fix indents

src/bootstrap.jl

@@ -167,18 +167,18 @@ end
 
 """
  confint(pr::MixedModelBootstrap; level::Real=0.95)
- 
+
 Compute bootstrap confidence intervals for coefficients and variance components, with confidence level level (by default 95%).
 
 !!! note
- The API guarantee is for a Tables.jl compatible table. The exact return type is an 
+ The API guarantee is for a Tables.jl compatible table. The exact return type is an
  implementation detail and may change in a future minor release without being considered
  breaking.
- 
-!!! note 
- The "row names" indicating the associated parameter name are guaranteed to be unambiguous,
- but their precise naming scheme is not yet stable and may change in a future release
- without being considered breaking.
+
+!!! note
+  The "row names" indicating the associated parameter name are guaranteed to be unambiguous,
+  but their precise naming scheme is not yet stable and may change in a future release
+  without being considered breaking.
 
 See also [`shortestcovint`](@ref).
 """

src/profile/profile.jl

@@ -1,13 +1,13 @@
 """
  MixedModelProfile{T<:AbstractFloat}
- 
+
 Type representing a likelihood profile of a [`LinearMixedModel`](@ref), including associated interpolation splines.
 
 The function [`profile`](@ref) is used for computing profiles, while [`confint`](@ref) provides a useful method for constructing confidence intervals from a `MixedModelProfile`.
 
 !!! note
- The exact fields and their representation are considered implementation details and are 
- **not** part of the public API.
+  The exact fields and their representation are considered implementation details and are
+  **not** part of the public API.
 """
 struct MixedModelProfile{T<:AbstractFloat}
  m::LinearMixedModel{T} # Model that has been profiled
@@ -56,18 +56,18 @@ end
 
 """
  confint(pr::MixedModelProfile; level::Real=0.95)
- 
+
 Compute profile confidence intervals for coefficients and variance components, with confidence level level (by default 95%).
 
 !!! note
- The API guarantee is for a Tables.jl compatible table. The exact return type is an 
+ The API guarantee is for a Tables.jl compatible table. The exact return type is an
  implementation detail and may change in a future minor release without being considered
  breaking.
- 
-!!! note 
- The "row names" indicating the associated parameter name are guaranteed to be unambiguous,
- but their precise naming scheme is not yet stable and may change in a future release
- without being considered breaking.
+
+!!! note
+  The "row names" indicating the associated parameter name are guaranteed to be unambiguous,
+  but their precise naming scheme is not yet stable and may change in a future release
+  without being considered breaking.
 """
 function StatsAPI.confint(pr::MixedModelProfile; level::Real=0.95)
  cutoff = sqrt(quantile(Chisq(1), level))

src/profile/sigmapr.jl

@@ -4,10 +4,10 @@
 Refit the model `m` with the given value of `σ` and return a NamedTuple of information about the fit.
 
 `obj` and `neg` allow for conversion of the objective to the `ζ` scale and `tc` is used to return a NamedTuple
-!!! note
- This method is internal and may change or disappear in a future release
- without being considered breaking.
 
+!!! note
+ This method is internal and may change or disappear in a future release
+ without being considered breaking.
 """
 function refitσ!(
  m::LinearMixedModel{T}, σ, tc::TableColumns{T}, obj::T, neg::Bool
@@ -34,9 +34,8 @@ end
 
 Return a Table of the profile of `σ` for model `m`. The profile extends to where the magnitude of ζ exceeds `threshold`.
 !!! note
- This method is called by `profile` and currently considered internal.
- As such, it may change or disappear in a future release without being considered breaking.
- 
+ This method is called by `profile` and currently considered internal.
+ As such, it may change or disappear in a future release without being considered breaking.
 """
 function profileσ(m::LinearMixedModel{T}, tc::TableColumns{T}; threshold=4) where {T}
  (; σ, optsum) = m

src/profile/utilities.jl

@@ -7,9 +7,8 @@ The struct also contains a Dict giving the column ranges for Symbols like `:σ`
 Finally it contains a scratch vector used to accumulate to values in a row of the profile table.
 
 !!! note
- This is an internal structure used in [`MixedModelProfile`](@ref).
- As such, it may change or disappear in a future release without being considered breaking.
-
+ This is an internal structure used in [`MixedModelProfile`](@ref).
+ As such, it may change or disappear in a future release without being considered breaking.
 """
 struct TableColumns{T<:AbstractFloat,N}
  cnames::NTuple{N,Symbol}

src/profile/vcpr.jl

@@ -5,8 +5,8 @@
 Profile an element of the variance components.
 
 !!! note
- This method is called by `profile` and currently considered internal.
- As such, it may change or disappear in a future release without being considered breaking.
+  This method is called by `profile` and currently considered internal.
+  As such, it may change or disappear in a future release without being considered breaking.
 """
 function profilevc(m::LinearMixedModel{T}, val::T, rowj::AbstractVector{T}) where {T}
  optsum = m.optsum
@@ -26,12 +26,12 @@ end
 
 """
  profileσs!(val::NamedTuple, tc::TableColumns{T}; nzlb=1.0e-8) where {T}
- 
+
 Profile the variance components.
 
 !!! note
- This method is called by `profile` and currently considered internal.
- As such, it may change or disappear in a future release without being considered breaking.
+  This method is called by `profile` and currently considered internal.
+  As such, it may change or disappear in a future release without being considered breaking.
 """
 function profileσs!(val::NamedTuple, tc::TableColumns{T}; nzlb=1.0e-8) where {T}
  m = val.m