diff --git a/changelog b/changelog index 63d2b41f1..b0dfd2e71 100644 --- a/changelog +++ b/changelog @@ -1,3 +1,9 @@ +================ +Release 0.8.0rc1 +================ + +see doc/releases/0.8.0-rc-1.txt + ================ Release 0.8beta2 ================ diff --git a/doc/conf.py b/doc/conf.py index a2369b4c9..bc03c7a88 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -78,7 +78,7 @@ class MockNESTModule(mock.Mock): # The short X.Y version. version = '0.8' # The full version, including alpha/beta/rc tags. -release = '0.8beta2' +release = '0.8.0rc1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/doc/installation.txt b/doc/installation.txt index c65242870..01889b0f0 100644 --- a/doc/installation.txt +++ b/doc/installation.txt @@ -32,8 +32,8 @@ If you are running Debian or Ubuntu, there are :doc:`binary packages ` available. If you would prefer to install manually, :doc:`download the latest source distribution `, then run the setup script, e.g.:: - $ tar xzf PyNN-0.8beta2.tar.gz - $ cd PyNN-0.8beta2 + $ tar xzf PyNN-0.8.0rc1.tar.gz + $ cd PyNN-0.8.0rc1 $ python setup.py install This will install it to your Python :file:`site-packages` directory, and may @@ -64,25 +64,29 @@ The PyNN installation will then compile PyNN-specific membrane mechanisms, which netstim2.mod refrac.mod reset.mod stdwa_guetig.mod stdwa_softlimits.mod stdwa_songabbott.mod stdwa_symm.mod tmgsyn.mod tmisyn.mod tsodyksmarkram.mod vecstim.mod -If you installed PyNN before installing NEURON, or if you update your PyNN installation, you will need to manually run :command:`nrnivmodl` in the :file:`pyNN/neuron/nmodl` directory. +If you installed PyNN before installing NEURON, or if you update your PyNN installation, +you will need to manually run :command:`nrnivmodl` in the :file:`pyNN/neuron/nmodl` directory. Installing NEURON ================= -Download the sources for the latest release of NEURON, in ``.tar.gz`` format, from ``_. Also download Interviews from the same location. +Download the sources for the latest release of NEURON, in ``.tar.gz`` format, from ``_. +Also download Interviews from the same location. -Compile Interviews and NEURON according to the instructions given at ``_, except that when you run :command:`configure`, add the options :option:`--with-nrnpython` and, optionally, :option:`--with-paranrn`, i.e.:: +Compile Interviews and NEURON according to the instructions given at ``_, +except that when you run :command:`configure`, add the options :option:`--with-nrnpython` and, optionally, :option:`--with-paranrn`, i.e.:: $ ./configure --prefix=`pwd` --with-nrnpython --with-paranrn $ make $ make install -Make sure that you add the Interviews and NEURON :file:`bin` directories to your path. Test that the Python support has been enabled by running:: +Make sure that you add the Interviews and NEURON :file:`bin` directories to your path. +Test that the Python support has been enabled by running:: $ nrniv -python - NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26 - Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008 - See http://www.neuron.yale.edu/credits.html + NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2014-04-04 + Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014 + See http://www.neuron.yale.edu/neuron/credits >>> import hoc >>> import nrn @@ -90,26 +94,15 @@ Make sure that you add the Interviews and NEURON :file:`bin` directories to your Now you can compile and install NEURON as a Python package:: $ cd src/nrnpython - # python setup.py install - -Note that the latter step requires running as root and will install to your global Python :file:`site-packages` directory. -If you would prefer to install it locally, replace the last step with:: - - $ python setup.py install --prefix=~ - -which will install into :file:`~/lib/python2.7/site-packages/` (or the equivalent for other Python versions; for more fine-grained control over where