Merge pull request #15 from gjbex/development

Update for Cython 3.x

Author: gjbex

python_for_hpc.pptx

@@ -0,0 +1 @@
+points.c

source-code/cython/Classes/.gitignore

@@ -0,0 +1,12 @@
+VERSION = cpython-311-x86_64-linux-gnu
+POINTS_LIB = points.$(VERSION).so
+POINTS_PURE_LIB = points_pure.$(VERSION).so
+
+all: $(POINTS_LIB)
+
+$(POINTS_LIB): points.pyx points_pure.py
+	python setup.py build_ext --inplace
+
+clean:
+	python setup.py clean
+	$(RM) points.c points_pure.c $(POINTS_LIB) $(POINTS_PURE_LIB)

source-code/cython/Classes/Makefile

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+# Classes
+
+Illustration of using Cython extension types (aka cdef classes).
+
+## What is it?
+
+1. `points.pyx`: implementation of a cdef class, and a Python
+   child class thereof.
+1. `points_pure.py`: implementation in Cython's pure Python
+   syntax.
+1. `points_python.py`: Python implementation of the class.
+1. `driver.py`: Python script that uses both classes.
+1. `setup.py`: Python installation file to build the Cython
+   extension.
+1. `distances_cython.py`: Python script to compute distances between
+   points using Cython class.
+1. `distances_python.py`: Python script to compute distances between
+   points using Python class.
+1. `distances_internal.py`: Python script to compute distances between
+   points using Cython class, computing the distances using a static
+   class method..
+1. `Makefile`: make file to build the extension.

source-code/cython/Classes/README.md

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+import argparse
+import itertools
+import pyximport
+pyximport.install(pyimport=True, language_level='3str')
+from points_pure import Point
+import random
+
+
+def main():
+    arg_parser = argparse.ArgumentParser(description='compute distances')
+    arg_parser.add_argument('--n', type=int, default=10,
+                            help='number of points')
+    options = arg_parser.parse_args()
+    points = [Point(random.random(), random.random()) for _ in range(options.n)]
+    min_distance = 2.0
+    max_distance = 0.0
+    for i, p1 in enumerate(points):
+        for p2 in points[i+1:]:
+            d = p1.distance(p2)
+            min_distance = min(d, min_distance)
+            max_distance = max(d, max_distance)
+    print(f'min. distance: {min_distance}')
+    print(f'max. distance: {max_distance}')
+
+if __name__ == '__main__':
+    main()

source-code/cython/Classes/distances_cython.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+import argparse
+import itertools
+import pyximport
+pyximport.install(pyimport=True, language_level='3str')
+from points_pure import Point
+import random
+
+
+def main():
+    arg_parser = argparse.ArgumentParser(description='compute distances')
+    arg_parser.add_argument('--n', type=int, default=10,
+                            help='number of points')
+    options = arg_parser.parse_args()
+    points = [Point(random.random(), random.random()) for _ in range(options.n)]
+    min_distance, max_distance = Point.min_max_distance(points)
+    print(f'min. distance: {min_distance}')
+    print(f'max. distance: {max_distance}')
+
+if __name__ == '__main__':
+    main()

source-code/cython/Classes/distances_internal.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+
+import argparse
+import itertools
+from points_python import Point
+import random
+
+
+def main():
+    arg_parser = argparse.ArgumentParser(description='compute distances')
+    arg_parser.add_argument('--n', type=int, default=10,
+                            help='number of points')
+    options = arg_parser.parse_args()
+    points = [Point(random.random(), random.random()) for _ in range(options.n)]
+    min_distance = 2.0
+    max_distance = 0.0
+    for i, p1 in enumerate(points):
+        for p2 in points[i+1:]:
+            d = p1.distance(p2)
+            min_distance = min(d, min_distance)
+            max_distance = max(d, max_distance)
+    print(f'min. distance: {min_distance}')
+    print(f'max. distance: {max_distance}')
+
+if __name__ == '__main__':
+    main()

source-code/cython/Classes/distances_python.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+
+from points import Point, ColoredPoint
+
+p = Point(1.0, -2.0)
+print(p)
+print(f'point = {p.x}, {p.y}')
+print(p.distance())
+
+p1 = ColoredPoint(1.0, -2.0, 'blue')
+print(p1.color)

source-code/cython/Classes/driver.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+
+import pyximport
+pyximport.install(pyimport=True, language_level='3str')
+
+from points_pure import Point, ColoredPoint
+
+p = Point(1.0, -2.0)
+print(p)
+print(f'point = {p.x}, {p.y}')
+print(p.distance())
+
+p1 = ColoredPoint(1.0, -2.0, 'blue')
+print(p1.color)

source-code/cython/Classes/driver_pure.py

@@ -0,0 +1,39 @@
+from libc.math cimport sqrt
+
+cdef class Point:
+    
+    cdef double _x, _y
+    
+    def __init__(self, x, y):
+        self._x = x
+        self._y = y
+        
+    cpdef distance(self, other):
+        return sqrt((self._x - other._x)**2 + (self._y - other._y)**2)
+    
+    property x:
+        def __get__(self):
+            return self._x
+        def __set__(self, value):
+            self._x = float(value)
+            
+    property y:
+        def __get__(self):
+            return self._y
+        def __set__(self, value):
+            self._y = float(value)            
+
+
+class ColoredPoint(Point):
+
+    def __init__(self, x, y, color):
+        super().__init__(x, y)
+        self._color = color
+
+    @property
+    def color(self):
+        return self._color
+
+    @color.setter
+    def color(self, value):
+        self._color = str(value)

