updated CMC code #474
updated CMC code #474
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…to be able to set tunable flag for individual parameters of the array. Added untune! utility function to set tunable flag to false on list elements.
…ctors and set standard connection weight to non-tunable
* add tests for AdjacencyMatrix * fix import and typo * fix names test
* more terms from connections to neurons * accumulate both states and parameters (values) for spike affects * match state with the correct parameter value in spike affect * allow for duplicate parameters to be passed in functional affect using Pairs * update comment & fix typo * rename variable for clarity * synchronize GraphDynamicsInterop with changes to the LIFExci / LIFInh neurons --------- Co-authored-by: Mason Protter <[email protected]>
* Add citation links * Add alternative method for creating edges from adjacency matrix * New PING network illustration Thanks to Annabel for creating a much cleaner version! * Final tweaks to address direct comments * Updating documentation for PING blocks Missing docstrings for API creation and Scott's right we should have that for tutorials * Adding bullet points to the intro * Suggestions are pretty much covered now Still missing API links though - will discuss further before merging. * Just seeing if this compiles the docs * and does this compile * try adding a note * add offset to last line --------- Co-authored-by: haris organtzidis <[email protected]>
* update Getting Started text * change title and fix link in parkinsons * add seed and update plot in resting_state * remove outdated phrase * Fix the Parkinson's circuit to match Liu et al. 2020 Looks like this replicates their dynamics now. Includes all the weights from their paper and splits the striatum into the three groups instead of wherever we got that one striatum block from. * Prettify the introduction * Fix Jansen-Rit docstring to show defaults * Add dispatch of powerspectrum for neural masses * Overhaul of Parkinson's JR tutorial This has some pretty significant changes that should address nearly all the points --------- Co-authored-by: agchesebro <[email protected]>
* fix mistake in LIFExciNeuron connections * increase test duration to catch the bug
…mics (#484) * remove soem junk * more junk * switch to using `ForeachConnectedSubsystem` instead of composite events * make connections subtypes of ConnectionRule * allow skipping building `ODESystem` * bump GraphDynamics compat * remove more unused comments
* move `t_warmup` to kwargs * more RL save test * add `run_warmup` function * update `run_trial!` function * add getter functions for states and times when actions and learning rules are evaluated * update `run_experiment!` dispatches * move RL tests in a single file * remove `save_idxs` kwarg * import `CSV.write` for RL save
* import Symbolics.variable
* add concrete types to learning rule fields
* add function to narrow Dict type
* narrow `learning_rules` type
* use a `Union{Nothing, Num}` instead of `Num` so that `maybe_set_state_*` works
* Add illustration to Parkinson's tutorial * rename `STH -> STN` for consistency with other tutorials * fix file path and rename file for consistency --------- Co-authored-by: Haris Orgn <[email protected]>
* initial DBS protocol for getting ERNAs * unify DBS and DBSProtocol into single type * add DBS protocol example * add docstrings for `DBS` and `protocol_dbs` constructors * add a tunable option to `paramscoping` function * set DBS and protocol_dbs parameters as not tunable * change constructor name to ProtocolDBS * change input frequency units to Hz * add tests for ProtocolDBS * adjust `frequency` in `compute_transition_times` --------- Co-authored-by: haris organtzidis <[email protected]>
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@MasonProtter @harisorgn Can you help me understand why the tests were cancelled here? Also why is the GraphDynamics3 failing? It doesn't fail on my local machine. Does this have to do with me adding a Project.toml to the test folder? Did that change the environment in which tests are run? (I remember you guys mentioned to add a relative path to Neuroblox, I dev'ed it to run it on my machine. Is that what's missing?) Thanks!! |
You need to
If one CI run fails then the rest are cancelled. Documentation is independent from the rest though.
Yes, basically since you added Also please delete the packages you ahve added in the main |
This is a bit odd though since in the documentation it says "In Julia 1.2 and later test dependencies can be declared in test/Project.toml. When running tests, Pkg will automatically merge this and the package Projects to create the test environment." I also noted that Okay, maybe better to move this to a fresh PR, this is getting more complicated than I had thought. |
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I'll try one thing and if it fails we can revert to the |
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We should probably remove Test from the main Project.toml too, I'm not sure why it's there. |
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oops, good catch |
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Ok test environment is sorted. I have not cleaned up |
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great, thanks! But can we not also remove |
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hmm, okay, doesn't seem to work remotely though... |
* switched from symbolic arrays to list of symbolic parameters. Needed to be able to set tunable flag for individual parameters of the array. Added untune! utility function to set tunable flag to false on list elements. * added new approach to set tunable flag for the connection matrix also to the tutorial * use generate_weight_param also in StimulusBlox and ObserverBlox connectors and set standard connection weight to non-tunable * fixed and cleaned code * minor changes * update MTK compat * added Project.toml to test * fixed MTK compat once more * added more packages to test environment needed in GraphDynamics tests * remove test deps and unnecessary deps * add Test to tect project * remove Test dep from main Project * add missing test deps * add Statistics dep * removed [extras] from Project.toml * added [extras] again. --------- Co-authored-by: haris organtzidis <[email protected]>
Canonical micro-circuit code updated. Use add_edge! with blox rather than indices, makes code more readable. Also updated blox connectors to use the helper function
generate_weight_param.