the package is installed, see the `distutils`_ documentation), then add this directory to your :envvar:`PYTHONPATH`:: - - $ export PYTHONPATH=$PYTHONPATH:~/lib/python2.7/site-packages + $ python setup.py install Now test everything worked:: $ python >>> import neuron - NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26 - Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008 - See http://www.neuron.yale.edu/credits.html - - >>> + NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2014-04-04 + Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014 + See http://www.neuron.yale.edu/neuron/credits If you run into problems, check out the `NEURON Forum`_. @@ -131,9 +124,9 @@ On Linux, most Unix variants and Mac OS X, installation is usually as simple as: $ ./configure --with-mpi $ make - # make install + $ make install -This will install PyNEST to your Python :file:`site-packages` directory, and may require root privileges. +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:: @@ -157,7 +150,7 @@ Installing Brian ================ Instructions for downloading and installing Brian_ are available from ``_. - +Note that this version of PyNN works with Brian 1.4, but not with Brian 2. .. _PyNN: http://neuralensemble.org/PyNN diff --git a/doc/release_notes.txt b/doc/release_notes.txt index 9ee85f53b..a1426e2ba 100644 --- a/doc/release_notes.txt +++ b/doc/release_notes.txt @@ -6,6 +6,7 @@ Release notes .. toctree:: :maxdepth: 1 + releases/0.8.0-rc-1.txt releases/0.8-beta-2.txt releases/0.8-beta-1.txt releases/0.8-alpha-2.txt diff --git a/doc/releases/0.8-beta-2.txt b/doc/releases/0.8-beta-2.txt index 34c4e7b93..cfdedd2a8 100644 --- a/doc/releases/0.8-beta-2.txt +++ b/doc/releases/0.8-beta-2.txt @@ -73,4 +73,4 @@ Other changes .. _Brian: http://http://briansimulator.org .. _NEST: http://www.nest-initiative.org/ .. _NEURON: http://www.neuron.yale.edu/neuron/ -.. _`Assorted bug fixes`: https://github.com/NeuralEnsemble/PyNN/issues?q=is%3Aclosed+closed%3A%3E2013-11-15+milestone%3A0.8.0 +.. _`Assorted bug fixes`: https://github.com/NeuralEnsemble/PyNN/issues?q=is%3Aclosed+closed%3A2013-11-15..2015-01-06+milestone%3A0.8.0 \ No newline at end of file diff --git a/doc/releases/0.8.0-rc-1.txt b/doc/releases/0.8.0-rc-1.txt new file mode 100644 index 000000000..bfe505e11 --- /dev/null +++ b/doc/releases/0.8.0-rc-1.txt @@ -0,0 +1,25 @@ +============================================ +PyNN 0.8.0 release candidate 1 release notes +============================================ + +August 19th 2015 + +Welcome to the first release candidate of PyNN 0.8.0! + +For full information about what's new in PyNN 0.8, see the :doc:`0.8-alpha-1`, :doc:`0.8-beta-1` and :doc:`0.8-beta-2` + +NEST 2.6 +-------- + +The main new feature in this release is support for NEST_ 2.6. Previous versions of NEST are no longer supported. + +Other changes +------------- + + * Travis CI now runs system tests as well as unit tests. + * `Assorted bug fixes`_ + + + +.. _NEST: http://www.nest-initiative.org/ +.. _`Assorted bug fixes`: https://github.com/NeuralEnsemble/PyNN/issues?q=is%3Aclosed+closed%3A2015-01-07..2015-08-19+milestone%3A0.8.0 \ No newline at end of file diff --git a/doc/testdocs.py b/doc/testdocs.py index 81153f55e..e6d063bca 100644 --- a/doc/testdocs.py +++ b/doc/testdocs.py @@ -76,7 +76,7 @@ def remove_data_files(): # Process command line parser = OptionParser(usage="usage: %prog [options] FILE") parser.add_option("-s", "--simulator", dest="simulator", - type="choice", choices=('nest', 'neuron', 'pcsim', 'brian'), + type="choice", choices=('nest', 'neuron', 'brian'), help="run doctests with SIMULATOR", metavar="SIMULATOR", default='nest') parser.add_option("--strict", action="store_true", dest="strict", default=False, diff --git a/examples/VAbenchmarks.py b/examples/VAbenchmarks.py index d3410bcfd..721927aa4 100644 --- a/examples/VAbenchmarks.py +++ b/examples/VAbenchmarks.py @@ -15,7 +15,7 @@ simulator benchmark positional arguments: - simulator neuron, nest, brian, pcsim or another backend simulator + simulator neuron, nest, brian or another backend simulator benchmark either CUBA or COBA optional arguments: diff --git a/examples/current_injection.py b/examples/current_injection.py index 7b696e6b9..fe1b7b1dc 100644 --- a/examples/current_injection.py +++ b/examples/current_injection.py @@ -14,7 +14,7 @@ Usage: current_injection.py [-h] [--plot-figure] simulator positional arguments: - simulator neuron, nest, brian, pcsim or another backend simulator + simulator neuron, nest, brian or another backend simulator optional arguments: -h, --help show this help message and exit diff --git a/examples/random_numbers.py b/examples/random_numbers.py index 5de0beaf6..008d6b993 100644 --- a/examples/random_numbers.py +++ b/examples/random_numbers.py @@ -14,7 +14,7 @@ Usage: random_numbers.py [-h] [--plot-figure] [--debug DEBUG] simulator positional arguments: - simulator neuron, nest, brian, pcsim or another backend simulator + simulator neuron, nest, brian or another backend simulator optional arguments: -h, --help show this help message and exit diff --git a/examples/small_network.py b/examples/small_network.py index d87318971..df84ed680 100644 --- a/examples/small_network.py +++ b/examples/small_network.py @@ -6,7 +6,7 @@ Usage: random_numbers.py [-h] [--plot-figure] [--debug DEBUG] simulator positional arguments: - simulator neuron, nest, brian, pcsim or another backend simulator + simulator neuron, nest, brian or another backend simulator optional arguments: -h, --help show this help message and exit diff --git a/examples/tsodyksmarkram.py b/examples/tsodyksmarkram.py index 8fda6056a..e9b098290 100644 --- a/examples/tsodyksmarkram.py +++ b/examples/tsodyksmarkram.py @@ -5,7 +5,7 @@ Usage: tsodyksmarkram.py [-h] [--plot-figure] [--debug DEBUG] simulator positional arguments: - simulator neuron, nest, brian, pcsim or another backend simulator + simulator neuron, nest, brian or another backend simulator optional arguments: -h, --help show this help message and exit diff --git a/examples/varying_poisson.py b/examples/varying_poisson.py index 4d860cc14..1065d2a21 100644 --- a/examples/varying_poisson.py +++ b/examples/varying_poisson.py @@ -7,7 +7,7 @@ Usage: varying_poisson.py [-h] [--plot-figure] simulator positional arguments: - simulator neuron, nest, brian, pcsim or another backend simulator + simulator neuron, nest, brian or another backend simulator optional arguments: -h, --help show this help message and exit diff --git a/pyNN/__init__.py b/pyNN/__init__.py index 56a96f8e1..fcf269018 100644 --- a/pyNN/__init__.py +++ b/pyNN/__init__.py @@ -69,7 +69,7 @@ :license: CeCILL, see LICENSE for details. """ -__version__ = '0.8dev' +__version__ = '0.8.0rc1' __all__ = ["common", "random", "nest", "neuron", "brian", "recording", "errors", "space", "descriptions", "standardmodels", "parameters", "core"] diff --git a/pyNN/utility/__init__.py b/pyNN/utility/__init__.py index f78dbce09..275c11c25 100644 --- a/pyNN/utility/__init__.py +++ b/pyNN/utility/__init__.py @@ -102,7 +102,7 @@ def get_simulator(*arguments): import argparse parser = argparse.ArgumentParser() parser.add_argument("simulator", - help="neuron, nest, brian, pcsim or another backend simulator") + help="neuron, nest, brian or another backend simulator") for argument in arguments: arg_name, help_text = argument[:2] extra_args = {} diff --git a/setup.py b/setup.py index 0d2939b56..eccc952ff 100644 --- a/setup.py +++ b/setup.py @@ -40,8 +40,8 @@ def find_nrnivmodl(self): setup( name = "PyNN", - version = "0.8dev", - packages = ['pyNN','pyNN.nest', 'pyNN.neuron', 'pyNN.nineml', + version = "0.8.0rc1", + packages = ['pyNN','pyNN.nest', 'pyNN.neuron', 'pyNN.brian', 'pyNN.common', 'pyNN.mock', 'pyNN.recording', 'pyNN.standardmodels', 'pyNN.descriptions', 'pyNN.nest.standardmodels',