Make FlowUtils (and Flowkit) compatible with NumPy >= 2.0

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ['setuptools>=61.0', 'oldest-supported-numpy']
+requires = ['setuptools>=61.0', 'numpy>=2']
 build-backend   = 'setuptools.build_meta'

setup.py

@@ -15,14 +15,15 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
+
 logicle_extension = Extension(
     'flowutils.logicle_c',
     sources=[
         'src/flowutils/logicle_c_ext/_logicle.c',
         'src/flowutils/logicle_c_ext/logicle.c'
     ],
     include_dirs=[np.get_include(), 'src/flowutils/logicle_c_ext'],
-    extra_compile_args=['-std=c99']
+    extra_compile_args=['-std=c99', '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION']
 )
 
 gating_extension = Extension(
@@ -32,7 +33,7 @@
         'src/flowutils/gating_c_ext/gate_helpers.c'
     ],
     include_dirs=[np.get_include(), 'src/flowutils/gating_c_ext'],
-    extra_compile_args=['-std=c99']
+    extra_compile_args=['-std=c99', '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION']
 )
 
 setup(
@@ -49,7 +50,7 @@
     license='BSD',
     url="https://github.com/whitews/flowutils",
     ext_modules=[logicle_extension, gating_extension],
-    install_requires=['numpy>=1.20,<2'],
+    install_requires=['numpy>=2.0,<3.0'],
     classifiers=[
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.11',

src/flowutils/gating_c_ext/_gate_helpers.c

@@ -1,4 +1,5 @@
 #include <Python.h>
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION // to avoid a warning
 #include <numpy/arrayobject.h>
 #include "gate_helpers.h"
 
@@ -12,7 +13,11 @@ static PyObject *wrap_calc_wind_count(PyObject *self, PyObject *args) {
         return NULL;
     }
 
-    PyObject *poly_vert_array = PyArray_FROM_OTF(poly_vertices, NPY_DOUBLE, NPY_IN_ARRAY);
+    PyArrayObject *poly_vert_array = (PyArrayObject *) PyArray_FROM_OTF(poly_vertices, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!poly_vert_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert poly_vertices to NumPy array");
+        return NULL;
+    }
     double *poly_vertices_c = (double *) PyArray_DATA(poly_vert_array);
 
     // now we can call our function!
@@ -34,10 +39,18 @@ static PyObject *wrap_points_in_polygon(PyObject *self, PyObject *args) {
         return NULL;
     }
 
-    PyObject *poly_vert_array = PyArray_FROM_OTF(poly_vertices, NPY_DOUBLE, NPY_IN_ARRAY);
+    PyArrayObject *poly_vert_array = (PyArrayObject *) PyArray_FROM_OTF(poly_vertices, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!poly_vert_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert poly_vertices to NumPy array");
+        return NULL;
+    }
     double *poly_vertices_c = (double *) PyArray_DATA(poly_vert_array);
 
-    PyObject *points_array = PyArray_FROM_OTF(points, NPY_DOUBLE, NPY_IN_ARRAY);
+    PyArrayObject *points_array = (PyArrayObject *) PyArray_FROM_OTF(points, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!points_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert points to NumPy array");
+        return NULL;
+    }
     double *points_c = (double *) PyArray_DATA(points_array);
 
     // now we can call our function!
@@ -67,28 +80,40 @@ static PyMethodDef module_methods[] = {
 
 #if PY_MAJOR_VERSION >= 3
 static struct PyModuleDef gatingdef = {
-        PyModuleDef_HEAD_INIT,
-        "gating_c",
-        NULL,
-        -1,
-        module_methods
+    PyModuleDef_HEAD_INIT, 
+    "gating_c", 
+    NULL, 
+    -1, 
+    module_methods
 };
-#endif
 
-#if PY_MAJOR_VERSION >= 3
 PyMODINIT_FUNC PyInit_gating_c(void) {
     PyObject *m = PyModule_Create(&gatingdef);
+    if (m == NULL) {
+        return NULL;
+    }
+
+    import_array();
+    if (PyErr_Occurred()) {
+        Py_DECREF(m);
+        return NULL;
+    }
+
+    return m;
+}
 #else
 PyMODINIT_FUNC initgating_c(void) {
     PyObject *m = Py_InitModule3("gating_c", module_methods, NULL);
-#endif
-
     if (m == NULL) {
-        return NULL;
+        return;
     }
+
     import_array();
+    if (PyErr_Occurred()) {
+        Py_DECREF(m);
+        return;
+    }
 
-#if PY_MAJOR_VERSION >= 3
-    return m;
+    return;
+}
 #endif
-}

src/flowutils/gating_c_ext/gate_helpers.c

@@ -70,7 +70,7 @@ int * points_in_polygon(int *wind_counts, double *poly_vertices, int vert_count,
 
     This implementation is based on the C implementation here:
 
-        http://geomalgorithms.com/a03-_inclusion.html
+        http://geomalgorithms.com/a03-_inclusion.html % This website seems to be a scam now ?
 
