Spike Order support (#39)0.6.0

* reorganized directionality module

* further refactoring of directionality

* completed python directionality backend

* added SPIKE-Sync based filtering

new function filter_by_spike_sync removes spikes that have a multi-variate
Spike Sync value below some threshold

not yet fully tested, python backend missing.

* spike sync filtering, cython sim ann

Added function for filtering out events based on a threshold for the spike
sync values. Usefull for focusing on synchronous events during directionality
analysis.
Also added cython version of simulated annealing for performance.

* added coincidence single profile to python backend

missing function in python backend added, identified and fixed a bug in the
implementation as well

* updated test case to new spike sync behavior

* python3 fixes

* another python3 fix

* reorganized directionality module

* further refactoring of directionality

* completed python directionality backend

* added SPIKE-Sync based filtering

new function filter_by_spike_sync removes spikes that have a multi-variate
Spike Sync value below some threshold

not yet fully tested, python backend missing.

* spike sync filtering, cython sim ann

Added function for filtering out events based on a threshold for the spike
sync values. Usefull for focusing on synchronous events during directionality
analysis.
Also added cython version of simulated annealing for performance.

* added coincidence single profile to python backend

missing function in python backend added, identified and fixed a bug in the
implementation as well

* updated test case to new spike sync behavior

* python3 fixes

* another python3 fix

* Fix absolute imports in directionality measures

* remove commented code

* Add directionality to docs, bump version

* Clean up directionality module, add doxy.

* Remove debug print from tests

* Fix bug in calling Python backend

* Fix incorrect integrals in PieceWiseConstFunc (#36)

* Add (some currently failing) tests for PieceWiseConstFunc.integral

* Fix implementation of PieceWiseConstFunc.integral

Just by adding a special condition for when we are only taking an
integral "between" two edges of a PieceWiseConstFunc
All tests now pass.
Fixes #33.

* Add PieceWiseConstFunc.integral tests for ValueError

* Add testing bounds of integral
* Raise ValueError in function implementation

* Fix incorrect integrals in PieceWiseLinFunc (#38)

Integrals of piece-wise linear functions were incorrect if the
requested interval lies completely between two support points.
This has been fixed, and a unit test exercising this behavior
was added.

Fixes #38

* Add Spike Order example and Tutorial section

Adds an example computing spike order profile and the optimal
spike train order. Also adds a section on spike train order to the
tutorial.

1 files changed, 22 insertions, 6 deletions

diff --git a/setup.py b/setup.py
index 5b9e677..b5b01a6 100644
--- a/setup.py
+++ b/setup.py
@@ -30,7 +30,9 @@ class numpy_include(object):
 
 if os.path.isfile("pyspike/cython/cython_add.c") and \
    os.path.isfile("pyspike/cython/cython_profiles.c") and \
-   os.path.isfile("pyspike/cython/cython_distances.c"):
+   os.path.isfile("pyspike/cython/cython_distances.c") and \
+   os.path.isfile("pyspike/cython/cython_directionality.c") and \
+   os.path.isfile("pyspike/cython/cython_simulated_annealing.c"):
     use_c = True
 else:
     use_c = False
@@ -45,7 +47,11 @@ if use_cython:  # Cython is available, compile .pyx -> .c
         Extension("pyspike.cython.cython_profiles",
                   ["pyspike/cython/cython_profiles.pyx"]),
         Extension("pyspike.cython.cython_distances",
-                  ["pyspike/cython/cython_distances.pyx"])
+                  ["pyspike/cython/cython_distances.pyx"]),
+        Extension("pyspike.cython.cython_directionality",
+                  ["pyspike/cython/cython_directionality.pyx"]),
+        Extension("pyspike.cython.cython_simulated_annealing",
+                  ["pyspike/cython/cython_simulated_annealing.pyx"])
     ]
     cmdclass.update({'build_ext': build_ext})
 elif use_c:  # c files are there, compile to binaries
@@ -55,14 +61,18 @@ elif use_c:  # c files are there, compile to binaries
         Extension("pyspike.cython.cython_profiles",
                   ["pyspike/cython/cython_profiles.c"]),
         Extension("pyspike.cython.cython_distances",
-                  ["pyspike/cython/cython_distances.c"])
+                  ["pyspike/cython/cython_distances.c"]),
+        Extension("pyspike.cython.cython_directionality",
+                  ["pyspike/cython/cython_directionality.c"]),
+        Extension("pyspike.cython.cython_simulated_annealing",
+                  ["pyspike/cython/cython_simulated_annealing.c"])
     ]
 # neither cython nor c files available -> automatic fall-back to python backend
 
 setup(
     name='pyspike',
     packages=find_packages(exclude=['doc']),
-    version='0.5.3',
+    version='0.6.0',
     cmdclass=cmdclass,
     ext_modules=ext_modules,
     include_dirs=[numpy_include()],
@@ -90,11 +100,17 @@ train similarity',
 
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
-
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6'
-    ]
+    ],
+    package_data={
+        'pyspike': ['cython/cython_add.c', 'cython/cython_profiles.c',
+                    'cython/cython_distances.c',
+                    'cython/cython_directionality.c',
+                    'cython/cython_simulated_annealing.c'],
+        'test': ['Spike_testdata.txt']
+    }
 )