Document Counts to Frequencies + Format

NEWS.md

@@ -2,10 +2,8 @@
 
 ### Changes from v2.21.0 to dev
 
-* *[Breaking change]* The `mapcolpairfreq!` and `mapseqpairfreq!` functions now uses the
-  boolean `usediagonal` keyword argument to indicate if the function should be applied to
-  the diagonal elements of the matrix (the default is `true`). Before, this was done passing
-  `Val{true}` or `Val{false}` as the last positional argument.
+* *[Breaking change]* The `Information` module deprecates the `Counts` type in favor of 
+  the new `Frequencies` type. The new type as the same signature and behavior as the old one.
 
 * *[Breaking change]* The `count` function on sequences has been deprecated in favor of the
   `frequencies` function, which has the same signature and behavior as the old one.
@@ -40,8 +38,13 @@
   accept arrays of `Residue`s of any dimension. Therefore, there is no need to use the
   `vec` function to convert the arrays to vectors.
 
+* *[Breaking change]* The `mapcolpairfreq!` and `mapseqpairfreq!` functions now uses the
+  boolean `usediagonal` keyword argument to indicate if the function should be applied to
+  the diagonal elements of the matrix (the default is `true`). Before, this was done passing
+  `Val{true}` or `Val{false}` as the last positional argument.
+
 * The `mapcolfreq!`, `mapseqfreq!`, `mapcolpairfreq!`, and `mapseqpairfreq!` methods using
-  keyword arguments, now pass the extra keyword arguments to mapped function.
+  keyword arguments, now pass the extra keyword arguments to the mapped function.
 
 * The `Information` module now exports the `mapfreq` function that offers a more high-level
   interface to the `mapcolfreq!`, `mapseqfreq!`, `mapcolpairfreq!`, and `mapseqpairfreq!`

src/Information/ContingencyTables.jl

@@ -53,7 +53,11 @@ mutable struct Counts{T,N,A} <: AbstractArray{T,N}
     table::ContingencyTable{T,N,A}
 end
 function Counts{T,N,A}(table::ContingencyTable{T,N,A}) where {T,N,A}
-    Base.depwarn("The `Counts` type is deprecated. Please use `Frequencies` instead.", :Counts, force=true)
+    Base.depwarn(
+        "The `Counts` type is deprecated. Please use `Frequencies` instead.",
+        :Counts,
+        force = true,
+    )
     Frequencies{T,N,A}(table)
 end
 

src/Information/InformationMeasures.jl

@@ -39,7 +39,9 @@ function shannon_entropy(table::Frequencies{T,N,A}; base::Number = ℯ) where {T
     end
 end
 
-function StatsBase.entropy(table::Union{Frequencies{T,N,A},Probabilities{T,N,A}}) where {T,N,A}
+function StatsBase.entropy(
+    table::Union{Frequencies{T,N,A},Probabilities{T,N,A}},
+) where {T,N,A}
     Base.depwarn(
         "entropy(table::Union{Frequencies,Probabilities}) is deprecated. Use shannon_entropy(table) instead.",
         :entropy,
@@ -495,8 +497,18 @@ alignment using the [`mapfreq`](@ref) function—all the keyword arguments are p
 `mapfreq`. $_DOC_NMI By default, it uses counts/frequencies to estimate the nMI, as it's
 faster than using probabilities.
 """
-function normalized_mutual_information(msa::AbstractArray{Residue}; rank::Int=2, probabilities::Bool=false,
-    kargs...)
+function normalized_mutual_information(
+    msa::AbstractArray{Residue};
+    rank::Int = 2,
+    probabilities::Bool = false,
+    kargs...,
+)
     @assert rank > 1 "rank must be greater than 1 for normalized_mutual_information"
-    mapfreq(normalized_mutual_information, msa, rank=rank, probabilities=probabilities, kargs...)
-end
+    mapfreq(
+        normalized_mutual_information,
+        msa,
+        rank = rank,
+        probabilities = probabilities,
+        kargs...,
+    )
+end