From 7a2a38c7538434fadff26402daea46294a92bc9f Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Thu, 27 Oct 2016 20:27:00 -0700 Subject: Added SoftwareX reference and Spike-Order note --- Readme.rst | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/Readme.rst b/Readme.rst index 542f4b3..d60d154 100644 --- a/Readme.rst +++ b/Readme.rst @@ -15,6 +15,13 @@ PySpike provides the same fundamental functionality as the SPIKY_ framework for All source codes are available on `Github `_ and are published under the BSD_License_. +Citing PySpike +---------------------------- +If you use PySpike in your research, please cite our SoftwareX publication on PySpike: + Mario Mulansky, Thomas Kreuz, *PySpike - A Python library for analyzing spike train synchrony*, SoftwareX, (2016), ISSN 2352-7110, http://dx.doi.org/10.1016/j.softx.2016.07.006. + +Additionally, depending on the methods you are using you should consider citation one or more of the following articles: + .. [#] Kreuz T, Haas JS, Morelli A, Abarbanel HDI, Politi A, *Measuring spike train synchrony.* J Neurosci Methods 165, 151 (2007) `[pdf] `_ .. [#] Kreuz T, Chicharro D, Houghton C, Andrzejak RG, Mormann F, *Monitoring spike train synchrony.* J Neurophysiol 109, 1457 (2013) `[pdf] `_ @@ -31,6 +38,12 @@ This is a breaking change in the function interfaces. Hence, programs written for older versions of PySpike (0.1.x) will not run with newer versions. +Upcoming Functionality +------------------------- + +In an upcoming release, new functionality for analyzing Synfire patterns based on the new measures SPIKE-Order and Spike-Train-Order method will become part of the PySpike library. +The new measures and algorithms are described in `this preprint `_. + Requirements and Installation ----------------------------- -- cgit v1.2.3 From 1b01bcfefbc4ccfc0f108aeedf2a518421333ea5 Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Sun, 30 Oct 2016 13:09:16 -0700 Subject: updated references --- Readme.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Readme.rst b/Readme.rst index d60d154..41e9c6c 100644 --- a/Readme.rst +++ b/Readme.rst @@ -7,7 +7,7 @@ PySpike :target: https://travis-ci.org/mariomulansky/PySpike PySpike is a Python library for the numerical analysis of spike train similarity. -Its core functionality is the implementation of the ISI_ and SPIKE_ distance [#]_ [#]_ as well as SPIKE-Synchronization_ [#]_. +Its core functionality is the implementation of the ISI_\-distance [#]_ and SPIKE_ distance [#]_ as well as SPIKE-Synchronization_ [#]_. It provides functions to compute multivariate profiles, distance matrices, as well as averaging and general spike train processing. All computation intensive parts are implemented in C via cython_ to reach a competitive performance (factor 100-200 over plain Python). @@ -20,13 +20,13 @@ Citing PySpike If you use PySpike in your research, please cite our SoftwareX publication on PySpike: Mario Mulansky, Thomas Kreuz, *PySpike - A Python library for analyzing spike train synchrony*, SoftwareX, (2016), ISSN 2352-7110, http://dx.doi.org/10.1016/j.softx.2016.07.006. -Additionally, depending on the methods you are using you should consider citation one or more of the following articles: +Additionally, depending on the used methods: ISI-distance [1], SPIKE-distance [2] or SPIKE-Synchronization [3], please cite one or more of the following publications: .. [#] Kreuz T, Haas JS, Morelli A, Abarbanel HDI, Politi A, *Measuring spike train synchrony.* J Neurosci Methods 165, 151 (2007) `[pdf] `_ .. [#] Kreuz T, Chicharro D, Houghton C, Andrzejak RG, Mormann F, *Monitoring spike train synchrony.* J Neurophysiol 109, 1457 (2013) `[pdf] `_ -.. [#] Kreuz T, Mulansky M and Bozanic N, *SPIKY: A graphical user interface for monitoring spike train synchrony*, J Neurophysiol, in press (2015) +.. [#] Kreuz T, Mulansky M and Bozanic N, *SPIKY: A graphical user interface for monitoring spike train synchrony*, J Neurophysiol, JNeurophysiol 113, 3432 (2015) Important Changelog ----------------------------- -- cgit v1.2.3 From 50b3d0bd1ceea236d8b4e95578cebf7c78a5035e Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Sun, 30 Oct 2016 13:13:38 -0700 Subject: fixed typo --- Readme.