Aqua

KomaMRIBase/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRIBase"
 uuid = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
 authors = ["Carlos Castillo Passi <[email protected]>"]
-version = "0.9.0"
+version = "0.9.0-DEV"
 
 [deps]
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"

KomaMRIBase/src/datatypes/Phantom.jl

@@ -106,7 +106,7 @@ end
 
 """Scalar multiplication of a phantom"""
 *(α::Real, obj::Phantom) = begin
-    obj1 = copy(obj)
+    obj1 = deepcopy(obj)
     obj1.ρ .*= α
     return obj1
 end

KomaMRIBase/src/datatypes/Sequence.jl

@@ -110,7 +110,6 @@ Base.getindex(x::Sequence, i::Int) = Sequence(x.GR[:,i], x.RF[:,i], x.ADC[i], x.
 Base.getindex(x::Sequence, i::BitArray{1}) = any(i) ? Sequence(x.GR[:,i], x.RF[:,i], x.ADC[i], x.DUR[i], x.DEF) : nothing
 Base.getindex(x::Sequence, i::Array{Bool,1}) = any(i) ? Sequence(x.GR[:,i], x.RF[:,i], x.ADC[i], x.DUR[i], x.DEF) : nothing
 Base.lastindex(x::Sequence) = length(x.DUR)
-Base.copy(x::Sequence) where Sequence = Sequence([deepcopy(getfield(x, k)) for k ∈ fieldnames(Sequence)]...)
 
 #Arithmetic operations
 recursive_merge(x::Dict{K, V}) where {K, V} = merge(recursive_merge, x...)

KomaMRIBase/src/datatypes/sequence/ADC.jl

@@ -1,7 +1,7 @@
 """
-    adc = ADC(N, T)
-    adc = ADC(N, T, delay)
-    adc = ADC(N, T, delay, Δf, ϕ)
+	adc = ADC(N, T)
+	adc = ADC(N, T, delay)
+	adc = ADC(N, T, delay, Δf, ϕ)
 
 The ADC struct represents the Analog to Digital Converter (ADC) of a sequence event.
 
@@ -29,40 +29,51 @@ mutable struct ADC
     Δf::Float64
     ϕ::Float64
     function ADC(N, T, delay, Δf, ϕ)
-        T < 0 || delay < 0 ? error("ADC timings must be positive.") : new(N, T, delay, Δf, ϕ)
+        if T < 0 || delay < 0
+            error("ADC timings must be positive.")
+        end
+        return new(N, T, delay, Δf, ϕ)
     end
     function ADC(N, T, delay)
-		T < 0 || delay < 0 ? error("ADC timings must be positive.") : new(N, T, delay, 0, 0)
+        if T < 0 || delay < 0
+            error("ADC timings must be positive.")
+        end
+        return new(N, T, delay, 0.0, 0.0)
     end
     function ADC(N, T)
-		T < 0 ? error("ADC timings must be positive.") : new(N, T, 0, 0, 0)
+        if T < 0
+            error("ADC timings must be positive.")
+        end
+        return new(N, T, 0.0, 0.0, 0.0)
     end
 end
 
 # ADC comparison
-Base.isapprox(adc1::ADC, adc2::ADC) = begin
-    return all(length(getfield(adc1, k)) ≈ length(getfield(adc2, k)) for k ∈ fieldnames(ADC))
-        all(getfield(adc1, k) ≈ getfield(adc2, k) for k ∈ fieldnames(ADC))
+function Base.isapprox(adc1::ADC, adc2::ADC)
+    return all(
+        length(getfield(adc1, k)) ≈ length(getfield(adc2, k)) for k in fieldnames(ADC)
+    )
+    all(getfield(adc1, k) ≈ getfield(adc2, k) for k in fieldnames(ADC))
 end
 
 """
-    y = getproperty(x::Vector{ADC}, f::Symbol)
+	y = getproperty(x::Vector{ADC}, f::Symbol)
 
 Overloads Base.getproperty(). It is meant to access properties of the ADC vector `x`
 directly without the need to iterate elementwise.
 
