Merge pull request #10 from PyCOMPLETE/develop

Develop

Author: aoeftiger

README.md

@@ -1,4 +1,9 @@
 PyHEADTAIL
 ==========
 
-CERN PyHEADTAIL numerical n-body simulation code for simulating macro-particle beam dynamics with collective effects
+CERN PyHEADTAIL numerical n-body simulation code 
+for simulating macro-particle beam dynamics with collective effects.
+
+Currently only a git-clone of the repository is supported.
+The available zip files on github are missing the versioning 
+and will not allow ./install to work.

_version.py

@@ -1,8 +1,11 @@
 import os, subprocess
 worktree = 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)
-__version__ = __version__.rstrip() # remove trailing \n
-__version__ = __version__[1:] # remove leading v
+try:
+    __version__ = subprocess.check_output(
+        'git --git-dir=' + gitdir + ' --work-tree=' +
+        worktree + ' describe --long --dirty --abbrev=10 --tags', shell=True)
+    __version__ = __version__.rstrip() # remove trailing \n
+    __version__ = __version__[1:] # remove leading v
+except:
+    __version__ = '(no git available to determine version)'

setup.py

@@ -4,15 +4,24 @@
 from _version import __version__
 
 import re, os, sys, subprocess
-#import cython_gsl
 import numpy as np
 
-from distutils.core import setup
-from distutils.extension import Extension
+#from distutils.core import setup
+#from distutils.extension import Extension
+from setuptools import setup, Extension
+
 from Cython.Distutils import build_ext
 from Cython.Build import cythonize
 
 
+import platform
+if platform.system() is 'Darwin':
+    print ("Info: since you are running Mac OS, you "
+           "may have to install with the following line:\n\n"
+           "$ CC=gcc-4.9 ./install\n"
+           "(or any equivalent version of gcc)")
+    raw_input('Hit any key to continue...')
+
 VERSIONFILE="_version.py"
 #verstrline = open(VERSIONFILE, "rt").read()
 #VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
@@ -23,6 +32,9 @@
 #    raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
 execfile(VERSIONFILE)
 verstr = __version__
+if not verstr[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
@@ -51,14 +63,6 @@
 # Set up extension and build
 cy_ext_options = {"compiler_directives": {"profile": True}, "annotate": True}
 cy_ext = [
-        # Extension("beams.bunch",
-        #           ["beams/bunch.pyx"],
-        #          include_dirs=[np.get_include()],
-        #          #extra_compile_args=["-g"],
-        #          #extra_link_args=["-g"],
-        #          libraries=["m"],
-        #          library_dirs=[],
-        #          ),
         Extension("solvers.grid_functions",
                  ["solvers/grid_functions.pyx"],
                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
@@ -70,59 +74,32 @@
                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
                  extra_compile_args=["-fopenmp"],
                  extra_link_args=["-fopenmp"],
-                 #extra_compile_args=["-g"],
-                 #extra_link_args=["-g"],
                  ),
-        #Extension("cobra_functions.random",
-                 #["cobra_functions/random.pyx"],
-                 #include_dirs=[np.get_include(), cython_gsl.get_cython_include_dir()],
-                 ##extra_compile_args=["-g"],
-                 ##extra_link_args=["-g"],
-                 #library_dirs=[], libraries=["gsl", "gslcblas"],
-                 #),
         Extension("solvers.compute_potential_fgreenm2m",
                  ["solvers/compute_potential_fgreenm2m.pyx"],
                   include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
-                 #extra_compile_args=["-g"],
-                 #extra_link_args=["-g"],
                  ),
-#        Extension("cobra_functions.interp1d",
-#                 ["cobra_functions/interp1d.pyx"],
-#                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
-#                 #extra_compile_args=["-g"],
-#                 #extra_link_args=["-g"],
-#                 ),
         Extension("trackers.transverse_tracking_cython",
                  ["trackers/transverse_tracking_cython.pyx"],
                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
                  extra_compile_args=["-fopenmp"],
                  extra_link_args=["-fopenmp"],
-                 #extra_compile_args=["-g"],
-                 #extra_link_args=["-g"],
                  ),
         Extension("trackers.detuners_cython",
                  ["trackers/detuners_cython.pyx"],
                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
                  extra_compile_args=["-fopenmp"],
                  extra_link_args=["-fopenmp"],
-                 #extra_compile_args=["-g"],
-                 #extra_link_args=["-g"],
                  ),
         Extension("rfq.rfq",
                  ["rfq/rfq.pyx"],
                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
                  extra_compile_args=["-fopenmp"],
                  extra_link_args=["-fopenmp"],
-                 #extra_compile_args=["-g"],
-                 #extra_link_args=["-g"],
                  ),
         Extension("aperture.aperture",
                  ["aperture/aperture.pyx"],
                  include_dirs=[np.get_include()], library_dirs=[], libraries=["m"],
-                 #extra_compile_args=["-fopenmp"],
-                 #extra_link_args=["-fopenmp"],
-                 #extra_compile_args=["-g"],
-                 #extra_link_args=["-g"],
                  )
           ]
 
@@ -134,4 +111,11 @@
     packages=['PyHEADTAIL'],
     cmdclass={'build_ext': build_ext},
     ext_modules=cythonize(cy_ext, **cy_ext_options),
+    install_requires=[
+        'numpy',
+        'scipy',
+        'hdf5',
+        'h5py',
+        'cython'
+    ]
     )

testing/interactive-tests/WakeTest.ipynb

@@ -9,8 +9,7 @@
    "outputs": [],
    "source": [
     "import sys, os\n",
-    "#BIN = os.path.expanduser(\"~/cern/git/PyHEADTAIL-new/\")\n",
-    "BIN = os.path.expanduser(\"../../../PyHEADTAIL/\")\n",
+    "BIN = os.path.expanduser(\"../../../\")\n",
     "sys.path.append(BIN)"
    ]
   },

testing/unittests/autoruntests/WakeTest.py

@@ -354,7 +354,7 @@ def track_n_show(bunch, slicer, map_woWakes, wake_field):
 
     # Definition of WakeField as a composition of different sources.
     resis_circ = CircularResistiveWall(pipe_radius=5e-2, resistive_wall_length=C,
-                                        conductivity=1e6, dz_min=1e-3)
+                                        conductivity=1e6, dt_min=1e-3)
     wake_field = WakeField(uniform_bin_slicer, resis_circ)
 
 
@@ -376,7 +376,7 @@ def track_n_show(bunch, slicer, map_woWakes, wake_field):
 
     # Definition of WakeField as a composition of different sources.
     resis_para = ParallelPlatesResistiveWall(pipe_radius=5e-2, resistive_wall_length=C,
-                                        conductivity=1e6, dz_min=1e-3)
+                                        conductivity=1e6, dt_min=1e-3)
     wake_field = WakeField(uniform_bin_slicer, resis_para)
 
 
@@ -398,7 +398,7 @@ def track_n_show(bunch, slicer, map_woWakes, wake_field):
 
     # Definition of WakeField as a composition of different sources.
     resis_circ = CircularResistiveWall(pipe_radius=5e-2, resistive_wall_length=C,
-                                        conductivity=1e6, dz_min=1e-3)
+                                        conductivity=1e6, dt_min=1e-3)
     reson_para = ParallelPlatesResonator(R_shunt=1e6, frequency=1e8, Q=1)
     wake_file_columns = ['time', 'dipole_x', 'dipole_y', 'quadrupole_x', 'quadrupole_y',
                          'dipole_xy', 'dipole_yx']