Bluecellulab

----------------
- First version of code that reads nrrp var from nrn.h5 (unvalidated)
[Werner Van Geit]
- Mention new way of using NEURON nix on CSCS viz in doc. [Werner Van
Geit]
- Remove modlibpath warning, it confuses people. [Werner Van Geit]
- Access 'OutputRoot' config key only when needed. [Arseny V.
Povolotsky]
- Mention --enable-unicode=ucs4 python compilation problem in doc.
[Werner Van Geit]
- Fix small things in doc. [Werner Van Geit]
- Merge branch 'remove_cmake' [Werner Van Geit]
- Fixed link to dep section in docs. [Werner Van Geit]
- Improve installation docs. [Werner Van Geit]
- Small renaming in test_ssim. [Werner Van Geit]
- Update README about how to recreate neurodamus test sims. [Werner Van
Geit]
- Remove soma2h5 script. [Werner Van Geit]
- Add mvr test, also rerun all neurodamus test sims. [Werner Van Geit]
- Refactor code to generate test sims using neurodamus. [Werner Van
Geit]
- Reran all neurodamus simulations, removed all soma.h5 files. [Werner
Van Geit]
- Remove all CMakeLists.txt. [Werner Van Geit]
- Changed doc upload string, add py3 tox target. [Werner Van Geit]
- Added test for threshold current in proj64, still disabled for now.
[Werner Van Geit]
- Let tox pass https_proxy variable. [Werner Van Geit]
- Add git proxy to .jenkins.sh. [Werner Van Geit]
- Recreate tox env in jenkins. [Werner Van Geit]
- Use github neuron instead of 'official' release for testing. [Werner
Van Geit]
- Fix importer warning message. [Werner Van Geit]
- Reenable some complicated gpfs tests. [Werner Van Geit]
- Remove the 'recreate' from tox. [Werner Van Geit]
- Raise exception in connection when pre_spiketrain has negative time.
[Werner Van Geit]
- Add mode for older cell templates. [Werner Van Geit]
- Enable proj64 test. [Werner Van Geit]
- Remove png-files delete from Makefile. [Werner Van Geit]
- Include hour:minutes in build time of sphinx doc. [Werner Van Geit]
- Fixing back-and-forth bluepy api changes. [Werner Van Geit]
- Fix destructor of ssim in case 'cells' doesn't exist. [Werner Van
Geit]
- Changed permission of .jenkins.sh. [Werner Van Geit]
- Add jenkins shell script. [Werner Van Geit]
- Incorporate fixes for bugs in bluepy.v2. [Werner Van Geit]
- Remove code that removes all old docs. [Werner Van Geit]
- Remove old docs. [Werner Van Geit]
- Fix version on doc server. [Werner Van Geit]
- Small fixes in doc_upload. [Werner Van Geit]
- Store all major.minor versions on doc server. [Werner Van Geit]
- Prevent uploading same doc dir twice. [Werner Van Geit]
- Fix doc metadata fields. [Werner Van Geit]
- Fix order in tox.ini again. [Werner Van Geit]
- Using config to register email again. [Werner Van Geit]
- Add bbprelman email address to commit. [Werner Van Geit]
- Print git log during doc upload. [Werner Van Geit]
- Print git log in upload_doc. [Werner Van Geit]
- Cleanup upload_docs. [Werner Van Geit]
- Clean old doc from jekyll before uploading new. [Werner Van Geit]
- Fix devpi in tox. [Werner Van Geit]
- Switch to zip for devpi. [Werner Van Geit]
- More fixes in jekyll template. [Werner Van Geit]
- Fix jekyll template. [Werner Van Geit]
- Python to other file for upload2repo. [Werner Van Geit]
- Whitelisting upload2repo. [Werner Van Geit]
- Add bbprelman email address to upload doc script. [Werner Van Geit]
- Call python to run upload doc script. [Werner Van Geit]
- Remove -Q from sphinx build. [Werner Van Geit]
- Made doc upload more verbose. [Werner Van Geit]
- Change order of test/doc in tox. [Werner Van Geit]
- Add push master to doc upload. [Werner Van Geit]
- Added doc upload target. [Werner Van Geit]
- Upload to dev devpi instead of release. [Werner Van Geit]
- Add test-gpfs target. [Werner Van Geit]
- Update setup.py metadata. [Werner Van Geit]
- Make HOC_LIBRARY_PATH not found an exception. [Werner Van Geit]
- Remove dist dir before building sdist. [Werner Van Geit]
- Test for HOC_LIBRARY_PATH in importer. [Werner Van Geit]
- Add devpi target, started doc target. [Werner Van Geit]
- Add manifest file. [Werner Van Geit]
- Added versioneer versions. [Werner Van Geit]
- Fix yet another typo in package.json. [Liesbeth Vanherpe]
- Fix another typo in package.json. [Liesbeth Vanherpe]
- Fix typo in package.json. [Liesbeth Vanherpe]
- Fix package.json: switched fields. [Liesbeth Vanherpe]

