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Merge dev into master - #236

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rgerkin wants to merge 419 commits into

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Commits on Aug 29, 2018
- merge from remote
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- sync to shared folder
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Commits on Aug 30, 2018
- folding in BPO
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- folding bpo into NU
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- folding bpo into NU
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Commits on Aug 31, 2018
- folded in bpo
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Commits on Sep 6, 2018
- refactor run_ref_range.py
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- temporary refactor
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- Clear descriptions of all Druckmann tests
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Commits on Sep 7, 2018
- development changes
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Commits on Sep 13, 2018
- Static model usable by tests
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  d05b035
- Bug fixes related to quantities handling; changes to verbosity
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Commits on Sep 14, 2018
- Merge pull request #2 from scidash/rj-fixes
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Commits on Sep 15, 2018
- Update optimization_management.py
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- from linux
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- merge head conclusion
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Commits on Sep 18, 2018
- changes that went missing
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- changes that went missing
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- default test params
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Commits on Sep 19, 2018
- Added fetching of waveforms from NeuroML-DB.org
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- 5 more Druckmann tests implemented
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- AIBS API change fix
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Commits on Sep 20, 2018
- Update the AIBS skd requirement
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- Backwards compatibility with previous AIBS sdk versions
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- More druckmann tests
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- Restored requirement for prev AIBS sdk
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Commits on Sep 21, 2018
- Support for pulling waveforms from nmldb based on current amplitude
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- One more druckmann test
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Commits on Sep 22, 2018
- Add files via upload
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- Update rawpy.py
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Commits on Sep 25, 2018
- evidence of faster backend
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- evidence of faster backend
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- evidence of faster backend
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- closer to correct NEURON models due to more accurate unit translation
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Commits on Sep 26, 2018
Commits on Sep 28, 2018
- round trip testing
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- outside optimization
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Commits on Oct 1, 2018
- actual NEURON capacitance sensing
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- dev changes
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- backend updates for real (as opposed to perceived NEURON capacitance update)
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Commits on Oct 3, 2018
- committing changes
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- dev changes
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- dev changes
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- Fixes
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- Merge branch 'dev' of http://github.com/russelljjarvis/neuronunit into dev
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- Optimization fixes
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- dev changes
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- opt manager
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- merged without notebook
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Commits on Oct 22, 2018
- force MU to be divisible by 4
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Commits on Nov 7, 2018
- cleansing of bad rheobase genes, cripled exhaustive search, visualisation improvements
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Commits on Nov 9, 2018
- 30/31 druckmann tests
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Commits on Nov 13, 2018
- 31/31 druckmann tests. 14/31 verified with one model
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Commits on Nov 14, 2018
- 27/31 druckmann tests verified with one model
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- All druckmann tests validated with one model
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- Druckmann 2013 tests part of unit_test suite
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  e81e794
- Druckmann tests python 3 unit test fixes
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- python 3 dictionary key parsing issue fix
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Commits on Nov 20, 2018
- rheobase search indipendent of testing, neuronunit tests, indipendent of each other
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- Debugged Druckmann tests using all NML-DB models
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- Druckmann tests python 3 bug fix
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Commits on Nov 25, 2018
- fixed broken rheobase algorithm
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Commits on Nov 26, 2018
- code refactor and cleanup
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- stuff
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Commits on Nov 27, 2018
- rheobase and passive test patches, to deal with inf, -inf and nan
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Commits on Dec 5, 2018
- Added params validation for the VmTest class
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Commits on Dec 9, 2018
- dev changes
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  4aa4e8f
- demonstration of rheobase speed up
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  46b6fc1
- demonstration of rheobase speed up
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  4494cb9
- parallel evaluation of DM tests gives ~2 speed up
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Commits on Dec 14, 2018
- two new backends
  russelljjarvis
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  ef96af9
- added bind score and judge to some appropriate DM tests
  russelljjarvis
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  b48e900
- 2 new backends, 2 DM tests
  russelljjarvis
  committed
  cb1236d
- Expanded exception for pip installation
  rgerkin
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  5a2e66c
- Update requirements.txt
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- Update requirements.txt
  rgerkin
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- Update requirements.txt
  rgerkin
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- Update setup.py
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- Update requirements.txt
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- Update setup.py
  rgerkin
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  cc3ee3e
- almost working dynamic bind
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- almost working dynamic bind
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Commits on Dec 17, 2018
- setup.py fixes
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- Fixes
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  68a7346
- Update pip
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  82f2735
- Try with no requirements file
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  4aae190
- Simplified
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- expanded available backends, improved test robustness etc
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- justas file
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Commits on Jan 7, 2019
- start of begginer friendly
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- Add files via upload
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  24e8b42
- Update begginer_friendly_intro.ipynb
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Commits on Jan 9, 2019
- to facilitate merge
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- commit for merge
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Commits on Jan 11, 2019
- before remerge
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Commits on Jan 12, 2019
