Release 0.2.0 cleanup (#52)

* migrate to top-level test project and add compats

* CI config

* docs update

* add YAS enforcer

* README update

* s/hide_progress/progress and remove threads in nonparametricbootstrap

* s/hide_progress/progress and remove threads in permutation

* fix deprecation warning for Cholesky

* YAS

* update author list

.github/workflows/FormatCheck.yml

@@ -0,0 +1,52 @@
+---
+name: YAS Enforcer
+on:
+  push:
+    branches:
+      - main
+      - /^release-.*$/
+    tags: ["*"]
+    paths:
+      - "**/*.jl"
+      - ".github/workflows/FormatCheck.yml"
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths:
+      - "**/*.jl"
+      - ".github/workflows/FormatCheck.yml"
+jobs:
+  format-check:
+    name: YASStyle
+    # These permissions are needed to:
+    # - Delete old caches: https://github.com/julia-actions/cache#usage
+    # - Post formatting suggestions: https://github.com/reviewdog/action-suggester#required-permissions
+    permissions:
+      actions: write
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+        fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: "1"
+      - uses: julia-actions/cache@v1
+      - name: Install JuliaFormatter
+        shell: julia --project=@format --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.add(PackageSpec(; name="JuliaFormatter", version="1"))
+      - name: Check formatting
+        shell: julia --project=@format --color=yes {0}
+        run: |
+          using JuliaFormatter
+          format(["src", "test", "docs"], YASStyle(); verbose=true)
+      # Add formatting suggestions to non-draft PRs when "Check formatting" fails
+      - uses: reviewdog/action-suggester@v1
+        if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true

.github/workflows/ci.yml

@@ -17,20 +17,19 @@ on:
       - 'README.md'
 jobs:
   ci:
+    name: CI - ${{ matrix.os }} - Julia ${{ matrix.julia }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        version: [1.6] # add 1 later
-        arch: [x64]
-        os: [ubuntu-20.04] # macos-10.15, windows-2019
+        julia: [1.9]
+        os: [ubuntu-latest] # macos-10.15, windows-2019, macOS-14
     steps:
       - name: Checkout
         uses: actions/checkout@v4
       - name: Julia Setup
         uses: julia-actions/setup-julia@v2
         with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
+          version: ${{ matrix.julia }}
       - name: Cache
         uses: julia-actions/cache@v1
         with:

Project.toml

@@ -1,7 +1,7 @@
 name = "MixedModelsPermutations"
 uuid = "647c4018-d7ef-4d03-a0cc-8889a722319e"
-authors = ["Phillip Alday <[email protected]> and contributors"]
-version = "0.2.1"
+authors = ["Phillip Alday <[email protected]>", "Benedikt Ehinger <[email protected]>", "Jaromil Frossard <[email protected]>"]
+version = "0.2.0"
 
 [deps]
 BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0"
@@ -16,11 +16,25 @@ StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [compat]
+Aqua = "0.8"
+DataFrames = "1"
 BlockDiagonals = "0.1.18"
-MixedModels = "4.2.1"
+MixedModels = "4.22"
+MixedModelsSim = "0.2.9"
+StableRNGs = "1"
 StaticArrays = "1.0"
 Statistics = "1"
 StatsBase = "0.33, 0.34"
 StatsModels = "0.6, 0.7"
-Tables = "1.0"
-julia = "1.6"
+Tables = "1"
+julia = "1.9"
+
+[extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+MixedModelsSim = "d5ae56c5-23ca-4a1f-b505-9fc4796fc1fe"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Aqua", "Test", "DataFrames", "MixedModelsSim", "StableRNGs"]

README.md

@@ -5,6 +5,7 @@
 [![Dev Docs][docs-dev-img]][docs-dev-url]
 [![Codecov](https://codecov.io/gh/palday/MixedModelsPermutations.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/palday/MixedModelsPermutations.jl)
 [![DOI](https://zenodo.org/badge/337080334.svg)](https://zenodo.org/badge/latestdoi/337080334)
+[![Code Style: YAS](https://img.shields.io/badge/code%20style-yas-1fdcb3.svg)](https://github.com/jrevels/YASGuide)
 
 [docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
 [docs-dev-url]: https://palday.github.io/MixedModelsPermutations.jl/dev

docs/Project.toml

@@ -4,5 +4,5 @@ MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
 MixedModelsPermutations = "647c4018-d7ef-4d03-a0cc-8889a722319e"
 
