Issue #113 fixes (#114)

* updated/added install instructions for Ubuntu 18.04 LTS * docstring fformatting * adding Python 3.7 to travis testing * 3.7 not ready for prime time * documentation updates, updated recipe for NEURON source install on Ubuntu * removed use of h.SectionList.allsec method * build NEURON against github master * fix test with NEURON@github:master * prep next release 2.0.1 * debug py27 travis build * debug travis python27 * send NEURON .configure output to null * v2.0.1 version number * removed csa from dependency_links list * neuron 7.6.4 a requirement for this version * add NEURON >= v7.6.4 version testing * Update README.md * Update README.md * LFPy.__version__ = '2.0.1'
LFPy · Jan 3, 2019 · 2e0db05 · 2e0db05
1 parent 2e5797a
commit 2e0db05
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Showing 9 changed files with 234 additions and 138 deletions.
diff --git a/LFPy/__init__.py b/LFPy/__init__.py
@@ -41,7 +41,7 @@
   * run_simulations - Functions to run NEURON simulations
 """
 
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 
 from .pointprocess import Synapse, PointProcess, StimIntElectrode
 from .recextelectrode import RecExtElectrode, RecMEAElectrode

diff --git a/LFPy/cell.py b/LFPy/cell.py
@@ -28,6 +28,15 @@
 from .run_simulation import _collect_geometry_neuron
 from .alias_method import alias_method
 
+# check neuron version:
+try:
+    try:
+        assert(neuron.version >= '7.6.4')
+    except AttributeError:
+        warn('LFPy could not read NEURON version info. v7.6.4 or newer required')
+except AssertionError:
+    warn('LFPy requires NEURON v7.6.4 or newer. Found v{}'.format(neuron.version))
+
 
 class Cell(object):
     """
@@ -2169,7 +2178,7 @@ def get_axial_currents_from_vmem(self, timepoints=None):
                      self.zend - self.zmid]
 
         children_dict = self.get_dict_of_children_idx()
-        for sec in self.allseclist.allsec():
+        for sec in self.allseclist:
             if not neuron.h.SectionRef(sec.name()).has_parent():
                 if sec.nseg == 1:
                     # skip soma, since soma is an orphan
@@ -2262,6 +2271,7 @@ def get_axial_currents_from_vmem(self, timepoints=None):
     def get_axial_resistance(self):
         """
         Return NEURON axial resistance for all cell compartments.
+        
         Returns
         -------
         ri_list : ndarray, dtype=float
@@ -2289,6 +2299,7 @@ def get_axial_resistance(self):
     def get_dict_of_children_idx(self):
         """
         Return dictionary with children segment indices for all sections.
+        
         Returns
         -------
         children_dict : dictionary
@@ -2298,7 +2309,7 @@ def get_dict_of_children_idx(self):
             sibling of a segment.
         """
         children_dict = {}
-        for sec in self.allseclist.allsec():
+        for sec in self.allseclist:
             children_dict[sec.name()] = []
             for child in neuron.h.SectionRef(sec.name()).child:
                 # add index of first segment of each child
@@ -2310,6 +2321,7 @@ def get_dict_of_children_idx(self):
     def get_dict_parent_connections(self):
         """
         Return dictionary with parent connection point for all sections.
+        
         Returns
         -------
         connection_dict : dictionary
@@ -2330,6 +2342,7 @@ def _parent_and_segment_current(self, seg_idx, parent_idx, bottom_seg,
         """
         Return axial current from segment (seg_idx) mid to segment start,
         and current from parent segment (parent_idx) end to parent segment mid.
+        
         Parameters
         ----------
         seg_idx : int