- script to run on cluster
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- script to run on cluster
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Commits on Jan 13, 2019
- Added git attributes file to handle line endings
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- Merge pull request #195 from scidash/dev-install-fix
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  b3fe022
- seed population best found from first pass of coarse grained grid search
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- seed population best found from first pass of coarse grained grid search
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- seed population best found from first pass of coarse grained grid search
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- seed population best found from first pass of coarse grained grid search
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- before merge
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- before merge
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Commits on Jan 15, 2019
- add a whole heap of backends, including HH, and general pyNN
  russelljjarvis
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  2114c37
- fixes to snippet extraction
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  03036f5
- added many backends and examples directory
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  6738221
- druckmann differences
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- refactor
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Commits on Jan 16, 2019
- Merged
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- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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- cluster script
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Commits on Jan 18, 2019
- dev changes
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  142e51a
- fixed begginer friendly intro
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  7b3e883
- fixed begginer friendly intro
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  90ac30d
- Merge branch 'unmerged_dev' of https://github.com/russelljjarvis/neuronunit into dev
  russelljjarvis
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  fc3ccb4
- fixed begginer friendly intro
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  370f1f9
- fixed begginer friendly intro
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  4fb3f40
- fixed begginer friendly intro
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- fixed begginer friendly intro
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- dev changes
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Commits on Jan 19, 2019
- documentation enrichment
  russelljjarvis
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  c111d60
- Bug fixes to make all unit tests pass locally
  rgerkin
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  5df8fd2
- Merge branch 'dev' of http://github.com/russelljjarvis/neuronunit into dev2
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- Bug fixes
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Commits on Jan 22, 2019
- Update requirements.txt
  rgerkin
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  630451d
- Catch import error for pyNN.neuron
  rgerkin
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  9f9c513
- Update bindings.py
  rgerkin
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  813246c
- Fixes for Python 2
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  f54cb53
- Added __future__ imports for Python 2
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  88284c0
- Used platform information to conditionally ignore NEURON errors
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  d65a0f0
- added back in glif support for optimization
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- latest change for olf_mit
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- update pertaining to GH issue olf_mit
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- glif debug progress
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- Use _backend_run instead of _local_run
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- Python 2 fixes
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- Post-merge fixes
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- Update .travis.yml
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Commits on Jan 23, 2019
- glif backend seems to be working
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- dev changes
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- dev changes
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Commits on Jan 25, 2019
- Merge branch 'unmerged_dev' of http://github.com/russelljjarvis/neuronunit into russell_dev
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Commits on Jan 26, 2019
- Many updates/fixes to the rheobase tests
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  85b706c
- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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- Update cellmodelp.py
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Commits on Jan 30, 2019
- NEURONBackend API fix
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Commits on Jan 31, 2019
- All unit tests pass with NEURON backend
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Commits on Feb 12, 2019
- Fixes for pyNN support
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  c2ba029
- Added example
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Commits on Feb 14, 2019
- Hotfix to pip install dash branch
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- Update requirements.txt
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Commits on Feb 18, 2019
- Delete bash_process.sh
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  authored
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Commits on Feb 20, 2019
- Expanded test for parameter validation; gave example for getting units
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  committed
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Commits on Mar 1, 2019
- Update druckmann2013.py
  russelljjarvis
  authored
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Commits on Mar 8, 2019
- Morphology tests using hoc2swc and pyLMeasure
  JustasB
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  3b4bee6
- Revert "Morphology tests using hoc2swc and pyLMeasure"
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  50be27b
- Merge pull request #1 from scidash/dev
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- Morphology tests using hoc2swc and pyLMeasure
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- Cleanup
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- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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- Morphology unit tests, documentation, and pyLM install as extra
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Commits on Mar 10, 2019
- Fixed RestingPotentialTest
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  dfdaa1a
- Delete check_speed.py
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Commits on Mar 12, 2019
- Merge pull request #202 from JustasB/dev
  rgerkin
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Commits on Mar 18, 2019
- Added observation schema names
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- Style compliance
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Commits on Mar 29, 2019
- Morphology test update
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  9492dc4
- Merge remote-tracking branch 'scidash/dev' into dev
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- Removed fragmentation tests
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Commits on Apr 1, 2019
- Merge pull request #204 from JustasB/dev
  rgerkin
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Commits on Apr 10, 2019
- Update optimization_management.py
  russelljjarvis
  authored
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Commits on Apr 11, 2019
- Merge branch 'dev' into dash
  rgerkin
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  051d4cc
- Merge pull request #210 from scidash/dash
  rgerkin
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  0e63889
- Merge branch 'dash' of http://github.com/scidash/neuronunit into dash
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  committed
  3b8927e
- Demonstration of cache and hash; make model state match just-before-run state
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Commits on Apr 12, 2019
- Merge branch 'dash' into dev
  rgerkin
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  2fac34a
- Merge pull request #2 from scidash/dev
  JustasB
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- Unit test fix test
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  dce017e
- Druckmann test fix
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  2a79b4c
- Merge pull request #211 from JustasB/dev
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Commits on Apr 13, 2019
- Delete optimization_management.py.orig
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- Simple instance less capability cheks
  
