Bluecellulab

------

* Decouple Cell and Synapse from RNGSettings
* Have a single way of isolating processes via IsolatedProcess
* Implement: Add missing unit tests for tools functions 76
* Remove redundancies in tools.py
* RNGSettings.get_instance() replaces constructor

------

* Add StimulusFactory enabling Python generated Stimulus creation
* Stimulus creation through StimulusFactory is decoupled from the Cell object
* Cell.add_step and Cell.add_ramp use StimulusFactory
* Move stimuli module to stimulus/circuit_stimulus_definitions
* [DOCS] Add list of stimuli page that describe, generate and plot the stimuli
* Add jupyter notebook displaying how to inject the StimulusFactory Stimulus into Cell

-------

* Cell class no longer serialises the following attributes
- secname_to_hsection
- secname_to_isec
- serialized
- cellname
* The direct access to hsection option is removed. The access is through psection.
* solves the dependency issue between init_psections and get_psections
* avoids storing lists of NEURON sections for each Cell. Instead turns them into properties.
* Dendrogram plotting functions are decoupled from PSection

----------------
- Fixed pylint / pep8 after setup.py introduction. [Werner Van Geit]
- Made setup.py changes run on lviz. [Werner Van Geit]
- Tests run after setup.py changes. [Werner Van Geit]
- First installation using setup.py works. [Werner Van Geit]
- Started with making bglibpy pip installable. [Werner Van Geit]
- Added switches to cmake scripts to disable coverage / xunits. [Werner
Van Geit]
- Made sure right bluepy gets picked up by pylint. [Werner Van Geit]
- Added restriction of coverage to bglibpy. [Werner Van Geit]
- Cleaned up runtests.sh.in. [Werner Van Geit]
- Updated runtests to ignore .coverage. [Werner Van Geit]
- Added xunit and coverage output. [Werner Van Geit]
- Fixed pep8 warning in cell.py. [Werner Van Geit]
- Added pep8 target, introduced pep8 error on purpose in cell.py.
[Werner Van Geit]
- All pylint warnings are solved. [Werner Van Geit]
- Solved pylint warnings in psection and simulation. [Werner Van Geit]
- Fixed pylint issues. Also solved an error introduced in previous
commit. [Werner Van Geit]
- Solved pylint errors ssim. [Werner Van Geit]
- Solved more pylint issues. [Werner Van Geit]
- Solved some pylint errors. [Werner Van Geit]
- Disabled I0011 (prevents locally disabling warnings) in pylint.
[Werner Van Geit]
- Added pylint target. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]

Conflicts:
src/cell.py
- Disabled 'use of eval' pylint warning. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Made small change to let Jenkins push the changes. [Werner Van Geit]
- Updated build.sh.lviz.example. [Werner Van Geit]
- Pylint fix in cell.py. [Werner Van Geit]
- Added info_dict() to Cell, Synapse and Connection. [Werner Van Geit]
- Small cleanup in cell.py. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Added a comment to src/cell.py. [Werner Van Geit]
- Pylinting. [Werner Van Geit]
- Raise exception when encountering stimulus that is not supported.
[Werner Van Geit]
- Fixed some pylint warnings. [Werner Van Geit]
- Disabled some pylint warnings. [Werner Van Geit]
- Fixed pep8 error in cell.py. [Werner Van Geit]
- Fixed code to read site-packages dir in case a virtualenv print "using
..." messages when starting python. [Werner Van Geit]
- Moved creation of current_version.txt. [Werner Van Geit]
- Fixed 'too many arguments' error in doc upload. [Werner Van Geit]
- Documentation uploading is now done by a shell script. [Werner Van
Geit]
- Added hbpcol build example. [Werner Van Geit]
- Removed install location module file. [Werner Van Geit]
- Removed adding cmake output files from documentation upload. [Werner
Van Geit]
- Fixed a bug so that index.html gets upload to the bbp documentation.
[Werner Van Geit]
- Changed order so to git add in doc_upload adds all files including
index.html. [Werner Van Geit]
- Fixed a doc_upload dependencies issue. [Werner Van Geit]
- Disabled upload of dirty source directories. [Werner Van Geit]
- Put git push in dry-run mode. [Werner Van Geit]
- Define BGLIBPY_MAINVERSION in CMake. [Werner Van Geit]

