Fix/numpy2 (#37)

* fix: install for numpy<2
* fix: code style issues with Black
* ci: update versions
* ci: add setuptools to tox
* style: flake8 compatibility
* ci: remove macos python3.7
* ci: updated action versions
* tests: use pip install

.github/workflows/lint.yml

@@ -18,10 +18,10 @@ jobs:
 
     steps:
       - name: Check out Git repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
 

.github/workflows/run-tests.yml

@@ -15,12 +15,16 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, windows-latest, ubuntu-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        exclude:
+          - os: macos-latest
+            python-version: "3.7"
+
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox and dependencies

.github/workflows/wheels-deploy.yml

@@ -15,25 +15,25 @@ jobs:
         os: [macos-latest, windows-latest, ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.10.2
+        uses: pypa/cibuildwheel@v2.21.1
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build sdist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -45,7 +45,7 @@ jobs:
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           # unpacks default artifact into dist/
           # if `name: artifact` is omitted, the action will create extra parent dir
@@ -57,7 +57,7 @@ jobs:
           artifacts: "dist/*.whl,dist/*.tar.gz"
           token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: pypa/gh-action-pypi-publish@v1.5.0
+      - uses: pypa/gh-action-pypi-publish@v1.10.2
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

.pre-commit-config.yaml

@@ -1,7 +1,13 @@
 exclude: '^docs/'
 repos:
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: ["--profile", "black", "--filter-files"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.6.0
   hooks:
   -   id: trailing-whitespace
       exclude: '^.bumpversion.cfg$'
@@ -10,19 +16,19 @@ repos:
   -   id: pretty-format-json
       args: ['--autofix', '--no-sort-keys']
 - repo: https://github.com/ambv/black
-  rev: 22.6.0
+  rev: 24.8.0
   hooks:
   - id: black
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 4.0.1
+- repo: https://github.com/PyCQA/flake8
+  rev: '7.1.1'
   hooks:
-  - id: flake8
+  -   id: flake8
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.961
+  rev: v1.11.2
   hooks:
   -   id: mypy
 - repo: https://github.com/codespell-project/codespell
-  rev: 'v2.1.0'
+  rev: 'v2.3.0'
   hooks:
   -   id: codespell
       name: codespell

pyproject.toml

@@ -1,5 +1,7 @@
 [build-system]
-requires = ["setuptools", "wheel", "oldest-supported-numpy"]
+requires = ["setuptools", "wheel", "numpy<2.0"]
+build-backend = "setuptools.build_meta"
+
 
 [tool.cibuildwheel]
 test-requires = ["pytest", "tqdm", "tifffile"]

pystackreg/util/__init__.py

@@ -1,6 +1,7 @@
 """
 Collection of utility functions for pystackreg
 """
+
 import numpy as np
 
 
@@ -44,7 +45,7 @@ def to_int_dtype(arr: np.ndarray, dtype: type):
     :rtype:  ndarray(Ni..., Nj..., Nk...)
     :return: Input array clipped & rounded to integer dtype
     """
-    assert type(arr) == np.ndarray, "Input must be a numpy array"
+    assert isinstance(arr, np.ndarray), "Input must be a numpy array"
 
     if not np.issubdtype(dtype, np.integer):
         return arr

setup.py

@@ -3,8 +3,6 @@
 import os
 from setuptools import setup, Extension, find_packages
 
-# cannot directly import because __init__.py imports pystackreg which imports the
-# compiled plugin, which is not available before setup.py is run
 __version__ = ""  # placeholder for linters
 exec(open("pystackreg/version.py").read())
 
@@ -26,13 +24,17 @@ def __str__(self):
 
     setup(
         name="pystackreg",
-        description="Image registration tool (python implementation of the ImageJ/FIJI "
-        "Plugin TurboReg/StackReg)",
+        description=(
+            "Image registration tool (python implementation of the ImageJ/FIJI "
+            "Plugin TurboReg/StackReg)"
+        ),
         long_description="\n\n".join([readme, change]),
         version=__version__,
-        author="Gregor Lichtner (python/C++ port);"
-        "TurboReg Author: Philippe Thévenaz, Biomedical Imaging Group,"
-        "Swiss Federal Institute of Technology Lausanne",
+        author=(
+            "Gregor Lichtner (python/C++ port);"
+            "TurboReg Author: Philippe Thévenaz, Biomedical Imaging Group,"
+            "Swiss Federal Institute of Technology Lausanne"
+        ),
         url="https://github.com/glichtner/pystackreg",
         packages=find_packages("."),
         ext_modules=[
@@ -51,7 +53,7 @@ def __str__(self):
             )
         ],
         setup_requires=["numpy"],
-        install_requires=["numpy", "tqdm"],
+        install_requires=["numpy<2", "tqdm"],
         classifiers=[
             # complete list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
             "Development Status :: 5 - Production/Stable",
@@ -62,12 +64,12 @@ def __str__(self):
             "Operating System :: POSIX",
             "Programming Language :: C++",
             "Programming Language :: Python",
-            "Programming Language :: Python :: 2.7",
-            "Programming Language :: Python :: 3.5",
-            "Programming Language :: Python :: 3.6",
             "Programming Language :: Python :: 3.7",
             "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
+            "Programming Language :: Python :: 3.10",
+            "Programming Language :: Python :: 3.11",
+            "Programming Language :: Python :: 3.12",
             "Topic :: Scientific/Engineering :: Image Processing",
             "Topic :: Utilities",
         ],

tox.ini

@@ -8,8 +8,10 @@ deps=
   -rrequirements.txt
   tifffile
   pytest
+  setuptools
+  numpy<2
 
 commands=
-  python setup.py build_ext --inplace
+  pip install -e .
   python setup.py install
   pytest {posargs:}