 [compat]
-Documenter = "0.27"
-julia = "1.6"
+Documenter = "1.3"
+julia = "1.9"

docs/make.jl

@@ -1,12 +1,9 @@
 using Documenter
 using MixedModelsPermutations
 
-makedocs(
-    sitename = "MixedModelsPermutations",
-    doctest = true,
-    pages = [
-        "index.md",
-    ],
-)
+makedocs(; sitename="MixedModelsPermutations",
+         doctest=true,
+         pages=["index.md"])
 
-deploydocs(repo = "github.com/palday/MixedModelsPermutations.jl.git", push_preview=true, devbranch="main")
+deploydocs(; repo="github.com/palday/MixedModelsPermutations.jl.git", push_preview=true,
+           devbranch="main")

docs/src/index.md

@@ -4,7 +4,7 @@
 CurrentModule = MixedModelsPermutations
 ```
 
-*MixedModelsPermutations.jl* is a Julia package providing extra capabilities for models fit with [MixedModels.jl](https://juliastats.org/MixedModels.jl/stable/).
+*MixedModelsPermutations.jl* is a Julia package providing nonparametric testing capabilities for models fit with [MixedModels.jl](https://juliastats.org/MixedModels.jl/stable/).
 
 ```@contents
 Pages = [

sim/nb_mwe-unshrunken.jl

@@ -7,7 +7,14 @@ using InteractiveUtils
 # This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
 macro bind(def, element)
     quote
-        local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end
+        local iv = try
+            Base.loaded_modules[Base.PkgId(
+                Base.UUID("6e696c72-6542-2067-7265-42206c756150"),
+                "AbstractPlutoDingetjes",
+            )].Bonds.initial_value
+        catch
+            b -> missing
+        end
         local el = $(esc(element))
         global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el)
         el
@@ -16,20 +23,20 @@ end
 
 # ╔═╡ f92470d8-c28e-4057-87bd-12383b43c158
 begin
-	using Pkg
-	Pkg.activate(; temp=true)
-	Pkg.add("Revise")
-	using Revise
-	Pkg.add(path="..")
-	Pkg.add(["PlutoUI", "MixedModelsSim", "MixedModels", "DataFrames","StableRNGs"])
-	using PlutoUI
-	using MixedModelsSim
-	using MixedModelsPermutations
-	using MixedModels
-	using DataFrames
-	using StableRNGs
-	using LinearAlgebra
-	using Statistics
+    using Pkg
+    Pkg.activate(; temp = true)
+    Pkg.add("Revise")
+    using Revise
+    Pkg.add(path = "..")
+    Pkg.add(["PlutoUI", "MixedModelsSim", "MixedModels", "DataFrames", "StableRNGs"])
+    using PlutoUI
+    using MixedModelsSim
+    using MixedModelsPermutations
+    using MixedModels
+    using DataFrames
+    using StableRNGs
+    using LinearAlgebra
+    using Statistics
 end
 
 # ╔═╡ f5830c4e-a8d0-47f2-baca-bc734720b1e0
@@ -48,14 +55,21 @@ md"seed $(@bind seed_val Slider(1:100; default=1., show_value=true))"
 rng = StableRNG(Int(seed_val))
 
 # ╔═╡ 2141edd4-c8ed-4d1b-a5ec-9913b19a2d4a
-	md"Subjects: $(@bind nsub Slider(2:2:50; default=30, show_value=true))"
+md"Subjects: $(@bind nsub Slider(2:2:50; default=30, show_value=true))"
 
 
 # ╔═╡ bac32d2f-fb1f-4f02-b2f5-49df029b7b92
 md"Items per Subject: $(@bind nitem Slider(2:2:50; default=30, show_value=true))"
 
 # ╔═╡ 461f6470-359e-406a-b32d-5455647e36b8
-@bind inflate Radio(["ols" => "inflation_factor from OLS blups", "yes" => "inflation_factor from original blups/residuals", "no" => "identity"],"ols")
+@bind inflate Radio(
+    [
+        "ols" => "inflation_factor from OLS blups",
+        "yes" => "inflation_factor from original blups/residuals",
+        "no" => "identity",
+    ],
+    "ols",
+)
 
 # ╔═╡ a44e5f9f-5a23-46b6-adbd-228b893ac81f
 md"### Calculate 50 permutations"
@@ -64,19 +78,20 @@ md"### Calculate 50 permutations"
 md"### How the saussage is simulated"
 
 # ╔═╡ 0cbf776c-8e56-4d32-8a55-da22f8bf1940
-f =  @formula(dv ~ 1 + condition + (1 + condition | subj));
+f = @formula(dv ~ 1 + condition + (1 + condition | subj));
 
