Created Class nest_build_nineml_synapsetype to read synapses in nimeml format

AUTHORS

@@ -1,6 +1,6 @@
 The following people have contributed to PyNN. Their affiliations at the time of the contributions are shown below.
 
-* Andrew Davison [1]
+* Andrew Davison [1, 20]
 * Pierre Yger [1, 9]
 * Eilif Muller [7, 13]
 * Jens Kremkow [5,6]
@@ -22,9 +22,14 @@ The following people have contributed to PyNN. Their affiliations at the time of
 * Jannis Schücker [16]
 * Maximilian Schmidt [16]
 * Christian Roessert [13]
-* Shailesh Appukuttan [1]
+* Shailesh Appukuttan [1, 20]
 * Elodie Legouée [1]
 * Joffrey Gonin [1]
+* Ankur Sinha [18]
+* Håkon Mørk [19]
+* Andrei Moise [20]
+* Onur Ates [20]
+* Rémy Cagnol [21]
 
 
 1.  Unité de Neuroscience, Information et Complexité, CNRS, Gif sur Yvette, France
@@ -44,3 +49,7 @@ The following people have contributed to PyNN. Their affiliations at the time of
 15. PDC, KTH, Stockholm, Sweden
 16. Institute of Neuroscience and Medicine (INM-6), Jülich Research Center, Jülich, Germany
 17. Okinawa Institute of Science and Technology (OIST), Onna-son, Okinawa, Japan
+18. Biocomputation group, University of Hertfordshire, Hatfield, United Kingdom.
+19. Norwegian University of Life Sciences, Ås, Norway
+20. Paris-Saclay Institute of Neuroscience, CNRS/Université Paris-Saclay, Gif sur Yvette, France
+21. Faculty of Mathematics and Physics, Charles University, Prague, Czechia

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at pynn-maintainers@protonmail.com. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -0,0 +1 @@
+See http://neuralensemble.org/docs/PyNN/developers/contributing.html

MANIFEST.in

@@ -10,6 +10,7 @@ include test/system/scenarios/*.py
 include test/unittests/*.py
 include examples/*.py
 include doc/*.txt
+include doc/*/*.txt
 include LICENSE
 include AUTHORS
 include README.rst

README.rst

@@ -30,7 +30,7 @@ your simulator, and are not restricted to the standard models.
 - Bug reports: https://github.com/NeuralEnsemble/PyNN/issues
 
 
-:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
+:copyright: Copyright 2006-2020 by the PyNN team, see AUTHORS.
 :license: CeCILL, see LICENSE for details.
 
 .. image:: https://travis-ci.org/NeuralEnsemble/PyNN.png?branch=master

ci/install.sh

@@ -2,7 +2,6 @@
 
 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

ci/install_brian.sh

@@ -8,3 +8,8 @@ if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ]; then
     pip install sympy;
     pip install brian;
 fi
+if [ "$TRAVIS_PYTHON_VERSION" == "3.7" ]; then
+    echo -e "\n========== Installing Brian 2 ==========\n"
+    pip install cython;
+    pip install brian2;
+fi

ci/install_nest.sh

@@ -2,20 +2,20 @@
 
 set -e  # stop execution in case of errors
 
-if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ] || [ "$TRAVIS_PYTHON_VERSION" == "3.5" ]; then
+if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ] || [ "$TRAVIS_PYTHON_VERSION" == "3.7" ]; then
     echo -e "\n========== Installing NEST ==========\n"
     # Specify which version of NEST to install
     #export NEST_VERSION="master"
-    export NEST_VERSION="2.14.0"
+    export NEST_VERSION="2.20.0"
 
-    pip install cython==0.23.4
+    pip install cython  #==0.28.1
 
     if [ "$NEST_VERSION" = "master" ]; then
       export NEST="nest-simulator-$NEST_VERSION"
       wget https://github.com/nest/nest-simulator/archive/$NEST_VERSION.tar.gz -O $HOME/$NEST.tar.gz;
     else
-      export NEST="nest-$NEST_VERSION"
-      wget https://github.com/nest/nest-simulator/releases/download/v$NEST_VERSION/nest-$NEST_VERSION.tar.gz -O $HOME/$NEST.tar.gz
+      export NEST="nest-simulator-$NEST_VERSION"
+      wget https://github.com/nest/nest-simulator/archive/v$NEST_VERSION.tar.gz -O $HOME/$NEST.tar.gz;
     fi
 
     pushd $HOME;
@@ -26,11 +26,13 @@ if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ] || [ "$TRAVIS_PYTHON_VERSION" == "3.5"
     mkdir -p $HOME/build/$NEST
     pushd $HOME/build/$NEST
     export VENV=`python -c "import sys; print(sys.prefix)"`;
-    ln -s /opt/python/2.7.14/lib/libpython2.7.so $VENV/lib/libpython2.7.so;
-    ln -s /opt/python/3.5.4/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
-        export PYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIR}m;
+    if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ]; then
+      ln -s /opt/python/2.7/lib/libpython2.7.so $VENV/lib/libpython2.7.so;
+      export PYTHON_INCLUDE_DIR=$VENV/include/python${TRAVIS_PYTHON_VERSION}
+    fi
+    if [ "$TRAVIS_PYTHON_VERSION" == "3.7" ]; then
+      ln -s /opt/python/3.7/lib/libpython3.7m.so $VENV/lib/libpython3.7.so;
+      export PYTHON_INCLUDE_DIR=$VENV/include/python${TRAVIS_PYTHON_VERSION}m
     fi
     cython --version;
     cmake --version;

