Spellcheck CI (#726)

* spellcheck CI

* typos

Author: palday

.github/workflows/spellcheck.yml

@@ -0,0 +1,21 @@
+# 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
+        with:
+            config: _typos.toml
+            write_changes: true
+      - uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: Typos
+          fail_on_error: true

NEWS.md

@@ -2,7 +2,7 @@ MixedModels v4.22.0 Release Notes
 ==============================
 * Support for equal-tail confidence intervals for `MixedModelBootstrap`. [#715]
 * Basic `show` methods for `MixedModelBootstrap` and `MixedModelProfile`. [#715]
-* The `hide_progress` keyword argument to `parametricbootstrap` is now deprecated. Users should isntead use `progress` (which is consistent with e.g. `fit`). [#717]
+* The `hide_progress` keyword argument to `parametricbootstrap` is now deprecated. Users should instead use `progress` (which is consistent with e.g. `fit`). [#717]
 
 MixedModels v4.21.0 Release Notes
 ==============================

_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

src/Xymat.jl

@@ -48,7 +48,7 @@ end
 
 Convenience constructor for a sparse [`FeTerm`](@ref) assuming full rank, identity pivot and unit weights.
 
-Note: automatic rank deficiency handling may be added to this method in the future, as discused in
+Note: automatic rank deficiency handling may be added to this method in the future, as discussed in
 the vignette "[Rank deficiency in mixed-effects models](@ref)" for general `FeTerm`.
 """
 function FeTerm(X::SparseMatrixCSC, cnms::AbstractVector{String})

src/bootstrap.jl

@@ -75,7 +75,7 @@ end
 
 Restore replicates from `f`, using `m` to create the desired subtype of [`MixedModelFitCollection`](@ref).
 
-`f` can be any entity suppored by `Arrow.Table`. `m` does not have to be fitted, but it must have
+`f` can be any entity supported by `Arrow.Table`. `m` does not have to be fitted, but it must have
 been constructed with the same structure as the source of the saved replicates.
 
 The two-argument method constructs a [`MixedModelBootstrap`](@ref) with the same eltype as `m`.
@@ -92,7 +92,7 @@ end
 # why this weird second method? it allows us to define custom types and write methods
 # to load into those types directly. For example, we could define a `PowerAnalysis <: MixedModelFitCollection`
 # in MixedModelsSim and then overload this method to get a convenient object. 
-# Also, this allows us to write `restorereplicateS(f, m, ::Type{<:MixedModelNonparametricBoostrap})` for
+# Also, this allows us to write `restorereplicateS(f, m, ::Type{<:MixedModelNonparametricBootstrap})` for
 # entities in MixedModels bootstrap
 function restorereplicates(
     f, m::MixedModel, ctype::Type{<:MixedModelFitCollection{T}}
@@ -193,7 +193,7 @@ performance benefits.
 - `β`, `σ`, and `θ` are the values of `m`'s parameters for simulating the responses.
 - `σ` is only valid for `LinearMixedModel` and `GeneralizedLinearMixedModel` for
 families with a dispersion parameter.
-- `progress` controls whehter the progress bar is shown. Note that the progress
+- `progress` controls whether the progress bar is shown. Note that the progress
 bar is automatically disabled for non-interactive (i.e. logging) contexts.
 - `optsum_overrides` is used to override values of [OptSummary](@ref) in the models
 fit during the bootstrapping process. For example, `optsum_overrides=(;ftol_rel=1e-08)`

src/serialization.jl

@@ -15,7 +15,7 @@ function restoreoptsum!(
         all(ops.lowerbd .≤ dict.initial) &&
         all(ops.lowerbd .≤ dict.final)
     if !okay
-        throw(ArgumentError("initial or final parameters in io do not satify lowerbd"))
+        throw(ArgumentError("initial or final parameters in io do not satisfy lowerbd"))
     end
     for fld in (:feval, :finitial, :fmin, :ftol_rel, :ftol_abs, :maxfeval, :nAGQ, :REML)
         setproperty!(ops, fld, getproperty(dict, fld))

test/FactorReTerm.jl

@@ -185,7 +185,7 @@ end
                                                  1 0 1 0
                                                  1 0 0 1]
 
-        # implict intercept
+        # implicit intercept
         ff = apply_schema(@formula(y ~ 1 + (f | g)), schema(dat), MixedModel)
         rem = modelcols(last(ff.rhs), dat)
         @test size(rem) == (18, 18)