----------------
- Disable wget output when installing neuron, writing to log file.
[Werner Van Geit]
- Use bluepy spikereport to parse out.dat. [Werner Van Geit]
- Reenable wget output in install neuron. [Werner Van Geit]
- Call tox with -v in Makefile. [Werner Van Geit]
- Fix test target makefile. [Werner Van Geit]
- Merge branch 'remove_cmake' of ssh://bbpcode.epfl.ch/sim/BGLibPy into
remove_cmake. [Werner Van Geit]
- Bump version. [Werner Van Geit]
- First working version with new bluepy. [Werner Van Geit]
- Merge branch 'master' into remove_cmake. [Werner Van Geit]
- Updated package.json: needs patch version filled in. [Liesbeth
Vanherpe]
- Updated package.json. [Liesbeth Vanherpe]
- Added metadata (package.json) for documentation purposes. [Liesbeth
Vanherpe]
- Fix setup.py.in. [Liesbeth Vanherpe]
- Switch Documentation dir to jekylltest. [Werner Van Geit]
- Fixing doc_upload. [Werner Van Geit]
- Updated metadata for documentation purposes. [Liesbeth Vanherpe]
- Make long name in test a bit longer. [Werner Van Geit]
- Add test template for long name test. [Werner Van Geit]
- Short template name if too long. [Werner Van Geit]
- Ramove cmake installer, switch to pip. [Werner Van Geit]
- Showing bluepy version in exception added in last commit. [Werner Van
Geit]
- Merge branch 'master' of ssh://bbpcode.epfl.ch/sim/BGLibPy. [Werner
Van Geit]
- Add exception for ttx to make_passive. [Werner Van Geit]
- Add check for version BluePy and message why not to use >=0.10.0.
[Werner Van Geit]
- Removed some useless print statements. [Werner Van Geit]
- Fixing holding_current() in test_tools to accommodate non-backward-
compatible changes in BluePy. [Werner Van Geit]
- Added use_random123_stochkv option to simulator. [Werner Van Geit]
- Fixed create example doc. [Werner Van Geit]
- Reran regression tests after fix in Neurodamus regarding tsyn global
var. [Werner Van Geit]
- Make sure /bgscratch isn't referenced. [Mike Gevaert]

* some of the jenkins tests nodes have issues w/
nfs, so don't let the tests even lookup /bgscratch
* add .gitreview file
- Added BG/Q target in CMake. [Werner Van Geit]
- Fixed issue when user specified synapse_detail=2 and add_minis=False.
[Werner Van Geit]
- One more pylint fix. [Werner Van Geit]
- Pylint fixes. [Werner Van Geit]
- Updating regression tests to work with fix in Neurodamus train() /
Pulse function
https://bbpteam.epfl.ch/project/issues/browse/BBPBGLIB-246. [Werner
Van Geit]
- Only serialize sections when really necessary. [Werner Van Geit]
- Disable bgscratch tests until soma-connection issue is resolved
(import3d changes connect soma at different point to dendrites,
changes results) [Werner Van Geit]
- Updated two cell test sims to reflect import3d change in neurodamus.
[Werner Van Geit]
- Fixed bluepy deprecation warnings. [Werner Van Geit]
- Fixed pep8 warning. [Werner Van Geit]

----------------
- Updated to use the new BlueConfig parsing. [Mike Gevaert]
- Disable warning in dendrogram.py. [Werner Van Geit]
- Added test for existence of neurodamus dirs. [Werner Van Geit]
- Added 'show figure' switch in add_dendrogram. [Werner Van Geit]
- Improved dendrogram plotting. [Werner Van Geit]
- Ignoring two new hdf5 file introduced in Neurodamus. [Werner Van Geit]
- Updated doc to reflect new repo url. [Werner Van Geit]
- Fix an issue with relative linear stimuli. [Werner Van Geit]
- Small commit to test new repo. [Werner Van Geit]
- Added support RelativeLinear BlueConfig stimulus. [Werner Van Geit]
- Fixed pylint warning in cell.py. [Werner Van Geit]
- Unit tests for pulsestim now working All two circuit simulations have
been rerun. [Werner Van Geit]
- Merge branch 'sideloadsyn' of ssh://bbpgit.epfl.ch/sim/BGLibPy into
sideloadsyn. [Werner Van Geit]