     Original copyright notice:
         Copyright 2000 softSurfer, 2012 Dan Sunday

src/flowutils/logicle_c_ext/_logicle.c

@@ -1,4 +1,5 @@
 #include <Python.h>
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION // to avoid a warning
 #include <numpy/arrayobject.h>
 #include "logicle.h"
 
@@ -11,12 +12,10 @@ static PyObject *wrap_logicle_scale(PyObject *self, PyObject *args) {
         return NULL;
     }
 
-    // read the numpy array
-    PyObject *x_array = PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_IN_ARRAY);
-
+    PyArrayObject *x_array = (PyArrayObject *) PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
     // throw exception if the array doesn't exist
-    if (x_array == NULL) {
-        Py_XDECREF(x_array);
+    if (!x_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert x to NumPy array");
         return NULL;
     }
 
@@ -29,7 +28,7 @@ static PyObject *wrap_logicle_scale(PyObject *self, PyObject *args) {
     // now we can call our function!
     logicle_scale(t, w, m, a, xc, n);
 
-    return x_array;
+    return (PyObject *) x_array;
 }
 
 static PyObject *wrap_logicle_inverse(PyObject *self, PyObject *args) {
@@ -42,11 +41,9 @@ static PyObject *wrap_logicle_inverse(PyObject *self, PyObject *args) {
     }
 
     // read the numpy array
-    PyObject *x_array = PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_IN_ARRAY);
-
-    // throw exception if the array doesn't exist
-    if (x_array == NULL) {
-        Py_XDECREF(x_array);
+    PyArrayObject *x_array = (PyArrayObject *) PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!x_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert x to NumPy array");
         return NULL;
     }
 
@@ -59,7 +56,7 @@ static PyObject *wrap_logicle_inverse(PyObject *self, PyObject *args) {
     // now we can call our function!
     logicle_inverse(t, w, m, a, xc, n);
 
-    return x_array;
+    return (PyObject *) x_array;
 }
 
 static PyObject *wrap_hyperlog_scale(PyObject *self, PyObject *args) {
@@ -72,11 +69,9 @@ static PyObject *wrap_hyperlog_scale(PyObject *self, PyObject *args) {
     }
 
     // read the numpy array
-    PyObject *x_array = PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_IN_ARRAY);
-
-    // throw exception if the array doesn't exist
-    if (x_array == NULL) {
-        Py_XDECREF(x_array);
+    PyArrayObject *x_array = (PyArrayObject *) PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!x_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert x to NumPy array");
         return NULL;
     }
 
@@ -89,7 +84,7 @@ static PyObject *wrap_hyperlog_scale(PyObject *self, PyObject *args) {
     // now we can call our function!
     hyperlog_scale(t, w, m, a, xc, n);
 
-    return x_array;
+    return (PyObject *) x_array;
 }
 
 static PyObject *wrap_hyperlog_inverse(PyObject *self, PyObject *args) {
@@ -102,11 +97,9 @@ static PyObject *wrap_hyperlog_inverse(PyObject *self, PyObject *args) {
     }
 
     // read the numpy array
-    PyObject *x_array = PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_IN_ARRAY);
-
-    // throw exception if the array doesn't exist
-    if (x_array == NULL) {
-        Py_XDECREF(x_array);
+    PyArrayObject *x_array = (PyArrayObject *) PyArray_FROM_OTF(x, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY);
+    if (!x_array) {
+        PyErr_SetString(PyExc_RuntimeError, "Failed to convert x to NumPy array");
         return NULL;
     }
 
@@ -119,7 +112,7 @@ static PyObject *wrap_hyperlog_inverse(PyObject *self, PyObject *args) {
     // now we can call our function!
     hyperlog_inverse(t, w, m, a, xc, n);
 
-    return x_array;
+    return (PyObject *) x_array;
 }
 
 
@@ -133,29 +126,41 @@ static PyMethodDef module_methods[] = {
 
 #if PY_MAJOR_VERSION >= 3
 static struct PyModuleDef logicledef = {
-        PyModuleDef_HEAD_INIT,
-        "logicle_c",
-        NULL,
-        -1,
-        module_methods
+    PyModuleDef_HEAD_INIT,
+    "logicle_c",
+    NULL,
+    -1,
+    module_methods
 };
-#endif
 
-#if PY_MAJOR_VERSION >= 3
 PyMODINIT_FUNC PyInit_logicle_c(void) {
     PyObject *m = PyModule_Create(&logicledef);
+    if (m == NULL) {
+        return NULL;
+    }
+
+    import_array(); 
+    if (PyErr_Occurred()) {  
+        Py_DECREF(m);
+        return NULL;
+    }
+
+    return m;
+}
 #else
 PyMODINIT_FUNC initlogicle_c(void) {
     PyObject *m = Py_InitModule3("logicle_c", module_methods, NULL);
-#endif
-
     if (m == NULL) {
-        return NULL;
+        return;
     }
 
-    import_array();
+    import_array();  
+    if (PyErr_Occurred()) {
+        Py_DECREF(m);
+        return;
+    }
 
-#if PY_MAJOR_VERSION >= 3
-    return m;
-#endif
+    return;
 }
+#endif
+