Merge branch 'nest-dev' of github.com:NeuralEnsemble/PyNN into nest-dev

# Conflicts:
#	ci/install_nest.sh

.gitignore

@@ -21,6 +21,7 @@
 x86_64
 i386
 i686
+_build
 
 # Python files
 build

.travis.yml

@@ -18,8 +18,8 @@ after_success:
   - coveralls
 cache:
   directories:
-    - $HOME/nest-master
+    - $HOME/nest-2.12.0
     - $HOME/nrn-7.4
-    - $HOME/build/nest-master
+    - $HOME/build/nest-2.12.0
     - $HOME/build/nrn-7.4
     - $HOME/.cache/pip

MANIFEST.in

@@ -1,4 +1,8 @@
 include pyNN/neuron/nmodl/*.mod
+include pyNN/nest/extensions/*.h
+include pyNN/nest/extensions/*.cpp
+include pyNN/nest/extensions/CMakeLists.txt
+include pyNN/nest/extensions/sli/*
 include pyNN/descriptions/templates/*/*.txt
 include test/parameters/*
 include test/system/*.py
@@ -10,3 +14,4 @@ include LICENSE
 include AUTHORS
 include README.rst
 include changelog
+include requirements.txt

ci/install.sh

@@ -3,9 +3,9 @@
 set -e  # stop execution in case of errors
 
 sudo apt-get install -qq python-numpy python3-numpy python-scipy python3-scipy libgsl0-dev  openmpi-bin libopenmpi-dev
-
 pip install -r requirements.txt
 pip install coverage coveralls
+pip install nose-testconfig
 source ci/install_brian.sh
 source ci/install_nest.sh
 source ci/install_neuron.sh

ci/install_nest.sh

@@ -4,18 +4,28 @@ set -e  # stop execution in case of errors
 
 if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ] || [ "$TRAVIS_PYTHON_VERSION" == "3.5" ]; then
     echo -e "\n========== Installing NEST ==========\n"
+    # Specify which version of NEST to install
     export NEST_VERSION="master"
+    #export NEST_VERSION="2.12.0"
+
     export NEST="nest-simulator-$NEST_VERSION"
     pip install cython==0.23.4
-    wget https://github.com/nest/nest-simulator/archive/$NEST_VERSION.tar.gz -O $HOME/$NEST.tar.gz;
+
+    if [ "$NEST_VERSION" = "master" ]; then
+      wget https://github.com/nest/nest-simulator/archive/$NEST_VERSION.tar.gz -O $HOME/$NEST.tar.gz;
+    else
+      wget https://github.com/nest/nest-simulator/releases/download/v$NEST_VERSION/nest-$NEST_VERSION.tar.gz -O $HOME/$NEST.tar.gz
+    fi
+
     pushd $HOME;
     tar xzf $NEST.tar.gz;
+    ls;
     popd;
 
     mkdir -p $HOME/build/$NEST
     pushd $HOME/build/$NEST
     export VENV=`python -c "import sys; print(sys.prefix)"`;
-    ln -s /opt/python/2.7.12/lib/libpython2.7.so $VENV/lib/libpython2.7.so;
+    ln -s /opt/python/2.7.13/lib/libpython2.7.so $VENV/lib/libpython2.7.so;
     ln -s /opt/python/3.5.2/lib/libpython3.5m.so $VENV/lib/libpython3.5.so;
     export PYTHON_INCLUDE_DIR=$VENV/include/python${TRAVIS_PYTHON_VERSION}
     if [ "$TRAVIS_PYTHON_VERSION" == "3.5" ]; then

doc/build_examples.py

@@ -35,6 +35,8 @@
     "synaptic_input.py",
     "tsodyksmarkram.py",
     "varying_poisson.py",
+    "stochastic_synapses.py",
+    "stochastic_deterministic_comparison.py"
 )
 
 # todo: add line numbering to code examples
@@ -62,8 +64,9 @@
 tmp_dir = tempfile.mkdtemp()
 results_dir = os.path.join(tmp_dir, "Results")
 
-if not os.path.exists(image_dir):
-    os.makedirs(image_dir)
+for dir_name in (image_dir, results_dir):
+    if not os.path.exists(dir_name):
+        os.makedirs(dir_name)
 
 
 def run(python_script, simulator, *extra_args):
@@ -92,8 +95,9 @@ def list_files(filter):
                 for filename in x[2]
                 if filter in filename])
 
