cleanup PR for Neuroblox 0.3 #324
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
I just noticed that the next version will be Neuroblox 0.3 |
* Deleted `jansen_rit_component_tests.jl`. * Renamed `jansen_rit_component_tests_new_timing.jl` to `jansen_rit_component_tests.jl` (removing old examples in favor of updated blocks with ms timing defaults). * Deleted `temp_test.jl` * Deleted `jansen_rit_hemodynamic_tests.jl` * Deleted `test/old_component_tests/*`. These were all old neural mass model tests from pre-`BloxConnector` days that I kept around just in case. Seem redundant now. * @hstrey I think `test/ode_from_graph.jl` can be deleted - looks like old Jansen Rit code that we've incorporated elsewhere or removed entirely.
* Documented new blox * Deleted old blox
Fix last commit because I deleted the wrong one @@
* Add comments to new blox * Remove old blox @hstrey I kept the defaults for all these parameters except for omega which needed to be updated to ms. Any citation you'd like for this parameter set? It's just a harmonic oscillator so I'm assuming it's general enough to not need one unless we really want to highlight a particular paper.
* Deleted old blox * Updated new blox * Fixed docstring issue from other blocks (I think - we'll see after the next tests run)
Also removed a couple other old blocks. One more commit and I should be done with this
The following tests have been commented out because they used the deprecated (now removed) Jansen Rit blox: * Canonical & Jansen-Rit Network * OUBlox & Jansen-Rit network * Time-series output @hstrey do we need these? If so then I'll modify to the new blocks - if not we can delete. They're just commented out for now.
Cleaned up the comments for WilsonCowan and LarterBreakspear blocks.
Commented out "ODE from Graph and simulate" from `graph_to_dataframe.jl` because these are also built using old blocks.
…ogress_scope into paramscoping. This works fine for the current code but it will not work if models have many layers of hierarchies. However, if I understand it correctly with the new system from graph structure we won't run into that issue. This new structure also allowed us to get rid of LinHemo which had required the separation into progress_scope and compileparameterlist in the earlier version.
Removing old blocks
* Remove old examples * Add new examples of Jansen-Rit with delays and Larter-Breakspear with DTI-derived connections * Add additional function for Balloon model convolution after simulation * Test documentation formatting
…a generic solution rather than having a special JR block to deal with the sigmoidal connection function
…er than ODEfromGraph
…into cleanup04
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
@anandpathak31 @david-hofmann @harisorgn @agchesebro
Please add all your cleanup to this PR. We should have this done by early next week.