diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml index 7aaf269..a4c1188 100644 --- a/.github/workflows/cibuildwheel.yml +++ b/.github/workflows/cibuildwheel.yml @@ -24,7 +24,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-20.04, windows-2019, macos-13] - py: [cp39, cp310, cp311] + py: [cp39, cp310, cp311, cp312] steps: - uses: actions/checkout@v3 @@ -79,7 +79,7 @@ jobs: CIBW_TEST_COMMAND: pytest -v --cov=spotiflow {project} - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 name: Upload wheels with: name: dist @@ -120,5 +120,3 @@ jobs: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} verbose: true - - diff --git a/README.md b/README.md index 41c2cbf..84f0ba1 100644 --- a/README.md +++ b/README.md @@ -19,10 +19,10 @@ The documentation of the software can be found [here](https://weigertlab.github.io/spotiflow/). ## Installation (pip, recommended) -Create and activate a fresh conda environment (we currently support Python 3.9 to 3.11): +Create and activate a fresh conda environment (we currently support Python 3.9 to 3.12): ```console -conda create -n spotiflow python=3.9 +conda create -n spotiflow python=3.12 conda activate spotiflow ``` @@ -31,7 +31,7 @@ conda activate spotiflow For Linux/Windows with a CUDA device, install PyTorch using conda/mamba (one might need to change the cuda version accordingly): ```console -conda install pytorch torchvision pytorch-cuda=11.8 -c pytorch -c nvidia # Might need to change the cuda version accordingly +conda install pytorch torchvision pytorch-cuda=12.1 -c pytorch -c nvidia # Might need to change the cuda version accordingly ``` **Note (for Windows users):** if using Windows, please install the latest [Build Tools for Visual Studio](https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2022) (make sure to select the C++ build tools during installation) before proceeding to install Spotiflow. diff --git a/pyproject.toml b/pyproject.toml index ac68f64..6b77c07 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,7 +2,7 @@ requires = ["setuptools<=71.0", "setuptools_scm[toml]>=6.2", "wheel", - "oldest-supported-numpy"] + "numpy"] build-backend = "setuptools.build_meta" [tool.setuptools_scm] diff --git a/setup.cfg b/setup.cfg index c01cef7..da5df2a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -15,6 +15,7 @@ classifiers = Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 [options] packages = find: @@ -25,7 +26,7 @@ install_requires = dask lightning networkx - numpy<2.0.0 + numpy pandas Pillow pydash @@ -40,7 +41,7 @@ install_requires = typing-extensions wandb zarr -python_requires = >=3.9, <3.12 +python_requires = >=3.9, <3.13 [options.entry_points] console_scripts = diff --git a/setup.py b/setup.py index baf1ead..07c96fa 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from __future__ import absolute_import, print_function from setuptools import setup, Extension from setuptools.command.build_ext import build_ext -from numpy.distutils.misc_util import get_numpy_include_dirs +from numpy import get_include from os import path # ------------------------------------------------------------------------------------ @@ -76,37 +76,37 @@ def compile_patched(obj, src, ext, cc_args, extra_postargs, pp_opts): "spotiflow.lib.spotflow2d", sources=["spotiflow/lib/spotflow2d.cpp"], extra_compile_args=["-std=c++11"], - include_dirs=get_numpy_include_dirs() + [nanoflann_root], + include_dirs=[get_include()] + [nanoflann_root], ), Extension( "spotiflow.lib.spotflow3d", sources=["spotiflow/lib/spotflow3d.cpp"], extra_compile_args=["-std=c++11"], - include_dirs=get_numpy_include_dirs() + [nanoflann_root], + include_dirs=[get_include()] + [nanoflann_root], ), Extension( "spotiflow.lib.point_nms", sources=["spotiflow/lib/point_nms.cpp"], extra_compile_args=["-std=c++11"], - include_dirs=get_numpy_include_dirs() + [nanoflann_root], + include_dirs=[get_include()] + [nanoflann_root], ), Extension( "spotiflow.lib.point_nms3d", sources=["spotiflow/lib/point_nms3d.cpp"], extra_compile_args=["-std=c++11"], - include_dirs=get_numpy_include_dirs() + [nanoflann_root], + include_dirs=[get_include()] + [nanoflann_root], ), Extension( "spotiflow.lib.filters", sources=["spotiflow/lib/filters.cpp"], extra_compile_args=["-std=c++11"], - include_dirs=get_numpy_include_dirs() + [nanoflann_root], + include_dirs=[get_include()] + [nanoflann_root], ), Extension( "spotiflow.lib.filters3d", sources=["spotiflow/lib/filters3d.cpp"], extra_compile_args=["-std=c++11"], - include_dirs=get_numpy_include_dirs() + [nanoflann_root], + include_dirs=[get_include()] + [nanoflann_root], ), ], include_package_data=True,