refactor(config): Update pyproject.toml version pinning and add tasks

docs/developinstall.rst

@@ -10,7 +10,7 @@ guide is described for **Linux**. For *Windows*, see :ref:`developinstallwin:Adv
 Requirements
 ^^^^^^^^^^^^
 
-Install `git <https://github.com/git-guides/install-git>`_, python and `pixi <https://pixi.sh/latest/#installation>`_.
+Install `git <https://github.com/git-guides/install-git>`_ and `pixi <https://pixi.sh/latest/#installation>`_.
 Some operating systems might require the python headers (e.g python-dev on ubuntu) or other supporting
 libraries/packages (e.g. Visual Studio on Windows needs the c++ compiler components).
 

docs/developinstallwin.rst

@@ -10,7 +10,7 @@ guide is described for **Windows**. For *Linux*, see :ref:`developinstall:Advanc
 Requirements
 ^^^^^^^^^^^^
 
-Install `git <https://github.com/git-guides/install-git>`_, python and `pixi <https://pixi.sh/latest/#installation>`_.
+Install `git <https://github.com/git-guides/install-git>`_ and `pixi <https://pixi.sh/latest/#installation>`_.
 
 Install `Microsoft C++ compiler <https://wiki.python.org/moin/WindowsCompilers>`_.
 Follow the installation steps for the version corresponding to the installed python version.
@@ -43,7 +43,7 @@ Compile the cython com1DFA part::
    You will have to do this compilation every time something changes in the cython code. We also suggest
    to do this everytime updates from the repositories are pulled.
 
-   **Before** compilation in Windows, make sure to delete ``AvaFrame/build`` directory, in addition to any .pyd, .c, and
+   **Before** compilation in Windows, make sure to delete ``AvaFrame/build`` directory, in addition to any .pyc, .c, and
    .pycache files in ``AvaFrame/avaframe/com1DFA``
 
 This installs avaframe in editable mode, so every time you import avaframe the

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 # Cython dependency is optional, see setup.py for details.
 # For the package (run-time) dependencies, see setup.cfg.
-requires = ["setuptools", "numpy", "Cython", "setuptools-scm"]
+requires = ["setuptools", "numpy<2.0", "Cython>=3.0.10", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -26,13 +26,13 @@ classifiers = [
 requires-python = ">=3.9,<3.14"
 dependencies = [
     "numpy<2.0", # numpy 2.0 introduces breaking changes in relation to qgis versions
-    "salib<1.5.1", # this is the last aversion that works with numpy <2.
-    "pyshp<3.0", # pin until 3.0.3 is out, there's a known bug for certain polygon types
+    "salib", # this is the last aversion that works with numpy <2.
+    "pyshp>=3.0.3", # pin until 3.0.3 is out, there's a known bug for certain polygon types
     "matplotlib",
     "scipy",
     "cmcrameri",
     "seaborn",
-    "cython<3.0", # cython 3.x compiles code that needs numpy > 2.0
+    "cython>=3.0.10", # Cython 3.x is required for Python 3.12/3.13, configured for numpy < 2.0 in setup.py
     "pandas",
     "shapely",
     "configUpdater",
@@ -64,7 +64,7 @@ version_file = "avaframe/RELEASE-VERSION.txt"
 #build = ["cp312-*"]
 skip = ["*musllinux*","*-win32"]
 build-verbosity = 1
-before-build = "pip install cython numpy"
+before-build = "pip install 'cython>=3.0.10' 'numpy<2.0'"
 
 
 [tool.cibuildwheel.linux]
@@ -86,7 +86,7 @@ channels = ["https://prefix.dev/conda-forge"]
 platforms = ["linux-64", "win-64", "osx-64"]
 
 [tool.pixi.dependencies]
-python = "<3.14"
+python = ">=3.9,<3.14"
 setuptools = "*"
 setuptools-scm = "*"
 cibuildwheel = "*"
@@ -114,17 +114,13 @@ sphinxcontrib-bibtex = "*"
 [tool.pixi.feature.prod.pypi-dependencies]
 avaframe = "*"
 
-#Feature py313
-[tool.pixi.feature.py313.dependencies]
-python = "==3.13.7"
-
 #Feature rcs
 #[tool.pixi.feature.rcs.pypi-dependencies]
 #avaframe = "==1.13rc4"
 
 [tool.pixi.tasks]
 build = "python setup.py build_ext --inplace"
-clean = "find avaframe -type f \\( -name '*.so' -o -name '*.c' \\) -delete"
+clean = "python -c \"import pathlib; [f.unlink() for f in pathlib.Path('avaframe').rglob('*.so')]; [f.unlink() for f in pathlib.Path('avaframe').rglob('*.c')]\""
 rebuild = { depends-on = ["clean", "build"] }
 
 #Feature qgis
@@ -139,6 +135,4 @@ dev = ["dev"]
 doc = ["doc", "dev"]
 prod = ["prod"]
 #rcs = ["rcs"]
-py313 = ["py313", "dev"]
 qgis = ["qgis", "dev"]
-

setup.py

@@ -13,11 +13,20 @@
     'avaframe/com1DFA/damCom1DFA.pyx',
 ]
 
+# Define macros to ensure NumPy 1.x API compatibility
+# This allows Cython 3.x to generate code that works with numpy < 2.0
+define_macros = [
+    ("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"),
+    # Target NumPy 1.x C API even when building with Cython 3.x
+    ("NPY_TARGET_VERSION", "NPY_1_22_API_VERSION"),
+]
+
 extensions = [
     Extension(
         name=file.replace('/', '.').replace('.pyx', ''),
         sources=[file],
-        include_dirs=[numpy.get_include()]
+        include_dirs=[numpy.get_include()],
+        define_macros=define_macros,  # Add the macros here
     )
     for file in cython_files
 ]
@@ -27,6 +36,8 @@
     compiler_directives={
         'language_level': '3',
         'linetrace': True,
+        # Ensure Cython generates code compatible with older NumPy
+        'binding': True,
     }
 )
 
@@ -43,4 +54,4 @@
     #     'pandas'
     # ],
     # python_requires='>=3.8',
-)
+)