Prepare for package registration

.JuliaFormatter.toml

@@ -1,13 +1,3 @@
-indent = 2
-margin = 68
-format_markdown = true
-verbose = true
-always_for_in = true
-whitespace_ops_in_indices = true
-remove_extra_newlines = true
-pipe_to_function_call = true
-always_use_return = true
-whitespace_in_kwargs = false
+style = "yas"
 format_docstrings = true
-conditional_to_if = true
-trailing_comma = true
+format_markdown = true

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/ci.yml

@@ -0,0 +1,43 @@
+name: CI
+on:
+  push:
+      paths-ignore:
+        - 'README.md'
+      branches:
+        - main
+  pull_request:
+      paths-ignore:
+        - 'README.md'
+      branches:
+        - main
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+          - 'min'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+      - name: Cache
+        uses: julia-actions/cache@v2
+        with:
+            cache-compiled: "true"
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/formatcheck.yml

@@ -0,0 +1,48 @@
+---
+  name: Format Check
+  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: Julia
+      # 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
+      steps:
+        - uses: actions/checkout@v4
+        - uses: julia-actions/setup-julia@v2
+          with:
+            version: "1"
+        - uses: julia-actions/cache@v2
+        - 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("."; verbose=true) || exit(1)
+        # Add formatting suggestions to non-draft PRs even if when "Check formatting" fails
+        - uses: reviewdog/action-suggester@db4abb16fbaabe386831e5addb7be1485d0d63d3 # v1.18.0
+          if: ${{ !cancelled() && github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
+          with:
+            tool_name: JuliaFormatter

.gitignore

@@ -16,3 +16,5 @@ data/
 /.quarto/
 
 /.luarc.json
+lcov.info
+*.cov

.zenodo.json

@@ -0,0 +1,24 @@
+{
+    "access_right": "open",
+    "license": "MIT",
+    "title": "Embrace Uncertainty",
+    "description": "A Julia package accompanying the online book Embrace Uncertainty",
+    "upload_type": "software",
+    "creators": [
+        {
+            "affiliation": "Beacon Biosignals",
+            "name": "Alday, Phillip M.",
+            "orcid": "0000-0002-9984-5745"
+        },
+        {
+            "affiliation": "University of Potsdam",
+            "name": "Kliegl, Reinhold",
+            "orcid": "0000-0002-0180-8488"
+        },
+        {
+            "affiliation": "University of Wisconsin - Madison",
+            "name": "Bates, Douglas",
+            "orcid": "0000-0001-8316-9503"
+        }
+    ]
+}

LDT_accuracy.qmd

@@ -27,20 +27,17 @@ and define some constants
 ```{julia}
 #| code-fold: true
 #| output: false
-@isdefined(contrasts) || const contrasts = Dict{Symbol, Any}()
+@isdefined(contrasts) || const contrasts = Dict{Symbol,Any}()
 @isdefined(progress) || const progress = false
 ```
 
 ## Create the dataset
 
-
 ```{julia}
 #| output: false
-trials = innerjoin(
-    DataFrame(dataset(:ELP_ldt_trial)),
-    select(DataFrame(dataset(:ELP_ldt_item)), :item, :isword, :wrdlen),
-    on = :item
-)
+trials = innerjoin(DataFrame(dataset(:ELP_ldt_trial)),
+                   select(DataFrame(dataset(:ELP_ldt_item)), :item, :isword, :wrdlen);
+                   on=:item)
 ```
 
 ```{julia}
@@ -54,20 +51,18 @@ This takes about ten to fifteen minutes on a recent laptop
 ```{julia}
 contrasts[:isword] = EffectsCoding()
 contrasts[:wrdlen] = Center(8)
-@time gm1 = let f = @formula(acc ~ 1 + isword * wrdlen + (1|item) + (1|subj))
+@time gm1 = let f = @formula(acc ~ 1 + isword * wrdlen + (1 | item) + (1 | subj))
     fit(MixedModel, f, trials, Bernoulli(); contrasts, progress, init_from_lmm=(:β, :θ))
 end
 ```
 
-
 ```{julia}
 print(gm1)
 ```
 
-
 ```{julia}
 #| fig-cap: Conditional modes and 95% prediction intervals on random effects for subject in model gm1
 #| label: fig-gm1condmodesubj
 #| code-fold: true
-qqcaterpillar!(Figure(; size=(800,800)), gm1, :subj)
-```
+qqcaterpillar!(Figure(; size=(800, 800)), gm1, :subj)
+```

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020-2024 Phillip Alday, Reinhold Kliegl and Douglas Bates
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

@@ -1,6 +1,6 @@
 name = "EmbraceUncertainty"
 uuid = "81be8970-b14c-4107-8889-06289fef228c"
-authors = ["Phillip Alday <[email protected]>, Reinhold Kliegl <[email protected]>, Douglas Bates <[email protected]>"]
+authors = ["Phillip Alday <[email protected]>", "Reinhold Kliegl <[email protected]>", "Douglas Bates <[email protected]>"]
 version = "0.1.0"
 
 [deps]
@@ -44,25 +44,32 @@ ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
 
 [compat]
 AlgebraOfGraphics = "0.6, 0.7, 0.8"
+Aqua = "0.8.7"
 Arrow = "2"
+BenchmarkTools = "1"
 CSV = "0.10"
 CairoMakie = "0.11, 0.12"
 CategoricalArrays = "0.10"
 Chain = "0.5,0.6"
 DataAPI = "1"
 DataFrameMacros = "0.3,0.4"
 DataFrames = "1.3"
+Dates = "1"
 Distributions = "0.25"
 Downloads = "1"
 Effects = "1"
 FreqTables = "0.4"
 GLM = "1"
 LinearAlgebra = "1"
+Markdown = "1"
 MixedModels = "4,5"
+MixedModelsDatasets = "0.1.1"
 MixedModelsMakie = "0.4"
 NLopt = "1"
+Pkg = "1"
 PooledArrays = "1"
 RCall = "0.13,0.14"
+RectangularFullPacked = "0.2"
 Random = "1"
 SHA = "0.7"
 Scratch = "1"
@@ -71,6 +78,17 @@ StatsAPI = "1"
 StatsBase = "0.33, 0.34"
 StatsModels = "0.7"
 Tables = "1"
+TidierPlots = "0.8"
+Test = "1.11.0"
+TestSetExtensions = "3.0.0"
 TypedTables = "1"
 ZipFile = "0.10"
-julia = "1.8"
+julia = "1.10"
+
+[extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestSetExtensions = "98d24dd4-01ad-11ea-1b02-c9a08f80db04"
+
+[targets]
+test = ["Aqua", "Test", "TestSetExtensions"]