Merge pull request #167 from ComputationalPsychiatry/dev

0.7.1

Author: PTWaade

.github/workflows/CompatHelper.yml

@@ -41,10 +41,4 @@ jobs:
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          # This repo uses Documenter, so we can reuse our [Documenter SSH key](https://documenter.juliadocs.org/stable/man/hosting/walkthrough/).
-          # If we didn't have one of those setup, we could configure a dedicated ssh deploy key `COMPATHELPER_PRIV` following https://juliaregistries.github.io/CompatHelper.jl/dev/#Creating-SSH-Key.
-          # Either way, we need an SSH key if we want the PRs that CompatHelper creates to be able to trigger CI workflows themselves.
-          # That is because GITHUB_TOKEN's can't trigger other workflows (see https://docs.github.com/en/actions/security-for-github-actions/security-guides/automatic-token-authentication#using-the-github_token-in-a-workflow).
-          # Check if you have a deploy key setup using these docs: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/reviewing-your-deploy-keys.
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -1,7 +1,7 @@
 name = "ActionModels"
 uuid = "320cf53b-cc3b-4b34-9a10-0ecb113566a3"
 authors = ["Peter Thestrup Waade [email protected]", "Luke Ring [email protected]", "Malte Lau Møller", "Christoph Mathys [email protected]"]
-version = "0.7.0"
+version = "0.7.1"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"

README.md

@@ -2,7 +2,7 @@
 [![Stable](https://img.shields.io/badge/docs-dev-blue.svg)](https://ComputationalPsychiatry.github.io/ActionModels.jl/dev/)
 [![Build Status](https://github.com/ComputationalPsychiatry/ActionModels.jl/actions/workflows/CI_full.yml/badge.svg?branch=main)](https://github.com/ComputationalPsychiatry/ActionModels.jl/actions/workflows/CI_full.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/ComputationalPsychiatry/ActionModels.jl/branch/main/graph/badge.svg?token=NVFiiPydFA)](https://codecov.io/gh/ComputationalPsychiatry/ActionModels.jl)
-[![License: GNU](https://img.shields.io/badge/License-GNU-yellow)](<https://www.gnu.org/licenses/>)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 # Welcome to ActionModels!

docs/julia_files/B_user_guide/7_using_submodels.jl

@@ -38,7 +38,7 @@ end
 # The attributes object, or whichvever subpart of it that will contain the states and parameters, needs to be mutable, as it will be updated during the model fitting process.
 # Additionally, in order to function with Turing, the attributes struct needs to have type parameters that are subtypes of Real for continuous (Float64) and discrete (Int64) parameters and states.
 # This is because some AD backends like ForwardDiff and ReverseDiff need to switch between different subtypes of Real to calculate gradients.
-# Notably, users may in some situations want to use the same type for the attributes object as for the submodel object above. This is possible.
+# Notably, users may in some situations want to use the same type for the attributes object as for the submodel object above. This is possible, since `AbstractSubmodelAttributes` is a subtype of `AbstractSubmodel`.
 
 Base.@kwdef mutable struct RescorlaWagnerAttributes{T<:Real} <:
                            ActionModels.AbstractSubmodelAttributes

docs/julia_files/README.jl

@@ -2,7 +2,7 @@
 # [![Stable](https://img.shields.io/badge/docs-dev-blue.svg)](https://ComputationalPsychiatry.github.io/ActionModels.jl/dev/)
 # [![Build Status](https://github.com/ComputationalPsychiatry/ActionModels.jl/actions/workflows/CI_full.yml/badge.svg?branch=main)](https://github.com/ComputationalPsychiatry/ActionModels.jl/actions/workflows/CI_full.yml?query=branch%3Amain)
 # [![Coverage](https://codecov.io/gh/ComputationalPsychiatry/ActionModels.jl/branch/main/graph/badge.svg?token=NVFiiPydFA)](https://codecov.io/gh/ComputationalPsychiatry/ActionModels.jl)
-# [![License: GNU](https://img.shields.io/badge/License-GNU-yellow)](<https://www.gnu.org/licenses/>)
+# [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 # [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 # # Welcome to ActionModels! 

src/ActionModels.jl

@@ -39,7 +39,8 @@ export set_parameters!, set_states!, set_actions!, reset!
 
 ## For fitting models ##
 export create_model
-export Regression, RegressionPrior, exp, logistic
+export Regression, RegressionPrior
+export exp, logistic, softmax #export commonly used LogExpFunctions functions
 export sample_prior!, sample_posterior!, SampleSaveResume
 export get_session_parameters!, get_state_trajectories!, summarize
 # export parameter_recovery

src/defining_models/structs.jl

@@ -459,7 +459,8 @@ end
 ### TYPES FOR USE IN THE ACTION MODEL ###
 #########################################
 ## Abstract type for submodel attributes ##
-abstract type AbstractSubmodelAttributes end
+# It is a subtype of AbstractSubmodel, so that attributes can be as Submodels too
+abstract type AbstractSubmodelAttributes <: AbstractSubmodel end
 
 struct NoSubModelAttributes <: AbstractSubmodelAttributes end
 

src/simulation/plots/plot_trajectory.jl

@@ -30,7 +30,7 @@ Plot{Plots.GRBackend() n=1}
     state_history = get_history(agent, target_state)
 
     if !isnothing(index) && !(first(state_history) isa AbstractArray)
-        @error "And index was provided, but the state is not an array."
+        @error "An index was provided, but the state is not an array."
     end
 
     if isnothing(index) && first(state_history) isa AbstractArray
@@ -48,8 +48,8 @@ Plot{Plots.GRBackend() n=1}
     #Replace missings with NaNs for plotting
     state_history = replace(state_history, missing => NaN)
 
-    #The x-axis starts at 0
-    x_axis = collect(0:(length(state_history)-1))
+    #The x-axis starts at 0 and goes to the number of timesteps
+    x_axis = collect(0:agent.n_timesteps.value)
 
     xlabel --> "Timestep"
     yguide --> "$target_state"

src/simulation/structs.jl

@@ -1,5 +1,5 @@
 """
-    Agent{TH}
+    Agent{T<:AbstractSubmodel}
 
 Container for a simulated agent, including the action model, model attributes, state history, and number of timesteps.
 
@@ -19,10 +19,10 @@ Action model: rescorla_wagner_act_after_update
 This agent has received 0 observations
 ```
 """
-struct Agent{TH<:NamedTuple}
+struct Agent{T<:AbstractSubmodel}
     action_model::Function
     model_attributes::ModelAttributes
-    history::TH
+    history::NamedTuple
     n_timesteps::Variable{Int64}
 end
 
@@ -105,6 +105,9 @@ function init_agent(
         push!(state, get_states(model_attributes, state_name))
     end
 
+    #Get submodel type
+    submodel_type = typeof(action_model.submodel)
+
     ## Create agent ##
-    Agent(action_model.action_model, model_attributes, history, Variable{Int64}(0))
+    Agent{submodel_type}(action_model.action_model, model_attributes, history, Variable{Int64}(0))
 end