root/trunk/changelog

===========
Release 0.4 (r342)
===========

* Added a `quit_on_end` extra argument to `neuron.setup()`

* Added a `synapse_types` attribute to all standard cell classes.

* Removed `Projection.setThreshold()` from API

* In the `neuron` module, `load_mechanisms()` now takes a path to search from as an optional argument, in order to allow loading user-defined mechanisms

* Added `get_script_args()` (process command line arguments) and `colour()` (print coloured output) functions to the `utility` module.

* Added `rank()` to the API (returns the MPI rank)

* Removed `setRNGseeds()` from the API, since each simulator is so different in its requirements. The seeds may be provided using the `extra_params` argument to `setup()`.

* The headers of output files now contain the first and last ids in the Population (not fully implemented yet 
for recording with the low-level API)

* Global variables such as the time step and minimum delay have been replaced
with functions `get_time_step()`, `get_min_delay()` and `get_current_time()`. This
ensures that values are always up-to-date.

* Removed `cellclass` arg from `set()` function. All cells should now know their own cellclass.

* Added `get()` method to `Population` class.

* Default value for the `duration` parameter in `SpikeSourcePoisson` changed
from 1e12 ms to 1e6 ms.

* Reimplemented `Population.set()`, `tset()`, `rset()` in a more consistent way
which avoids exposing the translation machinery and fixes various bugs with
computed parameters. The new implementation is likely to be slower, but several
optimisations are possible.

* Added `simple_parameters()`, `scaled_parameters()` and `computed_parameters()`
methods to the `StandardModelType` class. Their intended use is in making
`set()` methods/functions more efficient for non-computed parameters when
setting on many nodes.

* Multiple calls to `Population.record()` no longer record the same cell twice.

* Changed `common.ID` to `common.IDMixin`, which allows the type used for the id
to vary (`int` for `neuron` and `nest1/2`, `long` for pcsim).

* In `common.StandardModelType`, changed most of the methods to be classmethods,
since they do not act on instance data.

* Added a `ModelNotAvailable` class to allow more informative error messages 
when people try to use a model with a simulator that doesn't support it.

* hoc and mod files are now correctly packaged, installed and compiled with
`distutils`.

* Added a check that argument names to `setup()` are not mis-spelled. This is
possible because of `extra_params`.

* It is now possible to instantiate Timer objects, i.e. to have multiple,
independent Timers

* Some re-naming of function/method arguments to conform more closely to
Python style guidelines, e.g. `methodParameters` to `method_parameters` and
`paramDict` to `param_dict`.

* Added `getWeights()` and `getDelays()` methods to `Projection` class. NOTE:
check for which simulators this is available. XXX

* Added a `RoundingWarning` exception, to warn the user when rounding is
occurring.

* Can now change the `spike_times` attribute of a `SpikeSourceArray` during a
simulation without reinitialising. This reduces memory for long simulations,
since it is not necessary to load all the spike times into memory at once.
NOTE: check for which simulators this works. XXX

* The `neuron` module now requires NEURON v6.1 or later.

* For developers, changes to the layout of the code: 
    (1) Simulator modules have been moved to a `src` subdirectory - this is to
    make distribution/installation of PyNN easier.
    (2) Several of the modules have been split into multiple files, in their own
    subdirectories, e.g.: `nest2.py` --> `nest2/__init__.py`, `nest2/cells.py`
    and `nest2/connectors.py`. The reason for this is that the individual files
    were getting very long and difficult to navigate.

* Added `index()` method to `Population` class - what does it do?? XXX

* Added `getSpikes()` method to `Population` class - returns spike times/ids as
a numpy array.

* Added support for the Stage 1 FACETS hardware.

* Changed the default weight to zero (was 1.0 nA)

* New STDP API, with implementations for `neuron` and `nest2`, based on
discussions at the CodeSprint.

* Distance calculations can now use periodic boundary conditions.

* Parameter translation system now fully supports reverse translation
(including units). The syntax for specifying translations is now simpler,
which makes it easier to define new standard cell models.

* All simulator modules now have a `list_standard_models()` function, which
returns a list of all the models that are available for that simulator.

* The `connect()` function now returns a `Connection` object, which has
`weight` and `delay` properties. This allows accessing/changing weights/delays
of individual connections in the low-level API. NOTE: only available in `nest2`?
Implement for all sims or delete from this release. XXX

* Added `record_c()` and `print_c()` methods to the `Population` class, to allow
recording synaptic conductances. NOTE: only in `nest2` - should add to
`neuron` or delete from this release. XXX

* Procedures for connecting `Population`s can now be defined as classes
(subclasses of an abstract `Connector` class) rather than given as a string.
This should make it easier for users to add their own connection methods.
Weights and delays can also be specified in the `Connector` constructor,
removing the need to call `setWeights()` and `setDelays()` after the building
of the connections.
We keep the string specification for backwards compatibility, but this is
deprecated and will be removed in a future API version. 

* Added new standard models: EIF_cond_alpha_isfa_ista, IF_cond_exp_gsfa_grr,
HodgkinHuxley. NOTE: check names, and that all models are supported by at
least two simulators.

* Version 2 of the NEST simulator is now supported, with the `nest2` module.
The `nest` module is now called `nest1`.

