BluePyOpt

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Arbor cable cell exporter

10

I'm working on an [Arbor cable cell](https://docs.arbor-sim.org/en/stable/python/cable_cell.html) exporter for BluePyOpt optimized cell models (related to https://github.com/arbor-sim/arbor/issues/1839) and looking for feedback here. I've added a `create_acc` module analogous to `create_hoc` in...

lukasgd

Implement LFPy backend

19

### LFPy-related changes - Added LFPy as a backend for simulation - [LFPyCellModel](https://github.com/alejoe91/BluePyOpt/blob/merging/bluepyopt/ephys/models.py#L484) - [LFPySimulator](https://github.com/alejoe91/BluePyOpt/blob/merging/bluepyopt/ephys/simulators.py#L178) - [LFPySquarePulse](https://github.com/alejoe91/BluePyOpt/blob/merging/bluepyopt/ephys/stimuli.py#L341) - [TimeLFPResponse](https://github.com/alejoe91/BluePyOpt/blob/merging/bluepyopt/ephys/responses.py#L89) - Added extracellular efeatures class [extraFELFeature](https://github.com/alejoe91/BluePyOpt/blob/merging/bluepyopt/ephys/efeatures.py#L248) that supports computing features from...

alejoe91

Neuronunit reduced cells

6

Hi @wvangeit and @rgerkin, This represents the long proposed pull request that reconciles BluePyOpt and Neuronunit optimization. In the examples directory, there is a neuronunit sub-directory with three notebooks demonstrating...

russelljjarvis

- Add a check that raises an exception if the voltage gets unrealistic - Replace h.run by hfadvance in the NrnSimulator

DrTaDa

increase max_ngen in CMA

2

arnaudon

fix python crash with NEURON8.1.0

7

this is fix related to CELLS-42

arnaudon

Increase coverage

3

Now that the coverage reporting is fixed we can see that the coverage has regressed over time. @AurelienJaquier @DrTaDa @anilbey, can you help getting the coverage closer to 100% again?...

wvangeit

error when running simplecell code

8

When I ran the code simplecell as is, I encountered errors as follows. Please help. default_params = {'gnabar_hh': 0.1, 'gkbar_hh': 0.03} responses = twostep_protocol.run(cell_model=simple_cell, param_values=default_params, sim=nrn) Errors: RemoteTraceback Traceback (most...

gincru

This commit: https://github.com/BlueBrain/BluePyOpt/commit/71a94b0ffa853133b688bcf4ef1755c9de415426 disables the comparison of the values in the dict returned by the l5pc evaluator. This was also the case when using nosetests. It seems these values are...

wvangeit

Add a way to record features extracted during optimisations

6

At the moment the scores of the parameters are returned to the master process. We should also have a way to e.g. get the raw efeature values out. This would...

wvangeit