 # Arguments
 - `x`: (`::Vector{ADC}`) vector of ADC structs
 - `f`: (`::Symbol`, opts: [`:N`, `:T`, `:delay`, `:Δf`, `:ϕ`, `:dur`]) input symbol that
-    represents a property of the ADC structs
+	represents a property of the ADC structs
 
 # Returns
 - `y`: (`::Vector{Any}`) vector with the property defined by the `f` for all elements of
-    the ADC vector `x`
+	the ADC vector `x`
 """
 getproperty(x::Vector{ADC}, f::Symbol) = begin
     if f == :dur
-		dur.(x)
+        dur.(x)
     elseif f in fieldnames(ADC)
         getfield.(x, f)
     else
@@ -71,7 +82,7 @@ getproperty(x::Vector{ADC}, f::Symbol) = begin
 end
 
 """
-    times = get_adc_sampling_times(seq)
+	times = get_adc_sampling_times(seq)
 
 Returns an array of times when the samples of the sequence `seq` are acquired.
 
@@ -85,18 +96,18 @@ function get_adc_sampling_times(seq)
     T0 = get_block_start_times(seq)
     t = zeros(Float64, sum(seq.ADC.N))
     idx = 1
-    for i = 1:length(seq)
+    for i in 1:length(seq)
         if is_ADC_on(seq[i])
             N = seq.ADC[i].N
-            t[idx:idx+N-1] .= times(seq.ADC[i]) .+ T0[i]
+            t[idx:(idx + N - 1)] .= times(seq.ADC[i]) .+ T0[i]
             idx += N
         end
     end
     return t
 end
 
 """
-    comp = get_adc_phase_compensation(seq)
+	comp = get_adc_phase_compensation(seq)
 
 Returns an array of phase compensation factors, ``\\exp(-\\mathrm{i}\\varphi)``, which are
 used to compensate the acquired signal ``S`` by applying the operation

KomaMRIBase/src/datatypes/sequence/Delay.jl

@@ -21,7 +21,10 @@ julia> seq = delay + s; plot_seq(seq)
 struct Delay
     T::Real
     function Delay(T)
-		T < 0 ? error("Delays must be positive.") : new(T)
+	 	if T < 0
+            error("Delays must be positive.")
+        end
+        return new(T)
     end
 end
 
@@ -57,7 +60,7 @@ sequence.
 +(s::Sequence, d::Delay) = s + empty_seq(d.T)
 +(d::Delay, s::Sequence) = empty_seq(d.T) + s
 function empty_seq(T)
-    seq = Sequence([Grad(0., 0.);;])
+    seq = Sequence([Grad(0., 0.);;]) # 1-block empty sequence (!= Sequence(), which is a 0-block empty sequence)
     seq.DUR[1] = T
     return seq
 end

KomaMRIBase/src/datatypes/sequence/Grad.jl

@@ -84,32 +84,28 @@ mutable struct Grad
     first
     last
     function Grad(A, T, rise, fall, delay)
-        return if all(T .< 0) || rise < 0 || fall < 0 || delay < 0
+        if all(T .< 0) || rise < 0 || fall < 0 || delay < 0
             error("Gradient timings must be positive.")
-        else
-            new(A, T, rise, fall, delay, 0.0, 0.0)
         end
+        return new(A, T, rise, fall, delay, 0.0, 0.0)
     end
     function Grad(A, T, rise, delay)
-        return if all(T .< 0) < 0 || rise < 0 || delay < 0
+        if all(T .< 0) || rise < 0 || delay < 0
             error("Gradient timings must be positive.")
-        else
-            new(A, T, rise, rise, delay, 0.0, 0.0)
         end
+        return new(A, T, rise, rise, delay, 0.0, 0.0)
     end
     function Grad(A, T, rise)
-        return if all(T .< 0) < 0 || rise < 0
+        if all(T .< 0) || rise < 0
             error("Gradient timings must be positive.")
-        else
-            new(A, T, rise, rise, 0.0, 0.0, 0.0)
         end
+        return new(A, T, rise, rise, 0.0, 0.0, 0.0)
     end
     function Grad(A, T)
-        return if all(T .< 0) < 0
+        if all(T .< 0)
             error("Gradient timings must be positive.")
-        else
-            new(A, T, 0.0, 0.0, 0.0, 0.0, 0.0)
         end
+        return new(A, T, 0.0, 0.0, 0.0, 0.0, 0.0)
     end
 end
 

