Adams model on ketamine

[anandpathak31]

No description provided.

[MasonProtter]

Pluto and Plots shouldn't be in the Neuroblox project.

The way I'd recommend doing this would be to add a Project.toml in the examples folder that has things like Plots and Pluto in it.

[anandpathak31]

@MasonProtter thanks for checking out. Once the code is straightened, I always remove those packages before merging. Its not an oversight I assure.

[MasonProtter]

Sure, but I think it'd actually be helpful to have those tools in a separate project so that users can use them in the examples.

The way this would be done is you'd do something like

cd Neuroblox
julia --project=examples

and then from within julia you'd do

julia> using Pkg; pkg"dev ." # add Neuroblox itself to the current environment

julia> pkg"add Plots Pluto DifferentialEquations Graphs MetaGraphs"

and then whenever you work on code that goes in the examples, you just need to activate the Neuroblox/examples folder instead of the Neuroblox folder itself.

[MasonProtter]

Okay, so it turns out that what I did here with the SDESystems acutally does cause problems, so I'm going to undo that merge. Sorry about that.

[anandpathak31]

Okay, so it turns out that what I did here with the SDESystems acutally does cause problems, so I'm going to undo that merge. Sorry about that.

@MasonProtter Just curious, what was the problem with noise_eqs ?

[anandpathak31]

@harisorgn the utils test is failing. Could not figure out.

[harisorgn]

@harisorgn the utils test is failing. Could not figure out.

You overwrote some lines from master when resolving conflicts. Your inner_namespaced_nameof is the master's namespaced_nameof and in master inner_namespaced_nameof does not exist.

Check here how it is in master

Neuroblox.jl/src/blox/blox_utilities.jl

Lines 75 to 77 in d3708aa

	namespaced_nameof(blox) = namespaced_name(inner_namespaceof(blox), nameof(blox))

And the error comes from using the wrong namespacing function here

Neuroblox.jl/src/blox/blox_utilities.jl

Lines 422 to 429 in d3708aa

	function voltage_timeseries(blox::AbstractNeuronBlox, sol::SciMLBase.AbstractSolution)
	namespaced_name = namespaced_nameof(blox)
	state_name = Symbol(namespaced_name, "₊V")
	s = only(@variables $(state_name)(t))
	return sol[s]
	end

So basically replace your inner_namespaced_nameof with namespaced_nameof having the definition above from master in the first link.

Also please make sure that no other changes were overwritten using diff.

[anandpathak31]

@harisorgn the utils test is failing. Could not figure out.

You overwrote some lines from master when resolving conflicts. Your inner_namespaced_nameof is the master's namespaced_nameof and in master inner_namespaced_nameof does not exist.

Check here how it is in master

Neuroblox.jl/src/blox/blox_utilities.jl

Lines 75 to 77 in d3708aa

	namespaced_nameof(blox) = namespaced_name(inner_namespaceof(blox), nameof(blox))

And the error comes from using the wrong namespacing function here

Neuroblox.jl/src/blox/blox_utilities.jl

Lines 422 to 429 in d3708aa

	function voltage_timeseries(blox::AbstractNeuronBlox, sol::SciMLBase.AbstractSolution)
	namespaced_name = namespaced_nameof(blox)
	state_name = Symbol(namespaced_name, "₊V")
	s = only(@variables $(state_name)(t))
	return sol[s]
	end

So basically replace your inner_namespaced_nameof with namespaced_nameof having the definition above from master in the first link.

Also please make sure that no other changes were overwritten using diff.

That's weird. I always accepted incoming changes, not the current changes during conflict resilution.
I think the safer thing to do now is to ditch this PR, start a new branch and copy my changes into that new branch.
Otherwise there is not other way to ensure that every thing else is same as master.