76c061fb some work on the software engineering part

examples/profiling/diffusion_numba.py

@@ -4,7 +4,7 @@
 
 
 import numpy as np
-from numba import jit
+from numba import jit, njit
 
 # parameters (global, for convenience)
 n_iterations = 10
@@ -33,11 +33,11 @@ def init(val=0.5):
     return grid
 
 
-@jit(nopython=True)
 def main_loop(evolve_func, grid):
     """Main loop function, calling evolve_func on grid."""
     grid_tmp = np.empty_like(grid)
     for i in range(1, n_iterations+1):
+        apply_periodic_bc_python(grid, n_points)
         evolve_func(grid, grid_tmp, n_points, dt, D)
         # swap references, do not copy
         if grid_tmp is not None:
@@ -47,7 +47,7 @@ def main_loop(evolve_func, grid):
     return grid
 
 
-@jit(nopython=True)
+@njit()
 def apply_periodic_bc_python(grid, n_points):
     """Explicitly apply periodic boundary conditions, via Python loops."""
     for j in range(n_points + 2):
@@ -58,9 +58,8 @@ def apply_periodic_bc_python(grid, n_points):
         grid[ i, 0] = grid[ i,-2]
 
 
-@jit(nopython=True)
+@njit
 def evolve_python(grid, grid_tmp, n_points, dt, D):
-    apply_periodic_bc_python(grid, n_points)
     for i in range(1, n_points+1):
         for j in range(1, n_points+1):
             # stencil formula

examples/setuptools/hello_world_with_sphinx/setup.py

-from setuptools import setup
-setup(
-    name="HelloWorld",
-    version="0.1",
-    # specify a list of the packages (subdirectory with __init__.py file)
-    packages=["HelloWorld"],
-    # executable that comes with the package (if applicable)
-    scripts=['say_hello.py'],
-    # software dependencies (if necessary)
-    # install_requires=['docutils>=0.3'],
-    # metadata for upload to PyPI
-    author="Me",
-    author_email="me@example.com",
-    description="This is an Example Package",
-    license="PSF",
-    keywords="hello world example examples",
-    url="http://example.com/HelloWorld/",   # project home page, if any
-)

examples/setuptools/hello_world_with_tests/HelloWorld/__init__.py → examples/setuptools/minimal/helloworld/__init__.py

-# init file of the HelloWorld example package, is automatically executed at 'import'
+# init file of the helloworld example package, is automatically executed at 'import'
 from .lib import *

examples/setuptools/hello_world/HelloWorld/lib.py → examples/setuptools/minimal/helloworld/lib.py

-# implementation file, part of the "HelloWorld" demo Python package
+# implementation file, part of the "helloworld" demo Python package
 
 def say_hello():
     print("Hello World!")

examples/setuptools/hello_world_with_tests/say_hello.py → examples/setuptools/minimal/say_hello.py

 #!/usr/bin/env python3
-import HelloWorld
-HelloWorld.say_hello()
+import helloworld
+helloworld.say_hello()

examples/setuptools/minimal/setup.py

+from setuptools import setup
+
+setup(
+    # name of the software package (as it would appear on PyPI)
+    name="helloworld",
+    version="0.1",
+    # list of the Python modules provided by the package
+    packages=["helloworld"],
+    # list of executable(s) that come with the package (if applicable)
+    scripts=['say_hello.py'],
+    # list of package dependencies (if necessary)
+    #install_requires=['numpy'],
+    # more information, necessary for an upload to PyPI
+    author="John Doe",
+    author_email="john.doe@example.mpg.de",
+    description="example package that prints hello world",
+    license="PSF",
+    keywords="hello world example",
+    url="https://example.mpg.de/helloworld/",   # project home page, if any
+)