Conflicts:
test/test_ssim.py
- Pylint pulse stimp test. [Werner Van Geit]
- Merge branch 'sideloadsyn' of ssh://bbpgit.epfl.ch/sim/BGLibPy into
sideloadsyn. [Werner Van Geit]
- Added simple test for pulse stimulus. [Giuseppe Chindemi]
- Added partial support for Pulse stimulus, missing Offset handling.
[Giuseppe Chindemi]
- Added simple test for pulse stimulus. [Giuseppe Chindemi]
- Added partial support for Pulse stimulus, missing Offset handling.
[Giuseppe Chindemi]
- Pylint pulse stimp test. [Werner Van Geit]
- Added simple test for pulse stimulus. [Giuseppe Chindemi]
- Added partial support for Pulse stimulus, missing Offset handling.
[Giuseppe Chindemi]
- Recreated simulation results regression tests on two cell circuit for
on CSCS viz. [Werner Van Geit]
- Made two_cell circuit tests independent of bgscratch Little bit of
pylinting in test_ssim. [Werner Van Geit]
- Fixed an error in the documentation of intersect_pre_gids. [Werner Van
Geit]
- Disabled pylint message. [Werner Van Geit]
- Added ability to specify cvode minstep and maxstep to simulation.
[Werner Van Geit]
- Fixed pylint warning. [Werner Van Geit]
- Added sentence to forwardskip documentation. [Werner Van Geit]
- Added forward_skip_value to simulation and ssim. [Werner Van Geit]
- Added more verbosity. [Werner Van Geit]
- Raise exception if add_replay is used with synapse_detail < 1. [Werner
Van Geit]
- Added base_noise_seed to ssim constructor. [Werner Van Geit]
- Merge branch 'ttx' [Werner Van Geit]
- Replaced 'pip' with 'python -m pip.__main__' to work around long path
lengths on CSCS viz. [Werner Van Geit]
- Merge branch 'master' into ttx. [Werner Van Geit]
- Added ttx tests to BGLibPy. [Werner Van Geit]
- Replaced 'pip' with 'python -m pip.__main__' to work around long path
lengths on CSCS viz. [Werner Van Geit]
- Added show_progress to ssim.run() [Werner Van Geit]
- Fixed pep8 error. [Werner Van Geit]
- Fixed pep8 error. [Werner Van Geit]
- Fixed pylint warnings. [Werner Van Geit]
- Don't call re_init_rng when cell is made passive. [Werner Van Geit]
- Ignore .coverage. [Werner Van Geit]
- Disabled automatic printing of header when importing BGLibPy Added
function print_header to replace printing of header, can be called by
user Simulation is no longer checking if t < maxtime, this was a bug.
[Werner Van Geit]
- Replaced implementation of add_ramp with that of add_stim_ramp.
[Werner Van Geit]
- Removed dt argument from add_tstim_ramp. [Werner Van Geit]

-----

* Breaking Change: sim.run() no longer takes celsius and v_init
* NeuronGlobals is added to control the global NEURON parameters such as celsius and v_init
* removed use_random123_stochkv param from re_init_rng

------

* add analysis/inject_sequence.py to inject multiple stim to the same cell in isolation
* core.py:: rename attribute 'all' to 'sections'
* have a class TemplateParams to represent all template related values

----------------
- Added add_voltage_recording / get_voltage_recording. [Werner Van Geit]
- Added add_step method to cell that adds a traditional iclamp. [Werner
Van Geit]
- Changed behavior of HOC_LIBRARY_PATH. If environment already has a
HOC_LIBRARY_PATH it will be appended after the BGLibPy
HOC_LIBRARY_PATH. [Werner Van Geit]
- Made method a static function. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Now possible to specify section/segx in add_ramp. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Update cell info_dict to caste some strings to integers. [Werner Van
Geit]
- Remove useless print statement. [Werner Van Geit]
- Removed synutils.inc dependence. [Werner Van Geit]
- Reraise exception if neuron import fails. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Fixed small bug introduced by previous commit. [Werner Van Geit]
- Create python connection objects even if no real connection to
presynaptic cell or replay spiketrain. [Werner Van Geit]
- Now we raise original exception when bluepy import fails. [Werner Van
Geit]
- Fixed apical trunk function, it added apic[0] twice. [Werner Van Geit]
- Disable cvode for holding_current. [Werner Van Geit]
- Added tools.holding_current function. [Werner Van Geit]
- Fixed an issue in grindaway because an integer division instead of a
float division. [Werner Van Geit]
- Applied a fix to euclid_section_distance. [Werner Van Geit]
- Added function to find the euclidian distance between two sections in
a morphology. [Werner Van Geit]
- Fixed small bug in apical trunk calculation function. [Werner Van
Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Added more documentation to ssim. [Werner Van Geit]
- Disabled load_nrnmech test, because its not working yet. [Werner Van
Geit]
- Added ability to enable cvode in ssim Added ability to specify seed in
ssim. [Werner Van Geit]
- Pushing soma when creating cell, adding time recording requires a
section to have been pushed. [Werner Van Geit]
- Moved test python files to binary directory before running tests.
[Werner Van Geit]
- Merge branch 'master' of ssh://bbpgit.epfl.ch/sim/BGLibPy. [Werner Van
Geit]
- Add synapses even when there is no connection block in the BlueConfig
Show syn_type in info_dict of synapse. [Werner Van Geit]
- Added some verbosity. [Werner Van Geit]
- Made ENABLE_PIP=OFF work correctly. [Werner Van Geit]
- Added version to bglibpy python package. [Werner Van Geit]
- Disabled I0012 in pylint. [Werner Van Geit]