Merge ebe697a into 0d822e8

LFPy · Jul 11, 2019 · cfafa9f · cfafa9f
2 parents 0d822e8 + ebe697a
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,4 +1,7 @@
 conda:
   file: doc/environment.yml
 python:
-   setup_py_install: true
+  version: 3.6
+  setup_py_install: true
+requirements_file: doc/requirements.txt
+system_packages: false
diff --git a/LFPy/__init__.py b/LFPy/__init__.py
@@ -41,7 +41,7 @@
   * run_simulations - Functions to run NEURON simulations
 """
 
-__version__ = "2.0.2"
+__version__ = "2.0.3"
 
 from .pointprocess import Synapse, PointProcess, StimIntElectrode
 from .recextelectrode import RecExtElectrode, RecMEAElectrode

diff --git a/LFPy/cell.py b/LFPy/cell.py
@@ -2129,8 +2129,7 @@ def insert_v_ext(self, v_ext, t_ext):
         return
 
     def get_axial_currents_from_vmem(self, timepoints=None):
-        """
-        Compute axial currents from cell sim: get current magnitude,
+        """Compute axial currents from cell sim: get current magnitude,
         distance vectors and position vectors.
 
         Parameters
@@ -2159,6 +2158,7 @@ def get_axial_currents_from_vmem(self, timepoints=None):
             the mid point of each axial current in i_axial in units of (µm). The
             indices of the first axis, correspond to the first axis
             of i_axial and d_vectors.
+        
         Raises
         ------
         AttributeError

diff --git a/README.md b/README.md
@@ -37,6 +37,7 @@ This scientific software is released under the GNU Public License GPLv3.
 
 Code status
 ===========
+[![PyPI version](https://badge.fury.io/py/LFPy.svg)](https://badge.fury.io/py/LFPy)
 [![Build Status](https://travis-ci.org/LFPy/LFPy.svg?branch=master)](https://travis-ci.org/LFPy/LFPy)
 [![Coverage Status](https://coveralls.io/repos/github/LFPy/LFPy/badge.svg?branch=master)](https://coveralls.io/github/LFPy/LFPy?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/lfpy/badge/?version=latest)](http://lfpy.readthedocs.io/en/latest/?badge=latest)
@@ -109,9 +110,9 @@ There are few options to install LFPy:
 5. Anaconda Python (macos/linux):
 
         conda install lfpy neuron=*=mpi* # installs LFPy and Neuron in the current conda environment
-    
+
     or
-    
+
         conda create -n lfpy lfpy neuron=*=mpi* # creates new conda environment with LFPy and Neuron
 
 Uninstall

diff --git a/doc/classes.rst b/doc/classes.rst
@@ -18,7 +18,7 @@ Module :mod:`LFPy`
         :members:
         :show-inheritance:
         :undoc-members:
-    
+
     class :class:`NetworkCell`
     ===========================
     .. autoclass:: NetworkCell
@@ -74,7 +74,7 @@ Module :mod:`LFPy`
         :members:
         :show-inheritance:
         :undoc-members:
-    
+
     class :class:`OneSphereVolumeConductor`
     =======================================
     .. autoclass:: OneSphereVolumeConductor
@@ -105,16 +105,15 @@ Module :mod:`LFPy`
     .. automodule:: LFPy.lfpcalc
         :members:
         :undoc-members:
-    
+
     submodule :mod:`tools`
     ======================
     .. automodule:: LFPy.tools
         :members:
         :undoc-members:
-    
+
     submodule :mod:`inputgenerators`
     ================================
     .. automodule:: LFPy.inputgenerators
         :members:
         :undoc-members:
-
diff --git a/doc/conf.py b/doc/conf.py
@@ -25,7 +25,8 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.doctest',
               'sphinx.ext.autosummary',
               'sphinx.ext.viewcode',
               'sphinx.ext.mathjax',
@@ -54,7 +55,7 @@
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.2'
+release = '2.0.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/environment.yml b/doc/environment.yml
@@ -12,6 +12,5 @@ dependencies:
   - mpi4py
   - numpydoc
   - sphinx
+  - sphinx_rtd_theme
   - neuron
-  - pip:
-    - sphinx-rtd-theme
diff --git a/doc/index.rst b/doc/index.rst
@@ -56,17 +56,12 @@ This scientific software is released under the GNU Public License `GPLv3 <http:/
 Tutorial slides on LFPy
 -----------------------
 
