Changeset 78

Timestamp:

05/24/07 14:58:23 (1 year ago)

Author:

apdavison

Message:

The documentation is now 'good enough' for release.

Files:

• branches/0.3/common.py (modified) (1 diff)
• branches/0.3/doc/highlevelapi.txt (modified) (1 diff)
• branches/0.3/doc/installation.txt (modified) (4 diffs)
• branches/0.3/doc/introduction.txt (modified) (1 diff)
• branches/0.3/doc/lowlevelapi.txt (modified) (1 diff)
• branches/0.3/doc/standardmodels.txt (modified) (1 diff)

branches/0.3/common.py

@@ +1 @@
+# encoding: utf-8
-"""
-Defines the PyNN classes and functions, and hence the FACETS API.

branches/0.3/doc/highlevelapi.txt

@@ -353 +353 @@
-=======
-
-
+ of the source distribution

branches/0.3/doc/installation.txt

@@ -3 +3 @@
-============
-
-
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+
-
-We assume this is installed on your machine already. If not, we suggest you install it via the package manager of your Linux distribution [OS X instructions?]. If this is not possible, go to `<http://www.python.org>`_ and follow the instructions you find there.
-
-Installing NEURON
@@ -13 +11 @@
-Download the sources for the latest release of NEURON, in ``.tar.gz`` format, from `<http://www.neuron.yale.edu/neuron/install/install.html>`_. Also download Interviews from the same location.
-
- [what about OS X?], except that when you run ``configure``, add the options ``--with-nrnpython`` and ``--with-mpi`` (the latter assumes you have the MPICH library installed on your machine [should we give instructions?]
+, except that when you run ``configure``, add the options ``--with-nrnpython`` and, optionally, ``--with-mpi`` (the latter assumes you have the MPICH library installed on your machine
-
-    $ ./configure --prefix=`pwd` --with-nrnpython --with-mpi
@@ -22 +20 @@
-
-    $ nrniv -python
-
+
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+
+
-    >>> import hoc
-    >>> import nrn   
@@ -29 +30 @@
-==========================
-
+NEST can be downloaded from `<http://www.nest-initiative.org/?page=Software&subpage=Download>`_.
+Installation instructions are available from `<http://www.nest-initiative.uni-freiburg.de/helpdesk/synod2/doc/install.html>`_.
+
+Check out PyNEST from the following Subversion repository (contact the NEST developers for access)::
+
+    $ svn co svn+ssh://facets@www.nest-initiative.uni-freiburg.de/facets/trunk pynest
+    $ cd pynest
+    
+Set the ``SLIHOME`` environment variable to your NEST source installation and ``SLIBUILD`` to your NEST build directory, e.g. (for bash)::
+
+    $ export SLIHOME=/usr/src/nest-1.0.13
+    $ export SLIBUILD=$SLIHOME/build
+    
+Finally, build and install PyNEST::
+
+    $ python setup.py install
+    
+This will install it to your python ``site-packages`` directory, and may require root privileges.
+If you wish to install it elsewhere::
+
+    $ python setup.py install --prefix=/where/to/install/pynest
+    
+and then set the ``PYTHONPATH`` environment variable appropriately, e.g.::
+    
+    $ export PYTHONPATH=$PYTHONPATH:/where/to/install/pynest/lib/python2.4/site-packages/
+
+Now try it out::
+
+    $ cd ~ 
+    $ python 
+    >>> import pynest 
+    >>> pynest.sps([1,2,3]) 
+    >>> pynest.spp() 
+    [1, 2, 3]
+
+
+Installing PCSIM
+================
+
+PCSIM_ is available by svn as follows:
+
+    $ svn co https://pcsim.svn.sourceforge.net/svnroot/pcsim pcsim
+
+For compilation instructions, see the files in the ``HowTos`` directory.
+
+
-Installing PyNN
-===============
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branches/0.3/doc/introduction.txt

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-Introduction
-============
+
+PyNN (pronounced 'pine' ) is a Python package for simulator-independent specification of neuronal network models. 
+
+In other words, you can write the code for a model once, using the PyNN API, and then run it without modification on any simulator that PyNN supports (currently NEURON_, NEST_ and PCSIM_). 
+
+The API has two parts, a low-level, procedural API, similar to that in PyNEST (functions ``create()``, ``connect()``, ``set()``, ``record()``, ``record_v()``), and a [wiki:HighLevelAPI high-level, object-oriented API] (classes ``Population`` and ``Projection``, which have methods like ``set()``, ``record()``, ``setWeights()``, etc.). 
+
+The low-level API is good for small networks, and perhaps gives more flexibility. The high-level API is good for hiding the details and the book-keeping.
+
+The other thing that is required to write a model once and run it on multiple simulators is standard cell models. PyNN translates standard cell-model names and parameter names into simulator-specific names, e.g. standard model ``IF_curr_alpha`` is ``iaf_neuron`` in NEST and ``StandardIF`` in NEURON, while ``SpikeSourcePoisson`` is a ``poisson_generator`` in NEST and a ``NetStim`` in NEURON. Only a few cell models have been implemented so far.
+
+Please note that PyNN is currently very experimental. The code is released under the CeCILL_ licence.
+ 
+.. _CeCILL: http://www.cecill.info/
+.. _NEURON: http://www.neuron.yale.edu/neuron/
+.. _NEST:   http://www.nest-initiative.org/?page=Software
+.. _PCSIM:  http://sourceforge.net/projects/pcsim/

branches/0.3/doc/lowlevelapi.txt

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branches/0.3/doc/standardmodels.txt

@@ -96 +96 @@
-Name          Default value  Units   Description
-============  =============  ======  ==========================
- 
+`
-``start``     0.0            ms      Start time
-``duration``  10^9           ms      Duration of spike sequence