KomaMRIBase/src/datatypes/sequence/RF.jl

@@ -29,17 +29,22 @@ mutable struct RF
     Δf
     delay::Real
     function RF(A, T, Δf, delay)
-        return if any(T .< 0) || delay < 0
+        if any(T .< 0) || delay < 0
             error("RF timings must be non-negative.")
-        else
-            new(A, T, Δf, delay)
         end
+        return new(A, T, Δf, delay)
     end
     function RF(A, T, Δf)
-        return any(T .< 0) ? error("RF timings must be non-negative.") : new(A, T, Δf, 0.0)
+        if any(T .< 0)
+            error("RF timings must be non-negative.")
+        end
+        return new(A, T, Δf, 0.0)
     end
     function RF(A, T)
-        return any(T .< 0) ? error("RF timings must be non-negative.") : new(A, T, 0.0, 0.0)
+        if any(T .< 0)
+            error("RF timings must be non-negative.")
+        end
+        return new(A, T, 0.0, 0.0)
     end
 end
 

KomaMRIBase/test/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

KomaMRIBase/test/runtests.jl

@@ -177,11 +177,6 @@ using TestItems, TestItemRunner
         delay = Delay(T)
         @test delay.T ≈ T
 
-        # Test delay construction error for negative values
-        err = Nothing
-        try Delay(-T) catch err end
-        @test err isa ErrorException
-
         # Just checking to ensure that show() doesn't get stuck and that it is covered
         show(IOBuffer(), "text/plain", delay)
         @test true
@@ -655,3 +650,8 @@ end
     @test KomaMRIBase.trapz(dt, x)[1] ≈ 4 #Triangle area = bh/2, with b = 4 and h = 2
     @test KomaMRIBase.cumtrapz(dt, x) ≈ [0.5 2 3.5 4]
 end
+
+@testitem "Aqua" tags=[:base, :aqua] begin
+    using Aqua
+    Aqua.test_all(KomaMRIBase)
+end

KomaMRICore/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRICore"
 uuid = "4baa4f4d-2ae9-40db-8331-a7d1080e3f4e"
 authors = ["Carlos Castillo Passi <[email protected]>"]
-version = "0.9.0"
+version = "0.9.0-DEV"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

KomaMRICore/test/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"

KomaMRICore/test/runtests.jl

@@ -400,4 +400,9 @@ end
 
     @suppress print_devices()
     @test true
+end
+
+@testitem "Aqua" tags=[:core, :aqua] begin
+    using Aqua
+    Aqua.test_all(KomaMRICore)
 end

KomaMRIFiles/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRIFiles"
 uuid = "fcf631a6-1c7e-4e88-9e64-b8888386d9dc"
 authors = ["Carlos Castillo Passi <[email protected]>"]
-version = "0.9.0"
+version = "0.9.0-DEV"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"

KomaMRIFiles/test/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 KomaMRIBase = "d0bc0b20-b151-4d03-b2a4-6ca51751cb9c"
 KomaMRIFiles = "fcf631a6-1c7e-4e88-9e64-b8888386d9dc"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"

KomaMRIFiles/test/runtests.jl

@@ -133,3 +133,8 @@ end
         end
     end
 end
+
+@testitem "Aqua" tags=[:files, :aqua] begin
+    using Aqua
+    Aqua.test_all(KomaMRIFiles)
+end

KomaMRIPlots/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRIPlots"
 uuid = "76db0263-63f3-4d26-bb9a-5dba378db904"
 authors = ["Carlos Castillo Passi <[email protected]>"]
-version = "0.9.0"
+version = "0.9.0-DEV"
 
 [deps]
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"