source-code/cython/Classes/points.pyx

@@ -0,0 +1,74 @@
+import cython
+from cython.cimports.libc.math import sqrt
+
+
+@cython.cfunc
+def _min_max_distance(points: cython.list) -> cython.tuple[cython.double, cython.double]:
+    min_distance : cython.double = 2.0   
+    max_distance : cython.double = 0.0
+    for i in range(len(points)):
+        p1 : Point = points[i]
+        for j in range(i+1, len(points)):
+            p2 : Point = points[j]
+            distance = sqrt((p1._x - p2._x)*(p1._x - p2._x) + (p1._y - p2._y)*(p1._y - p2._y))
+            if distance < min_distance:
+                min_distance = distance
+            if distance > max_distance:
+                max_distance = distance
+    return min_distance, max_distance
+
+
+@cython.cclass
+class Point:
+    
+    _x: cython.double
+    _y: cython.double
+    
+    def __init__(self, x: cython.double, y: cython.double) -> None:
+        self._x = x
+        self._y = y
+        
+    @cython.ccall
+    def distance(self, other: Point) -> cython.double:
+        return sqrt((self._x - other._x)*(self._x - other._x) + (self._y - other._y)*(self._y - other._y))
+    
+    @staticmethod
+    def min_max_distance(points: list) -> tuple[float, float]:
+        return _min_max_distance(points)
+
+    @property
+    def x(self) -> cython.double:
+        return self._x
+
+    @x.setter
+    def x(self, value: cython.double) -> None:
+        self._x = float(value)
+
+    @property
+    def y(self) -> cython.double:
+        return self._y
+
+    @y.setter
+    def y(self, value: cython.double) -> None:
+        self._y = float(value)
+
+    def __str__(self) -> str:
+        return f"Point({self.x}, {self.y})"
+
+
+class ColoredPoint(Point):
+
+    def __init__(self, x, y, color):
+        super().__init__(x, y)
+        self._color = color
+
+    @property
+    def color(self):
+        return self._color
+
+    @color.setter
+    def color(self, value):
+        self._color = str(value)
+
+    def __str__(self):
+        return f"ColoredPoint({self.x}, {self.y}, {self.color})"

source-code/cython/Classes/points_pure.py

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+from math import sqrt
+
+class Point:
+    
+    _x: float
+    _y: float
+    
+    def __init__(self, x: float, y: float) -> None:
+        self.x = x
+        self.y = y
+        
+    def distance(self, other) -> float:
+        return sqrt((self.x - other.x)*(self.x - other.x) + (self.y - other.y)*(self.y - other.y))
+    
+    @property
+    def x(self) -> float:
+        return self._x
+
+    @x.setter
+    def x(self, value: float) -> None:
+        self._x = float(value)
+
+    @property
+    def y(self) -> float:
+        return self._y
+
+    @y.setter
+    def y(self, value: float) -> None:
+        self._y = float(value)
+
+    def __str__(self) -> str:
+        return f"Point({self.x}, {self.y})"
+
+
+class ColoredPoint(Point):
+
+    def __init__(self, x, y, color):
+        super().__init__(x, y)
+        self._color = color
+
+    @property
+    def color(self):
+        return self._color
+
+    @color.setter
+    def color(self, value):
+        self._color = str(value)
+
+    def __str__(self):
+        return f"ColoredPoint({self.x}, {self.y}, {self.color})"

source-code/cython/Classes/points_python.py

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+#!/usr/bin/env python
+
+from distutils.core import setup
+from Cython.Build import cythonize
+
+setup(
+    ext_modules=cythonize(['points.pyx', 'points_pure.py'],
+                          language_level='3str')
+)

source-code/cython/Classes/setup.py

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+hello_world.c

source-code/cython/HelloWorld/.gitignore

@@ -0,0 +1,22 @@
+cmake_minimum_required(VERSION 3.22)
+
+project(HelloWorld LANGUAGES C)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
+find_package(Cython REQUIRED)
+find_package(PythonExtensions REQUIRED)
+# include_directories(${PYTHON_INCLUDE_DIRS})
+
+add_cython_target(hello_world hello_world.pyx PY3 OUTPUT_VAR hello_world_src)
+add_library(hello_world MODULE ${hello_world_src})
+target_include_directories(hello_world PRIVATE ${PYTHON_INCLUDE_DIRS})
+set_target_properties(hello_world PROPERTIES PREFIX "")
+
+install(TARGETS hello_world DESTINATION .)
+install(FILES say_hello.py
+    DESTINATION .
+    RENAME say_hello
+    PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+)

source-code/cython/HelloWorld/CMakeLists.txt

@@ -1,4 +1,4 @@
-VERSION = cpython-34m
+VERSION = cpython-311-x86_64-linux-gnu
 HELLO_WORLD_LIB = hello_world.$(VERSION).so
 
 all: $(HELLO_WORLD_LIB)
@@ -8,4 +8,5 @@ $(HELLO_WORLD_LIB): hello_world.pyx
 
 clean:
 	python setup.py clean
-	rm -f hello_world.c $(HELLO_WORLD_LIB)
+	$(RM)  $(HELLO_WORLD_LIB) hello_world.c
+	$(RM) -r build