diff --git a/LFPy/test/test_cell.py b/LFPy/test/test_cell.py
@@ -907,7 +907,7 @@ def test_cell_get_axial_currents_from_vmem_14(self):
         dend1.connect(soma(1), 0)
         dend2.connect(soma(1), 0)
         morphology = neuron.h.SectionList()
-        morphology.wholetree()
+        morphology.wholetree(sec=soma)
         cell = cell_w_synapse_from_sections(morphology)
         iaxial, d_list, pos_list = cell.get_axial_currents_from_vmem()
         new_x = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
@@ -925,7 +925,7 @@ def test_cell_get_axial_currents_from_vmem_14(self):
         cell._collect_geometry()
         cell2 = cell_w_synapse_from_sections(morphology)
         iaxial2, d_list2, pos_list2 = cell2.get_axial_currents_from_vmem()
-        mid_current_positions = np.array([[0., 0., 5], [0., 0., 12.5], [0., 0., 5.], [0., 0., 20.]])
+        mid_current_positions = np.array([[0., 0., 5], [0., 0., 20], [0., 0., 5.], [0., 0., 12.5]])
         np.testing.assert_almost_equal(mid_current_positions, pos_list2, decimal=9)
         np.testing.assert_allclose(mid_current_positions, pos_list2, rtol=1E-4)
 
@@ -942,7 +942,7 @@ def test_cell_get_axial_currents_from_vmem_15(self):
         dend2.connect(dend1(1.), 0)
         dend3.connect(dend1(.5), 0)
         morphology = neuron.h.SectionList()
-        morphology.wholetree()
+        morphology.wholetree(sec=soma)
         cell = cell_w_synapse_from_sections(morphology)
         iaxial1, d_list1, pos_list1 = cell.get_axial_currents_from_vmem()
         new_x = [[0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 5, 10]]
@@ -961,8 +961,8 @@ def test_cell_get_axial_currents_from_vmem_15(self):
         cell2 = cell_w_synapse_from_sections(morphology)
         iaxial2, d_list2, pos_list2 = cell2.get_axial_currents_from_vmem()
         mid_current_positions = np.array([[0., 0., 5.], [0., 0., 12.5],
-                                          [0., 0., 17.5], [0., 0., 25],
-                                          [0., 0., 15.],[2.5, 0., 15.]])
+                                          [0., 0., 15.], [2.5, 0., 15.],
+                                          [0., 0., 17.5], [0, 0., 25.]])
         np.testing.assert_almost_equal(mid_current_positions, pos_list2, decimal=9)
         np.testing.assert_allclose(mid_current_positions, pos_list2, rtol=1E-4)
 
@@ -991,7 +991,7 @@ def test_cell_simulate_recorder_00(self):
         self.assertTrue(np.all(stick.vmem == stick.v_init))
         self.assertTrue(np.all(stick.imem == 0.))
         self.assertTrue(np.all(stick.current_dipole_moment == 0.))
-        
+
 
     def test_cell_simulate_recorder_01(self):
         stickParams = {
@@ -1068,7 +1068,7 @@ def test_cell_simulate_recorder_03(self):
         self.assertTrue(np.all(stick.vmem == stick.v_init))
         self.assertTrue(np.all(stick.imem == 0.))
         self.assertTrue(np.all(stick.current_dipole_moment == 0.))
-        
+
 
     def test_cell_simulate_recorder_04(self):
         stickParams = {
@@ -1415,7 +1415,7 @@ def test_cell_with_recextelectrode_02(self):
         self.assertTrue(stick.tvec.size == stick.imem.shape[1] ==
                         electrode.LFP.shape[1] == electrode1.LFP.shape[1] ==
                         int(stick.tstop/stick.dt)+1)
-        
+
     def test_cell_with_recextelectrode_03(self):
         stickParams = {
             'morphology' : os.path.join(LFPy.__path__[0], 'test', 'stick.hoc'),

diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ MEG scalp surface magnetic fields, as described in the bioRXiv preprint "Multimo
 
 Citing LFPy:
 
-- LFPy v2.x: Hagen E, Naess S, Ness TV and Einevoll GT (2018). Multimodal modeling of neural network activity: computing LFP, ECoG, EEG and MEG signals with LFPy2.0. bioRXiv. doi: 10.1101/281717
+- LFPy v2.x: Hagen E, Næss S, Ness TV and Einevoll GT (2018) Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0. Front. Neuroinform. 12:92. doi: 10.3389/fninf.2018.00092
 - LFPy v1.x: Linden H, Hagen E, Leski S, Norheim ES, Pettersen KH and Einevoll GT (2013). LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons. Front. Neuroinform. 7:41. doi: 10.3389/fninf.2013.00041
 
