Merge branch 'main' into unify_landingpage

Author: xuyg16

.pre-commit-config.yaml

@@ -40,7 +40,7 @@ repos:
         types_or: [yaml, json]
         exclude: ".copier-answers.yml"
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
+    rev: v1.37.0
     hooks:
       - id: yamllint
   - repo: https://github.com/domluna/JuliaFormatter.jl

Project.toml

@@ -1,7 +1,7 @@
 name = "Unfold"
 uuid = "181c99d8-e21b-4ff3-b70b-c233eddec679"
 authors = ["Benedikt Ehinger <[email protected]>"]
-version = "0.8.1"
+version = "0.8.4"
 
 [deps]
 AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
@@ -21,11 +21,8 @@ IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-<<<<<<< HEAD
-=======
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
->>>>>>> 7f44b0a (Update doc links to the respective UnfoldDocs pages)
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MLBase = "f0e99cf1-93fa-52ec-9ecc-5026115318e0"
 Missings = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
@@ -61,6 +58,7 @@ UnfoldRobustModelsExt = "RobustModels"
 [compat]
 AlgebraOfGraphics = "0.9.4"
 BSplineKit = "0.16,0.17, 0.18"
+BSplineKit = "0.16,0.17"
 CUDA = "4,5"
 DSP = "0.7, 0.8"
 DataFrames = "1"
@@ -76,11 +74,8 @@ IterativeSolvers = "0.9"
 JLD2 = "0.5"
 Krylov = "0.9"
 LinearAlgebra = "1"
-<<<<<<< HEAD
-=======
 Literate = "2.20.1"
 LiveServer = "1.4.0"
->>>>>>> 7f44b0a (Update doc links to the respective UnfoldDocs pages)
 Logging = "1"
 MLBase = "0.9"
 Missings = "1"

docs/literate/explanations/nonlinear_effects.jl

@@ -2,7 +2,8 @@
 
 
 
-using BSplineKit, Unfold
+import BSplineKit
+using Unfold
 using CairoMakie
 using DataFrames
 using Random

docs/src/index.md

@@ -4,8 +4,10 @@ CurrentModule = Unfold
 
 # Unfold.jl Documentation
 
+
 Welcome to [Unfold.jl](https://unfoldtoolbox.github.io/UnfoldDocs/Unfold.jl/stable/): a Julia Package for regression and event-based time series analysis, with a focus on regression ERPs for EEG analysis. The modular approach allows for easy modification to other context, like iEEG, pupil dilation, fMRI etc. - while maintaining the speed of Julia!
 
+
 ```@raw html
 <div style="width:100%; margin: auto;">
 

docs/src/references/extensions.md

@@ -17,7 +17,7 @@ using Unfold
 To use robust (outlier-"safe") solvers support as described in @Ref(custom_solvers) you have to:
 
 ```julia
-using RobustSolvers
+import RobustSolvers
 using Unfold
 ```
 
@@ -26,7 +26,7 @@ using Unfold
 Finally to use non-linear effects/splines like in `@formula 0~1+spl(continuous,5)` you have to use:
 
 ```julia
-using BSplineKit
+import BSplineKit
 using Unfold
 ```
 

ext/UnfoldBSplineKitExt/UnfoldBSplineKitExt.jl

@@ -1,6 +1,12 @@
 module UnfoldBSplineKitExt
 using Unfold
-using BSplineKit
+import BSplineKit:
+    BSplineOrder,
+    BSplineBasis,
+    boundaries,
+    period,
+    PeriodicBSplineBasis,
+    basis_to_array_index
 using StatsModels
 import StatsModels: termvars, width, coefnames, modelcols, apply_schema
 import Base: show

ext/UnfoldBSplineKitExt/basisfunctions.jl

@@ -25,7 +25,7 @@ end
 
 function splinekernel(e, times, nsplines)
     breakpoints = spl_breakpoints(times, nsplines)
-    basis = BSplineKit.BSplineBasis(BSplineOrder(4), breakpoints)  # 4= cubic
+    basis = BSplineBasis(BSplineOrder(4), breakpoints)  # 4= cubic
     return sparse(splFunction(times, basis))
 end
 

ext/UnfoldBSplineKitExt/splinepredictors.jl

@@ -100,7 +100,7 @@ function splFunction(x::AbstractVector, spl::PeriodicBSplineTerm)
 end
 
 function splFunction(x::AbstractVector, spl::BSplineTerm)
-    basis = BSplineKit.BSplineBasis(BSplineOrder(spl.order), deepcopy(spl.breakpoints))
+    basis = BSplineBasis(BSplineOrder(spl.order), deepcopy(spl.breakpoints))
     _splFunction(x, basis)
 end
 #spl(x,df) = Splines2.bs(x,df=df,intercept=true) # assumes intercept

test/Project.toml

@@ -26,5 +26,4 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Unfold = "181c99d8-e21b-4ff3-b70b-c233eddec679"
 UnfoldSim = "ed8ae6d2-84d3-44c6-ab46-0baf21700804"

test/setup.jl

@@ -10,7 +10,7 @@ using StatsBase
 using Missings
 using StableRNGs
 
-using RobustModels, BSplineKit # extensionTriggers
+import RobustModels, BSplineKit # extensionTriggers
 using SparseArrays
 using UnfoldSim
 using Interpolations