+print("Running examples in {}".format(tmp_dir))
 for example in examples:
-    new_files = run(example, simulators.next())
+    new_files = run(example, next(simulators))
     if len(new_files) > 1:
         raise Exception("Multiple image files")
     img_path, = new_files

doc/conf.py

@@ -78,9 +78,9 @@ class MockNESTModule(mock.Mock):
 # built documents.
 #
 # The short X.Y version.
-version = '0.8'
+version = '0.9'
 # The full version, including alpha/beta/rc tags.
-release = '0.8.3'
+release = '0.9.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/data_handling.txt

@@ -22,8 +22,8 @@ top-level data container, which contains one or more :class:`Segment`\s. Each
 :class:`Segment` is a container for data sharing a common time basis - a new
 :class:`Segment` is added every time the :func:`reset` function is called.
 
-A :class:`Segment` can contain lists of :class:`AnalogSignal`,
-:class:`AnalogSignalArray` and :class:`SpikeTrain` objects. These data objects
+A :class:`Segment` can contain lists of :class:`AnalogSignal` and :class:`SpikeTrain` objects.
+These data objects
 inherit from NumPy's array class, and so can be treated in further processing
 (analysis, visualization, etc.) in exactly the same way as NumPy arrays, but in
 addition they carry metadata about units, sampling interval, etc.

doc/developers/contributing.txt

@@ -114,6 +114,23 @@ The suggested way to do this is to write test functions, in a separate file,
 that take a simulator module as an argument, and then call these functions from
 ``test_neuron.py``, ``test_nest.py``, etc.
 
+System tests defined in the scenarios directory are treated as a single test 
+(test_scenarios()) while running nosetests. To run only the tests within a file
+named 'test_electrodes' located inside system/scenarios, use::
+
+    $ nosetests -s --tc=testFile:test_electrodes test_nest.py
+
+To run a single specific test named 'test_changing_electrode' located within 
+some file (and added to registry) inside system/scenarios, use::
+
+    $ nosetests -s --tc=testName:test_changing_electrode test_nest.py
+
+Note that this would also run the tests specified within the simulator specific
+files such as test_brian.py, test_nest.py and test_neuron.py. To avoid 
+this, specify the 'test_scenarios function' on the command line::
+
+    $ nosetests -s --tc=testName:test_changing_electrode test_nest.py:test_scenarios
+
 The ``test/unsorted`` directory contains a number of old tests that are either
 no longer useful or have not yet been adapted to the nose framework. These are
 not part of the test suite, but we are gradually adapting those tests that are
@@ -249,4 +266,4 @@ If this is a final release, there are a few more steps:
 .. _`issue tracker`: https://github.com/NeuralEnsemble/PyNN/issues/
 .. _fork: https://github.com/NeuralEnsemble/PyNN/fork
 .. _`PyNN repository`: https://github.com/NeuralEnsemble/PyNN/
-.. _contents: http://software.incf.org/software/pynn/pynn/folder_contents
+.. _contents: http://software.incf.org/software/pynn/pynn/folder_contents

doc/examples.txt

@@ -15,4 +15,6 @@ Examples
    examples/synaptic_input
    examples/tsodyksmarkram
    examples/varying_poisson
+   examples/stochastic_synapses
+   examples/stochastic_deterministic_comparison
    examples/VAbenchmarks

doc/examples/Izhikevich.txt

@@ -1,7 +1,7 @@
 A selection of Izhikevich neurons
 =================================
 
-.. image:: ../images/examples/Izhikevich_nest_np1_20151005-081145.png
+.. image:: ../images/examples/Izhikevich_nest_np1_20170505-150315.png
 
 .. literalinclude:: ../../examples/Izhikevich.py
 

doc/examples/VAbenchmarks.txt

@@ -1,7 +1,7 @@
 Balanced network of excitatory and inhibitory neurons
 =====================================================
 
-.. image:: ../images/examples/VAbenchmarks_CUBA_20151005-081325.png
+.. image:: ../images/examples/VAbenchmarks_CUBA_20170505-150538.png
 
 .. literalinclude:: ../../examples/VAbenchmarks.py
 

doc/examples/cell_type_demonstration.txt

@@ -1,7 +1,7 @@
 A demonstration of the responses of different standard neuron models to current injection
 =========================================================================================
 