ci/install_neuron.sh

@@ -2,11 +2,11 @@
 
 set -e  # stop execution in case of errors
 
-if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ]; then
+if [ "$TRAVIS_PYTHON_VERSION" == "3.7" ]; then
     echo -e "\n========== Installing NEURON ==========\n"
-    export NRN_VERSION="nrn-7.5"
+    export NRN_VERSION="nrn-7.7"
     if [ ! -f "$HOME/$NRN_VERSION/configure" ]; then
-        wget http://www.neuron.yale.edu/ftp/neuron/versions/v7.5/$NRN_VERSION.tar.gz -O $HOME/$NRN_VERSION.tar.gz;
+        wget http://www.neuron.yale.edu/ftp/neuron/versions/v7.7/$NRN_VERSION.tar.gz -O $HOME/$NRN_VERSION.tar.gz;
         pushd $HOME;
         tar xzf $NRN_VERSION.tar.gz;
         popd;

ci/test_script.sh

@@ -2,9 +2,8 @@
 
 set -e  # stop execution in case of errors
 
-if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ] || [ "$TRAVIS_PYTHON_VERSION" == "3.5" ]; then
-    nosetests --with-coverage --cover-package=pyNN -e backends -v test/unittests;
-    nosetests --with-coverage --cover-package=pyNN -v test/system;
+if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ] || [ "$TRAVIS_PYTHON_VERSION" == "3.7" ]; then
+    python setup.py nosetests --with-coverage --cover-package=pyNN -v --tests=test;
 else
-    nosetests -e backends test/unittests;
-fi
+    python setup.py nosetests -e backends -v --tests=test/unittests;
+fi

doc/backends/NEST.txt

@@ -24,17 +24,12 @@ or the conventional grid-constrained scheme
 
     setup(spike_precision='on_grid')
 
-where `'on_grid'` is the default.
+where `'off_grid'` is the default.
 
-.. todo:: consider changing the default to off_grid, since PyNN's defaults are
-          supposed to prefer accuracy/comparability over performance.
-
-As of NEST 2.0.0, the following PyNN standard models have an off-grid
-implementation: :class:`IF_curr_alpha` (in preparation), :class:`IF_curr_exp`,
+The following PyNN standard models have an off-grid
+implementation: :class:`IF_curr_exp`, :class:`SpikeSourcePoisson`
 :class:`EIF_cond_alpha_isfa_ista`.
 
-.. todo:: check the accuracy of the above list before release
-
 .. todo:: add a list of native NEST models with off-grid capability
 
 Here is an example showing how to specify the option in a PyNN script

doc/backends/NEURON.txt

@@ -28,7 +28,7 @@ If using *cvode*, there are two more optional parameters:
 
 .. testcode:: cvode
 
-    setup(cvode=True,
+    setup(use_cvode=True,
           rtol=0.001, # specify relative error tolerance
           atol=1e-4)  # specify absolute error tolerance
 
@@ -137,55 +137,15 @@ If your model relies on other NMODL mechanisms, call the
 :func:`~pyNN.neuron.load_mechanisms` function with the path to the directory
 containing the :file:`.mod` files.
 
+It is also possible to use NEURON "ARTIFICIAL_CELL" models, such as :class:`IntFire1`,
+ :class:`IntFire2` and :class:`IntFire4`:
 
-Using native synaptic plasticity models
-=======================================
-
-A native NEURON synaptic plasticity model should be implemented in NMODL using the "weight adjuster"
-approach. The mechanism should be a ``POINT_PROCESS`` which defines a ``POINTER wsyn``.
-This mechanism will receive ``NetCon``s from both the presynaptic and postsynaptic neurons
-(at least for the common case where the mechanism depends on post-synaptic spike times
-but not on state variables of the postsynaptic cell such as the membrane potential.
-The latter scenario is possible, but is not documented here.) 
-The ``wsyn`` pointer will be connected to the weight variable of the post-synaptic response mechanism.
-See the :file:`pyNN/neuron/nmodl` directory for some examples of such mechanisms.
-
-Call the :func:`~pyNN.neuron.load_mechanisms` function with the path to the directory
-containing the :file:`.mod` file.
-
-For each synaptic plasticity model you must also define a synapse type class:
-
-.. codeblock:: python
-
-    from pyNN.neuron import NativeSynapseType
-    from pyNN.neuron.simulator import Connection
-
-    class MySTDP(NativeSynapseType):
-        default_parameters = {
-            "weight": 0.0, "delay": None,
-            "tauLTP": 20.0, "tauLTD": 20.0,
-            "aLTP": 0.01, "aLTD": 0.012,
-            "wmin": 0, "wmax": 0.0000001,
-            "dendritic_delay_fraction": 1.0
-        }
-        model = "MySTDPMechanism"  # this is the POINT_PROCESS name
-        connection_type = Connection
-        presynaptic_type = None
-        postsynaptic_variable = "spikes"
-
-The parameters "weight", "delay" and "dendritic_delay_fraction" are obligatory,
-and will be handled by PyNN. All other parameters will be passed on to the NMODL mechanism.
-
-It is now straightforward to use this synapse type in PyNN:
-
-.. codeblock:: python
+.. testcode:: nativemodel
 
