Bluecellulab

----------------
- Change behavior delayed connection blocks, weight is now a scaler
instead of absolute value. [Werner Van Geit]
- Enforce pyrsistent<0.17.1 for the py27 build. [Anil Tuncel]

pyrsistent requires python>3.5 from that version on
- Fix printv in synapses.py. [Werner Van Geit]
- When get time trace from mainsim, only look at 1 gid to save memory.
[Werner Van Geit]
- Removed all_targets_dict, since it uses too much memory in new
circuits, replaced with direct bluepy call and lru_cache. [Werner Van
Geit]
- Added explicit delete() method to ssim. [Werner Van Geit]
- Added a setting to ignore missing population id in projection blocks.
[Anil Tuncel]

* added docstring for rng_mode in SSim constructor
* added a module for custom exceptions
* rename: ignore_missing_populationid -> ignore_populationid_error
- Added support for MorphologyType field in BlueConfig. [Werner Van
Geit]
- Small fix of typo that shouldn't affect output. [Werner Van Geit]
- Use analytical solution for hill coefficient. [Werner Van Geit]
- Add support for a* targets in connections. [Werner Van Geit]
- Merge "vectorised usage of Bluepy api for get_sonata_mecombo_emodels"
[Werner Van Geit]
- Vectorised usage of Bluepy api for get_sonata_mecombo_emodels. [Anil
Tuncel]

* bc_circuit.cells.get use None to get all cells
* don't use mecombo_emodels dict if node_properties_available
* get_sonata_mecombo_emodels to return 2 dicts for threshold and holding currs
- Merge "use issubset for checking node properties" [Werner Van Geit]
- Use issubset for checking node properties. [Anil Tuncel]
- Made thalamus test trace shorter, removed 1st time point until we
understand change in ND. [Werner Van Geit]
- Merge "added sonata nodes.h5 support" [Werner Van Geit]
- Added sonata nodes.h5 support. [Anil Tuncel]

* updated changelog
* get_sonata_mecombo_emodels to extract nodes.h5 properties
* node_properties_available to check if nodes.h5 can be used
* setup.py to use bluepy[sonata]>=0.14.12
* merged ssim changes on sonata branch
* get_sonata_mecombo_emodels indentation fix after merge
- Added thalamus tests to jenkins plan * change the thalamus test path
to the recently run ND simulation below. /INTERNAL_PATH/pro
j55/tuncel/simulations/release/2020-08-06-v2/bglibpy-thal-test-with-
projections. [Anil Tuncel]
- Use nosepipe to isolate tests. [Werner Van Geit]
- Fix lru_cache in python2. [Werner Van Geit]
- Isolating nose tests. [Werner Van Geit]

----------------
- Fixing sonata properties check. [Werner Van Geit]
- Use bluepy available_properties, no need to check h5 version anymore.
[Werner Van Geit]
- Added reading of inh/exc minis freq from nodes file, use hill
coefficients and cond ratios from nodes file. [Werner Van Geit]
- Merge changes from topic 'remove-unused' [Werner Van Geit]

* changes:
removed unused tests depending on the data that no longer exist
removed unused psp_bglib test directory
- Removed unused tests depending on the data that no longer exist. [Anil
Tuncel]

These tests used to depend on the data stored at /bgscratch
- Removed unused psp_bglib test directory. [Anil Tuncel]

The code here cannot be executed since the directories to the config files no longer exist
- Corrected rst link. [Anil Tuncel]
- Update dependencies: mention rpm and deb packages for python compiled
neurons. [Anil Tuncel]
- BGLibPy tutorial is updated. [Anil Tuncel]

Changelog:
* Tutorial to use an existing BlueConfig file from the examples directory
* Mention of paired simulations via PSP validation
* Code block is added to enable spontMinis and synapses
- Temporary fix for documentation theme failing. [Andrew Hale]
- Removed Python 2.7 usage suggestion. [Anil Tuncel]
- Updated dependencies docs. [Anil Tuncel]
- Removed viz cluster info. [Anil Tuncel]
- Merged .gitignores. [Anil Tuncel]
- Merge changes from topic 'small-fixes' [Werner Van Geit]

* changes:
using not to check if dict is empty
string comparison to literal use ==
compare the string value, not its reference
- Using not to check if dict is empty. [Anil Tuncel]

Before it was compared to an empty list
- String comparison to literal use == [Anil Tuncel]
- Compare the string value, not its reference. [Anil Tuncel]
- Removed empty lines. [Anil Tuncel]
- Removed spontminis_set flag. [Anil Tuncel]
- Removed the default value for SpontMinis. [Anil Tuncel]
- In case of multiple spontminis take the latest. [Tuncel Anil]
- Updated .gitignore. [Tuncel Anil]
- Merge changes from topic 'test_thalamus' [Werner Van Geit]