------

* Add default value for segx param, improve docs vcs: minor (127)

----------------
- Updated documentation repo to point to bbpcode. [Werner Van Geit]
- Changed commit message for doc build. [Werner Van Geit]
- Added doc upload to BBP documentation server, still need to activate
actual push. [Werner Van Geit]
- Update Lausanne viz build example script. [Werner Van Geit]
- Added version check of neuron to disable/enable renaming templates.
[Werner Van Geit]
- Merge branch 'master' into samenametemplate. [Werner Van Geit]
- Removed CMake/oss directory. [Werner Van Geit]
- Merge branch 'master' into samenametemplate. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Added lbgq build script. [Werner Van Geit]
- Enabled repeating template fix. [Werner Van Geit]
- Started adding code to rename a template in case a template with the
same was already loaded before. Disabled final functionality because
neuron crashes when loading a template using HocObject. [Werner Van
Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Updated installation instructions to point to new bbpcode repo of
Neurodamus. [Werner Van Geit]
- Fixed small syntax warning in CMakeLists.txt. [Werner Van Geit]
- Increase timeout on multiprocessing call, Jenkins plan was sometimes
failing because it was too slow. [Werner Van Geit]
- Updated documentation to reflect the location change of the BluePy
repository (-> Gerrit) [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Removed parse error of runtests.sh.in on Ubuntu 13.10. [Werner Van
Geit]
- Updated installation documentation to reflect the new location of the
BluePy setup.py. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Removed a double installation of tools.py. [Werner Van Geit]
- Disabled xunit output of nosetests, since the ancient version of
nosetests on the Jenkin build nodes / Viz cluster doesn't support
this. [Werner Van Geit]
- Added junit output of nosetests. [Werner Van Geit]
- Commented out nose attribute selector code, since this is plugin is
not available on our test machines with an ancient OS. [Werner Van
Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Let CMake print the hostname to stdout. [Werner Van Geit]
- Added capability to disable unit tests that require bgscratch Small
fix in pre_gid search. [Werner Van Geit]
- Print the neuron installation path from cmake Added an example build
script for bglibpy on the Lugano viz cluster. [Werner Van Geit]
- Added functionality to get the gids of the presynaptic cells of a
cell. [Werner Van Geit]
- Add common CMake files. [Werner Van Geit]
- Added BBPSaucy to CMakelists. [Werner Van Geit]
- Expanded the comment of the SSim constructor. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Shortened one line. [Werner Van Geit]
- Cleaned up code. [Werner Van Geit]
- Cleaned up code. [Werner Van Geit]
- Cleaned up psection.py. [Werner Van Geit]
- Prevented loading of out.dat if add_replay=True is not specified.
[Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Cleaned up comments in cell.py. [Werner Van Geit]
- Fixed an issue for user for which the neuron binaries are install in
$PREFIX/bin instead of $PREFIX/$ARCH/bin. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Fixing doc in cell.py to comply PEP257. [Werner Van Geit]
- Cleaned up code. [Werner Van Geit]
- Cleaned up the SSim code. [Werner Van Geit]
- Cleaned up the code. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Changed path of nrnpython on santiago test machine. [Werner Van Geit]
- Fixed segment.x in cell.py. [Werner Van Geit]
- Cleaned up Simulation progress bar. [Werner Van Geit]
- Improved the progress bar. [Werner Van Geit]
- Added progress bar to Simulation. [Werner Van Geit]
- Added area calculation to cell.py. [Werner Van Geit]
- Fixed small bug in dendrogram. [Werner Van Geit]
- Added functions that return the release morphologies and ccelss
directories. [Werner Van Geit]
- Brought cell.py to comply to pep8 standard. [Werner Van Geit]
- Added a function to cell to make a neuron passive. [Werner Van Geit]
- Implemented ForwardSkip in BGLibPy and added a unit test for it.
[Werner Van Geit]
- Added ssim support for replay to bonus projection synapses, with
example. Does not parse BlueConfig yet for BonusSynapseFile params,
because this syntax is about to change in bglib to support multiple
projections. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Connection blocks with dest or src targets that don't exist are now
ignored. [Werner Van Geit]
- Using numpy.testing.assert_array_almost_equal to compare arrays for
tapering test. [Werner Van Geit]
- Replaced assert_equal with assert_almost_equal for tapering test.
[Werner Van Geit]
- Added a test for tapering when using delete_axon with arguments in
BGLib. [Werner Van Geit]
- Fixing teardown in SSim test suite. [Werner Van Geit]
- Added the properties syns and hsynapses back to the cell object.
[Werner Van Geit]
- Changed if statement for pre_cell and pre_spiketrain in Connection, so
that it can handle generators as spiketrains. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Changed api.rst, so that source links are shown again in the
documentation. [Werner Van Geit]
- Renamed Bluebrain to bbp. [Werner Van Geit]
- Added functions to synapse to check if the synapse is inhibitory or
excitatory. [Werner Van Geit]
- Added new functionality in instantiate_gids to independendly
enable/disable noise and hyperpolarizing stimuli. [Werner Van Geit]
- Added build dir to .gitignore. [Werner Van Geit]
- Updated README. [Werner Van Geit]
- Removed some useless comments. [Werner Van Geit]
- Finished added an internal representation for section. [Werner Van
Geit]
- Starting to create an internal BGLibPy structure of a cell with
psections and psegments. [Werner Van Geit]
- Removed architecture reference from module help. [Werner Van Geit]
- Added support for environment modules. [Werner Van Geit]
- Remove showdenddiam function because it's deprecated. [Werner Van
Geit]
- Added r in front of regular expression string. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Updated doc of bglibpy.tools.search_hyp_current_replay_gidlist.
[Werner Van Geit]
- Added date to button of doc pages. [Werner Van Geit]
- Merge branch 'ebmuller' [Werner Van Geit]
- Updated the documentation of a set of functions. [Werner Van Geit]
- Removed namespace polution in SSim. [Werner Van Geit]
- Cleanup. [Werner Van Geit]
- Got Ben's unit tests for get_gids_of_mtypes() running. [Werner Van
Geit]
- Fixed problems in Ben's unit tests because pickled files were not
saved in the repo. [Werner Van Geit]
- Fixed an bug after renaming get_section to get_hsection. [Werner Van
Geit]
- Merge branch 'btn' [Werner Van Geit]