-    from pyNN.neuron import setup, run, Population, Projection, AllToAllConnector, StaticSynapse
+    from pyNN.neuron import setup, Population, IntFire1
     setup()
-    p1 = Population(10, sim.IF_cond_exp())
-    syn = MySTDP(weight=0.01, delay=0.5, wmax=0.02)
-    prj = Projection(p1, p1, AllToAllConnector(), syn, receptor_type='excitatory')
-    run(100.0)
+    p1 = Population(10, IntFire1(tau=10.0, refrac=2.5))
+    p1.record('m')
 
 
 .. _`CVode documentation`: http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/cvode.html

doc/conf.py

@@ -71,7 +71,7 @@ class MockNESTModule(mock.Mock):
 # General information about the project.
 project = u'PyNN'
 authors = u'the PyNN community'
-copyright = u'2006-2017, ' + authors
+copyright = u'2006-2020, ' + authors
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -80,7 +80,7 @@ class MockNESTModule(mock.Mock):
 # The short X.Y version.
 version = '0.9'
 # The full version, including alpha/beta/rc tags.
-release = '0.9.2'
+release = '0.9.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/connections.txt

@@ -57,10 +57,14 @@ The simplest, and default synapse type in PyNN has constant synaptic weight:
 .. testcode::
 
     syn = StaticSynapse(weight=0.04, delay=0.5)
-    
+
 .. note:: weights are in microsiemens or nanoamps, depending on whether the
           post-synaptic mechanism implements a change in conductance or current,
-          and delays are in milliseconds (see :doc:`units`).
+          and delays are in milliseconds (see :doc:`units`). Weights should always
+          be positive, *except* for the case of inhibitory (see `receptor_type`
+          argument below), current-based synapses, for which they should be negative.
+          Inhibitory, conductance-based synapses have positive weights, because
+          it is the reversal potential which makes it inhibitory.
 
 It is also possible to add variability to synaptic weights and delays by
 specifying a :class:`RandomDistribution` object as the parameter value:
@@ -110,7 +114,7 @@ timing-dependence components, e.g.:
               timing_dependence=SpikePairRule(tau_plus=20.0, tau_minus=20.0,
                                               A_plus=0.01, A_minus=0.012),
               weight_dependence=AdditiveWeightDependence(w_min=0, w_max=0.04))
-    
+
 Note that not all simulators will support all possible combinations of synaptic
 plasticity components.
 
@@ -312,8 +316,8 @@ Reading connection patterns to/from a file
 
 Connection patterns can be read in from a text file. The file should contain
 a header specifying which parameter is in which column, e.g.::
- 
-    # columns = ["i", "j", "weight", "delay", "U", "tau_rec"]   
+
+    # columns = ["i", "j", "weight", "delay", "U", "tau_rec"]
 
 and then the connection data should be in columns separated by spaces. The
 connections are read using:
@@ -373,7 +377,8 @@ level of the simulator. To create a :class:`Projection` we must specify:
 Optionally, we can also specify:
 
     * the name of the post-synaptic mechanism (e.g. ‘excitatory’, ‘NMDA’)
-      (by default, this is 'excitatory');
+      (if not specified, PyNN picks a default depending on the weight
+       parameter of the synapse type);
     * a label (autogenerated if not specified);
     * a :class:`Space` object, which determines how distances should be
       calculated for distance-dependent wiring schemes or parameter values.

doc/contributors.txt

@@ -1,6 +1,6 @@
-========================
-Contributors and licence
-========================
+=================================
+Contributors, licence and funding
+=================================
 
 .. include:: ../AUTHORS
 
@@ -17,6 +17,18 @@ software in computational neuroscience, such as NEURON (GPL) and Brian (CeCILL).
 
 If you are interested in using PyNN, but the choice of licence is a problem for you, please contact us to discuss dual-licensing.
 
+
 .. centered:: LICENSE AGREEMENT
 
 .. include:: ../LICENSE
+
+
+Funding
+=======
+
+Development of PyNN has been partially funded by the European Union Sixth Framework Program (FP6) under
+grant agreement FETPI-015879 (FACETS), by the European Union Seventh Framework Program (FP7/2007­-2013)
+under grant agreements no. 269921 (BrainScaleS) and no. 604102 (HBP),
+and by the European Union’s Horizon 2020 Framework Programme for
+Research and Innovation under the Specific Grant Agreements No. 720270 (Human Brain Project SGA1)
+and No. 785907 (Human Brain Project SGA2).