----------------
- Updated version to 2.0. [Werner Van Geit]
- Updated the documentation string of instantiate_gids to reflect the
multi-cell changes Fixed a bug in Connection concerning the variable
name of the netcon added an example for a multicell replay. [Werner
Van Geit]
- Finished implementation of multi cell functionality of BGLibPy
Connection now correctly sets the weight of the real connections Added
unit test for real connections. [Werner Van Geit]
- Trying to get connect2target working, waiting for response from
M.Hines. [Werner Van Geit]
- Implemented connections between multiple cells, but it still core
dumps. [Werner Van Geit]
- Added a new synapse class. Still in an inconsistent state before
multicell works. [Werner Van Geit]
- Large rewrite of ssim to make it more readable. Separate functions to
add the stimuli, synapses, cells etc. This code is not finished, and
will not function correctly. [Werner Van Geit]
- Preparing to make it possible to connect several cells in a network: -
created a Connection class that represents a network connection in
BGLibPy. [Werner Van Geit]
- Renamed some variables in ssim to make them more readable only parse
out.dat once. [Werner Van Geit]
- Moved installation guide into separate file. [Werner Van Geit]
- Enforced CMake 2.8, since we're not testing for CMake 2.6. [Werner Van
Geit]
- Added two simple examples of BGLibPy usecases. [Werner Van Geit]
- Solved an issue in CMakeLists.txt in which some interference with
apparently BuildYard or something, make the configure_file to write
the paths.config in the wrong directroy. [Werner Van Geit]
- Starting with installation tutorial. [Werner Van Geit]
- Added other modules to documentation conf.py for the doc now get's the
right location of BGLibPY. [Werner Van Geit]
- Starting doc making in CMakeLists.txt. [Werner Van Geit]
- Merge branch 'imap_parallel' [Werner Van Geit]
Conflicts:
src/tools.py
- Search_hyp_current_replay_imap now internally uses asynchronous
parallelization. It returns a generator, so that the user can, one by
one retreive the asynchronous results. [Werner Van Geit]
- Added imap function to calculate hypvoltage. [Werner Van Geit]
- Merge branch 'btn' [Werner Van Geit]
- Cleaned up the doc directory. TODO: resolve issue with autosummary in
api.rst. [Ben Torben-Nielsen]
- First: commit, second: clean up the doc mess. [Ben Torben-Nielsen]
- Too much documentation. [Ben Torben-Nielsen]
- Merge remote-tracking branch 'origin/master' into btn. [Ben Torben-
Nielsen]
- Werner revised the intersect_pre_gid for loop. [Ben Torben-Nielsen]
- Fixed a bug in tools.py where the same variable full_voltage was
erroneously used twice. [Werner Van Geit]
- Changed the behavior of search_hyp_current_replay_gidlist so that it
implements a timeout in case one of the subpool workers doesn't return
in time. [Werner Van Geit]
- Merge branch 'ebmuller' [Werner Van Geit]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Minor fixes: consistency of return values for return_fullrange modes,
multiprocessing map uses cpu count, additional doc clarifications.
[Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Minor fixes: consistency of return values for return_fullrange modes,
multiprocessing map uses cpu count, additional doc clarifications.
[Eilif Muller]
- Added code to the delete() function of cells, so that they destroy the
circular dependencies introduced by FInitializeHandler SSim will now
call this delete() function on all its cells during destruction.
[Werner Van Geit]
- Add support for the 'delay' field of a connection block in a
BlueConfig. [Werner Van Geit]
- Hardened the SSim connection block reader against ignoring any
unsupported fields in these block. [Werner Van Geit]
- Merge branch 'ebmuller' [Werner Van Geit]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Added option to check for spiking (and if so, return None) for
calculate_SS_voltage_subprocess. Default behaviour unchanged. [Eilif
Muller]
- Added methods to reset synapse state. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Added sections keyword to execute_neuronconfigure method. [Eilif
Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Merge with origin/master. [Eilif Muller]
- Added failure status for add_replay_synapse, instantiate_gids now has
a synapse_detail=0 option. [Eilif Muller]
- Made default edgecolor of psegment 'black' [Werner Van Geit]
- Removed finitialize from constructor of dendrogram. [Werner Van Geit]
- Made a warning in runtest.sh more visible. [Werner Van Geit]
- Removed all reference in other modules to getTime and getSomaVoltage.
[Werner Van Geit]
- Removed all references to addRamp in other modules. [Werner Van Geit]
- Dendrogram is working again Refactored some functions in cell.py.
[Werner Van Geit]
- Reenabled to ability to add live plots. This time the code is using
cvode.event callback function, so that it doesn't interfere with the
time step of the simulation. [Werner Van Geit]
- Renamed function that parses the out.dat in ssim Created a unit test
for this function Added script that runs coverage analysis on the unit
tests. [Werner Van Geit]
- Added a warning to runtests.sh to warn users to rebuild BGLibPy before
executing runtests.sh. [Werner Van Geit]
- Added a unit test for search_hyp_current_replay_gidlist Slight changed
the API of search_hyp_current_replay_gidlist, so that it also returns
the time trace, in addition to the voltage trace. [Werner Van Geit]
- Updated the BlueConfigs in the unit tests to reflect the changes in
bgscratch directory structure on BG/Q. [Werner Van Geit]
- Adding kwargs to search_hyp_current_replay_gidlist, instead of a
specifying an entire list of kwargs that have to percolate down.
[Werner Van Geit]
- Disable show_progress by default in the run() of Simulation. [Werner
Van Geit]
- Made it possible to specify the test as an argument to runtests.sh.
[Werner Van Geit]
- Small cleanup of comments in test_ssim. [Werner Van Geit]
- Added the ability to show the progress of a simulation to the run()
function of Simulation. [Werner Van Geit]
- Calculate_SS_voltage_replay_subprocess now returns a voltage of a
'full time range' of the simulation after it is done, not just the
time between start_time / stop_time. [Werner Van Geit]
- Added function documentation to search_hyp_current_replay_gidlist.
[Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Add --tags to the git describe, so that we don't depend on annotated
tags. [Werner Van Geit]
- Changed the verbose level of some messages in ssim to level 2. [Werner
Van Geit]
- Added a function to tools.py called search_hyp_current_replay_gidlist
It search for a list of gids, the current injection amplitude
necessary to bring the cells to a target voltage. [Werner Van Geit]
- Added CMake code that checks for the version of Neuron and BGLib used
during compilation. The versions can be accessed by the variable
build_versions of the module. [Werner Van Geit]
- Added __version__, version and VERSION variables to the module that
contain the git-repository version of BGLibPy. [Werner Van Geit]
- Dummy commit, trying out versioning. [Werner Van Geit]