-.. image:: ../images/examples/cell_type_demonstration_nest_20151005-081150.png
+.. image:: ../images/examples/cell_type_demonstration_nest_20170505-150320.png
 
 .. literalinclude:: ../../examples/cell_type_demonstration.py
 

doc/examples/current_injection.txt

@@ -1,7 +1,7 @@
 Injecting time-varying current into a cell
 ==========================================
 
-.. image:: ../images/examples/current_injection_neuron_20151005-081148.png
+.. image:: ../images/examples/current_injection_neuron_20170505-150317.png
 
 .. literalinclude:: ../../examples/current_injection.py
 

doc/examples/random_numbers.txt

@@ -1,7 +1,7 @@
 An example to illustrate random number handling in PyNN
 =======================================================
 
-.. image:: ../images/examples/random_numbers_neuron_20151005-081153.png
+.. image:: ../images/examples/random_numbers_neuron_20170505-150323.png
 
 .. literalinclude:: ../../examples/random_numbers.py
 

doc/examples/simple_STDP.txt

@@ -1,7 +1,7 @@
 A very simple example of using STDP
 ===================================
 
-.. image:: ../images/examples/simple_stdp_neuron_20151005-081202.png
+.. image:: ../images/examples/simple_stdp_neuron_20170505-150331.png
 
 .. literalinclude:: ../../examples/simple_STDP.py
 

doc/examples/small_network.txt

@@ -1,7 +1,7 @@
 Small network created with the Population and Projection classes
 ================================================================
 
-.. image:: ../images/examples/small_network_nest_np1_20151005-081205.png
+.. image:: ../images/examples/small_network_nest_np1_20170505-150334.png
 
 .. literalinclude:: ../../examples/small_network.py
 

doc/examples/stochastic_deterministic_comparison.txt

@@ -0,0 +1,7 @@
+Example of facilitating and depressing synapses in deterministic and stochastic versions
+========================================================================================
+
+.. image:: ../images/examples/stochastic_comparison_neuron_20170505-150418.png
+
+.. literalinclude:: ../../examples/stochastic_deterministic_comparison.py
+

doc/examples/stochastic_synapses.txt

@@ -0,0 +1,7 @@
+Example of simple stochastic synapses
+=====================================
+
+.. image:: ../images/examples/stochastic_synapses__nest_20170505-150345.png
+
+.. literalinclude:: ../../examples/stochastic_synapses.py
+

doc/examples/synaptic_input.txt

@@ -1,7 +1,7 @@
 A demonstration of the responses of different standard neuron models to synaptic input
 ======================================================================================
 
-.. image:: ../images/examples/synaptic_input_neuron_20151005-081208.png
+.. image:: ../images/examples/synaptic_input_neuron_20170505-150337.png
 
 .. literalinclude:: ../../examples/synaptic_input.py
 

doc/examples/tsodyksmarkram.txt

@@ -1,7 +1,7 @@
 Example of depressing and facilitating synapses
 ===============================================
 
-.. image:: ../images/examples/tsodyksmarkram_nest_20151005-081211.png
+.. image:: ../images/examples/tsodyksmarkram_nest_20170505-150340.png
 
 .. literalinclude:: ../../examples/tsodyksmarkram.py
 

doc/examples/varying_poisson.txt

@@ -1,7 +1,7 @@
 A demonstration of the use of callbacks to vary the rate of a SpikeSourcePoisson
 ================================================================================
 
-.. image:: ../images/examples/varying_poisson_neuron_20151005-081216.png
+.. image:: ../images/examples/varying_poisson_neuron_20170505-150343.png
 
 .. literalinclude:: ../../examples/varying_poisson.py
 

doc/index.txt

@@ -2,9 +2,6 @@
 PyNN: documentation
 ===================
 
-This is the documentation for version |release|. For versions 0.7 and earlier,
-see http://neuralensemble.org/trac/PyNN
-
 .. toctree::
    :maxdepth: 1
 
@@ -25,6 +22,13 @@ see http://neuralensemble.org/trac/PyNN
    contributors
    release_notes
 
+.. note::
+
+   This is the documentation for version |release|. Earlier versions:
+
+     - `version 0.8`_
+     - `version 0.7 and earlier`_
+
 .. add 'logging' after 'units' once configure_logging() implemented.
 