 # ╔═╡ 72f5e910-e40d-11eb-3725-f19a95c9b3c1
 begin
-	subj_btwn = Dict("age" => ["O", "Y"])
+    subj_btwn = Dict("age" => ["O", "Y"])
     # there are no between-item factors in this design so you can omit it or set it to nothing
     item_btwn = Dict("stimType" => ["I", "II"])
 
     # put within-subject/item factors in a Dict
     both_win = Dict("condition" => ["A", "B"])
 
     # simulate data
-    dat = simdat_crossed(rng,
+    dat = simdat_crossed(
+        rng,
         nsub,
         nitem,
         subj_btwn = subj_btwn,
@@ -88,59 +103,61 @@ end
 # ╔═╡ cd9b3fb7-06c7-4c44-81ac-d8a4a3e0c22e
 # generate simulated "y" vector
 begin
-	β = [1., 1.];
-	σs = [1, 1, 0.2];
-	simMod = fit(MixedModel, f, dat)
-	simMod = MixedModelsSim.update!(simMod,[create_re(x...) for x in σs]...)
-	simMod = simulate!(rng, simMod; β, σ = 1.)
+    β = [1.0, 1.0]
+    σs = [1, 1, 0.2]
+    simMod = fit(MixedModel, f, dat)
+    simMod = MixedModelsSim.update!(simMod, [create_re(x...) for x in σs]...)
+    simMod = simulate!(rng, simMod; β, σ = 1.0)
 end;
 
 # ╔═╡ cfd225bb-1eec-41b1-b6c1-ebc036b7e1d2
 begin
-	# fit a LMM mod to the y (separate models to maybe have separate formulas later
-	datSim = DataFrame(dat)
-	datSim[!, :dv] .= response(simMod)
-	morig = fit(MixedModel, f, datSim; REML=false)
+    # fit a LMM mod to the y (separate models to maybe have separate formulas later
+    datSim = DataFrame(dat)
+    datSim[!, :dv] .= response(simMod)
+    morig = fit(MixedModel, f, datSim; REML = false)
 end;
 
 # ╔═╡ a26a8327-8342-472e-841f-a9a68e5b15a8
 MixedModelsPermutations.inflation_factor(morig)
 
 # ╔═╡ 58fa0d39-65e0-4ec7-aeb0-e8bde381379a
 begin
-	samps = DataFrame()
-	seed = Int(seed_val)
-	
-	for p = 1:50
-		local m_new = deepcopy(morig)
-
-		sample_func = MixedModelsPermutations.permute!
-
-
-		sample_rng = StableRNG(seed+p)
-		blups = olsranef(m_new)
-		resids = residuals(m_new, blups)
-		if inflate == "ols"
-			scalings = MixedModelsPermutations.inflation_factor(m_new, blups, resids)
-		elseif inflate == "yes"
-			scalings = MixedModelsPermutations.inflation_factor(m_new)
-		else
-			# assumes that we have exactly 2 blocking vars
-			scalings = [I, I, 1]
-		end
-		sample_func(sample_rng, m_new; β, blups, resids, scalings)
-		
-		refit!(m_new)
-		push!(samps, (; σ=m_new.σ, β=m_new.β ))
-	
-	end
+    samps = DataFrame()
+    seed = Int(seed_val)
+
+    for p = 1:50
+        local m_new = deepcopy(morig)
+
+        sample_func = MixedModelsPermutations.permute!
+
+
+        sample_rng = StableRNG(seed + p)
+        blups = olsranef(m_new)
+        resids = residuals(m_new, blups)
+        if inflate == "ols"
+            scalings = MixedModelsPermutations.inflation_factor(m_new, blups, resids)
+        elseif inflate == "yes"
+            scalings = MixedModelsPermutations.inflation_factor(m_new)
+        else
+            # assumes that we have exactly 2 blocking vars
+            scalings = [I, I, 1]
+        end
+        sample_func(sample_rng, m_new; β, blups, resids, scalings)
+
+        refit!(m_new)
+        push!(samps, (; σ = m_new.σ, β = m_new.β))
+
+    end
 end
 
 # ╔═╡ 64d2509b-d94e-4e48-8f81-fa13d5f9e9be
-let	# convenience tuple :-)
-	("non parametric resampling"=>samps.σ,
-		"emprical σ"=>morig.σ,
-	"mean of resampled σ" => mean(samps.σ))
+let# convenience tuple :-)
+    (
+        "non parametric resampling" => samps.σ,
+        "emprical σ" => morig.σ,
+        "mean of resampled σ" => mean(samps.σ),
+    )
 end
 
 # ╔═╡ Cell order: