Merge port_ids branch into master.

.gitignore

@@ -0,0 +1,18 @@
+# ignore compiled python
+*.pyc
+
+#
+*.mat
+*.mp4
+*.avi
+*.prof
+*.png
+*.h5
+*.log
+*.file
+*qsub.py
+*gexf.gz
+*temp*
+neurokernel.egg-info
+neurokernel/neurokernel.log
+!neurokernel/examples/retina_lamina/image1.mat

INSTALL.rst

@@ -2,6 +2,27 @@
 
 Installation
 ============
+Prerequisites
+-------------
+Neurokernel requires Python 2.7, at least one NVIDIA GPU, NVIDIA's `GPU drivers 
+<http://www.nvidia.com/content/drivers/>`_, and `CUDA 
+<http://www.nvidia.com/object/cuda_home_new.html>`_ 5.0 or later.  To check what 
+GPUs are in your system, you can use the `inxi 
+<https://code.google.com/p/inxi/>`_ command available on most Linux 
+distributions::
+
+  inxi -G
+
+You can verify that the drivers are loaded as follows::
+
+  lsmod | grep nvidia
+
+If no drivers are present, you may have to manually load them by running 
+something like::
+
+  modprobe nvidia
+
+as root.
 
 Prerequisites
 -------------
@@ -39,8 +60,8 @@ following dependencies as follows::
 
 If installation of PyCUDA fails because some of the CUDA development files or 
 libraries are not found, you may need to specify where they are explicitly. For 
-example, if CUDA is installed in ``/usr/local/cuda/``, try installing PyCUDA as 
-follows::
+example, if CUDA is installed in ``/usr/local/cuda/``, try installing PyCUDA
+as follows::
 
   CUDA_ROOT=/usr/local/cuda/ CFLAGS=-I${CUDA_ROOT}/include \
   LDFLAGS=-L${CUDA_ROOT}/lib64 pip install pycuda
@@ -52,9 +73,9 @@ Linux. If you continue to encounter installation problems, see the `PyCUDA Wiki
 
 You will also need to have `ffmpeg <http://www.fmpeg.org>`_ or `libav 
 <http://libav.org>`_ installed to generate some of the demo visualizations.
-
-Run the following to install the remaining dependencies and the latest 
-Neurokernel code::
+  
+Run the following to install the remaining dependencies and the 
+latest Neurokernel code::
 
   git clone https://github.com/neurokernel/neurokernel.git
   pip install -e git+./neurokernel#egg=neurokernel
@@ -76,10 +97,11 @@ Neurokernel currently requires the following Python packages:
 * `lxml <http://lxml.de/>`_ 3.3.0 or later.
 * `matplotlib <http://matplotlib.org/>`_ 1.3.0 or later.
 * `msgpack-numpy <http://pypi.python.org/pypi/msgpack-numpy>`_ 0.3.1.1 or later.
-* `networkx <https://networkx.github.io>`_ 1.9 or later
+* `networkx <https://networkx.github.io>`_ 1.9 or later.
 * `numexpr <https://github.com/pydata/numexpr>`_ 2.3 or later.
 * `numpy <http://numpy.scipy.org>`_ 1.2.0 or later.
 * `pandas <http://pandas.pydata.org>`_ 0.14.1 or later.
+* `ply <http://www.dabeaz.com/ply/>`_ 3.4 or later.
 * `pycuda <http://mathema.tician.de/software/pycuda>`_ 2014.1 or later.
 * `pyzmq <http://zeromq.github.io/pyzmq/>`_ 13.0 or later.
 * `scipy <http://www.scipy.org>`_ 0.11.0 or later.

LICENSE.rst

@@ -1,33 +1,61 @@
 .. -*- rst -*-
 
-License
-=======
+Licenses
+========
 
+Neurokernel
+-----------
 Copyright (c) 2012-2014, Neurokernel Development Team
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
 met:
 
-* Redistributions of source code must retain the above copyright
-  notice, this list of conditions and the following disclaimer.
-* Redistributions in binary form must reproduce the above
-  copyright notice, this list of conditions and the following
-  disclaimer in the documentation and/or other materials provided
-  with the distribution.
-* Neither the names of the Neurokernel Development Team nor the names of any
-  contributors may be used to endorse or promote products derived
-  from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+* Neither the names of the copyright holders nor the names of any contributors
+  may be used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+libNeuroML
+----------
+Copyright (c) 2012, libNeuroML authors and contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+* Neither the names of the copyright holders nor the names of the contributors
+  may be used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

docs/source/conf.py

@@ -37,12 +37,14 @@ def __getattr__(cls, name):
     def __getitem__(self, v):
         return Mock()
 