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Readme.rst b/Readme.rst index 41e9c6c..0422dad 100644 --- a/Readme.rst +++ b/Readme.rst @@ -7,7 +7,7 @@ PySpike :target: https://travis-ci.org/mariomulansky/PySpike PySpike is a Python library for the numerical analysis of spike train similarity. -Its core functionality is the implementation of the ISI_\-distance [#]_ and SPIKE_ distance [#]_ as well as SPIKE-Synchronization_ [#]_. +Its core functionality is the implementation of the ISI_\-distance [#]_ and SPIKE_\-distance [#]_ as well as SPIKE-Synchronization_ [#]_. It provides functions to compute multivariate profiles, distance matrices, as well as averaging and general spike train processing. All computation intensive parts are implemented in C via cython_ to reach a competitive performance (factor 100-200 over plain Python). -- cgit v1.2.3 From 564f9ba9df3c6837b102f370ad32a65c233c209f Mon Sep 17 00:00:00 2001 From: Dan Meliza Date: Mon, 2 Oct 2017 12:15:36 -0400 Subject: defer numpy import to allow install_requires to do its job (fixes #24) --- setup.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index b53304b..76a27e4 100644 --- a/setup.py +++ b/setup.py @@ -12,7 +12,6 @@ Distributed under the BSD License from setuptools import setup, find_packages from distutils.extension import Extension import os.path -import numpy try: from Cython.Distutils import build_ext @@ -21,6 +20,14 @@ except ImportError: else: use_cython = True + +class numpy_include(object): + """Defers import of numpy until install_requires is through""" + def __str__(self): + import numpy + return numpy.get_include() + + 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"): @@ -58,7 +65,7 @@ setup( version='0.5.1', cmdclass=cmdclass, ext_modules=ext_modules, - include_dirs=[numpy.get_include()], + include_dirs=[numpy_include()], description='A Python library for the numerical analysis of spike\ train similarity', author='Mario Mulansky', -- cgit v1.2.3 From 9fa10fe30e3216170f41ce47797c7a3a56e17a5f Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Wed, 4 Oct 2017 21:57:27 -0700 Subject: Update version in docs --- doc/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 807dec6..f9ec320 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -57,7 +57,7 @@ master_doc = 'index' # General information about the project. project = u'PySpike' -copyright = u'2014-2015, Mario Mulansky' +copyright = u'2014-2017, Mario Mulansky' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -66,7 +66,7 @@ copyright = u'2014-2015, Mario Mulansky' # The short X.Y version. version = '0.5' # The full version, including alpha/beta/rc tags. -release = '0.5.1' +release = '0.5.2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -- cgit v1.2.3 From 7d661660f143c1e690efa6dc2d526db635dc079a Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Wed, 4 Oct 2017 22:08:35 -0700 Subject: Fix typo in email --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index afcfa16..76fce07 100644 --- a/setup.py +++ b/setup.py @@ -69,7 +69,7 @@ setup( description='A Python library for the numerical analysis of spike\ train similarity', author='Mario Mulansky', - author_email='mario.mulanskygmx.net', + author_email='mario.mulansky@gmx.net', license='BSD', url='https://github.com/mariomulansky/PySpike', install_requires=['numpy'], -- cgit v1.2.3 From ece06870ab729f28fa1771f49725f25c6a25576d Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Wed, 4 Oct 2017 22:27:44 -0700 Subject: Fix library status string --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 76fce07..be5d209 100644 --- a/setup.py +++ b/setup.py @@ -79,7 +79,7 @@ train similarity', # 3 - Alpha # 4 - Beta # 5 - Production/Stable - 'Development Status :: 3 - Beta', + 'Development Status :: 4 - Beta', # Indicate who your project is intended for 'Intended Audience :: Science/Research', -- cgit v1.2.3 From 16040c3fb9f61f7753172f6d67ac7b22c961dcaa Mon Sep 17 00:00:00 2001 From: Mario Mulansky Date: Wed, 4 Oct 2017 22:35:08 -0700 Subject: Version bump --- doc/conf.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index f9ec320..25aa9c9 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -66,7 +66,7 @@ copyright = u'2014-2017, Mario Mulansky' # The short X.Y version. version = '0.5' # The full version, including alpha/beta/rc tags. -release = '0.5.2' +release = '0.5.3' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/setup.py b/setup.py index be5d209..5b9e677 100644 --- a/setup.py +++ b/setup.py @@ -62,7 +62,7 @@ elif use_c: # c files are there, compile to binaries setup( name='pyspike', packages=find_packages(exclude=['doc']), - version='0.5.2', + version='0.5.3', cmdclass=cmdclass, ext_modules=ext_modules, include_dirs=[numpy_include()], -- cgit v1.2.3