Merge branch 'main' into permutationtest

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CompatHelper.yml

@@ -13,4 +13,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+        run: julia -e 'using CompatHelper; CompatHelper.main(; bump_version=true)'

.github/workflows/ci.yml

@@ -1,4 +1,7 @@
-name: continuous-integration
+name: CI
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
 on:
   push:
     branches:
@@ -19,26 +22,19 @@ jobs:
       matrix:
         version: [1.6] # add 1 later
         arch: [x64]
-        os: [ubuntu-18.04] # macos-10.15, windows-2019
+        os: [ubuntu-20.04] # macos-10.15, windows-2019
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Julia Setup
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - name: Cache
-        uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
+        uses: julia-actions/cache@v1
         with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+          cache-compiled: "true"        
       - name: Build
         uses: julia-actions/julia-buildpkg@v1
       - name: Test
@@ -47,9 +43,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Coverage Process
         uses: julia-actions/julia-processcoverage@v1
-        if:  ${{ startsWith(matrix.os, 'ubuntu') && (matrix.version == '1') }}
       - name: Coverage Upload
-        uses: codecov/codecov-action@v1
-        if:  ${{ startsWith(matrix.os, 'ubuntu') && (matrix.version == '1') }}
+        uses: codecov/codecov-action@v4
         with:
           file: lcov.info

.github/workflows/documenter.yml

@@ -1,4 +1,7 @@
 name: Documenter
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
 on:
   push:
     branches: [main]
@@ -11,7 +14,11 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+      - name: Cache
+        uses: julia-actions/cache@v1
+        with:
+          cache-compiled: "true"              
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-docdeploy@latest
         env:

.github/workflows/spellcheck.yml

@@ -0,0 +1,23 @@
+# adapted from https://github.com/JuliaDocs/Documenter.jl/blob/master/.github/workflows/SpellCheck.yml
+# see docs at https://github.com/crate-ci/typos
+name: Spell Check
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@master
+        # don't fail on typos in files not impacted by this PR
+        continue-on-error: true
+        with:
+            config: _typos.toml
+            write_changes: true
+      - uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: Typos
+          fail_on_error: true

Project.toml

@@ -1,7 +1,7 @@
 name = "MixedModelsPermutations"
 uuid = "647c4018-d7ef-4d03-a0cc-8889a722319e"
 authors = ["Phillip Alday <[email protected]> and contributors"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0"
@@ -19,7 +19,8 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 BlockDiagonals = "0.1.18"
 MixedModels = "4.2.1"
 StaticArrays = "1.0"
-StatsBase = "0.33"
-StatsModels = "0.6"
+Statistics = "1"
+StatsBase = "0.33, 0.34"
+StatsModels = "0.6, 0.7"
 Tables = "1.0"
 julia = "1.6"

_typos.toml

@@ -0,0 +1,20 @@
+# https://github.com/crate-ci/typos#false-positives
+[default]
+
+[default.extend-identifiers]
+Lik = "Lik"
+missings = "missings"
+
+[default.extend-words]
+Lik = "Lik"
+missings = "missings"
+
+[type.package_toml]
+# Don't check spellings in these files
+extend-glob = ["Manifest.toml", "Project.toml"]
+check-file = false
+
+[type.bib]
+# contain lots of names, which are a great spot for false positives
+extend-glob = ["*.bib"]
+check-file = false

sim/permutation.jl

@@ -21,7 +21,7 @@ The default random number generator is `Random.GLOBAL_RNG`.
 
 !!! note
     Note that `use_threads=true` may not offer a performance boost and may even
-    decrease peformance if multithreaded linear algebra (BLAS) routines are available.
+    decrease performance if multithreaded linear algebra (BLAS) routines are available.
     In this case, threads at the level of the linear algebra may already occupy all
     processors/processor cores. There are plans to provide better support in coordinating
     Julia- and BLAS-level threads in the future.

src/nonparametricbootstrap.jl

@@ -13,7 +13,7 @@ The default random number generator is `Random.GLOBAL_RNG`.
 
 !!! note
     Note that `use_threads=true` may not offer a performance boost and may even
-    decrease peformance if multithreaded linear algebra (BLAS) routines are available.
+    decrease performance if multithreaded linear algebra (BLAS) routines are available.
     In this case, threads at the level of the linear algebra may already occupy all
     processors/processor cores. There are plans to provide better support in coordinating
     Julia- and BLAS-level threads in the future.
@@ -33,7 +33,7 @@ However, if the design matrix for the random effects is rank deficient (e.g., th
 of `MixedModels.fulldummy` or missing cells in the data), then this method will fail.
 See [`olsranef`](@ref) and `MixedModels.ranef` for more information.
 
-`residual_method` provides options for how observation-level residuals are passed for permuation.
+`residual_method` provides options for how observation-level residuals are passed for permutation.
 This should be a two-argument function, taking the model and the BLUPs (as computed with `blup_method`)
 as arguments. If you wish to ignore the BLUPs as computed with `blup_method`, then you still need
 the second argument, but you can simply not use it in your function.

src/permutation.jl

@@ -22,7 +22,7 @@ The default random number generator is `Random.GLOBAL_RNG`.
 
 !!! note
     Note that `use_threads=true` may not offer a performance boost and may even
-    decrease peformance if multithreaded linear algebra (BLAS) routines are available.
+    decrease performance if multithreaded linear algebra (BLAS) routines are available.
     In this case, threads at the level of the linear algebra may already occupy all
     processors/processor cores. There are plans to provide better support in coordinating
     Julia- and BLAS-level threads in the future.
@@ -46,7 +46,7 @@ However, if the design matrix for the random effects is rank deficient (e.g., th
 of `MixedModels.fulldummy` or missing cells in the data), then this method will fail.
 See [`olsranef`](@ref) and `MixedModels.ranef` for more information.
 
-`residual_method` provides options for how observation-level residuals are passed for permuation.
+`residual_method` provides options for how observation-level residuals are passed for permutation.
 This should be a two-argument function, taking the model and the BLUPs (as computed with `blup_method`)
 as arguments. If you wish to ignore the BLUPs as computed with `blup_method`, then you still need
 the second argument, but you can simply not use it in your function.