* changes:
added test for thalamus The simulation contains multiple projections and stimuli
restrict the compilation of neocortexv5 to test&v5 It is not needed to be compiled for the other settings. When thalamus tests are introduced it should not be compiled for those
- Added test for thalamus The simulation contains multiple projections
and stimuli. [Tuncel Anil]
- Restrict the compilation of neocortexv5 to test&v5 It is not needed to
be compiled for the other settings. When thalamus tests are introduced
it should not be compiled for those. [Tuncel Anil]
- Downgrading virtualenv on ubuntu 16.04. [Werner Van Geit]
- Try older nrn commit. [Werner Van Geit]
- Fix git checkout. [Werner Van Geit]
- Trying build with other nrn commit. [Werner Van Geit]
- Cloning neuron deeper. [Werner Van Geit]
- Pull older version of neuron for testing. [Werner Van Geit]
- Removed unnecessary cp operations from install_neurodamus. [Tuncel
Anil]
- BUGFIX: check&remove NRRP using the Enum value Other were getting
removed before in case of multiple projections, since the check was
missing. [Tuncel Anil]
- Fix class and module docs. [Andrew Hale]

Class and module documentation was being generated, however it
was not linked anywhere that was useful on the docs pages.
This commit cleans up some code that was required with older
versions of sphinx.

This commit puts all class/module documentation on the same
page as the class/module itself.
- Fixing v5 tests. [Werner Van Geit]
- Fixing tests. [Werner Van Geit]

----------------
- Fix target_popid in synapse. [Werner Van Geit]
- Changes related to minis with projections. [Werner Van Geit]
- Switch to BBP doc theme. [Werner Van Geit]
- Handle case with no patch version in bglibpy version. [Werner Van
Geit]
- Libsonata is now a dependency. [Werner Van Geit]
- Remove versions.py which is a relic from the past. [Werner Van Geit]
- Surround synapseconf statements by {} [Werner Van Geit]
- Remove unused libs in upload_docs. [Werner Van Geit]

----------------
- Change the synids provided by bluepy so that they match nd. [Werner
Van Geit]
- Merge branch 'master' of ssh://bbpcode.epfl.ch/sim/BGLibPy. [Werner
Van Geit]
- Use new options for uploading docs. [Andrew Hale]

Utilise options from docs-internal-upload to manage
uploading docs (or not) depending on whether they are duplicates.

Requires docs-internal-upload>=0.0.8
- Pass USER env variable to tox envs. [Andrew Hale]
- Use docs-internal-upload for docs release. [Andrew Hale]

Transition the upload of documentation to use the
docs-internal-upload package. This simplifies the logic
in .upload_docs.py and removes any need for interacting
with the docs repo directly.
- Add depth to neurodamus core clone. [Werner Van Geit]
- Remove vangeit from neurodamus download. [Werner Van Geit]
- Finalized move to nd core. [Werner Van Geit]
- Switching to neurodamus core. [Werner Van Geit]
- Improved importer, bglibpy_modlib_path can now be list. [Werner Van
Geit]
- Remove presynaptic location request to bluepy. [Werner Van Geit]
- Merge branch 'master' into add_projections. [Werner Van Geit]
- Extend numpy encoder for json in python3. [Werner Van Geit]
- Lowered precision of some tests because of change in nrnsim repo.
[Werner Van Geit]
- Make sure we have absolute path of doc html dir. [Werner Van Geit]
- Fix for hocobjects not having len() in new nrn release. [Werner Van
Geit]
- Add a projections field to ssim instantantie gid. [Werner Van Geit]
- Temporarily pin version of tox to make tests work. [Werner Van Geit]
- Small text edit. [Werner Van Geit]
- Update package version. [Werner Van Geit]
- Merge branch 'master' of ssh://bbpcode.epfl.ch/sim/BGLibPy. [Werner
Van Geit]
- Fix verbose level from env. [Werner Van Geit]
- Fix syn id iterator in ssim. [Werner Van Geit]
- Add numpy encoder to convert dict to json string. [Werner Van Geit]
- Add default rng mode. [Werner Van Geit]
- Fix issue in previous commit (nrrp check) [Werner Van Geit]
- Add test for non-integer nrrp values. [Werner Van Geit]
- Fix sonata test in ssim. [Werner Van Geit]
- Raise exception when section with particual isec not found. [Werner
Van Geit]
- Add check for sonata connectome, switch nrrp behavior based on it.
[Werner Van Geit]
- Add hack to handle situation where ascii subdir doesnt' exist. [Werner
Van Geit]
- Catch indexerror when no threshold/holding current value found.
[Werner Van Geit]
- Fix python title in doc. [Werner Van Geit]
- Add python 3 version to classifiers in setup.py. [Werner Van Geit]
- Make v5 test py3 compatible. [Werner Van Geit]
- Remove 'vangeit' from neurodamus clone. [Werner Van Geit]
- Make BGLibPy python3 compatible. [Werner Van Geit]

