release-script: Merge branch 'release/v1.11.3'

MANIFEST.in

@@ -1,4 +1,3 @@
-recursive-include PyHEADTAIL *.pxd *.pyx *.c
-recursive-include PyHEADTAIL/testing *.py *.ipynb *.wake *.dat *.pkl
-include README.md
-include _version.py
+recursive-include PyHEADTAIL *.pxd *.pyx *.c *.f90 *.cu
+recursive-include PyHEADTAIL/testing *.py *.dat
+include README.rst

Makefile

@@ -2,9 +2,9 @@
 NVCC_RESULT := $(shell which nvcc)
 NVCC_TEST := $(notdir $(NVCC_RESULT))
 
-.PHONY: clean PyHEADTAIL PyHEADTAILGPU
+.PHONY: clean PyHEADTAIL PyHEADTAILGPU errfff
 
-all: PyHEADTAIL PyHEADTAILGPU
+all: PyHEADTAIL PyHEADTAILGPU errfff
 
 PyHEADTAIL:
 	python setup.py build_ext --inplace
@@ -16,6 +16,10 @@ else
 	@echo "GPU: Thrust interface not compiled because nvcc compiler not found."
 endif
 
+errfff:
+	f2py -c PyHEADTAIL/general/errfff.f90 -m errfff
+	mv errfff.so PyHEADTAIL/general/
+
 clean:
 	python setup.py build_ext --inplace cleanall
 	rm -f PyHEADTAIL/gpu/thrust.so

PyHEADTAIL/__init__.py

@@ -4,9 +4,11 @@
     worktree = os.path.dirname(
         os.path.dirname(os.path.abspath(__file__)))
     gitdir = worktree + '/.git/'
-    __version__ = subprocess.check_output(
-        'git --git-dir=' + gitdir + ' --work-tree=' +
-        worktree + ' describe --long --dirty --abbrev=10 --tags', shell=True)
+    with open(os.devnull, 'w') as devnull:
+        __version__ = subprocess.check_output(
+            'git --git-dir=' + gitdir + ' --work-tree=' +
+            worktree + ' describe --long --dirty --abbrev=10 --tags',
+            shell=True, stderr=devnull)
     __version__ = __version__.decode('utf-8').rstrip() # remove trailing \n
     __version__ = __version__[1:] # remove leading v
     # remove commit hash to conform to PEP440:

PyHEADTAIL/_version.py

@@ -1 +1 @@
-__version__ = '1.11.1'
+__version__ = '1.11.3'

PyHEADTAIL/general/pmath.py

@@ -6,14 +6,14 @@
 '''
 import numpy as np
 from ..cobra_functions import stats as cp
-from ..gpu import gpu_utils
-from ..gpu import gpu_wrap
 try:
     import pycuda.cumath
     import pycuda.gpuarray
     import pycuda.tools
+    from ..gpu import gpu_utils
+    from ..gpu import gpu_wrap
     has_pycuda = gpu_wrap.has_pycuda
-except ImportError:
+except (ImportError, OSError):
     # print ('No Pycuda in pmath.py import statement found')
     has_pycuda = False
 try:

PyHEADTAIL/trackers/longitudinal_tracking.py

@@ -719,7 +719,6 @@ def __init__(self, alpha_array, circumference, Q_s, D_x=0, D_y=0,*args, **kwargs
     def Qs(self):
         return self.Q_s
 
-    @clean_slices
     def track(self, beam):
         try:
             self.track_with_dispersion(beam)
@@ -743,6 +742,7 @@ def track_with_dispersion(self, beam):
         beam.x += self.D_x*beam.dp
         beam.y += self.D_y*beam.dp
 
+    @clean_slices
     def track_without_dispersion(self, beam):
         omega_0 = 2 * np.pi * beam.beta * c / self.circumference
         omega_s = self.Q_s * omega_0

README.rst

@@ -36,7 +36,7 @@ And there you go, start using PyHEADTAIL!
 
     In [1]: import PyHEADTAIL
 
-    PyHEADTAIL v1.11.1
+    PyHEADTAIL v1.11.2
 
 
 -------------------------------------------------------------------------------

setup.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 
 # thanks to Nick Foti for his cython skeleton, cf.
 # http://nfoti.github.io/a-creative-blog-name/posts/2013/02/07/cleaning-cython-build-files/
@@ -24,11 +24,6 @@
     raw_input('Hit any key to continue...')
 
 
-if not __version__[0].isdigit():
-    raise RuntimeError("Unable to determine version from _version.py, "
-                       "perhaps no git-describe available?")
-
-
 args = sys.argv[1:]
 # Make a `cleanall` rule to get rid of intermediate and library files
 if "cleanall" in args:
@@ -58,7 +53,11 @@
 
 
 # Set up extension and build
-cy_ext_options = {"compiler_directives": {"profile": True}, "annotate": True}
+cy_ext_options = {
+    "compiler_directives": {"profile": True, # SLOW!!!
+                            "embedsignature": True},
+    "annotate": True,
+}
 cy_ext = [
     Extension("PyHEADTAIL.cobra_functions.stats",
               ["PyHEADTAIL/cobra_functions/stats.pyx"],
@@ -87,6 +86,10 @@
     description='CERN PyHEADTAIL numerical n-body simulation code '
         'for simulating macro-particle beam dynamics with collective effects.',
     url='https://github.com/PyCOMPLETE/PyHEADTAIL',
+    author='Kevin Li',
+    author_email='Kevin.Li@cern.ch',
+    maintainer='Adrian Oeftiger',
+    maintainer_email='Adrian.Oeftiger@cern.ch',
     packages=find_packages(),
     long_description=long_description,
     cmdclass={'build_ext': build_ext},
@@ -98,10 +101,10 @@
         'h5py',
         'cython',
     ]
-    )
-
-from numpy.distutils.core import setup, Extension
-setup(
-    ext_modules = [Extension('PyHEADTAIL.general.errfff',
-                             ['PyHEADTAIL/general/errfff.f90'])],
 )
+
+# from numpy.distutils.core import setup, Extension
+# setup(
+#     ext_modules = [Extension('PyHEADTAIL.general.errfff',
+#                              ['PyHEADTAIL/general/errfff.f90'])],
+# )