 .. add 'descriptions' after logging
@@ -62,3 +66,6 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+.. _`version 0.8`: http://neuralensemble.org/docs/PyNN/0.8/
+.. _`version 0.7 and earlier`: http://neuralensemble.org/docs/PyNN/0.7/

doc/installation.txt

@@ -10,7 +10,7 @@ Installing PyNN requires:
     * Python (version 2.6, 2.7, 3.3-3.6)
     * a recent version of the NumPy_ package
     * the lazyarray_ package
-    * the Neo_ package
+    * the Neo_ package (>= 0.5.0)
     * at least one of the supported simulators: e.g. NEURON, NEST, or Brian.
 
 Optional dependencies are:
@@ -22,7 +22,7 @@ Optional dependencies are:
 Installing PyNN
 ===============
 
-.. note:: if using NEURON, it is easiest if you install NEURON *before* you install PyNN (see below).
+.. note:: if using NEURON or NEST, it is easiest if you install NEURON/NEST *before* you install PyNN (see below).
 
 The easiest way to get PyNN is to use pip_::
 
@@ -32,8 +32,8 @@ If you are running Debian or Ubuntu, there are :doc:`binary packages <download>`
 available. If you would prefer to install manually, :doc:`download the latest
 source distribution <download>`, then run the setup script, e.g.::
 
-    $ tar xzf PyNN-0.8.3.tar.gz
-    $ cd PyNN-0.8.3
+    $ tar xzf PyNN-0.9.1.tar.gz
+    $ cd PyNN-0.9.1
     $ python setup.py install
 
 This will install it to your Python :file:`site-packages` directory, and may
@@ -49,6 +49,8 @@ Test it using something like the following::
     >>> sim.end()
 
 (This assumes you have NEST installed).
+If you get a warning "Unable to install NEST extensions. Certain models may not be available" then ensure the
+program :command:`nest-config` is on your system PATH.
 
 With NEURON as the simulator, make sure you install NEURON *before* you install PyNN.
 The PyNN installation will then compile PyNN-specific membrane mechanisms, which are loaded when importing the :mod:`neuron` module::
@@ -116,20 +118,6 @@ Earlier versions of NEST will not work with this version of PyNN.
 The full installation instructions are available in the file INSTALL, which you can find in the NEST source package,
 or at `<http://www.nest-simulator.org/installation/>`_.
 
-.. note:: NumPy must be installed *before* installing NEST.
-
-.. note:: Make sure you have the GNU Scientific Library (GSL) installed,
-          otherwise some PyNN standard models (e.g. :class:`IF_cond_exp`) will not be available.
-
-On Linux, most Unix variants and Mac OS X, installation is usually as simple as::
-
-    $ ./configure --with-mpi
-    $ make
-    $ make install
-
-This will install PyNEST to your Python :file:`site-packages` directory.
-If you wish to install it elsewhere, see the full installation instructions.
-
 Now try it out::
 
     $ cd ~

doc/neurons.txt

@@ -378,8 +378,8 @@ or written to file using :meth:`write_data()`:
 Neo see the documentation at http://packages.python.org/neo. Here, it will
 suffice to note that a :class:`Block` is the top-level container, and contains
 one or more :class:`Segments`. Each :class:`Segment` is a container for data
-that share a common time basis, and can contain lists of :class:`AnalogSignal`,
-:class:`AnalogSignalArray` and :class:`SpikeTrain` objects. These data objects
+that share a common time basis, and can contain lists of :class:`AnalogSignal`
+and :class:`SpikeTrain` objects. These data objects
 inherit from NumPy array, and so can be treated in further processing (analysis,
 visualization, etc.) in exactly the same way as plain arrays, but in addition
 they carry metadata about units, sampling interval, etc.

doc/pyplots/ac_source.py

@@ -18,7 +18,7 @@
 sim.run(500.0)
 
 t, i_inj = sine._get_data()
-v = population.get_data().segments[0].analogsignalarrays[0]
+v = population.get_data().segments[0].analogsignals[0]
 
 plot_current_source(t, i_inj, v,
                     v_range=(-66, -49),

doc/pyplots/continuous_time_spiking.py

@@ -17,7 +17,7 @@ def test_sim(on_or_off_grid, sim_time):
     prj = Projection(src, nrn, OneToOneConnector(), StaticSynapse(weight=weight))
     nrn.record('v')
     run(sim_time)
-    return nrn.get_data().segments[0].analogsignalarrays[0]
+    return nrn.get_data().segments[0].analogsignals[0]
 
 sim_time = 10.0
 off = test_sim('off_grid', sim_time)