 LFPy was developed in the Computational Neuroscience Group, Department of Mathemathical Sciences and Technology (http://www.nmbu.no/imt),
@@ -47,11 +47,11 @@ Requirements
 
 To install LFPy you will need the following:
 
-- Python modules numpy, scipy and matplotlib
-- NEURON (from http://www.neuron.yale.edu) compiled as a Python module, so the following should execute without error in Python console::
+- Python modules numpy, scipy, matplotlib, h5py, mpi4py, csa, Cython
+- NEURON (from http://www.neuron.yale.edu, v7.6.4 or newer) and corresponding Python module. The following should execute without error in a Python console:
 
-    import neuron
-    neuron.test()
+        import neuron
+        neuron.test()
 
 - Cython (C-extensions for python, http://cython.org) to speed up simulations of extracellular fields
 
@@ -61,46 +61,38 @@ Installation
 
 There are few options to install LFPy:
 
-1.  From the Python Package Index with only local access using pip
-    ::
+1.  From the Python Package Index with only local access using pip:
 
         pip install LFPy --user 
 
     as sudoer (in general not recommended as system Python files may be overwritten):
-    ::
 
         sudo pip install LFPy
 
     Upgrading LFPy from the Python package index (without attempts at upgrading dependencies):
-    ::
 
         pip install --upgrade --no-deps LFPy --user
 
-    LFPy release candidates can be installed as
-    ::
+    LFPy release candidates can be installed as:
 
         pip install --pre --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple LFPy --user
 
 
-2.  From the Python Package Index with only local access using easy_install
-    ::
+2.  From the Python Package Index with only local access using easy_install:
 
         easy_install --user LFPy
 
-    as sudoer:
-    ::
+    As sudoer:
 
         sudo easy_install LFPy
 
 3.  From source:
-    ::
 
         tar -xzf LFPy-x.x.tar.gz
         cd LFPy-x.x
         (sudo) python setup.py develop (--user)
 
 4.  Development version from the GitHub repository:
-    ::
 
         git clone https://github.com/LFPy/LFPy.git
         cd LFPy
@@ -112,7 +104,6 @@ Uninstall
 =========
 
 To remove installed LFPy files it should suffice to issue (repeat until no more LFPy files are found):
-::
 
     (sudo) pip uninstall LFPy
 
@@ -121,12 +112,10 @@ Documentation
 =============
 
 To generate the html documentation using Sphinx, issue from the LFPy source code directory:
-::
 
     sphinx-build -b html <path to LFPy>/doc <path to output>
 
 The main html file is in ``<path to output>/index.html``. Numpydoc and the ReadTheDocs theme may be needed:
-::
 
     pip install numpydoc --user
     pip install sphinx-rtd-theme --user

diff --git a/continuous_integration/install.sh b/continuous_integration/install.sh
@@ -2,14 +2,14 @@
 export PATH=$HOME/.local/nrn/x86_64/bin:$PATH
 
 cd $HOME
-wget https://neuron.yale.edu/ftp/neuron/versions/v7.5/nrn-7.5.tar.gz
-tar -xf nrn-7.5.tar.gz
-cd nrn-7.5
+wget https://github.com/neuronsimulator/nrn/archive/master.tar.gz
+tar -xf master.tar.gz
+cd nrn-master
 echo "installing NEURON:"
 echo "running sh build.sh"
 sh build.sh > /dev/null
 echo "running ./configure"
-./configure --prefix=$HOME/.local/nrn --without-iv --with-nrnpython --with-mpi > /dev/null
+./configure --prefix=$HOME/.local/nrn --without-iv --with-nrnpython=python --with-mpi > /dev/null
 echo "running make"
 make > /dev/null
 echo "running make install"

diff --git a/doc/conf.py b/doc/conf.py
@@ -54,7 +54,7 @@
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.0'
+release = '2.0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.