-MOCK_MODULES = ['bidict', 'matplotlib', 'matplotlib.pyplot',
+MOCK_MODULES = ['bidict', 'chash', 'lxml', 'matplotlib', 'matplotlib.pyplot',
                 'msgpack', 'msgpack_numpy', 'networkx', 'numpy', 'pandas',
+                'ply', 'ply.lex', 'ply.yacc',
                 'pycuda', 'pycuda.compiler', 'pycuda.driver',
                 'pycuda.elementwise', 'pycuda.gpuarray',
                 'pycuda.reduction', 'pycuda.scan', 'pycuda.tools', 'pytools',
-                'scipy', 'scipy.sparse', 'twiggy', 'zmq', 'zmq.eventloop',
+                'scipy', 'scipy.sparse', 'twiggy', 'xxh',
+                'zmq', 'zmq.eventloop',
                 'zmq.eventloop.ioloop', 'zmq.eventloop.zmqstream']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()
@@ -57,6 +59,7 @@ def __getitem__(self, v):
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.append(os.path.abspath('../sphinxext'))
 sys.path.append(os.path.abspath('../../neurokernel'))
+sys.path.append(os.path.abspath('../../neurokernel/neuroml'))
 sys.path.append(os.path.abspath('../../'))
 
 # -- General configuration -----------------------------------------------------
@@ -307,6 +310,5 @@ def __getitem__(self, v):
     'http://documen.tician.de/pycuda/': None,
 }
 
-# Prevent methods/class attributes from automatically being added twice:                       
+# Prevent methods/class attributes from automatically being added twice:
 numpydoc_show_class_members = False
-

docs/source/reference_emulation.rst

@@ -9,14 +9,15 @@ Construction and Execution
    :toctree: generated/
    :nosignatures:
 
-   neurokernel.base.Broker
-   neurokernel.core.Manager
+    neurokernel.base.BaseManager
+    neurokernel.base.Broker
+    neurokernel.core.Manager
 
 Support Classes
 ---------------
 .. autosummary::
    :toctree: generated/
    :nosignatures:
 
-   neurokernel.ctrl_proc.ControlledProcess
-   neurokernel.routing_table.RoutingTable
+    neurokernel.ctrl_proc.ControlledProcess
+    neurokernel.routing_table.RoutingTable

docs/source/reference_model.rst

@@ -18,6 +18,5 @@ Inter-LPU Connectivity
    :toctree: generated/
    :nosignatures:
 
-   neurokernel.base.BaseConnectivity
-   neurokernel.core.Connectivity
-   neurokernel.core.IntervalIndex
+   neurokernel.pattern.Interface
+   neurokernel.pattern.Pattern

docs/source/reference_support.rst

@@ -3,6 +3,30 @@
 Support Classes and Functions
 =============================
 
+Path-Like Port Identifier Handling
+----------------------------------
+.. currentmodule:: neurokernel.plsel
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   PathLikeSelector
+   PortMapper
+
+XML Tools
+---------
+.. currentmodule:: neurokernel.neuroml.utils
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   graph_to_nml_module
+   graph_to_nml_pattern
+   load
+   nml_pattern_to_graph
+   nml_module_to_graph
+   write
+
 Context Managers
 ----------------
 .. currentmodule:: neurokernel.ctx_managers
@@ -27,17 +51,15 @@ Communication Tools
    is_poll_in
    ZMQOutput
 
-Graph Tools
------------
-.. currentmodule:: neurokernel.tools.graph
-.. autosummary::
-   :toctree: generated/
-   :nosignatures:
+.. reenable after these are rewritten to use the new Interface/Pattern classes
+   Graph Tools
+   -----------
+   .. currentmodule:: neurokernel.tools.graph
+   .. autosummary::
+      :toctree: generated/
+      :nosignatures:
 
-   conn_to_graph
-   graph_to_conn
-   graph_to_df
-   load_conn_all
+      graph_to_df
 
 Visualization Tools
 -------------------
@@ -52,6 +74,13 @@ Visualization Tools
 
 Other
 -----
+.. currentmodule:: neurokernel.mixins
+.. autosummary::
+    :toctree: generated/
+    :nosignatures:
+
+   LoggerMixin
+
 .. currentmodule:: neurokernel.tools.misc
 .. autosummary::
    :toctree: generated/