Bump codecov/codecov-action from 3 to 4

.JuliaFormatter.toml

@@ -0,0 +1,6 @@
+style = "blue"
+align_assignment = true
+align_struct_field = true
+align_conditional = true
+align_pair_arrow = true
+align_matrix = true

.github/workflows/CI.yml

@@ -39,7 +39,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           files: lcov.info
   docs:

docs/make.jl

@@ -1,23 +1,23 @@
 using SparseConnectivityTracer
 using Documenter
 
-DocMeta.setdocmeta!(SparseConnectivityTracer, :DocTestSetup, :(using SparseConnectivityTracer); recursive=true)
+DocMeta.setdocmeta!(
+    SparseConnectivityTracer,
+    :DocTestSetup,
+    :(using SparseConnectivityTracer);
+    recursive=true,
+)
 
 makedocs(;
     modules=[SparseConnectivityTracer],
     authors="Adrian Hill <[email protected]>",
     sitename="SparseConnectivityTracer.jl",
     format=Documenter.HTML(;
-        canonical="https://adrhill.github.io/SparseConnectivityTracer.jl",
-        edit_link="main",
-        assets=String[],
+        canonical = "https://adrhill.github.io/SparseConnectivityTracer.jl",
+        edit_link = "main",
+        assets    = String[],
     ),
-    pages=[
-        "Home" => "index.md",
-    ],
+    pages=["Home" => "index.md"],
 )
 
-deploydocs(;
-    repo="github.com/adrhill/SparseConnectivityTracer.jl",
-    devbranch="main",
-)
+deploydocs(; repo="github.com/adrhill/SparseConnectivityTracer.jl", devbranch="main")

src/SparseConnectivityTracer.jl

@@ -1,5 +1,68 @@
 module SparseConnectivityTracer
 
-# Write your package code here.
+# Input connectivity tracer
+struct Tracer <: Number
+    inputs::Set{UInt64} # indices of connected, enumerated inputs
+end
+
+Tracer(i::Integer) = Tracer(Set{UInt64}(i))
+Tracer(a::Tracer, b::Tracer) = Tracer(a.inputs ∪ b.inputs)
+
+# Enumerate inputs
+inputtrace(x) = inputtrace(x, 1)
+inputtrace(::Number, i) = Tracer(i)
+function inputtrace(x::AbstractArray, i)
+    indices = (i - 1) .+ reshape(1:length(x), size(x))
+    return Tracer.(indices)
+end
+
+include("ops.jl")
+
+# Extent core operators
+for fn in (:+, :-, :*, :/, :^)
+    @eval Base.$fn(a::Tracer, b::Tracer) = Tracer(a, b)
+    for T in (:Number,)
+        @eval Base.$fn(t::Tracer, ::$T) = t
+        @eval Base.$fn(::$T, t::Tracer) = t
+    end
+end
+
+Base.:^(a::Tracer, b::Tracer) = Tracer(a, b)
+for T in (:Number, :Integer, :Rational)
+    @eval Base.:^(t::Tracer, ::$T) = t
+    @eval Base.:^(::$T, t::Tracer) = t
+end
+Base.:^(t::Tracer, ::Irrational{:ℯ}) = t
+Base.:^(::Irrational{:ℯ}, t::Tracer) = t
+
+# Two-argument functions
+for fn in (:div, :fld, :cld)
+    @eval Base.$fn(a::Tracer, b::Tracer) = Tracer(a, b)
+    @eval Base.$fn(t::Tracer, ::Number) = t
+    @eval Base.$fn(::Number, t::Tracer) = t
+end
+
+# Single-argument functions
+for fn in scalar_operations
+    @eval Base.$fn(t::Tracer) = t
+end
+
+function connectivity(f, x)
+    xt = inputtrace(x)
+    yt = f(xt)
+    n, m = length(xt), length(yt)
+
+    # Construct connectivity matrix of size (ouput_dim, input_dim)
+    C = BitArray(undef, m, n)
+    for i in axes(C, 1)
+        tracer = yt[i]
+        for j in axes(C, 2)
+            C[i, j] = j ∈ tracer.inputs
+        end
+    end
+    return C
+end
+
+export connectivity
 
 end

src/enumerate.jl

@@ -0,0 +1,7 @@
+
+enumerate_tracers(x) = enumerate_tracers(x, 1)
+enumerate_tracers(::Number, i) = Tracer(i)
+function enumerate_tracers(x::AbstractArray, i)
+    indices = (i - 1) .+ reshape(1:length(x), size(x))
+    return Tracer.(indices)
+end

src/ops.jl

@@ -0,0 +1,20 @@
+#! format: off
+scalar_operations = (
+    :exp2, :deg2rad, :rad2deg,
+    :sincos, :sincospi,
+    :cos,  :cosd,  :cosh, :cospi, :cosc,
+    :sin,  :sind,  :sinh, :sinpi, :sinc,
+    :tan,  :tand,  :tanh,
+    :csc,  :cscd,  :csch,
+    :sec,  :secd,  :sech,
+    :cot,  :cotd,  :coth,
+    :acos, :acosd, :acosh,
+    :asin, :asind, :asinh,
+    :atan, :atand, :atanh,
+    :asec, :asech,
+    :acsc, :acsch,
+    :acot, :acoth,
+    :exp, :expm1, :exp10,
+    :frexp, :ldexp,
+)
+#! format: on

test/Project.toml

@@ -1,4 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/runtests.jl

@@ -1,14 +1,29 @@
 using SparseConnectivityTracer
 using Test
+using JuliaFormatter
 using Aqua
 using JET
 
+using LinearAlgebra
+using Random
+
 @testset "SparseConnectivityTracer.jl" begin
-    @testset "Code quality (Aqua.jl)" begin
+    @testset "Code formatting" begin
+        @test JuliaFormatter.format(
+            SparseConnectivityTracer; verbose=false, overwrite=false
+        )
+    end
+    @testset "Aqua.jl tests" begin
         Aqua.test_all(SparseConnectivityTracer)
     end
-    @testset "Code linting (JET.jl)" begin
-        JET.test_package(SparseConnectivityTracer; target_defined_modules = true)
+    @testset "JET tests" begin
+        JET.test_package(SparseConnectivityTracer; target_defined_modules=true)
+    end
+
+    @testset "Connectivity" begin
+        f(x) = [x[1]^2, 2 * x[1] * x[2]^2, sin(x[3])]
+        @test connectivity(f, rand(3)) == BitMatrix([1 0 0; 1 1 0; 0 0 1])
+
+        @test connectivity(identity, rand()) == BitMatrix([1;;])
     end
-    # Write your tests here.
 end