-Slides for OCNS 2018 meeting tutorial `T5: Modeling and analysis of extracellular potentials <https://www.cnsorg.org/cns-2018-tutorials#T5>`_ hosted in Seattle, USA on LFPy: `CNS2018_LFPy_tutorial.pdf  <http://LFPy.github.io/downloads/CNS2018_LFPy_tutorial.pdf>`_
-
-Slides for OCNS 2017 meeting tutorial `T4: Modeling and analysis of extracellular potentials <http://www.cnsorg.org/cns-2017-tutorials#t4>`_ hosted in Antwerp, Belgium on LFPy and hybridLFPy: `CNS2017_LFPy_tutorial.pdf  <http://LFPy.github.io/downloads/CNS2017_LFPy_tutorial.pdf>`_
-
-Slides from OCNS 2015 meeting tutorial `T2:  Modeling and analysis of extracellular potentials <http://www.cnsorg.org/cns-2015-tutorials#t2>`_ hosted in Prague, Czech Republic on LFPy and hybridLFPy: `CNS2015_LFPy_tutorial.pdf  <http://LFPy.github.io/downloads/CNS2015_LFPy_tutorial.pdf>`_
-
-Slides from OCNS 2014 meeting tutorial `T4:  Modeling and analysis of extracellular potentials <http://www.cnsorg.org/cns-2014-tutorials#T4>`_ hosted in Quebec City: `hybridlfpy_tutorial_OCNS2014.pdf  <http://LFPy.github.io/downloads/hybridlfpy_tutorial_OCNS2014.pdf>`_
-
-As part of the OCNS 2013 meeting workshop `Modeling and interpretation of extracellular potentials <http://www.cnsorg.org/cns-2013-tutorials#extracellular_potentials>`_,
-there was also a talk on LFPy.
-The slides can be found here: `lfpy-tutorial_OCNS2013.pdf  <http://LFPy.github.io/downloads/lfpy-tutorial_OCNS2013.pdf>`_.
+- Slides for OCNS 2018 meeting tutorial `T5: Modeling and analysis of extracellular potentials <https://www.cnsorg.org/cns-2018-tutorials#T5>`_ hosted in Seattle, USA on LFPy: `CNS2018_LFPy_tutorial.pdf  <http://LFPy.github.io/downloads/CNS2018_LFPy_tutorial.pdf>`_
+- Slides for OCNS 2017 meeting tutorial `T4: Modeling and analysis of extracellular potentials <http://www.cnsorg.org/cns-2017-tutorials#t4>`_ hosted in Antwerp, Belgium on LFPy and hybridLFPy: `CNS2017_LFPy_tutorial.pdf  <http://LFPy.github.io/downloads/CNS2017_LFPy_tutorial.pdf>`_
+- Slides from OCNS 2015 meeting tutorial `T2:  Modeling and analysis of extracellular potentials <http://www.cnsorg.org/cns-2015-tutorials#t2>`_ hosted in Prague, Czech Republic on LFPy and hybridLFPy: `CNS2015_LFPy_tutorial.pdf  <http://LFPy.github.io/downloads/CNS2015_LFPy_tutorial.pdf>`_
+- Slides from OCNS 2014 meeting tutorial `T4:  Modeling and analysis of extracellular potentials <http://www.cnsorg.org/cns-2014-tutorials#T4>`_ hosted in Quebec City: `hybridlfpy_tutorial_OCNS2014.pdf  <http://LFPy.github.io/downloads/hybridlfpy_tutorial_OCNS2014.pdf>`_
+- As part of the OCNS 2013 meeting workshop `Modeling and interpretation of extracellular potentials <http://www.cnsorg.org/cns-2013-tutorials#extracellular_potentials>`_,
+  there was also a talk on LFPy. The slides can be found here: `lfpy-tutorial_OCNS2013.pdf  <http://LFPy.github.io/downloads/lfpy-tutorial_OCNS2013.pdf>`_.
 
 
 Related projects

diff --git a/doc/information.rst b/doc/information.rst
@@ -419,7 +419,7 @@ Windows 10 Pro/Education (64-bit) install instructions:
 
         git clone https://github.com/LFPy/LFPy.git
 
-10.  Build LFPy from source (without moving files)
+10. Build LFPy from source (without moving files)
     ::
 
         python setup.py develop

diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -2,3 +2,4 @@
 numpy>=1.8.2
 numpydoc
 sphinx
+sphinx-rtd-theme
diff --git a/setup.py b/setup.py
@@ -14,27 +14,26 @@
 try:
     import numpy
     from Cython.Distutils import build_ext
-    cmdclass = { 'build_ext' : build_ext}
-    ext_modules = [
-        Extension('LFPy.run_simulation',
-        [os.path.join('LFPy', 'run_simulation.pyx')],
-        include_dirs=[numpy.get_include()]),
-        Extension('LFPy.alias_method',
-        [os.path.join('LFPy', 'alias_method.pyx')],
-        include_dirs=[numpy.get_include()]),
-        ]
-except ImportError as ie:
+    cmdclass = {'build_ext': build_ext}
+    ext_modules = [Extension('LFPy.run_simulation',
+                   [os.path.join('LFPy', 'run_simulation.pyx')],
+                   include_dirs=[numpy.get_include()]),
+                   Extension('LFPy.alias_method',
+                   [os.path.join('LFPy', 'alias_method.pyx')],
+                   include_dirs=[numpy.get_include()]),
+                    ]
+except ImportError:
     print("'from Cython.Distutils import build_ext' or 'import numpy' failed!")
     print("Cython extensions will not be compiled, and")
     print("simulations in LFPy may run slower")
     cmdclass = {}
     ext_modules = []
 