----------------
- Bumping version. [Werner Van Geit]

----------------
- Merge branch 'master' of ssh://bbpcode.epfl.ch/sim/BGLibPy. [Werner
Van Geit]
- Fixed access to proj_nrn.h5 files. [Arseny V. Povolotsky]
- Fixing init of neurodamus in importer after changes in neurodamus
master. [Werner Van Geit]
- Enable verbose tox in jenkins. [Werner Van Geit]
- Remove mpi file from neurodamus. [Werner Van Geit]
- Finalize tests vclamp, add doc. [Werner Van Geit]
- Add new add_voltage_clamp method. [Werner Van Geit]
- Added BGLIBPY_VERBOSE_LEVEL env variable. [Werner Van Geit]
- Fix python3 change in Neuron. [Werner Van Geit]
- Add ttx flag to tools.holding_current() [Werner Van Geit]
- Fix last commit in case CircuitConfig is used instead of BlueConfig.
[Werner Van Geit]
- Set neuron tstop in constructor of ssim because it used in TStim.hoc.
[Werner Van Geit]
- Merge branch 'master' of ssh://bbpcode.epfl.ch/sim/BGLibPy. [Werner
Van Geit]
- Open nrn.h5 in read-only mode. [Arseny V. Povolotsky]
- Force downgrade sphinx to avoid bug in latest sphinx release. [Werner
Van Geit]
- Temporariy disable 1 test because circuit disappeared. [Werner Van
Geit]
- Small fix in .jenkins.sh. [Werner Van Geit]
- Upload docs only on BB5. [Werner Van Geit]
- Run gpfs tests on BB5 in jenkins. [Werner Van Geit]
- Remove pybinreports from setup.py requirements. [Werner Van Geit]
- Read the nrn.h5 version from bglibpy instead of counting on bluepy.
[Werner Van Geit]
- Introduce get_time_trace and get_voltage_trace that return pos times.
[Werner Van Geit]
- Fixing case where hypamp is empty in tsv file, for hippocampus.
[Werner Van Geit]
- Random123 fixes. [Werner Van Geit]
- Merge branch 'master' into add_random123. [Werner Van Geit]
- Ignore error when we can't upload do release devpi. [Werner Van Geit]
- Add verbose message to add_replay_hypamp. [Werner Van Geit]
- Unpin Brain version, a bug has been fixed. [Werner Van Geit]
- Also upload package to devpi release. [Werner Van Geit]
- Add pybinreports to bbp extra. [Werner Van Geit]
- Upload docs and devpi from cscs viz instead of ubuntu. [Werner Van
Geit]
- Fall back to version 2.1.0 of Brain because of a bug in Brain. [Werner
Van Geit]
- Import RNGSettings.hoc, also remove version number from brain
dependency. [Werner Van Geit]
- Add bbp extra to tox.ini. [Werner Van Geit]
- Moved brain dependency to [bbp] extra. [Werner Van Geit]
- More small doc fixes. [Werner Van Geit]
- More doc fixes. [Werner Van Geit]
- Fixes in documentation. [Werner Van Geit]
- Add seeds to synapses, minis, etc. [Werner Van Geit]
- Adding rngsettings argument to synapse. [Werner Van Geit]
- Added new rngsettings class. [Werner Van Geit]
- Pin version of Brain to avoid bug in devpi package. [Werner Van Geit]
- Fix warning about pandas indexing. [Werner Van Geit]
- Fixing synapse ids when intersect_pre_gids is used. [Werner Van Geit]
- Make sure add_synapses is set to true if pre_spike_trains are
specified. [Werner Van Geit]
- Add a pre_spike_trains and projection option to instantiate_gids.
[Werner Van Geit]
- Update doc to solve nix trouble. [Werner Van Geit]
- Implement change in neurodamus that puts synapses at 0.99.. and
0.00..1. [Werner Van Geit]
- Add 1 more spot check to make sure nrrp value I get is correct.
[Werner Van Geit]
- Implementing getting threshold/holding from tsv and adding v6 test.
[Werner Van Geit]
- Add default implementation of enable/disable ttx. [Werner Van Geit]
- First version that runs (unvalidated) with Nrrp read from nrn.h5.
[Werner Van Geit]
- Fix for MVR nrrp. [Werner Van Geit]
- Add functionality to tools.holding_current to manage v6 templates.
[Werner Van Geit]
- Change how templates are loaded, in ssim, assume hoc has correct
morph. [Werner Van Geit]
- Fix tests that use circuits on gpfs. [Werner Van Geit]