* Changed the order of arguments in `random.RandomDistribution.__init__()` to
put `rng` last, since this is the argument for which the default is most often
used (moving it lets positional arguments be used for `distribution` and
`parameters` when `rng` is not specified).

* Changes to `ID` class:
  - `_cellclass` attribute renamed to `cellclass` and is now a [http://www.geocities.com/foetsch/python/new_style_classes.htm property].
  - Ditto for `_position` --> `position`
  - Methods `setPosition()`, `getPosition()`, `setCellClass()` removed (just use
  the `position` or `cellclass` properties).
  - `set(param,val=None)` changed to `setParameters(**parameters)`.
  - Added `getParameters()`
  - `__setattr__()` and `__getattr__()` overridden, so that cell parameters can
  be read/changed using dot notation, e.g. `id.tau_m = 20.0`
Note that one of the reasons for using properties is that it allows attributes
to be created only when needed, hopefully saving on memory.

* Added `positions` property to `Population` class, which allows the positions
of all cells in a population to be set/read at once as a numpy array.

* All positions are now in 3D space, irrespective of the shape of the
`Population`.

* Threads can now be used in `nest` and `pcsim`, via the `extra_param` option of
the `setup()` function. 

* Removed `oldneuron` module.

* Added `__iter__()` (iterates over ids) and `addresses()` (iterates over
addresses) to the `Population` class.

===========
Release 0.3
===========

* `pcsim` is now fully supported, although there are still one or two parts of
the API that are not implemented.

* The behaviour of the `run()` function in the `neuron` module has been changed to match the `nest` and `pcsim` modules, i.e., calling `run(simtime)` several times in succession will advance the simulation by `simtime` ms each time, whereas before, `neuron` would reset time to zero each time.

* PyTables is now optional with `pcsim`

* Change to `neuron` and `oldneuron` to match more closely the behaviour of
`nest` and `pcsim` when the `synapse_type` argument is not given in `connect()`.
Before, `neuron` would by default choose an excitatory synapse. Now, it chooses
an inhibitory synapse if the weight is negative. 

* `runtests.py` now runs tests for `pcsim` as well as `nest`, `neuron` and
`oldneuron`.

* Minor changes to arg names and doc-strings, to improve API-consistency between modules.

* Added users' guide (in `doc` directory).

* Renamed `neuron` module to `oldneuron` and `neuron2` to `neuron`.

* PyNN can now be installed using `distutils`, although this doesn't install
or compile hoc/mod files.

* Added a `compatible_output` argument to the `printX()` functions/methods, to
allow choosing a simulator's native format (faster) or a format that is
consistent across simulators.

* Temporary files used for saving spikes and membrane potential are now created
using the `tempfile` module, which means it should be safe to run multiple PyNN
simulations at the same time (before, they would all overwrite the same file).

* pygsl is no longer an absolute requirement but can be used if available

* Changed the behaviour of `Population` indexing in the `nest` module to be more
consistent with the `neuron2` module, in two ways. (i) negative addresses now
raise an Exception. (ii) Previously, an integer index `n` signified the `(n+1)`th
neuron in the population, e.g., `p[99]` would be the same as `p[10,10]` for a
10x10 population. Now, `p[99]` is the same as `p[99,]` and is only valid for a
1D population.

* Addition of `ID` class (inherits from `int`), allowing syntax like
`p[3,4].set('tau_m',20.0)` where `p` is a Population object.

=============
Release 0.2.0
=============

* `Population.tset()` now accepts arrays of arrays (e.g. conceptually a 2D array
of 1D arrays, actually a 3D array) as well as arrays of lists.

* setup() now returns the node id. This can be used in a parallel framework to
identify the master node.

* Unified output format for spikes and membrane potential for `nest` and
`neuron` modules.

* Added first experimental version of `pcsim` module

* `neuron2` module now supports distributed simulations using NEURON compiled
with both MPI and Python support.

* `Population[xx]` syntax for getting individual cell ids improved. You can now
write `p[2,3]` instead of `p[(2,3)]`.

* `v_init` added as a parameter to the `IF_curr_alpha`, etc, models.

* Trying to access a hoc variable that doesn't exist raises a Python exception,
`HocError`.

* If synaptic delay is not specified, delays are now set to `min_delay`, not zero.

* Random number API allows keeping control of the random numbers used in
simulations, by passing an RNG object as an argument to functions that use RNGs.
`random` module has wrappers for NumPy RNGs and GSL RNGs, as well as a stub
class to indicate the simulator's native RNG should be used (i.e., the `Random`
class in hoc).

* Translation of model and parameter names from standardised names to
simulator-specific names now uses one class per neuron model, rather than a
single class with one method per model. For users, the only difference is
that you have to use, e.g.,
    `create(IF_curr_alpha)`
instead of
    `create('IF_curr_alpha')`
i.e., pass the class instead of a string.
For developers, it should now be easier to add new standard models. 

* Added `neuron2` module, a reimplemtation of the PyNN API for NEURON, that uses
more Python and less hoc.


=============
Release 0.1.0
=============

Version 0.1 of the API was never really released. At this point the project used
the FACETSCOMMON svn repository.

First svn import of early stage of PyNN was on 9th May 2006.