Conflicts:
src/ssim.py
src/tools.py
- Ssim.get_gids_of_mtypes + tests. [Benjamin Torben-Nielsen]
- Added get_gitd_of_mtypes helper to ssim; uses the self.bc_simulation
to handle queries. TODO: add test. [Ben Torben-Nielsen]
- Moved get_gid_of_mtypes froom tools.py, to be moved to ssim. [Ben
Torben-Nielsen]
- Added automatic deprecation doc to deprecated function Extended
documentation of some cell functions. [Werner Van Geit]
- Added a haiku-bbp theme, to fix an issue with haiku and numpydoc
interaction. [Werner Van Geit]
- Added a ~ to links in the tutorial to shorten the linked name. [Werner
Van Geit]
- Replace ::code with ::code-block in rst files. [Werner Van Geit]
- Added pre_gid field to Synapse class. [Werner Van Geit]
- Added some example to the tutorial. [Werner Van Geit]
- Documentation now works with numpydoc. [Werner Van Geit]
- Documentation now generates autosummary for all the modules correctly.
[Werner Van Geit]
- Fixed a erroneous move of index.rst to introduction.rst. [Werner Van
Geit]
- Fixed Paramters to Parameters in ssim doc. [Werner Van Geit]
- Extended the documentation, and reordered things a bit. [Werner Van
Geit]
- Enabling numpydoc again. [Werner Van Geit]
- Disabled numpydoc temporarily until it works in the bamboo plans.
[Werner Van Geit]
- Added support for BBPQUANTAL in the CMakeLists.txt. [Werner Van Geit]
- Removed checks in instantiate_gids to see if no illegal combinations
of options are given, it clashes with the synapse_detail setting.
[Werner Van Geit]
- Search_hyp_current_replay_imap: support to override cpu_count, other
minor fix. [Eilif Muller]
- Search_hyp_current_replay: Making return values for non-convergence
conformant to layout for successful cases to avoid complex downstream
logic. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]
- Merge remote branch 'origin/master' into ebmuller. [Eilif Muller]