-#try and locate the nrnivmodl script of NEURON in PATH so that the
-#NEURON extension file LFPy/sinsyn.mod can be compiled in place and be copied
-#as part of the package_data, allowing unit tests to run
+# try and locate the nrnivmodl script of NEURON in PATH so that the
+# NEURON extension file LFPy/sinsyn.mod can be compiled in place and be copied
+# as part of the package_data, allowing unit tests to run
 from distutils.spawn import find_executable, spawn
-if not any(arg in sys.argv for arg in ['sdist', 'upload']): 
+if not any(arg in sys.argv for arg in ['sdist', 'upload']):
     if find_executable('nrnivmodl') is not None:
         os.chdir(os.path.join('LFPy', 'test'))
         for path in ['x86_64', 'i686', 'powerpc']:
@@ -43,33 +42,33 @@
         spawn([find_executable('nrnivmodl')])
         os.chdir(os.path.join('..', '..'))
     else:
-        print("nrnivmodl script not found in PATH, thus NEURON .mod files could" +
-              "not be compiled, and LFPy.test() functions will fail")
+        print("nrnivmodl script not found in PATH, thus NEURON .mod files" +
+              "could not be compiled, and LFPy.test() functions will fail")
 
 with open('README.md') as file:
     long_description = file.read()
 
 setup(
-    name = "LFPy",
-    version = "2.0.2",
-    maintainer = "Espen Hagen",
-    maintainer_email = 'espen.hagen@fys.uio.no',
-    packages = ['LFPy'],
-    package_data = {'LFPy' : [os.path.join('test', '*.hoc'),
-                              os.path.join('test', '*.py'),
-                              os.path.join('test', 'sinsyn.mod'),
-                              os.path.join('i686', '*'),
-                              os.path.join('i686', '.libs', '*'),
-                              os.path.join('x86_64', '*'),
-                              os.path.join('x86_64', '.libs', '*'),
-                              os.path.join('powerpc', '*'),
-                              os.path.join('powerpc', '.libs', '*'),
-                              ]},
+    name="LFPy",
+    version="2.0.3",
+    maintainer="Espen Hagen",
+    maintainer_email='espen.hagen@fys.uio.no',
+    packages=['LFPy'],
+    package_data={'LFPy': [os.path.join('test', '*.hoc'),
+                           os.path.join('test', '*.py'),
+                           os.path.join('test', 'sinsyn.mod'),
+                           os.path.join('i686', '*'),
+                           os.path.join('i686', '.libs', '*'),
+                           os.path.join('x86_64', '*'),
+                           os.path.join('x86_64', '.libs', '*'),
+                           os.path.join('powerpc', '*'),
+                           os.path.join('powerpc', '.libs', '*'),
+                           ]},
     include_package_data=True,
-    cmdclass = cmdclass,
-    ext_modules = ext_modules,
+    cmdclass=cmdclass,
+    ext_modules=ext_modules,
     url='http://LFPy.readthedocs.io',
-    download_url = 'https://github.com/LFPy/LFPy/tarball/v2.0.2',
+    download_url='https://github.com/LFPy/LFPy/tarball/v2.0.3',
     license='LICENSE',
     description='A module for modeling extracellular potentials of multicompartment neuron models built on NEURON',
     long_description=long_description,
@@ -80,6 +79,7 @@
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
         'Programming Language :: Cython',
         'Operating System :: OS Independent',
         'Topic :: Scientific/Engineering',
@@ -89,14 +89,16 @@
         'Intended Audience :: Science/Research',
         'Development Status :: 5 - Production/Stable',
         ],
-    install_requires = [
+    install_requires=[
         'numpy>=1.8',
         'scipy>=0.14',
         'Cython>=0.20',
         'h5py>=2.5',
         'mpi4py>=1.2',
         ],
-    extras_require = {'tests': ['pytest']},
-    dependency_links = [],
-    provides = ['LFPy'],
+    extras_require={'tests': ['pytest'],
+                    'docs': ['sphinx', 'numpydoc', 'sphinx_rtd_theme']
+                    },
+    dependency_links=[],
+    provides=['LFPy'],
     )