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Commits on Apr 16, 2019
- Separated out `condition_model` from `get_prediction`.
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Commits on Apr 17, 2019
- Delete exhaustive_search.py
  russelljjarvis
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- Delete progress_report_10thJuly-Copy1.ipynb
  russelljjarvis
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  31771d1
- Update optimization_management.py
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  25ffe4f
- Update optimization_management.py
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  27945e9
- Update optimization_management.py
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Commits on Apr 18, 2019
- New model zoo notebook showing different models taking different tests
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  4d3b6ba
- Better code reuse, especially for channel models
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- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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- Added back morphology file for unit tests
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Commits on Apr 19, 2019
- Merge pull request #1 from scidash/dev
  NeZanyat
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- Merge branch 'dev' into dash
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Commits on Apr 20, 2019
- Merge pull request #212 from NeZanyat/dash
  rgerkin
  authored
  b668559
- Merge pull request #3 from scidash/dev
  JustasB
  authored
  166f829
- Update base.py
  JustasB
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  fe1ef80
- Update base.py
  JustasB
  authored
  2690759
- Fixes urljoin import in Python 2
  JustasB
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  7322c9a
- Update base.py
  JustasB
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  06fad1d
- Update base.py
  JustasB
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  16e15ef
- Update base.py
  JustasB
  authored
  9ab7367
- Fewer side-effect test for NEURON package
  JustasB
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Commits on Apr 21, 2019
- hide neuron output during support test
  JustasB
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- Merge pull request #217 from JustasB/dev
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Commits on Apr 24, 2019
- Added observation schema to IVCurveTest
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  510e18d
- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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Commits on May 3, 2019
- Fixed bbp module and unit test
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  08fb5b4
- Added Geppetto backend
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  3100d8b
- Refactored some tests to use ProtocolsToFeaturesTest
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  e0242cc
- Change Druckmann unit test tolerance
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  cc9f712
- Added Geppetto Backend example
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  3a53be7
- Update gitignore
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Commits on May 8, 2019
- Added better support for default test parameters
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- Delete index.html
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- New examples
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  3542c5b
- Changed parameter usage in FI tests
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Commits on May 20, 2019
- Style cleanup
  rgerkin
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  bb0e05d
- Added default parameters and param schemas to more tests
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  339578a
- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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Commits on May 31, 2019
- Add files via upload
  rgerkin
  authored
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Commits on Jun 17, 2019
- Refactored channel tests for ProtocolToFeaturesTest
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  4bc226c
- Refactored channel analysis capabilities
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  93f7ec2
- Fixed channel tests to validate and use parameters
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Commits on Jun 20, 2019
- Added default ChannelModel backend
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Commits on Feb 13, 2020
- Backends cleanuo
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  d03d942
- Improved LEMS files parsing
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- Added file download to NeuroML-DB module
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  438bf88
- Added pylmeasure to requirements
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Commits on Feb 16, 2020
- Drop support for Python 2.7
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Commits on Jul 27, 2020
- Pre-create 'results' directory for some LEMS simulations
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  9cb9435
- Added reduced model simulation tutorial
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- Bug fix
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Commits on Aug 4, 2020
- Added function to return state variables
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Commits on Aug 14, 2020
- Added docstrings to get_state_variables function
  kedoxey
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  62501db
- Merge pull request #248 from kedoxey/dev
  rgerkin
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Commits on Sep 1, 2020
- Update Unit Test Cases and Other Improvements (#249)
  ChihweiLHBird
  authored
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Commits on Nov 8, 2020
- Removing duplicate jNeuroMLBackend import (#251)
  mwatts15
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Commits on Dec 19, 2020
- Added RandomVmModel
  rgerkin
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  20c78f8
- Added StaticBackend
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  1f7c038
- fixup! Added StaticBackend
  rgerkin
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  972490b
- Merge branch 'dev' of http://github.com/scidash/neuronunit into dev
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  96ac2be
- Fix mistake in Izhikevich equation markdown
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  701c33a
Commits on Mar 10, 2021
- optimization -> dev (#255) (#256)
  
  authored
  15ab9e5
Commits on Apr 22, 2021
- Fix merge conflicts in models.backends
  rgerkin
  authored
  835235e

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