = [ - "scyjava>=1.12.1", - "pyimagej>=1.7.0", - "JPype1>=1.5.0", + "scyjava>=1.12.4", + "pyimagej>=1.8.0", + "JPype1>=1.7.0", "numpy>=2.3.3", "matplotlib>=3.10.7", "xarray>=2025.10.1", @@ -37,16 +37,16 @@ dependencies = [ # Enhanced display and conversion features display = [ "pandas>=2.3.3", - "networkx>=3.0", + "networkx>=3.2.1", "cairosvg>=2.8.2", - "PyMuPDF>=1.26.3", + "PyMuPDF>=1.26.5", ] # Interactive GUI features gui = [ "pandasgui>=0.2.15", "ipykernel>=7.1.0", "pyobjc-core>=11.1; sys_platform == 'darwin'", - "pyobjc-framework-cocoa>=11.1; sys_platform == 'darwin'", + "pyobjc-framework-cocoa>=12.0; sys_platform == 'darwin'", ] # Optional Java auto-install support java = [ @@ -54,26 +54,26 @@ java = [ ] # Optional OME-Zarr support zarr = [ - "zarr>=2.10.0", - "fsspec>=2023.1.0", + "zarr>=2.18.2", + "fsspec>=2025.10.0", ] # All optional features all = [ "pandas>=2.3.3", - "networkx>=3.0", + "networkx>=3.2.1", "cairosvg>=2.8.2", - "PyMuPDF>=1.26.3", + "PyMuPDF>=1.26.5", "pandasgui>=0.2.15", "ipykernel>=7.1.0", "pyobjc-core>=11.1; sys_platform == 'darwin'", - "pyobjc-framework-cocoa>=11.1; sys_platform == 'darwin'", + "pyobjc-framework-cocoa>=12.0; sys_platform == 'darwin'", "install-jdk>=1.1.0", - "zarr>=2.10.0", - "fsspec>=2023.1.0", + "zarr>=2.18.2", + "fsspec>=2025.10.0", ] # Development dependencies dev = [ - "pytest>=6.0", + "pytest>=8.4.2", "pytest-cov", "black", "flake8", @@ -82,9 +82,9 @@ dev = [ ] # Documentation dependencies docs = [ - "sphinx>=5.0,<8.0", + "sphinx>=7.4.7,<8.0", "sphinx-design", - "myst-nb>=0.15.0,<1.4.0", + "myst-nb>=1.3.0,<1.4.0", "sphinx-copybutton", "pydata-sphinx-theme", ]