From 95eb7fd328c4f77a258e5ba7cc1b8c60309f73ff Mon Sep 17 00:00:00 2001
From: AlbertDominguez <albert.dominguezmantes@epfl.ch>
Date: Sat, 5 Oct 2024 10:44:50 +0200
Subject: [PATCH] add support for py312 and np2.x

---
 .github/workflows/cibuildwheel.yml |  6 ++----
 README.md                          |  6 +++---
 pyproject.toml                     |  2 +-
 setup.cfg                          |  5 +++--
 setup.py                           | 14 +++++++-------
 5 files changed, 16 insertions(+), 17 deletions(-)

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,